FamilyTreeDNA Thanksgiving Sale + New Comprehensive Health Report

FTDNA Thanksgiving.png

FamilyTreeDNA’s Thanksgiving Sale has begun. Almost everything is on sale. I don’t know about you, but I like to have all of my holiday planning and purchasing DONE before Thanksgiving. Some of the gifts I wanted for people this year are already sold out or backordered – but DNA testing is always available. The gift of history, and now of health too.

I wrote about the Big Y test and upgrades just a couple days ago, here, including the restructuring of the Big Y product resulting in a permanent $100 dollar reduction, in addition to sale prices.

FamilyTreeDNA has made a few product changes and introduced the new Tovana Health test.

I’ve included a special section of frequently asked questions (and answers) about tests and when upgrading does, and doesn’t, make sense.

Individual Tests

Let’s start with the sale prices for individual tests.

Test Sale Price Regular Price Savings
Family Finder (FF) $59 $79 $20
Y DNA 37 $99 $169 $70
Y DNA 111 *1 $199 $359 $160
Big Y-700 *2 $399 $649 $250
Mitochondrial Full Sequence *3 $139 $199 $60

*1 – You may notice that only the 37-marker and 111-marker tests are listed above. The 111-marker test was reduced to the 67-marker sale price, so, at least during the sale, the 67-marker test is not available. In other words, you get 111 markers for the price of 67.

*2 – The Big Y-700 test includes the Y 111 test plus another 589 STR markers (to equal or exceed 700 markers total) plus the SNP testing. You can read about the Big Y here.

*3 – The mitochondrial full sequence (FMS) aka mtFullSequence test is now the only mitochondrial DNA test available. I’m glad to see this change. The price of the mtFullSequence test has now dropped to the level of the less specific partial tests of yesteryear. Genealogists really need the granularity of the full test.

Bundles save even more – an additional $9 over purchasing the bundled items separately

Bundles

Test Sale Price Regular Price Savings
Family Finder + mtFullSequence $189 $278 $89
Family Finder + Y-37 $149 $248 $188
Family Finder + Y111 $249 $438 $189
Y-37 + mtFullSequence $229 $368 $139
Y-111 + mtFullSequence $329 $558 $229
Family Finder + Y-37 + mtFull $279 $447 $170
Family Finder + Y-111 + mtFull $379 $637 $258

When Does Upgrading Make Sense?

Y DNA Q&A

Q – If I have several Y DNA matches, will upgrading help?

A – If you need more specific or granular information to tease your line out of several matches – upgrading will help refine your matches and determine who is a closer match, assuming some of your matches have tested at a higher level.

Q – If I have tested at a lower level of STR markers and have no matches, will I have matches at a higher level?

A – Sometimes, but not usually. If your mutations just happen to fall in the lower panels, you may have matches on higher panels that allow for more mutations. If you do have matches on a higher test in this circumstance, the person may or may not have your surname. You can also join haplogroup and surname projects where thresholds are slightly lower for matching within projects.

If you don’t test, you’ll never know.

Q – If I have no matches on STR markers, meaning 12, 25, 37, 67 or 111, will upgrading to the Big Y be beneficial?

A – Possibly to probably – and here’s why, even if you don’t initially have matches:

  • The Big Y-700 provides multiple tools including matches at the SNP level, not just the STR level, so you are matched in two entirely different ways.
  • You may have same-surname matches at the SNP level that you do not have at the STR level which are further back in time, but still valuable and relevant to your family history.
  • You may have SNP matches that aren’t STR matches that are not your surname, but reflect your family history before the advent of surnames. These matches can tell you where your family came from before you can locate them in records. In fact, this is the ONLY way you can track your family before the advent of surnames.
  • Even if you don’t have matches, you’ll receive all of your SNP markers that allow you to view your results on the Block Tree, which is in essence a migration map back through time. You can read about the Block Tree here.
  • Your test contributes to building the phylotree – meaning the Y DNA tree of man – which benefits all genealogists. In just the first 10 months of 2019, 32,000 new SNPs have been placed on the tree, resulting in about 5,000 new individual branches. All because of Big Y-700
  • New people test every day and your DNA tests fish for you every minute of every day.

Mitochondrial DNA Q&A

If you’ve previously taken lower level mitochondrial HVR1 and HVR2 tests, now is the perfect time to upgrade.

Q – I have 5,000 <or fill in large number here> HVR1 level matches. Will upgrading reduce the number of matches to those that are more meaningful?

A – Absolutely! Your most genealogically relevant matches, meaning closest in time, are those that match you exactly at the full sequence level.

Q – I don’t know where my ancestor was from. Can a full sequence test help me?

A – Yes. You can use the Matches Map and see where the ancestors of your closest matches were from. That’s a huge hint. You can also utilize your haplogroup, which, in some instances, will point to a specific continent such as Africa, Europe, Asia or Native American and Jewish populations.

Q – If I have no matches at the HVR1 or HVR2 level? Will an upgrade help me?

A – Possibly. Both the HVR1 and HVR2 (now obsolete) tests only allowed for one mutation difference to be considered a match. The full sequence allows for many more differences. If you were unlucky and your mutations just happened to fall in the HVR1 or HVR2 levels, it would prevent a match which will occur at a higher level. Either way, you’ll receive information about your rare mutations – which may well explain why you don’t have matches (yet)! You’ll also receive a full haplogroup which will be useful, allowing you to use the mitochondrial haplotree to track back in time, which I wrote about here.

There are so many ways to obtain useful information. I wrote a step-by-step guide to using mitochondrial DNA, here.

Upgrade Options

Please note that if you are considering an upgrade, it maybe beneficial to upgrade to the maximum test available for either the Y or mitochondrial DNA, especially if you cannot obtain more of the sample. Of course, if it’s your own sample, you can always swab again, but others can’t.

Every time a vial is opened for testing, more DNA is used, until there is none left. Additionally, DNA degrades with time, depending on the quality of the original scraping and the amount of bacteria in the sample. Generally, the sample is viable for at least 5 years, but not always. Some older samples remain viable for many years. There’s no way to know in advance.

Test Sale Price Regular Price Savings
Y-12 to Y-37 $79 $109 $30
Y-12 to Y-67 $149 $199 $50
Y-12 to Y-111 $169 $359 $190
Y-25 to Y-37 $49 $59 $10
Y-25 to Y-67 $119 $159 $40
Y-25 to Y-111 $149 $269 $120
Y-37 to Y-67 $69 $109 $40
Y-37 to Y-111 $119 $228 $109
Y-67 to Y-111 $69 $99 $30
Y-12 to Big Y-700 $359 $629 $270
Y-25 to Big Y-700 $349 $599 $250
Y-37 to Big Y-700 $319 $569 $250
Y-67 to Big Y-700 $259 $499 $240
Y-111 to Big Y-700 $229 $499 $270
Big Y-500 to Big Y-700 $189 $249 $60
HVR1 to mtFullSequence $99 $159 $60
mtDNA Plus to mtFullSequence $99 $159 $60

Tovana – A New Limited Availability Exome Medical Report 

Recently, FamilyTreeDNA did a limited announcement about a medically supervised health exome health test for a subset of customers, specifically customers who:

  • Don’t live in Pennsylvania, New York, California or Maryland, due to state law restrictions.
  • Took the Family Finder test since October 2015 – meaning no transfers. The Family Finder test is used in conjunction with the exome chip to generate the customer report.

If you took the Family Finder test before October 2015, you are eligible but the rollout is being done in stages and your kit will be eligible in December.

This Tovana Genome Report is focused towards people who are health and wellness conscious. Meaning those who don’t want to die a premature death that might be preventable.

All genetic health tests focus on predispositions. You may or may not develop the condition, with a few notable exceptions, but forewarned is forearmed.

You might, however, be VERY interested in intervening, one way or another, BEFORE you develop potentially life-threatening conditions, or taking preventative actions to avoid developing those conditions. At the very least, you can be aware and monitor your health to catch them early, when they are treatable, manageable or potentially curable.

It only takes one, ONE, terrifying experience to convince you that health testing might make a difference.

Once you’re embroiled in that health nightmare, there is no going back in time to take a test and enact preventative measures.

My mother might still be with us had we known she was susceptible to blood clots. My sister had metastatic breast cancer.

Let me show you something from a Tovana report.

FTDNA Tovana.png

This portion of a page from an actual customer report shows this individual is positive for a mutation for a clotting disorder where clots are formed that can cause strokes, pulmonary embolisms and DVTs (deep vein thrombosis).

I’d give anything, any amount of money – to have had advance warning so we could have watched my mother more vigilantly and taken simple proactive measures that might have prevented her stroke and resulting death.

What would another 10 or 15 years with her have been worth?

We could have and would have discussed this with her doctors and asked about preventative measures, like taking aspirin or other measures as indicated by her health and other medications. (Please do not self-diagnose or medicate without discussing with your physician as drugs interact in ways patients may not be aware of.)

Compared to hospital (or funeral) bills, not to mention the sheer agony…the cost of this test at $799 is irrelevant. What better way to say, “I love you”?

I would pick up bottles by the side of the road, if I needed to, to be able to purchase this test for my Mom 15 years ago. Sadly, this type of testing wasn’t available then, but it is now.

Ignorance is not bliss.

I want to know if I or my children carry these predispositions so that we can take action.

The Tovana Test is Different

The Tovana test is different from and much more comprehensive than the tests offered by Ancestry, MyHeritage and 23andMe that utilize only your autosomal genealogy test.

To begin with, the Tovana test is run on an exome chip that tests over 50 million locations in addition to the 700,000+ locations tested in the Family Finder test.

The completed report that I viewed was 128 pages in length, with lots of graphics. This  explain explains autosomal dominant inheritance.

FTDNA Tovana autosomal dominant.png

The report is very user-friendly, including drawings, a risk-meter for polygenic conditions that involve more than a simple yes or no answer, explanations and recommendations for each condition reported.

FTDNA Tovana risk meter.png

And yes, in case you’re wondering, the report also includes the fun traits like ear wax and such that you can discuss if you’re bored beyond imagination at a cocktail party.

Each report is centered around and tailored to the family information you provide, such as known Jewish heritage, or known cases of cancer.

FTDNA Tovana Table of Contents.png

Comparisons

I’ve compiled a chart with some comparison details – although this test is in a class by itself where the other three tests compete directly with each other.

I’ve personally taken the other tests, except for the Ancestry upgrade. I also took an early exome test a few years ago, but THAT ONE CAME WITH NO REPORT OR EXPLANATIONS.

  23andme Ancestry Health Core MyHeritage Family Tree DNA Tovana Test
# DNA locations tested About 700,000 About 700,000 About 700,000 >50 million plus the 700,000 in the Family Finder test
# Results Provided to Customer 78 health + polygenic diabetes +34 traits such as freckles 84 88+ polygenic heart, diabetes, breast cancer 3000+ including many polygenic diseases including heart, diabetes & 35 genes associated with breast cancer
Physician Oversight No PWNHealth PWNHealth Tovana
Personal Clinical Analysis No No No Yes
Analysis, Interpretation by board certified geneticist No No No Yes
Genetic Counseling No Yes, limited Yes, limited $50 for 30-minute session
Updates Yes, episodic depending on test level, may not receive, sometimes have to purchase new test No, one time results only Yes, free for first year then with $99 per year subscription Not at this time, but under consideration
Cost – Initial Purchase $149 upgrade only after DNA test $199 new purchase -combined health plus ancestry $799 introductory price
Upgrade if Already Tested No $49 upgrade if have already tested $120 to upgrade if already tested, plus $99 year subscription after year 1 Not relevant
Requirements None This is an upgrade from an existing Ancestry test Must test with MyHeritage, not a transfer kit

Are You Eligible?

To see if you are one of the customers eligible to purchase the Tovane Genome Report, sign in, here, and then check your personal page under “Additional Features” to see if the Tovana Genome Report is available. If so, click for more information or to order.

FTDNA Tovana order.png

You’ve probably guessed what my family is receiving for Christmas😊. No one else is going to suffer from or die from something preventable if I can help it.

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Disclosure

I receive a small contribution when you click on some of the links to vendors in my articles. This does NOT increase the price you pay but helps me to keep the lights on and this informational blog free for everyone. Please click on the links in the articles or to the vendors below if you are purchasing products or DNA testing.

