Category Archives: Whole Genome Sequencing (WGS)

FamilyTreeDNA 2023 Update – Past, Present and Future

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At the FamilyTreeDNA International Conference on Genetic Genealogy, held November 3-5 in Houston for group project administrators, product and feature updates were scattered across both days in various presentations.

I’ve combined the updates from FamilyTreeDNA into one article.

I’ve already written two articles that pertain to the conference.

FamilyTreeDNA has already begun rolling the new Y DNA haplogroups from Family Finder autosomal tests, which I wrote about here:

I still have at least two more articles to publish from this conference that was chocked full of wonderful information from a wide range of talented speakers.

Past, Present, and Future with Katy Rowe-Schurwanz

Katy Rowe-Schurwanz, FamilyTreeDNA’s Product Manager, provided an update on what has been accomplished in the four and a half years since the last conference, what’s underway now, and her wish list for 2024.

Please note the word “wish list.” Wish list items are NOT commitments.

Recent Milestones

A lot has been happening at FamilyTreeDNA since the last conference.

Acquisition and Wellness Bundles

As everyone is aware, at the end of 2020, myDNA acquired Gene by Gene, the parent company of FamilyTreeDNA, which included the lab. As a result, the FamilyTreeDNA product menu has expanded, and wellness bundles are now available for FamilyTreeDNA customers.

If you’re interested, you can order the Wellness product in a bundle with a Family Finder test, here.

You can add the Wellness product for $39 if you’ve already tested.

New TIP (Time Prediction) STR Report

Did you notice that the old TIP report for Y DNA STR markers was replaced with an updated version several months ago?

To view the new report, sign on and select your Y DNA matches. At the far right of each match you’ll see these three icons representing a pedigree chart, notes, and the TIP (Time Predictor) report.

The updated TIP report includes wonderful new graphs and age estimates for each match category, which you can read about, here. Each category, such as 67-marker matches, has time estimates in which a common ancestor might have lived at each possible genetic distance.

Math is our friend, and thankfully, someone else has done it for us!

Please note that the Big Y SNP dates are MUCH more accurate for a variety of reasons, not limited to the instability and rapid mutation rate of STR mutations.

MyOrigins3

MyOrigins3, FamilyTreeDNA’s ethnicity offering, added over 60 new reference populations for a total of 90, plus chromosome painting. You can read about MyOrigins features here, and the white paper, here.

This is one of my favorite improvements because it allows me to identify the segment location of my population ancestries, which in turn allows me to identify people who share my minority segments such as Native American and African.

Due to a lack of records, these relationships are often exceedingly difficult to identify, and MyOrigins3 helps immensely.

Additional Releases

Additional products and features released since the last conference include:

Discover

Released in July 2022, Discover is the amazing new free product that details your ancestor’s Y DNA “story” and his walk through time and across the globe.

In the past 18 months, all of the Discover features are new, so I’m only making a brief list here. The great thing is that everyone can use Discover if you know or can discover (pardon the pun) the haplogroup of your ancestral lines. Surname projects are often beneficial for finding your lineages.

  • Haplogroup Story includes haplogroup location, ages derived from the earliest known ancestor (EKA) of your matches, and ancient DNA samples. Please be sure you’ve entered or updated your EKA, and that the information is current. You can find instructions for how to update or add your EKA here.
  • A recent addition to the haplogroup story includes Haplogroup Badges.
  • Country Frequency showing where this haplogroup is found with either a table view or an interactive map
  • Famous and infamous Notable Connections, including Mayflower passengers, Patriots from the American Revolution, US presidents, royal houses, artists, musicians, authors, pirates, sports figures, scientists, and more.

If you know of a proven connection to a notable figure, contact customer support and let them know! Notable connections are added every week.

One famous Discover connection is Ludwig von Beethoven which resulted from a joint academic study between FamilyTreeDNA and academic researchers. It’s quite a story and includes both a mystery and misattributed parentage. You can see if you match on Discover and read about the study, here.