Thank you so much.

DNA Purchases and Free Transfers

Genealogy Services

Genealogy Research

Big Y News and Stats + Sale

I must admit – this past January when FamilyTreeDNA announced the Big Y-700, an upgrade from the Big Y-500 product, I was skeptical. I wondered how much benefit testers would really see – but I was game to purchase a couple upgrades – and I did. Then, when the results came back, I purchased more!

I’m very pleased to announce that I’m no longer skeptical. I’m a believer.

The Big Y-700 has produced amazing results – and now FamilyTreeDNA has decoupled the price of the BAM file in addition to announcing substantial sale prices for their Thanksgiving Sale.

I’m going to discuss sale pricing for products other than the Big Y in a separate article because I’d like to focus on the progress that has been made on the phylogenetic tree (and in my own family history) as a result of the Big Y-700 this year.

Big Y Pricing Structure Change

FamilyTreeDNA recently anounced some product structure changes.

The Big Y-700 price has been permanently dropped by $100 by decoupling the BAM file download from the price of the test itself. This accomplishes multiple things:

  • The majority of testers don’t want or need the BAM file, so the price of the test has been dropped by $100 permanently in order to be able to price the Big Y-700 more attractively to encourage more testers. That’s good for all of us!!!
  • For people who ordered the Big Y-700 since November 1, 2019 (when the sale prices began) who do want the BAM file, they can purchase the BAM file separately through the “Add Ons and Upgrades” page, via the “Upgrades” tab for $100 after their test results are returned. There will also be a link on the Big Y-700 results page. The total net price for those testers is exactly the same, but it represents a $100 permanent price drop for everyone else.
  • This BAM file decoupling reduces the initial cost of the Big Y-700 test itself, and everyone still has the option of purchasing the BAM file later, which will make the Big Y-700 test more affordable. Additionally, it allows the tester who wants the BAM file to divide the purchase into two pieces, which will help as well.
  • The current sale price for the Big Y-700 for the tester who has taken NO PREVIOUS Y DNA testing is now just $399, formerly $649. That’s an amazing price drop, about 40%, in the 9 months since the Big Y-700 was introduced!
  • Upgrade pricing is available too, further down in this article.
  • If you order an upgrade from any earlier Big Y to the Big Y-700, you receive an upgraded BAM file because you already paid for the BAM file when you ordered your initial Big Y test.
  • The VCF file is still available for download at no additional cost with any Big Y test.
  • There is no change in the BAM file availability for current customers. Everyone who ordered before November 1, 2019 will be able to download their BAM file as always.

The above changes are permanent, except for the sale price.

2019 has been a Banner Year

I know how successful the Big Y-700 has been for kits and projects that I manage, but how successful has it been overall, in a scientific sense?

I asked FamilyTreeDNA for some stats about the number of SNPs discovered and the number of branches added to the Y phylotree.

Drum roll please…

Branches Added This Year Total Tree Branches Variants Added to Tree This Year Total Variants Added to Tree
2018 6,259 17,958 60,468 132.634
2019 4,394 22.352 32,193 164,827

The tests completed in 2019 are only representative for 10 months, through October, and not the entire year.

Haplotree Branches

Not every SNP discovered results in a new branch being added to the haplotree, but many do. This chart shows the number of actual branches added in 2018 and 2019 to date.

Big Y 700 haplotree branches.png

These stats, provided by FamilyTreeDNA, show the totals in the bottom row, which is a cumulative branch number total, not a monthly total. At the end of October 2019, the total number of individual branches were 22,352.

Big Y 700 haplotree branches small.png

This chart, above, shows some of the smaller haplogroups.

Big Y 700 haplotree branches large.png

This chart shows the larger haplogroups, including massive haplogroup R.

Haplotree Variants

The number of variants listed below is the number of SNPs that have been discovered, named and placed on the tree. You’ll notice that these numbers are a lot larger than the number of branches, above. That’s because roughly 168,000 of these are equivalent SNPs, meaning they don’t further branch the tree – at least not yet. These 168K variants are the candidates to be new branches as more people test and the tree can be further split.

Big Y 700 variants.png

These numbers also don’t include Private Variants, meaning SNPs that have not yet been named.

If you see Private Variants listed in your Big Y results, when enough people have tested positive for the same variant, and it makes sense, the variants will be given a SNP name and placed on the tree.

Big Y 700 variants small.png

The smaller haplogroups variants again, above, followed by the larger, below.

Big Y 700 variants large.png

Upgrades from the Big Y, or Big Y-500 to Big Y-700

Based on what I see in projects, roughly one third of the Big Y and Big Y-500 tests have upgraded to the Big Y-700.

For my Estes line, I wondered how much value the Big Y-700 upgrade would convey, if any, but I’m extremely glad I upgraded several kits. As a result of the Big Y-700, we’ve further divided the sons of Abraham, born in 1747. This granularity wasn’t accomplished by STR testing and wasn’t accomplished by the Big Y or Big Y-500 testing alone – although all of these together are building blocks. I’m ECSTATIC since it’s my own ancestral line that has the new lineage defining SNP.

Big Y 700 Estes.png

Every Estes man descended from Robert born in 1555 has R-BY482.

The sons of the immigrant, Abraham, through his father, Silvester, all have BY490, but the descendants of Silvester’s brother, Robert, do not.

Moses, son of Abraham has ZS3700, but the rest of Abraham’s sons don’t.

Then, someplace in the line of kit 831469, between Moses born in 1711 and the present-day tester, we find a new SNP, BY154784.

Big Y 700 Estes block tree.png

Looking at the block tree, we see the various SNPs that are entirely Estes, except for one gentleman who does not carry the Estes surname. I wrote about the Block Tree, here.

Without Big Y testing, none of these SNPs would have been found, meaning we could never have split these lines genealogically.

Every kit I’ve reviewed carries SNPs that the Big Y-700 has been able to discern that weren’t discovered previously.

Every. Single. One.

Now, even someone who hasn’t tested Y DNA before can get the whole enchilada – meaning 700+ STRs, testing for all previously discovered SNPs, and new branch defining SNPs, like my Estes men – for $399.

If a new Estes tester takes this test, without knowing anything about his genealogy, I can tell him a great deal about where to look for his lineage in the Estes tree.

Reduced Prices

FamilyTreeDNA has made purchasing the Big Y-700 outright, or upgrading, EXTREMELY attractive.

Test Price
Big Y-700 purchase with no previous Y DNA test

 

$399
Y-12 upgrade to Big Y-700 $359
Y-25 upgrade to Big Y-700 $349
Y-37 upgrade to Big Y-700 $319
Y-67 upgrade to Big Y-700 $259
Y-111 upgrade to Big Y-700 $229
Big Y or Big Y-500 upgrade to Big Y-700 $189

Note that the upgrades include all of the STR markers as yet untested. For example, the 12-marker to Big Y-700 includes all of the STRs between 25 and 111, in addition to the Big Y-700 itself. The Big Y-700 includes:

  • All of the already discovered SNPs, called Named Variants, extending your haplogroup all the way to the leaf at the end of your branch
  • Personal and previously undiscovered SNPs called Private Variants
  • All of the untested STR markers inclusive through 111 markers
  • A minimum of a total of 700 STR markers, including markers above 111 that are only available through Big Y-700 testing

With the refinements in the Big Y test over the past few years, and months, the Big Y is increasingly important to genealogy – equally or more so than traditional STR testing. In part, because SNPs are not prone to back mutations, and are therefore more stable than STR markers. Taken together, STRs and SNPs are extremely informative, helping to break down ancestral brick walls for people whose genealogy may not reach far back in time – and even those who do.

If you are a male and have not Y DNA tested, there’s never been a better opportunity. If you are a female, find a male on a brick wall line and sponsor a scholarship.

Click here to order or upgrade!

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Disclosure

I receive a small contribution when you click on some of the links to vendors in my articles. This does NOT increase the price you pay but helps me to keep the lights on and this informational blog free for everyone. Please click on the links in the articles or to the vendors below if you are purchasing products or DNA testing.

Thank you so much.

DNA Purchases and Free Transfers

Genealogy Services

Genealogy Research

Family Tree DNA Sale Prices Including Big Y-700 Upgrade

I was attempting to finish an article about the Family Tree DNA conference this past weekend and include special conference sale price information, but it looks like that article just isn’t going to happen right now.

Typically, the conference is held in November, so the Holiday Sale begins the last day of the conference. That’s not the case this year, so Bennett announced a special sale just for conference attendees, project members, and through me, you too! Read on, because these sale prices are NOT available to the general public although you can certainly share with your families.

Thank you Bennett!!!

The good news is that while I realize I just can’t get that article written right now, I’m providing the sale price information which is only valid through month end. These are really good prices.

  • $30 off Family Finder ($49) – Use Code: GGC19FF
  • $50 off Y-37 ($119) – Use Code: GGC19Y37
  • $70 off Y-67 ($198) – Use Code: GGC19Y67
  • $70 off Y-111 ($289) – Use Code: GGC19Y111
  • $200 off Big Y-700 meaning have never taken any Y DNA test ($449) – Use Code: GGC19BIGY
  • $50 off MtFull Sequence ($149) – Use Code: GGC19MTFULL

If you have taken one of the Y DNA STR tests, have never taken the Big Y-500 but want to upgrade from an existing 12, 25, 37, 67 or 111 marker STR test to the Big Y-700, here are the upgrade codes:

Upgrade Regular Price Final Price Code
Y12 to Big Y-700 $629 $449 GCC19122BY
Y25 to Big Y-700 $599 $449 GCC19252BY
Y37 to Big Y-700 $569 $449 GCC19372BY
Y67 to Big Y-700 $499 $399 GCC19BYUP
Y111 to Big Y-700 $449 $349 GCC19BYUP

All coupons codes expire March 31, 2019 and may not be used in conjunction with other promocodes, discounts, or offers.

Big Y-700 Upgrade – $179

The greatly anticipated Big Y-700 upgrade is now available.

In addition to the above sale prices for purchases, Bennett is offering the introductory upgrade price to move from the Y-500 to the Y-700 at just $179 through the end of the month. I was actually very surprised to see the price this low since it’s an actual rerun.

Family Tree DNA reviews each order to assure that enough DNA remains for the test. If not, they will reach out to you before processing begins to request another vial. If the tester is deceased, meaning they can’t provide an additional sample, please notify Family Tree DNA so that they can flag the sample for special handling in the lab, if necessary.

I wrote about the Big Y-700 here. If you want to read the scientific nitty-gritty, the Big Y-700 white paper is here. The white paper refers to the Big Y and compared to the Big Y-700. The Big Y is the same test as the Big Y-500, the difference being that Family Tree DNA added the additional STR markers for free (totaling 500) for all testers who had taken the Big Y and renamed the test at that time to Big Y-500.

To recap the benefits of a Big Y-700 as compared to the Big Y-500:

  • Big Y-700 provides 50% increase in quality SNPs over Big Y-500
  • Provides quality reads of Y chromosome regions not previously available
  • An additional 200 STR markers bringing the total from at least 500 to at least 700
  • Better coverage meaning fewer no-reads

Note that with the improved sequencing technology, it’s possible that men run on the Big Y-700 platform may not exactly match men run on the earlier Big Y-500 platform. If you’re working with a group of men who you “need” to be on the exact same platform in order to derive family lineages, then you’ll want all of the men on the same platform so you are comparing apples to apples. In the case of the Estes project, I’m hoping that the new technology will further divide my roughly 10 Big-Y men into distinct lineages in order to provide increased granularity.

I know that the price will increase after month-end and I don’t want anyone left behind. With my luck, the man I don’t upgrade will of course be the one with a newly-to-be-discovered mutation that I need.

If you are interested in upgrading from an existing Big Y-500 to a Big Y-700, there is no code needed. Click here to sign in to your account and then click on the upgrade button on your Y-DNA section of your personal page.

Y DNA Upgrade

You’ll then see the Big Y-700 upgrade, but only at this price for a few more days.

Big Y-700 upgrade

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Disclosure

I receive a small contribution when you click on some (but not all) of the links to vendors in my articles. This does NOT increase the price you pay but helps me to keep the lights on and this informational blog free for everyone. Please click on the links in the articles or to the vendors below if you are purchasing products or DNA testing.

Thank you so much.