  • Updated Migration Map, including locations of select ancient DNA sites
  • The Time Tree, probably the most popular Discover report, shows the most current version of the Y DNA phylotree, updated weekly, plus scientifically calculated ages for each branch. Tree node locations are determined by your matches and their EKA countries of origin. I wrote about the Time Tree, here.
  • Anticipated in early 2024, the EKA and block tree matches will also be shown on the Time Tree in Discover for individual Big Y testers, meaning they will need to sign in through their kits.
  • The Group Time Tree, visible through group projects, takes the Time Tree a step further by including the names of the EKA of each person on the Time Tree within a specific project. Information is only displayed for project members who have given permission to include their data. You can select specific project groupings to view, or the entire project. I wrote about the Group Time Tree here and here.
  • Globetrekker is an exclusive Big Y mapping feature discussed here, here, here, and here.
  • Ancient Connections includes more than 6,100 ancient Y DNA results from across the globe, which have been individually analyzed and added for matching in Discover. Ancient Connections serve to anchor haplogroups and provide important clues about matches, migration paths and culture. New connections are added weekly or as academic papers with adequate Y DNA coverage are released.
  • Your Ancestral Path, which lists the haplogroups through every step from the tester back to Y Adam and beyond. Additional information for each haplogroup in your path includes “Time Passed” between haplogroups, and “Immediate Descendants,” meaning haplogroups that descend from each subclade. New columns recently added include “Tested Modern Descendants” and “Ancient Connections.”
  • Suggested Projects include surname, haplogroup, and geographic projects. Katy said that people joining projects are more likely to collaborate and upgrade their tests. You can also see which projects other men with this haplogroup have joined, which may well be projects you want to join too.
  • Scientific Details provides additional information, such as each branch’s confidence intervals and equivalent variables (SNPs). You can read more here.
  • Compare Haplogroups is the most recent new feature, added just last month, which allows you to enter any two haplogroups and compare them to determine their most recent common ancestral haplogroup. You can read about Compare Haplogroups, here.

Please note that the Studies feature is coming soon, providing information about studies whose data has been included in Discover.

You can read about Discover here, here, here, and here.

If you’re interested, FamilyTreeDNA has released a one-minute introduction to Y DNA and Discover that would interest new testers, here.

Earliest Known Ancestor (EKA) Improvement

Another improvement is that the earliest known ancestor is MUCH easier to enter now, and the process has been simplified. The EKAs are critical for Discover, so PLEASE be sure you’ve entered and updated your EKA.

Under the dropdown beside your name in the upper right-hand corner of your personal page, select Account Settings, then Genealogy and Earliest Known Ancestors. Complete the information, then click on “Update Location” to find or enter the location on a map to record the coordinates.

It’s easy. Just type or drop a pin and “Save.”

Saving will take you back to the original EKA page. Save that page, too.

Recommended Projects on Haplogroups & SNPs Page

You’re probably aware that Discover suggests projects for Y DNA testers to join, but recommended haplogroup projects are available on each tester’s pages, under the Y DNA Haplotree & SNPs page, in the Y DNA STR results section.

If there isn’t a project for your immediate haplogroup, just scroll up to find the closest upstream project. You can also view this page by Variants, Surnames and Countries.

This is a super easy tool to use to view which surnames are clustered with and upstream of your haplogroup. With Family Finder haplogroups being assigned now, I check my upstream haplogroups almost daily to see what has been added.

For example, my Big Y Estes results are ten branches below R-DF49, but several men, including Estes testers, have been assigned at this level, thanks to Y DNA haplogroups from Family Finder testing. I can now look for these haplogroups in the STR and Family Finder matches lists and see if those men are receptive to Big Y testing.

Abandoned Projects

Sometimes group project administrators can no longer function in that capacity, resulting in the project becoming abandoned. FamilyTreeDNA has implemented a feature to help remedy that situation.

If you discover an abandoned project, you can adopt the project, spruce things up, and select the new project settings. Furthermore, administrators can choose to display this message to recruit co-administrators. I need to do this for several projects where I have no co-admin.

If you are looking for help with your project, you can choose to display the button
through the Project Profile page in GAP. For non-project administrators, if you’d like to help, please email the current project administrators.

New Kit Manager Feature

FamilyTreeDNA has added a “Kit Manager” feature so that an individual can designate another person as the manager of their kit.

This new setting provides an avenue for you to designate someone else as the manager of your DNA test. This alerts FamilyTreeDNA that they can share information with both of you – essentially treating your designated kit manager the same as you.

If you’re the kit manager for someone else, you NEED to be sure this is completed. If that person is unavailable for some reason, and support needs to verify that you have legitimate access to this kit, this form and the Beneficiary form are the ONLY ways they can do that.

If your family member has simply given you their kit number and password, and for some reason, a password reset is required, and their email address is the primary contact – you may be shut out of this kit if you don’t complete this form.