DNA Purchases and Free Transfers

Genealogy Services

Genealogy Research

The Big Y Test Increases Again to Big Y-700

In Japan, at the Tanabata or Star Festival, attendees write their wishes on tanzaku, or small ribbon-like colorful pieces of paper and hang them on the tanzaku bamboo tree. For a very long time, Y DNA project administrators pestered Bennett Greenspan at Family Tree DNA to add more STR markers, useful in determining relationships between and within family lines.

We’ve been getting our wishes granted at breakneck speed in this past year, with the addition of the Big Y-500 (that’s 500 free STR markers) in April 2018. Now, our wishes have been granted again as Family Tree DNA expands the Big Y to 700 included STR markers.

Big Y-700 Tanzaku tree.png

Family Tree DNA just announced the Big Y-700 which replaces the Big Y-500.

The Big Y test itself provides a scan of the majority of the Y chromosome, providing results to testers including:

  • All SNPs found, both ancestral (original value) and derived (mutated state)
  • New mutations never discovered before known as Private Variants. It’s exciting to be a part of scientific discovery AND these are useful genealogically as well. I wrote about using the Estes Big Y results here.
  • Reports for named SNPs and private variants, both
  • Matching for SNPs
  • SNP tree placement
  • The new Block Tree
  • First 500, now 700 STR values included for free. You can read about how these markers work, here.
  • Matching to other testers for both SNPs and STRs above 111 (STRs below 111 are handled separately). I wrote about how the new matching above 111 markers works here. You can read about the difference between STRs and SNPs here.

According to this announcement, testers whose Big Y-500 results are now pending will automatically receive the new Big Y-700 instead of the Big Y-500 that they ordered. Family Tree DNA added another 200 STR markers. No need to do anything on your part.

This is great news for everyone who ordered on or after November 1, 2018 or anyone who has not yet received Big Y results. For the first time in history, no one will bemoan delayed results!

Family Tree DNA provided the following schedule of when Big Y-700 results can be expected – some very soon!

Order Placed Results Expected By
Before November 1, 2018 February 8, 2019
November 2018 February 20, 2019
December 1, 2018 to present March 6, 2019

It looks like another benefit of the new genetic testing technology will be quicker delivery dates now and into the future. Family Tree DNA hopes to reduce their delivery time on the Big Y-700 after the current backlog is released to 2-4 weeks.

How Did They Squeeze Another 200 Markers Out?

New chemistry used in processing the Big Y-700 test results in more uniform coverage of the Y chromosome and includes a much broader target region. This combination does three things:

  • Allows quality reads of regions previously unavailable
  • Provides more consistent results
  • Provides better coverage, meaning fewer no-reads
  • Allows for more STRs to be accessed and reliably read, hence the Big Y-500 is replaced by the Big Y-700

Price

The Big Y-700 prices, according to the Family Tree DNA e-mail to group administrators:

Big Y-700 pricing.png

Upgrades

Since the new Big Y-700 test provides an additional 200 markers above and beyond the Big Y-500, many people will want to know if upgrades are available. The answer is yes, they will be but not just yet and the upgrade price has not been announced. Expect an e-mail with this information around mid-March if you have already taken a Big Y or Big Y-500 test.

Because the new chemistry is needed to obtain the Big Y-700 results, this isn’t just reprocessing the existing data. Therefore, a new test actually has to be run in the lab on the sample to facilitate the Big Y-700 upgrade from the Big Y-500.

Obviously, if not enough of the original sample remains, this could be a problematic situation. I would suggest thinking conservatively about upgrading a Big Y-500 test where the tester can’t provide a new sample for testing. Every situation will be different.

Will My Big Y-500 Markers Change?

If you upgrade to the Big Y-700, your STR markers values above 111 may change due to the improved quality of the technology involved.

This means three things:

  • You may not match people you did before, or vice versa, on some markers
  • You may have results for markers you did not have results for before
  • Your matches to people who have also taken the Big Y-700 test will likely be more accurate than to people who took a Big Y-500 test. Apples to apples, so to speak.

What If My Results Change and I Want to Keep the Old Results?

You won’t be able to mix and match at will between the results of the Big Y-500 and Big Y-700 tests. No merging or combining results of the two tests allowed!

I asked about the situation where a tester has results for a specific marker in the Big Y-500, but that location is a no-call using the new Big Y-700 technology. Family Tree DNA replied that they did not anticipate this being an issue. I hope they are right.

I also asked about the situation where a marker value changes to NOT match men who have taken the Big Y-500 of the same surname. Would the person who took the Big Y-700 be able to “revert” to the older value (in other words, merge values for the two tests) for that conflicting marker? The answer is no, that the Big Y-700 technology is superior and more accurate. Remember that matching, meaning who is on your match list, is actually determined by the first 111 STR markers, not the additional STR markers provided by the Big Y-500 or Big Y-700, so markers above 111 will not affect who you do and don’t see on your match list.

The long-term answer is of course to upgrade the other men to Big Y-700 as well. In cases where that isn’t possible, project administrators and family members comparing these results for ancestral line marker mutations will simply have to make a note of any discrepancy.

If you do upgrade once the Big Y-700 upgrade becomes available, I would recommend printing or otherwise storing a copy of your Big Y-500 results for reference.

New Match Comparison Tools Planned

While the Big Y-500 (and soon 700) results are compared on an individual tester’s results page, there is currently no tool to allow administrators to compare groups of men, which is often how surname project grouping is achieved. This also means that results above 111 markers aren’t available on the pubic project pages.

While you may not have noticed if you’re just looking at your own results, project administrators need grouping tools in order to discern line marker mutations for specific lineages. The usefulness of Y DNA testing is, after all, in the comparison of the results to other men and forming clusters of men who match into genetic families. Every family group who is participating in Y DNA testing wants to discover markers that delineate between various male lines descending from a specific progenitor.

Let me give you a quick example. In my Campbell line, we’re still trying to discover the identity of the father of Charles Campbell, born about 1750. We know that he’s from the Campbell Clan line (Duke of Argyll) of Scotland based on his descendants’ Y DNA tests, but we can’t figure out which Campbell male he descends from (probably in Virginia) before he moved to Hawkins County, Tennessee about 1780. Hopefully, these new Y DNA STR markers may provide enough granularity, if a sufficient number of men upgrade, to help us track our line back in time. We need markers that are found only in Charles’s descendants and his father’s other descendants, whoever they might be, to connect us with the correct lineage. Hey, I’m a desperate genealogist – I’ll take every hint I can find! Fingers crossed.

Family Tree DNA indicates that new grouping tools for project administrators, and I presume that means project displays as well, are coming soon. I realize that scrolling to the right forever to see beyond 111 markers would be a pain, but I can’t think of a better way to facilitate comparisons of many men. If you have an idea, give me a shout. If you’d like to see a surname project example, here’s a link to the Estes project.

I look forward to the new FREE and included Big Y markers and upcoming tools. Thanks again Family Tree DNA!

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Disclosure

I receive a small contribution when you click on some (but not all) of the links to vendors in my articles. This does NOT increase the price you pay but helps me to keep the lights on and this informational blog free for everyone. Please click on the links in the articles or to the vendors below if you are purchasing products or DNA testing.

Thank you so much.

DNA Purchases and Free Transfers

Genealogy Services

Genealogy Research

Family Tree DNA’s New Big Y Block Tree

Family Tree DNA just released their new very cool new Block Tree for people who have taken the Big Y DNA test. Furthermore, Family Tree DNA is working hand-in-hand with citizen scientists. At the bottom of their new tree you’ll see the credit, “Layout based on the Big Tree by Alexander R. Williamson.”

I love collaboration because it benefits everyone.

If you have taken the Big Y test, sign on to your account and follow along. If you haven’t and you’re a male, you can always upgrade and if you’re a female, you can sponsor a male with a surname of interest.

Let’s step through the new Block Tree and see what it can tell us about our ancestors and their history. There’s so much here.

After signing on to your account, look under the Big Y-500 section on your personal pge and you’ll see the new Block Tree icon. If you’ve taken this test, you receive the new Block Tree automatically.

Block Tree icon

Click on the Block Tree icon and you’ll see an introduction.

Block Tree Tutorial

block tree tutorial.png

Cool! Trees, SNPs and branches combined with countries AND myOrigins results.

By clicking on “Show Me Around” you can see the various features. Watch for is the little pink blob that expands and contracts, kind of like a heartbeat.

block tree tutorial 1.png

Full screen makes a BIG difference. Pardon the pun.

block tree tutorial 2.png

Display options controls which features you see.

block tree display options.png

You can disable some of these cool functions, but why would anyone want to do that?

Block tree tutorial 3.png

Reset, the ultimate bread crumb trail. Back to the trailhead.

Block tree tutorial 4.png

We’ll try each of these features after the tutorial.

block tree tutorial 5.png

Note that the equivalent SNPs for each branch are included too. In the future, it’s possible that branches maybe divided into two smaller branches between equivalent SNPs. At that point, they won’t be equivalent anymore, because a difference will have been found.

BLock tree tutorial 6.png

Note, at the top of the display are the parent branches of the tree above the SNP boxes shown.

BLock tree parent branches

Click to enlarge.

You can step yourself all the way back up the tree if you wish to do so. In this view, you can see R-M207, the root of haplogroup R at the upper left. Wow, look at all of those branches that are children beneath R-Z39589, the navy blue block.

If you click on R-M207, you’ll see R-M207 and then, upstream, haplogroup P-M45 which gave birth to R-M207 and brother brother branch, Q-M242.

BLock tree SNP path.png

If you get lost on this block tree trying to see major branches and how they relate, remember you can reference the main branching haplotree in pedigree format here.

By clicking on any haplogroup, you can quickly see how they relate to others. For example, here’s P showing Q-M242 and M207 underneath on the pedigree tree.

Block tree to pedigree tree.png

I wrote about how to use this tree in the article, Family Tree DNA’s PUBLIC Y DNA Haplotree.

The block tree is private, meaning not available publicly, because it’s designed to show the names of your matches who have given permission for matching and sharing.

Ok, let’s get down to the nitty gritty.

You and Your Matches on the Block Tree

After you review the tutorial, you’ll see the block tree as it relates to you and your test results.

block tree main view.png

I’m using the test of a man as compared to a group of men whose tests I manage as examples. They have all granted sharing permission, but it’s just easier to blur identities for privacy than to explain repeatedly why I didn’t.

Your own branch is shown to the far left and is labeled as such. To the right, you’ll see all of the neighbor branches. Some will be brother branches, descended from the same parent SNP, like BY482 and R-ZP276, above. Others will be more distantly related.

block tree origins legend.png

Below your branch, a legend referring to the colors in the circle rings in the Origins section is provided.

Family Tree DNA has given us a lot of information  to unpack.

block tree your branch.png

What are we actually looking at?

Your SNP branch block is the one with a white background and a black border, in this case, R-ZS3700.

The teal box underneath includes the average number of private variants, meaning SNP mutations not yet named and located on the tree. Multiple occurrences of private variant mutations must be documented in different men in a reliable genome location before the SNP can be named and placed in its correct position on a branch of the haplotree.

If you hover over the teal box below your “terminal” or currently end-of-line SNP, you’ll see a pop-up box describing the variants. Different men will have different numbers of private variants based on any number of factors, including de novo (one off) mutations and read errors. Therefore, an average is used.

If you click on R-ZS3700, or any SNP, you’ll see just that branch in the display, without neighbor branches.

block tree individual branch.png

There are two people in this branch – you and your match. You have a total of 8 combined origins.

Distance, Years and SNPs

One of the questions all genealogists seek to answer is when. We want to know when and how closely we’re related to these men we match, either closely or distantly.

Unfortunately, that question, without genealogy, is very difficult to answer. Many researchers have spent approaching two decades now attempting to reliably answer that question. The key word here is reliably.

The general consensus is that a SNP generation is someplace, on average, between 80 and roughly 140 years. The topic is hotly debated, and many factors can play into SNP age calculations.

Family Tree DNA has approached this a little differently. They have provided a scale of number of SNPs on the left hand side. Each SNP represents one grey block.

block tree SNP generations.png

Here’s what I can tell you positively about the men in this example. SNP R-BY490 was born about 1600. The father who is confirmed through testing of multiple sons was positive for BY482 but not BY490 and was born in 1555.

There are a total of 5 SNPs plus Private Variants between the current tester whose account we are viewing and the birth of R-BY490.

Ancestor birth Tester birth Difference SNPs Years per SNP
1600 1928 328 5 65.6
1711 1928 217 4 54.25

A second example is equally as relevant. ZS3700 was born in 1711, proven through testing of multiple sons’ lines.

You can see that the average can vary quite a bit. Trying to calculate many generations back in time, with many branches having gone extinct along the way, with no proven genealogical lineages to help the process is fraught with landmines.

Countries

I love the view that incorporates countries and geography which shows in a very visual way where different branches of the genetic family line migrated to and settled. At least, where their descendants are clustered today.

block tree countries.png

In the wide view, above, we can see the history and birth of various SNPs in the blue box portion of the chart.

For example, the first split shown, beneath the large dark blue block including BY347 at the bottom occurred 33 SNP generations ago. If a SNP generation is 100 years, on average, then that’s 3300 years ago.

As new private variants are placed in different locations on the tree, this number of SNP generations may increase over time.

There are only two branches shown as descending from the navy blue SNP box; the largest medium blue block showing R-BY336 at the top and the turquoise Private Variant block with 27 variants, at far right.

block tree SNPS and clusters.png

The medium blue block box that includes SNP R-BY336 at the top and Y93760 at the bottom spans 16-33 SNP generations. Each SNP listed represents a SNP generation which is why each SNP is shown on a separate row equating to one grey bar at left.

Looking at the bottom of your display, you see the country of the location of the earliest known ancestor as listed by testers.

block tree flag icon.png

By hovering over the flag, you can identify the country, and by clicking on the flag, you see the detailed view of myOrigins of the testers for the SNP that flag is associated with – in this case, BY390.

block tree SNP plus origins detail view.png

Family Tree DNA has incorporated the highest combined regional myOrigins results for the testers into the display for the Big Y as a ring, plus the location of the testers’ Earliest Known Ancestor as completed in their personal information, found under their profile picture, under the genealogy tab.

Of course, as more people test, this information is subject to change, so check periodically.

block tree countries plus origins.png

The red boxes above indicate the pieces of information that are relevant for SNP R-BY490.

By hovering your mouse over the Origins box, you’ll see that the people in the group who are positive for BY490 have a total of 12 origins of which the highest two are British Isles and West and Central Europe. It just so happens that the earliest known proven ancestor of these men is found in England in the 1400s.

The US flag means that testers are stuck here. A feather indicates that the individuals identified their earliest known ancestor as Native American. I always take that with a grain of salt barring other evidence, such as a cluster (not based on oral history alone) or a known Native haplogroup.

Hint – Please note that if you have “0 Origins” showing, in order for your Origins to be included, you must enable “Origins Sharing” as well as “Project Sharing” for this information to appear on the branch. These options can be found under “Manage Personal Information” below your photo on your personal page, under Account Settings, then “Privacy and Sharing” and “Project Preferences” tabs, respectively.

My Matches

Your matches are shown below the blocks that represent the various SNPs. When you exceed the match threshold of 30 SNPs, you are no longer shown as a match to individuals, and their names will no longer show on the block tree – but the block tree SNP information will remain without their names.

If you want to find out the surnames, locations and ancestors of those people who have tested but aren’t shown as matches, you have a couple of options.

  • If testers have granted permission in their privacy setting to allow their information to be shown in projects, you can visit the appropriate haplogroup project to view their surname and earliest known ancestor information, if they have provided such. Fingers crossed that they did.
  • A google search with the following text string will likely be productive:

<snp ID> haplogroup family tree dna projects

For those people who you do match, by clicking on the matches option in the upper left-hand corner of the block tree page, you will see the following display:

block tree my matches.png

Your matches are shown at left. You can see in this case that all 8 of this man’s matches are shown at BY482 or below, shown in the first three SNP blocks counting from the left on the block tree. The ancestor who produced BY482 was born approximately 16 SNP generations ago. If we use 100 years as an average, that’s 1600 years ago, or about the year 400. So far, all of the men who have tested and are positive for BY482 have a known ancestor in the British Isles.

You can see your matches on the block tree by:

  • viewing this list beside the block tree
  • viewing your matches in their respective haplogroup blocks
  • by clicking on their name to view their individual profile cards

block tree match profile.png

Of course, you can always go back to your account to view the matches on the Big Y-500 matches tab.

block tree Big Y options.png

You can learn more about the Big Y-500 Block Tree here.

In Summary

For me the real power in the Block Tree isn’t just the new visual view. I love that, but I can also use the Block Tree to “see through time” a bit.

I’m clicking back (up arrow on the tree) to view the base of haplogroup Q. As you may know, subgroups of haplogroup Q are found in many locations around the world.

BLock tree hap Q.png

If there was ever a graphic to show, using science, that we are truly all related, this is it. Haplogroup Q is divided into 3 primary blocks.

People of primarily Ashkenazi Jewish origin scattered throughout the world. People of European origins, and people of Native American, Mexican, Russian and Norwegian origins.

Of course, when you look deeper at these three parent SNPs, you’ll see further breakdowns that represent migrations in time and geography.

That is, after all, how we learn about our ancestors before surnames and before genealogical records.

That history is written in our DNA and the DNA of the people to whom we are related, whether we know it or not.

If you are a male and haven’t taken the Big Y-500, please order or upgrade today. Who is waiting on you?

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Disclosure

I receive a small contribution when you click on some (but not all) of the links to vendors in my articles. This does NOT increase the price you pay but helps me to keep the lights on and this informational blog free for everyone. Please click on the links in the articles or to the vendors below if you are purchasing products or DNA testing.

Thank you so much.

DNA Purchases and Free Transfers

Genealogy Services

Genealogy Research

2018 – The Year of the Segment

Looking in the rear view mirror, what a year! Some days it’s been hard to catch your breath things have been moving so fast.

What were the major happenings, how did they affect genetic genealogy and what’s coming in 2019?

The SNiPPY Award

First of all, I’m giving an award this year. The SNiPPY.

Yea, I know it’s kinda hokey, but it’s my way of saying a huge thank you to someone in this field who has made a remarkable contribution and that deserves special recognition.

Who will it be this year?

Drum roll…….

The 2018 SNiPPY goes to…

DNAPainter – The 2018 SNiPPY award goes to DNAPainter, without question. Applause, everyone, applause! And congratulations to Jonny Perl, pictured below at Rootstech!

Jonny Perl created this wonderful, visual tool that allows you to paint your matches with people on your chromosomes, assigning the match to specific ancestors.

I’ve written about how to use the tool  with different vendors results and have discovered many different ways to utilize the painted segments. The DNA Painter User Group is here on Facebook. I use DNAPainter EVERY SINGLE DAY to solve a wide variety of challenges.

What else has happened this year? A lot!

Ancient DNA – Academic research seldom reports on Y and mitochondrial DNA today and is firmly focused on sequencing ancient DNA. Ancient genome sequencing has only recently been developed to a state where at least some remains can be successfully sequenced, but it’s going great guns now. Take a look at Jennifer Raff’s article in Forbes that discusses ancient DNA findings in the Americas, Europe, Southeast Asia and perhaps most surprising, a first generation descendant of a Neanderthal and a Denisovan.

From Early human dispersals within the Americas by Moreno-Mayer et al, Science 07 Dec 2018

Inroads were made into deeper understanding of human migration in the Americas as well in the paper Early human dispersals within the Americas by Moreno-Mayer et al.

I look for 2019 and on into the future to hold many more revelations thanks to ancient DNA sequencing as well as using those sequences to assist in understanding the migration patterns of ancient people that eventually became us.

Barbara Rae-Venter and the Golden State Killer Case

Using techniques that adoptees use to identify their close relatives and eventually, their parents, Barbara Rae-Venter assisted law enforcement with identifying the man, Joseph DeAngelo, accused (not yet convicted) of being the Golden State Killer (GSK).

A very large congratulations to Barbara, a retired patent attorney who is also a genealogist. Nature recognized Ms. Rae-Venter as one of 2018’s 10 People Who Mattered in Science.

DNA in the News

DNA is also represented on the 2018 Nature list by Viviane Slon, a palaeogeneticist who discovered an ancient half Neanderthal, half Denisovan individual and sequenced their DNA and He JianKui, a Chinese scientist who claims to have created a gene-edited baby which has sparked widespread controversy. As of the end of the year, He Jiankui’s research activities have been suspended and he is reportedly sequestered in his apartment, under guard, although the details are far from clear.

In 2013, 23andMe patented the technology for designer babies and I removed my kit from their research program. I was concerned at the time that this technology knife could cut two ways, both for good, eliminating fatal disease-causing mutations and also for ethically questionable practices, such as eugenics. I was told at the time that my fears were unfounded, because that “couldn’t be done.” Well, 5 years later, here we are. I expect the debate about the ethics and eventual regulation of gene-editing will rage globally for years to come.

Elizabeth Warren’s DNA was also in the news when she took a DNA test in response to political challenges. I wrote about what those results meant scientifically, here. This topic became highly volatile and politicized, with everyone seeming to have a very strongly held opinion. Regardless of where you fall on that opinion spectrum (and no, please do not post political comments as they will not be approved), the topic is likely to surface again in 2019 due to the fact that Elizabeth Warren has just today announced her intention to run for President. The good news is that DNA testing will likely be discussed, sparking curiosity in some people, perhaps encouraging them to test. The bad news is that some of the discussion may be unpleasant at best, and incorrect click-bait at worst. We’ve already had a rather unpleasant sampling of this.

Law Enforcement and Genetic Genealogy

The Golden State Killer case sparked widespread controversy about using GedMatch and potentially other genetic genealogy data bases to assist in catching people who have committed violent crimes, such as rape and murder.

GedMatch, the database used for the GSK case has made it very clear in their terms and conditions that DNA matches may be used for both adoptees seeking their families and for other uses, such as law enforcement seeking matches to DNA sequenced during a criminal investigation. Since April 2018, more than 15 cold case investigations have been solved using the same technique and results at GedMatch. Initially some people removed their DNA from GedMatch, but it appears that the overwhelming sentiment, based on uploads, is that people either aren’t concerned or welcome the opportunity for their DNA matches to assist apprehending criminals.

Parabon Nanolabs in May established a genetic genealogy division headed by CeCe Moore who has worked in the adoptee community for the past several years. The division specializes in DNA testing forensic samples and then assisting law enforcement with the associated genetic genealogy.

Currently, GedMatch is the only vendor supporting the use of forensic sample matching. Neither 23anMe nor Ancestry allow uploaded data, and MyHeritage and Family Tree DNA’s terms of service currently preclude this type of use.

MyHeritage

Wow talk about coming onto the DNA world stage with a boom.

MyHeritage went from a somewhat wobbly DNA start about 2 years ago to rolling out a chromosome browser at the end of January and adding important features such as SmartMatching which matches your DNA and your family trees. Add triangulation to this mixture, along with record matching, and you’re got a #1 winning combination.

It was Gilad Japhet, the MyHeritage CEO who at Rootstech who christened 2018 “The Year of the Segment,” and I do believe he was right. Additionally, he announced that MyHeritage partnered with the adoption community by offering 15,000 free kits to adoptees.

In November, MyHeritage hosted MyHeritage LIVE, their first user conference in Oslo, Norway which focused on both their genealogical records offerings as well as DNA. This was a resounding success and I hope MyHeritage will continue to sponsor conferences and invest in DNA. You can test your DNA at MyHeritage or upload your results from other vendors (instructions here). You can follow my journey and the conference in Olso here, here, here, here and here.

GDPR

GDPR caused a lot of misery, and I’m glad the implementation is behind us, but the the ripples will be affecting everyone for years to come.

GDPR, the European Data Protection Regulation which went into effect on May 25,  2018 has been a mixed and confusing bag for genetic genealogy. I think the concept of users being in charge and understanding what is happened with their data, and in this case, their data plus their DNA, is absolutely sound. The requirements however, were created without any consideration to this industry – which is small by comparison to the Googles and Facebooks of the world. However, the Googles and Facebooks of the world along with many larger vendors seem to have skated, at least somewhat.

Other companies shut their doors or restricted their offerings in other ways, such as World Families Network and Oxford Ancestors. Vendors such as Ancestry and Family Tree DNA had to make unpopular changes in how their users interface with their software – in essence making genetic genealogy more difficult without any corresponding positive return. The potential fines, 20 million plus Euro for any company holding data for EU residents made it unwise to ignore the mandates.