Beneficiary Page

Additionally, everyone needs to be sure to complete the Beneficiary page so that in the event of your demise, FamilyTreeDNA knows who you’ve designated to access and manage your DNA account in perpetuity. If you’ve inherited a kit, you need to add a beneficiary to take over in the event of your death as well.

What is FamilyTreeDNA working on now?

Currently in the Works

Katy moved on to what’s currently underway.

Privacy and Security

Clearly, the unauthorized customer data exposure breach at 23andMe has reverberated through the entire online community, not just genetic genealogy. You can read about the incident here, here, here, and here.

FamilyTreeDNA has already taken several steps, and others are in development and will be released shortly.

Clearly, in this fast-moving situation, everything is subject to change.

Here’s what has happened and is currently planned as of today:

  • Group Project Administrators will be required to reset their password soon.

Why is this necessary?

Unauthorized access was gained to 23andMe accounts by people using the same password for multiple accounts, combined with their email as their user ID. Many people use the same password for every account so that they can remember it. That means that all a hacker needs to do is breach one account, and they can use that same information to “legitimately” sign in to other accounts. There is no way for the vendor to recognize this as unauthorized since they have both your user ID and password.

That’s exactly what happened at 23andMe. In other breaches, this information was exposed, and hackers simply tried the same username and password combination at 23andMe, exposing the entire account of the person whose account they signed in “as.” This includes all of their matches, genetic tree, shared matches, matches of matches, ethnicity, and segments. They could also have downloaded both the match list and the raw DNA file of the compromised account.

At FamilyTreeDNA, project administrators can select their own username, which could be their email, so they will be required to reset their password.

Additional precautions have been put in place on an interim basis:

  • A pause in the ability to download match and segment information.
  • A pause in accepting 23andMe uploads.

Administrators will also be required to use two-factor authentication (2FA.) To date, two of the four major vendors are requiring 2FA. I would not be surprised to see it more broadly. Facebook recently required me to implement 2FA there, too, due to the “reach” of my postings, but 2FA is not required of everyone on Facebook.

Please note that if you received an email or message that is supposedly from any vendor requiring 2FA, GO DIRECTLY TO THAT VENDOR SITE AND SIGN IN.  Never click on a link in an email you weren’t expecting. Bad actors exploit everything.

Customers who are not signing in as administrators are not required to implement 2FA, nor will they be required to reset their password.

Personally, I will implement 2FA as soon as it’s available.

While 2FA is an extra step, it’s easy to get used to, and it has already literally saved one of my friends from an authorized hack on their primary and backup email accounts this week. Another friend just lost their entire account on Facebook because someone signed in as them. Their account was gone within 15 minutes.

2FA is one of those things you don’t appreciate (at all) until it saves you, and then, suddenly, you’re incredibly grateful.

At this point in time, FamilyTreeDNA users will NOT be required to do a password reset or implement 2FA. This is because customers use a kit number for sign-in and not a username or email address. I would strongly recommend changing your password to something “not easy.” Never reuse passwords between accounts.

I really, really want you to visit this link at TechRepublic and scroll down to Figure A, which shows how long it takes a hacker to crack your password. I guarantee you, it’s MUCH quicker than you’d ever expect.

Kim Komando wrote about this topic two years ago, so compare the two charts to see how much easier this has become in just two years.

Again, if you receive an email about resetting your password, don’t click on a link. Sign in independently to the vendor’s system, but DO reset your password.

FamilyTreeDNA also engages in additional security efforts, such as ongoing penetration testing.

New Permissions

Additionally, at FamilyTreeDNA, changes were already in the works to separate out at least two permissions that testers can opt-in to without granting project administrators Advanced rights.

  • Download data
  • Purchase tests

The ability to purchase tests can be very important because it allows administrators to order and pay for tests or upgrades on behalf of this tester anytime in the future.

Family Finder Haplogroups

FamilyTreeDNA has already begun releasing mid-level Y DNA haplogroups for autosomal testers in a staggered rollout of several thousand a day.

I wrote about this in the article, FamilyTreeDNA Provides Y DNA Haplogroups from Family Finder Autosomal Tests, so I’m not repeating all of that information here – just highlights.