In the genetic genealogy space, the shuttering of both YSearch and MitoSearch was heartbreaking, because that was the only location where you could actually compare Y STR and mitochondrial HVR1/2 results. Not everyone uploaded their results, and the sites had not been updated in a number of years, but the closure due to GDPR was still a community loss.

Today, mitoydna.org, a nonprofit comprised of genetic genealogists, is making strides in replacing that lost functionality, plus, hopefully more.

On to more positive events.

Family Tree DNA

In April, Family Tree DNA announced a new version of the Big Y test, the Big Y-500 in which at least 389 additional STR markers are included with the Big Y test, for free. If you’re lucky, you’ll receive between 389 and 439 new markers, depending on how many STR markers above 111 have quality reads. All customers are guaranteed a minimum of 500 STR markers in total. Matching was implemented in December.

These additional STR markers allow genealogists to assemble additional line marker mutations to more granularly identify specific male lineages. In other words, maybe I can finally figure out a line marker mutation that will differentiate my ancestor’s line from other sons of my founding ancestor😊

In June, Family Tree DNA announced that they had named more than 100,000 SNPs which means many haplogroup additions to the Y tree. Then, in September, Family Tree DNA published their Y haplotree, with locations, publicly for all to reference.

I was very pleased to see this development, because Family Tree DNA clearly has the largest Y database in the industry, by far, and now everyone can reap the benefits.

In October, Family Tree DNA published their mitochondrial tree publicly as well, with corresponding haplogroup locations. It’s nice that Family Tree DNA continues to be the science company.

You can test your Y DNA, mitochondrial or autosomal (Family Finder) at Family Tree DNA. They are the only vendor offering full Y and mitochondrial services complete with matching.

2018 Conferences

Of course, there are always the national conferences we’re familiar with, but more and more, online conferences are becoming available, as well as some sessions from the more traditional conferences.

I attended Rootstech in Salt Lake City in February (brrrr), which was lots of fun because I got to meet and visit with so many people including Mags Gaulden, above, who is a WikiTree volunteer and writes at Grandma’s Genes, but as a relatively expensive conference to attend, Rootstech was pretty miserable. Rootstech has reportedly made changes and I hope it’s much better for attendees in 2019. My attendance is very doubtful, although I vacillate back and forth.

On the other hand, the MyHeritage LIVE conference was amazing with both livestreamed and recorded sessions which are now available free here along with many others at Legacy Family Tree Webinars.

Family Tree University held a Virtual DNA Conference in June and those sessions, along with others, are available for subscribers to view.

The Virtual Genealogical Association was formed for those who find it difficult or impossible to participate in local associations. They too are focused on education via webinars.

Genetic Genealogy Ireland continues to provide their yearly conference sessions both livestreamed and recorded for free. These aren’t just for people with Irish genealogy. Everyone can benefit and I enjoy them immensely.

Bottom line, you can sit at home and educate yourself now. Technology is wonderful!

2019 Conferences

In 2019, I’ll be speaking at the National Genealogical Society Family History Conference, Journey of Discovery, in St. Charles, providing the Special Thursday Session titled “DNA: King Arthur’s Mighty Genetic Lightsaber” about how to use DNA to break through brick walls. I’ll also see attendees at Saturday lunch when I’ll be providing a fun session titled “Twists and Turns in the Genetic Road.” This is going to be a great conference with a wonderful lineup of speakers. Hope to see you there.

There may be more speaking engagements at conferences on my 2019 schedule, so stay tuned!

The Leeds Method

In September, Dana Leeds publicized The Leeds Method, another way of grouping your matches that clusters matches in a way that indicates your four grandparents.

I combine the Leeds method with DNAPainter. Great job Dana!

Genetic Affairs

In December, Genetic Affairs introduced an inexpensive subscription reporting and visual clustering methodology, but you can try it for free.

I love this grouping tool. I have already found connections I didn’t know existed previously. I suggest joining the Genetic Affairs User Group on Facebook.

DNAGedcom.com

I wrote an article in January about how to use the DNAGedcom.com client to download the trees of all of your matches and sort to find specific surnames or locations of their ancestors.

However, in December, DNAGedcom.com added another feature with their new DNAGedcom client just released that downloads your match information from all vendors, compiles it and then forms clusters. They have worked with Dana Leeds on this, so it’s a combination of the various methodologies discussed above. I have not worked with the new tool yet, as it has just been released, but Kitty Cooper has and writes about it here.  If you are interested in this approach, I would suggest joining the Facebook DNAGedcom User Group.

Rootsfinder

I have not had a chance to work with Rootsfinder beyond the very basics, but Rootsfinder provides genetic network displays for people that you match, as well as triangulated views. Genetic networks visualizations are great ways to discern patterns. The tool creates match or triangulation groups automatically for you.

Training videos are available at the website and you can join the Rootsfinder DNA Tools group at Facebook.

Chips and Imputation

Illumina, the chip maker that provides the DNA chips that most vendors use to test changed from the OmniExpress to the GSA chip during the past year. Older chips have been available, but won’t be forever.

The newer GSA chip is only partially compatible with the OmniExpress chip, providing limited overlap between the older and the new results. This has forced the vendors to use imputation to equalize the playing field between the chips, so to speak.

This has also caused a significant hardship for GedMatch who is now in the position of trying to match reasonably between many different chips that sometimes overlap minimally. GedMatch introduced Genesis as a sandbox beta version previously, but are now in the process of combining regular GedMatch and Genesis into one. Yes, there are problems and matching challenges. Patience is the key word as the various vendors and GedMatch adapt and improve their required migration to imputation.

DNA Central

In June Blaine Bettinger announced DNACentral, an online monthly or yearly subscription site as well as a monthly newsletter that covers news in the genetic genealogy industry.

Many educators in the industry have created seminars for DNACentral. I just finished recording “Getting the Most out of Y DNA” for Blaine.

Even though I work in this industry, I still subscribed – initially to show support for Blaine, thinking I might not get much out of the newsletter. I’m pleased to say that I was wrong. I enjoy the newsletter and will be watching sessions in the Course Library and the Monthly Webinars soon.

If you or someone you know is looking for “how to” videos for each vendor, DNACentral offers “Now What” courses for Ancestry, MyHeritage, 23andMe, Family Tree DNA and Living DNA in addition to topic specific sessions like the X chromosome, for example.

Social Media

2018 has seen a huge jump in social media usage which is both bad and good. The good news is that many new people are engaged. The bad news is that people often given faulty advice and for new people, it’s very difficult (nigh on impossible) to tell who is credible and who isn’t. I created a Help page for just this reason.

You can help with this issue by recommending subscribing to these three blogs, not just reading an article, to newbies or people seeking answers.

Always feel free to post links to my articles on any social media platform. Share, retweet, whatever it takes to get the words out!

The general genetic genealogy social media group I would recommend if I were to select only one would be Genetic Genealogy Tips and Techniques. It’s quite large but well-managed and remains positive.

I’m a member of many additional groups, several of which are vendor or interest specific.

Genetic Snakeoil

Now the bad news. Everyone had noticed the popularity of DNA testing – including shady characters.

Be careful, very VERY careful who you purchase products from and where you upload your DNA data.

If something is free, and you’re not within a well-known community, then YOU ARE THE PRODUCT. If it sounds too good to be true, it probably is. If it sounds shady or questionable, it’s probably that and more, or less.

If reputable people and vendors tell you that no, they really can’t determine your Native American tribe, for example, no other vendor can either. Just yesterday, a cousin sent me a link to a “tribe” in Canada that will, “for $50, we find one of your aboriginal ancestors and the nation stamps it.” On their list of aboriginal people we find one of my ancestors who, based on mitochondrial DNA tests, is clearly NOT aboriginal. Snake oil comes in lots of flavors with snake oil salesmen looking to prey on other people’s desires.

When considering DNA testing or transfers, make sure you fully understand the terms and conditions, where your DNA is going, who is doing what with it, and your recourse. Yes, read every single word of those terms and conditions. For more about legalities, check out Judy Russell’s blog.

Recommended Vendors

All those DNA tests look yummy-good, but in terms of vendors, I heartily recommend staying within the known credible vendors, as follows (in alphabetical order).

For genetic genealogy for ethnicity AND matching:

  • 23andMe
  • Ancestry
  • Family Tree DNA
  • GedMatch (not a vendor because they don’t test DNA, but a reputable third party)
  • MyHeritage

You can read about Which DNA Test is Best here although I need to update this article to reflect the 2018 additions by MyHeritage.

Understand that both 23andMe and Ancestry will sell your DNA if you consent and if you consent, you will not know who is using your DNA, where, or for what purposes. Neither Family Tree DNA, GedMatch, MyHeritage, Genographic Project, Insitome, Promethease nor LivingDNA sell your DNA.

The next group of vendors offers ethnicity without matching:

  • Genographic Project by National Geographic Society
  • Insitome
  • LivingDNA (currently working on matching, but not released yet)

Health (as a consumer, meaning you receive the results)

Medical (as a contributor, meaning you are contributing your DNA for research)

  • 23andMe
  • Ancestry
  • DNA.Land (not a testing vendor, doesn’t test DNA)

There are a few other niche vendors known for specific things within the genetic genealogy community, many of whom are mentioned in this article, but other than known vendors, buyer beware. If you don’t see them listed or discussed on my blog, there’s probably a reason.

What’s Coming in 2019

Just like we couldn’t have foreseen much of what happened in 2018, we don’t have access to a 2019 crystal ball, but it looks like 2019 is taking off like a rocket. We do know about a few things to look for:

  • MyHeritage is waiting to see if envelope and stamp DNA extractions are successful so that they can be added to their database.
  • www.totheletterDNA.com is extracting (attempting to) and processing DNA from stamps and envelopes for several people in the community. Hopefully they will be successful.
  • LivingDNA has been working on matching since before I met with their representative in October of 2017 in Dublin. They are now in Beta testing for a few individuals, but they have also just changed their DNA processing chip – so how that will affect things and how soon they will have matching ready to roll out the door is unknown.
  • Ancestry did a 2018 ethnicity update, integrating ethnicity more tightly with Genetic Communities, offered genetic traits and made some minor improvements this year, along with adding one questionable feature – showing your matches the location where you live as recorded in your profile. (23andMe subsequently added the same feature.) Ancestry recently said that they are promising exciting new tools for 2019, but somehow I doubt that the chromosome browser that’s been on my Christmas list for years will be forthcoming. Fingers crossed for something new and really useful. In the mean time, we can download our DNA results and upload to MyHeritage, Family Tree DNA and GedMatch for segment matching, as well as utilize Ancestry’s internal matching tools. DNA+tree matching, those green leaf shared ancestor hints, is still their strongest feature.
  • The Family Tree DNA Conference for Project Administrators will be held March 22-24 in Houston this year, and I’m hopeful that they will have new tools and announcements at that event. I’m looking forward to seeing many old friends in Houston in March.

Here’s what I know for sure about 2019 – it’s going to be an amazing year. We as a community and also as individual genealogists will be making incredible discoveries and moving the ball forward. I can hardly wait to see what quandaries I’ve solved a year from now.

What mysteries do you want to unravel?

I’d like to offer a big thank you to everyone who made 2018 wonderful and a big toast to finding lots of new ancestors and breaking down those brick walls in 2019.

Happy New Year!!!

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Disclosure

I receive a small contribution when you click on some (but not all) of the links to vendors in my articles. This does NOT increase the price you pay but helps me to keep the lights on and this informational blog free for everyone. Please click on the links in the articles or to the vendors below if you are purchasing products or DNA testing.

Thank you so much.

DNA Purchases and Free Transfers

Genealogy Services

Genealogy Research

Big Y-500 STR Matching

Family Tree DNA recently introduced Big Y-500 STR matching for men who have taken  the Big Y-500 test. This is in addition to the SNP results and matching. If you’d like an introduction or definition of the terms STR and SNP, you can read about SNPs and STRs here.

Beginning in April 2018, Family Tree DNA included an additional 379+ STR markers for free for Big Y testers as a bonus, meaning for free, including all earlier testers.

While the Big Y-500 STR marker values have been included in customers’ results for several months, unless you contacted your matches directly, you didn’t know how many of those additional markers above 111 you matched on – until now.

If you haven’t taken the Big Y test, the article Why the Big Y Test? will explain why you might want to. In addition to the Big Y results, which refine your haplogroup and scan the entire gold standard region of the Y chromosome looking for SNPs, you’ll also receive at least 389 Y STR markers above the 111 STR panel for total of at least 500, for free – which is why the name of the Big Y test was changed to the Big Y-500. If you haven’t tested at the 111 marker level, don’t worry about that because the cost of the upgrade is bundled in the price of the Big Y-500 test. Click here to sign in to your account and then click on the blue upgrade button to view pricing.

Big Y-500 STR Matching

To view your matches and values above the traditional 111 makers, sign on to your account and click on Y DNA matches.

You’ll see the following display.

Y500 matches

The column “Big Y-500 STR Differences” is new. If you have not taken the Big Y-500 test, you won’t see this column.

If you have taken the Big Y-500, you’ll see results for any other man that you match who has taken the Big Y-500 test. In this example, 5 of this person’s matches have also taken the Big Y-500 test.

What Are Big Y-500 STR Differences?

The “Big Y-500 STR Differences” column values are expressed in the format “4 of 441” or something similar.

The first number represents the number of non-matching locations you have above 111 markers – in this case, 4. In the csv download file, this value is displayed in the “Big Y-500 Differences” column.

The second number represents the total number of markers above 111 that have a value for both of you – in this case, 441. In other words, you and the other man are being compared on 441 marker locations. In the csv download file, this value is displayed in the “Big Y-500 Compared” column.

Because the markers above 111 are processed using NGS (next generation sequencing) scan technology, virtually every kit will have some marker locations that have no-calls, meaning the test doesn’t read reliably at that location in spite of being scanned several times.

It’s more difficult to read STRs accurately using NGS scan technology, as compared to SNPs. SNPs are only one position in length, so only one position needs to be read correctly. STRs are repeated of a sequence of nucleotides. A 20 repeat sequence could consist of 20 copies of a series of 4 nucleotides, so a total of 80 positions in a row would need to be successfully read several times.

Let’s take a look at how matching works.

How Does Big Y-500 STR Matching Work?

If you have a total of 441 markers that read reliably, but your match has a total of 439 that produced results, the maximum number of markers possible to share would be 439. If you both have no calls on different marker locations, you would match on fewer than 439 locations. Here’s an example just using 9 fictitious markers.

Y500 match example

Based on the example above, we can see that the red cells can’t match because they experienced no-calls, and the yellow cells do have results, but don’t match.

Y500 summary

New Filter

There’s also a new filter option so you can view only matches that have taken the Big Y-500 test.

Y500 filter

Let’s look at some of the questions people have been asking.

Frequently Asked Questions

Question 1: Are the markers above 111 taken into account in the Genetic Distance column?

Answer: No, the values calculated in the genetic distance column are the number of mismatches for the marker level you are viewing using a combination of the step-wise and infinite alleles mutation models. (Stay with me here.)

In our example, we’re viewing the 111 marker level, so the genetic distance tells you the number of mismatches at 111 markers. If we were viewing the 67 marker level, then the genetic distance would be for 67 markers.

The number of mismatches above 111 markers shows separately in the “Big Y-500 STR Differences” column and is calculated using the infinite alleles model, meaning every mutation is counted as one difference. You can read more about genetic distance in the article, Concepts – Genetic Distance.

The good news is that you don’t need to calculate anything, but you may want to understand how the markers are scored and how the genetic distance is calculated. If so, go ahead and read question 2. If not, skip to question 3.

Question 2: What’s the difference between the step-wise model and the infinite alleles model?

Answer: The step-wise model assumes that a mutated value on a particular marker of multiple steps, meaning a difference between a 28 for one man and a 30 for another is a result of two separate mutation events that happened at different times, so counted as 2 mutations, 2 steps, so a genetic distance of 2.

However, this doesn’t work well with palindromic markers, explained here, where multi-copy markers, such as DYS464, often mutate more than one step at a time.

Counting multiple mathematical differences as only one mutation event is called the infinite alleles model. For example, a dual copy marker that has a value of 15-16 could mutate to 15-18 in one step and would be counted as one mutation event, and one difference and a genetic distance of one using the infinite alleles model. The same event would count as 2 mutation events (steps) and a genetic distance of 2 using the step-wise mutation model. In this article, I explain which markers are calculated using which methodology.

Another good infinite alleles example is when a location loses it’s DNA at a marker entirely. If the marker value for most men being compared is 10 and is being compared to a  person with no DNA at that location, resulting in a null value of 0 (which is not the same as a no-call which means the location couldn’t be read successfully), the mutation event happened in one step, and the difference should be counted as one event, one step and a genetic distance of one, not 10 events, 10 steps and a genetic distance of 10.

To recap, the values of markers 1-111 are calculated by a combination of the step-wise model and the infinite alleles model, depending on the marker number and situation. The differences in markers above 111 are calculated using the infinite alleles model where every mutation or difference equals a distance of one unless a zero (null) is encountered. In that case, the mutation event is considered a one. However, above 111 markers, using NGS technology, most instances where no DNA is encountered results in a no-read, not a null value.

Question 3: Has the TIP calculator been updated?

Answer: No, the TIP calculator does not take into account the new markers above 111. The TIP calculator relies upon the combined statistical mutation frequency for each marker and includes haplogroup differences. Therefore, it would be difficult to compensate for different numbers of markers, with various markers missing for each individual above 111 markers. The TIP calculator only utilizes markers 1-111.

Question 4: Do projects display more than 111 markers?

Answer: No, projects don’t display the additional markers, at least not yet. The 111 marker results require scrolling to the right significantly, and 500 markers would require 5 times as much scrolling to compare values. Anyone with an idea how to better accomplish a public project display/comparison should submit their idea to Family Tree DNA.

Question 5: Which markers above 111 are fast versus slow mutating?

Answer: Results for these markers are new and statistical compilations aren’t yet available. However, initial results for surname projects in which several men who share a surname and match have tested indicate that there’s not as much variation in these additional markers as we’ve seen in the previous 111 markers, meaning Family Tree DNA already selected the most informative genealogical markers initially. This suggests that the additional markers may provide additional mutations but probably not five times as many as the initial 111 markers.

Question 6: Why do I have more mutations in the first 111 markers than I do in the 389+ markers above the 111 panel?

Answer: That’s a really good question. You’ve probably noticed in our example that the men have dis-proportionally more mutations in the first 111 markers than in the markers above 111.

Y500 genetic distance

The trend is clearly for the first 111 markers to mutate more frequently than the 379+ markers above 111. This means that the first 111 markers are generally going to be more genealogically informative than the balance of the 379+ markers. However, and this is a big however, if the line marker mutation that you need to sort out your group of men occurs in the markers above 111, the number of mutations and the percentages don’t mean anything at all. The information that matters is how you can utilize these markers to differentiate men within the line you are working with, and what story those markers tell.

Of course, the markers above 111 are free as part of the Big Y-500 test which is designed to extract as much SNP information as possible. In essence, these STR markers are icing on the cake – a treat we never expected.

Bottom Line

Here’s the bottom line about the Big-Y 500 STR markers. You don’t know what you don’t know and these 379+ STR markers come along with the Big Y test as a bonus. If you’re looking for line-marker STR mutations in groups of men, the Big Y-500 is a logical next step after 111 marker testing.

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Disclosure

I receive a small contribution when you click on some (but not all) of the links to vendors in my articles. This does NOT increase the price you pay but helps me to keep the lights on and this informational blog free for everyone. Please click on the links in the articles or to the vendors below if you are purchasing products or DNA testing.

Thank you so much.

DNA Purchases and Free Transfers

Genealogy Services

Genealogy Research

Whole Genome Sequencing – Is It Ready for Prime Time?

Dante Labs is offering a whole genomes test for $199 this week as an early Black Friday special.

Please note that just as I was getting ready to push the publish button on this article, Veritas Genetics also jumped on the whole sequencing bandwagon for $199 for the first 1000 testers Nov. 19 and 20th. In this article, I discuss the Dante Labs test. I have NOT reviewed Veritas, their test nor terms, so the same cautions discussed below apply to them and any other company offering whole genome sequencing. The Veritas link is here.

Update – Veritas provides the VCF file for an additional $99, but does not provide FASTQ or BAM files, per their Tweet to me.

I have no affiliation with either company.

$199 (US) is actually a great price for a whole genome test, but before you click and purchase, there are some things you need to know about whole genome sequencing (WGS) and what it can and can’t do for you. Or maybe better stated, what you’ll have to do with your own results before you can utilize the information for genealogical purposes.

The four questions you need to ask yourself are:

  • Why do you want to consider whole genome testing?
  • What question(s) are you trying to answer?
  • What information do you seek?
  • What is your testing goal?

I’m going to say this once now, and I’ll say it again at the end of the article.

Whole genome sequencing tests are NOT A REPLACEMENT FOR GENEALOGICAL DNA TESTS for mitochondrial, Y or autosomal testing. Whole genome sequencing is not a genealogy magic bullet.

There are both pros and cons of this type of purchase, as with most everything. Whole genome tests are for the most experienced and technically savvy genetic genealogists who understand both working with genetics and this field well, who have already taken the vendors’ genealogy tests and are already in the Y, mitochondrial and autosomal comparison data bases.

If that’s you or you’re interested in medical information, you might want to consider a whole genome test.

Let’s start with some basics.

What Is Whole Genome Sequencing?

Whole Genome Sequencing will sequence most of your genome. Keep in mind that humans are more than 99% identical, so the only portions that you’ll care about either medically or genealogically are the portions that differ or tend to mutate. Comparing regions where you match everyone else tells you exactly nothing at all.

Exome Sequencing – A Subset of Whole Genome

Exome sequencing, a subset of whole genome sequencing is utilized for medical testing. The Exome is the region identified as the portions most likely to mutate and that hold medically relevant information. You can read about the benefits and challenges of exome testing here.

I have had my Exome sequenced twice, once at Helix and once at Genos, now owned by NantOmics. Currently, NantOmics does not have a customer sign-in and has acquired my DNA sequence as part of the absorption of Genos. I’ll be writing about that separately. There is always some level of consumer risk in dealing with a startup.

Helix sequences your Exome (plus) so that you can order a variety of DNA based or personally themed products from their marketplace, although I’m not convinced about the utility of even the legitimacy of some of the available tests, such as the “Wine Explorer.”

On the other hand, the world-class The National Geographic Society’s Genographic Project now utilizes Helix for their testing, as does Spencer Well’s company, Insitome.

You can also pay to download your Exome sequence data separately for $499.

Autosomal Testing for Genealogy

Both whole genome and Exome testing are autosomal testing, meaning that they test chromosomes 1-22 (as opposed to Y and mitochondrial DNA) but the number of autosomal locations varies vastly between the various types of tests.

The locations selected by the genealogy testing companies are a subset of both the whole genome and the Exome. The different vendors that compare your DNA for genealogy generally utilize between 600,000 and 900,000 chip-specific locations that they have selected as being inclined to mutate – meaning that we can obtain genealogically relevant information from those mutations.

Some vendors (for example, 23andMe and Ancestry) also include some medical SNPs (single nucleotide polymorphisms) on their chips, as both have formed medical research alliances with various companies.

Whole genome and Exome sequencing includes these same locations, BUT, the whole genome providers don’t compare the files to other testers nor reduce the files to the locations useful for genealogical comparisons. In other words, they don’t create upload files for you.

The following chart is not to scale, but is meant to convey the concept that the Exome is a subset of the whole genome, and the autosomal vendors’ selected SNPs, although not the same between the companies, are all subsets of the Exome and full genome.

I have not had my whole genome sequenced because I have seen no purpose for doing so, outside of curiosity.

This is NOT to imply that you shouldn’t. However, here are some things to think about.

Whole Genome Sequencing Questions

Coverage – Medical grade coverage is considered to be 30X, meaning an average of 30 scans of every targeted location in your genome. Some will have more and some will have less. This means that your DNA is scanned thirty different times to minimize errors. If a read error happens once or twice, it’s unlikely that the same error will happen several more times. You can read about coverage here and here.

Genomics Education Programme [CC BY 2.0 (https://creativecommons.org/licenses/by/2.

Here’s an example where the read length of Read 1 is 18, and the depth of the location shown in light blue is 4, meaning 4 actual reads were obtained. If the goal was 30X, then this result would be very poor. If the goal was 4X then this location is a high quality result for a 4X read.

In the above example, if the reference value, meaning the value at the light blue location for most people is T, then 4 instances of a T means you don’t have a mutation. On the other hand, if T is not the reference value, then 4 instances of T means that a mutation has occurred in that location.

Dante Labs coverage information is provided from their webpage as follows:

Other vendors coverage values will differ, but you should always know what you are purchasing.

Ownership – Who owns your data? What happens to your DNA itself (the sample) and results (the files) under normal circumstances and if the company is sold. Typically, the assets of the company, meaning your information, are included during any acquisition.

Does the company “share, lease or sell” your information as an additional revenue stream with other entities? If so, do they ask your permission each and every time? Do they perform internal medical research and then sell the results? What, if anything, is your DNA going to be used for other than the purpose for which you purchased the test? What control do you exercise over that usage?

Read the terms and conditions carefully for every vendor before purchasing.

File Delivery – Three types of files are generated during a whole genome test.

The VCF (Variant Call Format) which details your locations that are different from the reference file. A reference file is the “normal” value for humans.

A FASTQ file which includes the nucleotide sequence along with a corresponding quality score. Mutations in a messy area or that are not consistent may not be “real” and are considered false positives.

The BAM (Binary Alignment Map) file is used for Y DNA SNP alignment. The output from a BAM file is displayed in Family Tree DNA’s Big Y browser for their customers. Are these files delivered to you? If so, how? Family Tree DNA delivers their Big Y DNA BAM files as free downloads.

Typically whole genome data is too large for a download, so it is sent on a disc drive to you. Dante provides this disc for BAM and FASTQ files for 59 Euro ($69 US) plus shipping. VCF files are available free, but if you’re going to order this product, it would be a shame not to receive everything available.

Version – Discoveries are still being made to the human genome. If you thought we’re all done with that, we’re not. As new regions are mapped successfully, the addresses for the rest change, and a new genomic map is created. Think of this as street addresses and a new cluster of houses is now inserted between existing houses. All of the houses are periodically renumbered.

Today, typically results are delivered in either of two versions: hg19(GRVH37) or hg38(GRCH38). What happens when the next hg (human genome) version is released?

When you test with a vendor who uses your data for comparison as a part of a product they offer, they must realign your data so that the comparison will work for all of their customers (think Family Tree DNA and GedMatch, for example), but a vendor who only offers the testing service has no motivation to realign your output file for you. You only pay for sequencing, not for any after-the-fact services.

Platform – Multiple sequencing platforms are available, and not all platforms are entirely compatible with other competing platforms. For example, the Illumina platform and chips may or may not be compatible with the Affymetrix platform (now Thermo Fisher) and chips. Ask about chip compatibility if you have a specific usage in mind before you purchase.

Location – Where is your DNA actually being sequenced? Are you comfortable having your DNA sent to that geographic location for processing? I’m personally fine with anyplace in either the US, Canada or most of Europe, but other locations maybe not so much. I’d have to evaluate the privacy policies, applicable laws, non-citizen recourse and track record of those countries.

Last but perhaps most important, what do you want to DO with this file/information?

Utilization

What you receive from whole genome sequencing is files. What are you going to do with those files? How can you use them? What is your purpose or goal? How technically skilled are you, and how well do you understand what needs to be done to utilize those files?

A Specific Medical Question

If you have a particular question about a specific medical location, Dante allows you to ask the question as soon as you purchase, but you must know what question to ask as they note below.

You can click on their link to view their report on genetic diseases, but keep in mind, this is the disease you specifically ask about. You will very likely NOT be able to interpret this report without a genetic counselor or physician specializing in this field.

Take a look at both sample reports, here.

Health and Wellness in General

The Dante Labs Health and Wellness Report appears to be a collaborative effort with Sequencing.com and also appears to be included in the purchase price.

I uploaded both my Exome and my autosomal DNA results from the various testing companies (23andMe V3 and V4, Ancestry V1 and V2, Family Tree DNA, LivingDNA, DNA.Land) to Promethease for evaluation and there was very little difference between the health-related information returned based on my Exome data and the autosomal testing vendors. The difference is, of course, that the Exome coverage is much deeper (and therefore more reliable) because that test is a medical test, not a consumer genealogy test and more locations are covered. Whole genome testing would be more complete.

I wrote about Promethease here and here. Promethease does accept VCF files from various vendors who provide whole genome testing.

None of these tests are designed or meant for medical interpretation by non-professionals.

Medical Testing

If you plan to test with the idea that should your physician need a genetics test, you’re already ahead of the curve, don’t be so sure. It’s likely that your physician will want a genetics test using the latest technology, from their own lab, where they understand the quality measures in place as well as how the data is presented to them. They are unlikely to accept a test from any other source. I know, because I’ve already had this experience.

Genealogical Comparisons

The power of DNA testing for genealogy is comparing your data to others. Testing in isolation is not useful.

Mitochondrial DNA – I can’t tell for sure based on the sample reports, but it appears that you receive your full sequence haplogroup and probably your mutations as well from Dante. They don’t say which version of mitochondrial DNA they utilize.

However, without the ability to compare to other testers in a database, what genealogical benefit can you derive from this information?

Furthermore, mitochondrial DNA also has “versions,” and converting from an older to a newer version is anything but trivial. Haplogroups are renamed and branches sawed from one part of the mitochondrial haplotree and grafted onto another. A testing (only) vendor that does not provide comparisons has absolutely no reason to update your results and can’t be expected to do so. V17 is the current build, released in February 2016, with the earlier version history here.

Family Tree DNA is the only vendor who tests your full sequence mitochondrial DNA, compares it to other testers and updates your results when a new version is released. You can read more about this process, here and how to work with mtDNA results here.

Y DNA – Dante Labs provides BAM files, but other whole genome sequencers may not. Check before you purchase if you are interested in Y DNA. Again, you’ll need to be able to analyze the results and submit them for comparison. If you are not capable of doing that, you’ll need to pay a third party like either YFull or FGS (Full Genome Sequencing) or take the Big Y test at Family Tree DNA who has the largest Y Database worldwide and compares results.

Typically whole genome testers are looking for Y DNA SNPs, not STR values in BAM files. STR (short tandem repeat) values are the results that you receive when you purchase the 37, 67 or 111 tests at Family Tree DNA, as compared to the Big Y test which provides you with SNPs in order to resolve your haplogroup at the most granular level possible. You can read about the difference between SNPs and STRs here.

As with SNP data, you’ll need outside assistance to extract your STR information from the whole genome sequence information, none of which will be able to be compared with the testers in the Family Tree DNA data base. There is also an issue of copy-count standardization between vendors.

You can read about how to work with STR results and matches here and Big Y results here.

Autosomal DNA – None of the major providers that accept transfers (MyHeritage, Family Tree DNA, GedMatch) accept whole genome files. You would need to find a methodology of reducing the files from the whole genome to the autosomal SNPs accepted by the various vendors. If the vendors adopt the digital signature technology recently proposed in this paper by Yaniv Erlich et al to prevent “spoofed files,” modified files won’t be accepted by vendors.

Summary

Whole genome testing, in general, will and won’t provide you with the following:

Desired Feature Whole Genome Testing
Mitochondrial DNA Presumed full haplogroup and mutations provided, but no ability for comparison to other testers. Upload to Family Tree DNA, the only vendor doing comparisons not available.
Y DNA Presume Y chromosome mostly covered, but limited ability for comparison to other testers for either SNPs or STRs. Must utilize either YFull or FGS for SNP/STR analysis. Upload to Family Tree DNA, the vendor with the largest data base not available when testing elsewhere.
Autosomal DNA for genealogy Presume all SNPs covered, but file output needs to be reduced to SNPs offered/processed by vendors accepting transfers (Family Tree DNA, MyHeritage, GedMatch) and converted to their file formats. Modified files may not be accepted in the future.
Medical (consumer interest) Accuracy is a factor of targeted coverage rate and depth of actual reads. Whole genome vendors may or may not provide any analysis or reports. Dante does but for limited number of conditions. Promethease accepts VCF files from vendors and provides more.
Medical (physician accepted) Physician is likely to order a medical genetics test through their own institution. Physicians may not be willing to risk a misdiagnosis due to a factor outside of their control such as an incompatible human genome version.
Files VCF, FASTQ and BAM may or may not be included with results, and may or may not be free.
Coverage Coverage and depth may or may not be adequate. Multiple extractions (from multiple samples) may or may not be included with the initial purchase (if needed) or may be limited. Ask.
Updates Vendors who offer sequencing as a part of a products that include comparison to other testers will update your results version to the current reference version, such as hg38 and mitochondrial V17. Others do not, nor can they be expected to provide that service.
Version Inquire as to the human genome (hg) version or versions available to you, and which version(s) are acceptable to the third party vendors you wish to utilize. When the next version of the human genome is released, your file will no longer be compatible because WGS vendors are offering sequencing only, not results comparisons to databases for genealogy.
Ownership/Usage Who owns your sample? What will it be utilized for, other than the service you ordered, by whom and for what purposes? Will you we able to authorize or decline each usage?
Location Where geographically is your DNA actually being sequenced and stored? What happens to your actual DNA sample itself and the resulting files? This may not be the location where you return your swab kit.

The Question – Will I Order?

The bottom line is that if you are a genealogist, seeking genetic information for genealogical purposes, you’re much better off to test with the standard and well know genealogy vendors who offer compatibility and comparisons to other testers.

If you are a pioneer in this field, have the technical ability required to make use of a whole genome test and are willing to push the envelope, then perhaps whole genome sequencing is for you.

I am considering ordering the Dante Labs whole genome test out of simple curiosity and to upload to Promethease to determine if the whole genome test provides me with something potentially medically relevant (positive or negative) that autosomal and Exome testing did not.

I’m truly undecided. Somehow, I’m having trouble parting with the $199 plus $69 (hard drive delivery by request when ordering) plus shipping for this limited functionality. If I was a novice genetic genealogist or was not a technology expert, I would definitely NOT order this test for the reasons mentioned above.

A whole genome test is not in any way a genealogical replacement for a full sequence mitochondrial test, a Y STR test, a Y SNP test or an autosomal test along with respective comparison(s) in the data bases of vendors who don’t allow uploads for these various functions.

The simple fact that 30X whole genome testing is available for $199 plus $69 plus shipping is amazing, given that 15 years ago that same test cost 2.7 billion dollars. However, it’s still not the magic bullet for genealogy – at least, not yet.

Today, the necessary integration simply doesn’t exist. You pay the genealogy vendors not just for the basic sequencing, but for the additional matching and maintenance of their data bases, not to mention the upgrading of your sequence as needed over time.

If I had to choose between spending the money for the WGS test or taking the genealogy tests, hands down, I’d take the genealogy tests because of the comparisons available. Comparison and collaboration is absolutely crucial for genealogy. A raw data file buys me nothing genealogically.

If I had not previously taken an Exome test, I would order this test in order to obtain the free Dante Health and Wellness Report which provides limited reporting and to upload my raw data file to Promethease. The price is certainly right.

However, keep in mind that once you view health information, you cannot un-see it, so be sure you do really want to know.

What do you plan to do? Are you going to order a whole genome test?

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Disclosure

I receive a small contribution when you click on some (but not all) of the links to vendors in my articles. This does NOT increase the price you pay but helps me to keep the lights on and this informational blog free for everyone. Please click on the links in the articles or to the vendors below if you are purchasing products or DNA testing.

Thank you so much.

DNA Purchases and Free Transfers

Genealogy Services

Genealogy Research

Family Tree DNA’s PUBLIC Y DNA Haplotree

It’s well known that as a result of Big Y testing that Family Tree DNA has amassed a huge library of Y DNA full sequence results that have revealed new SNPs, meaning new haplotree branches, for testers. That’s how the Y haplotree is built. I wrote about this in the article, Family Tree DNA Names 100,000 New Y DNA SNPs.

Up until now, the tree was only available on each tester’s personal pages, but that’s not the case anymore.

Share the Wealth

Today, Family Tree DNA has made the tree public. Thank you, thank you, THANK YOU Family Tree DNA.

To access the tree, click here, but DON’T sign in. Scroll to the bottom of the page. Keep scrolling, and scrolling…until you see the link under Community that says “Y-DNA Haplotree.” Click there.

The New Public Haplotree

The new public haplotree is amazing.

This tree isn’t just for people who took the Big Y test, but includes anyone who has a haplogroup confirming SNP OR took the Big Y test. Predicted haplogroups, of course, aren’t included.

Each branch includes the location of the most recent known ancestor of individuals who carry that terminal SNP, shown with a flag.

The branches are color coded by the following:

  • Light blue = haplogroup root branches
  • Teal or blue/green = branches with no descendants
  • Dark blue = branches that aren’t roots and that do have at least one descendant branch

The flag location is determined by the most distant known ancestor, so if you don’t have a “Most Distant Known Ancestor” completed, with a location, please, please, complete that field by clicking on “Manage Personal Information” beneath your profile picture on your personal page, then on Genealogy, shown below. Be sure to click on Save when you’re finished!

View Haplotree By

Viewing the haplotree is not the same as searching. “View by” is how the tree is displayed.

Click on the “View By” link to display the options: country, surnames or variant.

You can view by the country (flags), which is the default, the surname or the variants.

Country view, with the flags, is the default. Surname view is shown below.

The third view is variant view. By the way, a variant is another word for SNP. For haplogroup R-M207, there are 8,202 variants, meaning SNPs occurring beneath, or branches.

Reports

On any of the branch links, you’ll see three dots at the far right.

To view reports by country or surname, click on the dots to view the menu, then click on the option you desire.

Country statistics above, surname below. How cool is this!

Searching

The search function is dependent on the view currently selected. If you are in the surname view, then the search function says “Search by Surname” which allows you to enter a surname. I entered Estes.

If I’m not currently on the haplogroup R link, the system tells me that there are 2 Estes results on R. If I’m on the R link, the system just tells me how many results it found for that surname on this branch and if there are others on other branches.

The tree then displays the direct path between R-M207 (haplogroup R root) and the Estes branch.

…lots of branches in-between…

The great thing about this is that I can now see the surnames directly above my ancestral surname, if they meet the criteria to be displayed.

Display criteria is that two people match on the same branch AND that they both have selected public sharing. Requiring two surnames per branch confirms that result.

If you want to look at a specific variant, you can enter that variant name (BY490) in the search box and see the surnames associated with the variant. The click on “View by” to change the view from country (maps) to surnames to variants.

Change from country to surname.

And from surname to variants.

What geeky fun!!!

Go to Branch Name

If you want to research a specific branch, you can go there directly by utilizing the “Go to Branch Name” function, but you must enter the haplogroup in front of the branch name. R-BY490 for example.

When you’re finished with this search, REMOVE THE BRANCH NAME from the search box, if you’re going to do any other searches, or the system thinks you’re searching within that branch name.

My Result Isn’t Showing

In order for your results to be included on the tree, you must have fulfilled all 3 of these criteria:

  • Taken either a SNP or Big Y test
  • Opted in for public sharing
  • More than one result for that branch with the same exact surname

If you think your results should be showing and they aren’t, check your privacy settings by clicking the orange “Manage Personal Information” under your profile picture on your main page, then on the Privacy and Sharing tab.

Still not showing? See if you match another male of the same surname on the Big Y or SNP test at the same level.

If your surname isn’t included, you can recruit testers from that branch of your family.

How Can I Use This?

I’m like a kid with a new toy.

If any of your family surnames are rather unique, search to see if they are on the tree.

Hey look, my Vannoy line is on haplogroup I! Hmmm, clear the schedule, I’m going to be busy all day!

Every haplogroup has a story – and that story belongs to the men, and their families, who carry that haplogroup! I gather the haplogroups for each of my family surnames and this public tree just made this task much, MUCH easier.

Discovering More

If the testers have joined the appropriate surname project, you may also be able to find them in that project to see if they descend from a common line with you. To check and see, click here and then scroll down to the “Search Surname” section of the main Family Tree DNA webpage and enter the surname.

You can see if there is a project for your surname, and if not, your surname may be included in other projects.

Click on any of those links to view the project or contact the (volunteer) project administrators.

Want to search for another surname, the project search box is shown at the right in this view.

What gems can you find?

Want to Test?

If you are a male and you want to take the Big Y test or order a haplogroup confirming SNP, or you are a female who would like to sponsor a test for a male with a surname you’re interested in, you can purchase the Big Y test, here. As a bonus, you will also receive all of the STR markers for genealogical comparison as well.

Wonder what you can learn? You will be searching for matches to other males with the same surname. You can learn about your history. Confirm your ancestral line. Learn where they came from. You can help the scientific effort and contribute to the tree. For more information, read the article, Working with Y DNA – Your Dad’s Story.

Have fun!!!

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Disclosure

I receive a small contribution when you click on some of the links to vendors in my articles. This does NOT increase the price you pay but helps me to keep the lights on and this informational blog free for everyone. Please click on the links in the articles or to the vendors below if you are purchasing products or DNA testing.

Thank you so much.

DNA Purchases and Free Transfers

Genealogy Services

Genealogy Research

 

 

 

 

Why Different Haplogroup Results?

“Why do vendors give me different haplogroups?”

This questions often comes up when people test with different vendors and receive different haplogroup results for both Y and mitochondrial DNA.

If you need a quick refresher on who carries which types of DNA, read 4 Kinds of DNA for Genetic Genealogy.

You’re the same person, right, so why would you receive different answers from different testing companies, and which answer is actually right?

The answer is pretty straightforward, conceptually – having to do with how vendors test and interpret your DNA.

Different companies test different pieces of your DNA, depending on:

  • The type of chip the company is using for testing
  • The way they have programmed the chip
  • The version of the reference “tree” they are using to assign haplogroups
  • The level they have decided to report

Therefore, their haplogroups reported may vary, and some may be more exact than others. Occasionally, a vendor outside the major testers is simply wrong.

Not All Tests are Created Equal

All haplogroups carry interesting information and can be at least somewhat genealogically useful. For example, haplogroups alone can tell you if your direct line DNA (paternal or matrilineal) is probably European, Asian, African or Native American. Note the word probably. This too may be subject to interpretation.

A basic haplogroup can rule out a genealogical match through a specific branch, but can’t confirm a genealogical match. You need to compare specific DNA locations not provided with haplogroup testing alone for genealogical matching. Plus you’ll need to add genealogical records where possible.

Let’s look at two examples.

Mitochondrial DNA

Your mitochondrial DNA is inherited from your mother’s direct line, on up you tree until you run out of mothers.  So, you, your mother, her mother, her mother…etc.

The red circles show the mitochondrial lineage in the pedigree chart, below.

If your mitochondrial haplogroup is H1a, for example, then your base haplogroup is “H”, the first branch is “1” and the next smaller branch is “a.”

Therefore, if you don’t match at H, your base haplogroup, you aren’t a possible match on that genealogical line. In other words, if you are H1a, or H plus anything, you can’t match on the direct matrilineal line of someone who is J1a, or J plus anything. H and J are different base haplogroups who haven’t shared a common ancestor in tens of thousands of years.

You can, however, potentially be related on any other line – just not on this specific line.

If your haplogroup does match, even exactly, that doesn’t mean you are related in a genealogically relevant timeframe. It means you share an ancestor, but that common ancestor may be back hundreds, thousands or even tens of thousands of years.

The further downstream, the younger the branches.  “H” is the oldest, then “1,” then “a” is the youngest.

Some companies might just test the locations for H, some for H1 and some for H1a.  Of course, there are even more haplogroups, like H1a2a. New, more refined haplogroups are discovered with each new version of the mitochondrial reference tree.

The only company that tests your haplogroup all the way to the end, meaning the most refined test possible to give you your complete haplogroup and all mutations, is Family Tree DNA with their mtFull Sequence test.

A quick comparison of my mitochondrial DNA at the following three vendors shows the following:

23andMe Living DNA Family Tree DNA Full Seqence
J1c2 J1c J1c2f

With Family Tree DNA’s full sequence test, you’ll receive your full haplogroup along with matching to other people who have taken mitochondrial DNA tests. They are the only vendor to offer Y and mitochondrial matching, because they are the only vendor that tests at that level.

Y DNA

Y DNA operates on the same principle. Specific locations called SNPs are tested by companies like 23andMe and Living DNA to provide customers with a branch level haplogroup. You don’t receive matching with these types of tests.

Just like with mitochondrial DNA, a basic branch level test can eliminate a match on the direct paternal (surname) branch but can’t confirm the genealogical match.

If your haplogroup branch is E-M2 and someone else’s is R-M269, you can’t share a common paternal ancestor because your base haplogroups don’t match, meaning E and R.

You can share an ancestor on any other line, just not on the direct Y line.

The blue squares show the Y DNA lineage on the pedigree chart below.

Family Tree DNA predicts your haplogroup for free if you take the 37, 67 or 111 marker Y-DNA STR test, but if you take the Big Y-500, your Y chromosome is completely tested and your haplogroup defined to the most refined level possible (often called your terminal SNP) – including mutations that may exist in only very few people. You also receive matching to other testers (with any Y test) which can be very genealogically relevant, plus bonus Y STR markers with the Y-500.

OK, But Why Do Different Companies Give Me Different Haplogroup Results?

Great question.

For this example, let’s say your haplogroup is H1a2a.

Let’s say that Company 1 uses a chip that they’ve programmed to test to the H1a level of haplogroup H1a2a.

Let’s say that Company 2 uses a chip that they’ve programmed to test to the H1 level of haplogroup H1a2a.

Let’s say that you take the full sequence test with Family Tree DNA and they fully test all 15,659 locations of your mitochondria and determine that you are H1a2a.

Company 1 will report your mitochondrial haplogroup as H1a, Company 2 as H1 and Family Tree DNA as H1a2a.

With mitochondrial DNA, you can at least see some consist pathway in naming practices, meaning H, H1, H1a, etc., so you can tell that you’re on the same branch.

With Y DNA, the only consistent part is the base haplogroup.

With Y DNA, let’s say that Company 1 programs their chip to test for specific SNP  locations, and they return a Y DNA haplogroup of R-L21.

Company 2 programs their chip to test for fewer or different locations and they return a Y DNA haplogroup of R-M269.

You purchase a Big Y-500 test at Family Tree DNA, and they return your haplogroup as R-CTS3386.

All three haplogroups can be correct, as far as they go. It’s just that they don’t test the same distance down the Y chromosome tree.

R-M269, R-L21 and R-CTS3386 are all increasingly smaller branches on the Y haplotree.

Furthermore, for both Y and mitochondrial DNA, there is always a remote possibility that a critical location won’t be able to be read in your DNA sample that might affect your haplogroup.

Obtaining Your Haplogroup

I strongly encourage people to test with and upload to only well-known major companies or organizations. Some companies provide haplogroup information that is simply wrong.

Companies that I am comfortable with relative to haplogroups include:

Neither MyHeritage nor Ancestry provide Y or mitochondrial haplogroups.

The chart below shows the various vendor offerings, including Y and mitochondrial DNA matching.

Company Offerings Matching
Family Tree DNA – Y DNA Y haplogroup is estimated with STR test. Haplogroup provided to most refined level possible with Big Y-500 test. Individual SNP tests also available. Yes
Family Tree DNA – mitochondrial At least base haplogroup provided with mtPlus test, plus more if possible, but full haplogroup plus additional mutations provided with mtFull Sequence test. Yes
Genographic Project (obsolete in 2019) More than base haplogroup for both Y and mitochondrial, but not full haplogroup on either. No
23andMe More than base haplogroup for both Y and mitochondrial, but not full haplogroup on either. No
Living DNA More than base haplogroup for both Y and mitochondrial, but not full haplogroup on either. No

Want More Detail?

If you’d like to read a more detailed answer about how haplogroups are determined, take a look at the article, Haplogroup Comparisons Between Family Tree DNA and 23andMe.

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Disclosure

I receive a small contribution when you click on some of the links to vendors in my articles. This does NOT increase the price you pay but helps me to keep the lights on and this informational blog free for everyone. Please click on the links in the articles or to the vendors below if you are purchasing products or DNA testing.

Thank you so much.

DNA Purchases and Free Transfers

Genealogy Services

Genealogy Research