  • The Family Finder haplogroup rollout is being staggered and began with customers on the most recent version of the testing chip, which was implemented in March of 2019.
  • Last will be transfers/uploads from third parties.
  • Haplogroups resulting from tests performed in the FTDNA labs will be visible to matches and within projects. They will also be used in both Discover and the haplotree statistics. This includes Family Finder plus MyHeritage and Vitagene uploads.
  • Both MyHeritage and Vitagene are uploaded or “transferred” via an intracompany secure link, meaning FamilyTreeDNA knows that their information is credible and has not been manipulated.
  • Haplogroups derived from tests performed elsewhere will only be visible to the user or a group administrator viewing a kit within a project. They will not be visible to matches or used in trees or for statistics.
  • Any man who has taken a Y DNA STR test will receive a SNP-confirmed, updated haplogroup from their Family Finder test that replaces their predicted haplogroup from the STR test.

Please read this article for more information.

New Discover Tools and Updates

Discover content continues to be updated, and new features are added regularly, creating an increasingly robust user experience.

Soon, group administrators will be able to view all Discover features (like Globetrekker) when viewing kits of project members who have granted an appropriate level of access.

Ancient and Notable connects are added weekly, and a new feature, Study Connections, will be added shortly.

Study Connections is a feature requested by customers that will show you which study your academic matches came from. Today, those results are used in the Y DNA tree, but the source is not detailed.

Anticipated in early 2024, the EKA and block tree matches will also be shown on the Time Tree in Discover for individual Big Y testers (not publicly).

Big Y FaceBook Group

FamilyTreeDNA has ramped up its social media presence. They launched the Big Y Facebook group in July 2023, here, which currently has just under 9000 members. Several project administrators have volunteered their time to help manage the group.

FamilyTreeDNA Blog

In addition, FamilyTreeDNA is publishing at least one blog article each week, and sometimes more. You can view or subscribe here. Some articles are written by FamilyTreeDNA staff, but project administrators and customers author other content.

Multi-Language Support

Translation of the main FamilyTreeDNA website and results pages to Spanish has begun, with more languages planned soon.

Paypal, Payments, and Gift Cards

Paypal has been added as a payment selection, along with a PayPal option that provides the ability to make payments.

Additionally, a gift card can be purchased from the main page.

Million Mito Project & Mitotree

Work on the Million Mito Project is ongoing.

The Million Mito Project was launched in 2020 as a collaborative effort between FamilyTreeDNA’s Research & Development Team and the scientific portion of the Genographic Project. I’m a team member and wrote about the Million Mito Project, here.

We’re picking up from where the Phylotree left off in 2016, analyzing 20 times more mtDNA full sequences and reimagining the mtDNA Haplotree. By examining more mtDNA data and applying the processes that allowed FamilyTreeDNA to build the world’s largest Y DNA Haplotree, we can also create the world’s largest Mitotree.

In 2022, the first update was released, authored by the Million Mito team, with the discovery of haplogroup L7. You can read about this amazing discovery rooted deep in the tree here, here, and here. (Full disclosure: I’m a co-author.)

Not only that, but “Nature Scientific Reports” selected this article as one of five named Editor’s Choice in the Mitogenomics category, here. In the science world, that’s a HUGE deal – like the genetic Emmy.

Here’s one example of the type of improvements that can be expected. Currently, the formation of haplogroup U5a2b2a reaches back to about 5000 years ago, but after reanalysis, current branches originated between 500 and 2,500 years ago, and testers are clustered more closely together.

This is SOOO exciting!!!

Just as Discover for Y DNA results was built one feature at a time, the same will be true for MitoDiscover. That’s my name, not theirs.

As the new Mitotree is rolled out, the user interface will also be updated, and matching will function somewhat differently. Specifically, it’s expected that many more haplogroups will be named, so today’s matching that requires an exact haplogroup match to be a full sequence match will no longer work. That and other matching adjustments will need to be made.

I can hardly wait. I have so many results I need to be able to view in a tree format and to place in a timeframe.

You can be included in this exciting project, learn more about your matrilineal (mother’s) line, and hopefully break down some of those brick walls by taking the full sequence mitochondrial DNA test, here.

After the new Mitotree is rolled out and the Y DNA Family Finder haplogroups are completed, Family Finder customers, where possible, will also receive at least a basic-level mitochondrial haplogroup. Not all upload files from other vendors include mtDNA SNPs in their autosomal files. The mitochondrial Family Finder haplogroup feature isn’t expected until sometime in 2025, after the new tree and MitoDiscover are complete.

The Future

What’s coming later in 2024, or is ongoing?

Privacy Laws

Most people aren’t aware of the new privacy laws in various states, each of which has to be evaluated and complied with.

The effects of these changes will be felt in various areas as they are implemented.

New Kits Opted Out of IGG

Since late August, all new FTDNA kits are automatically opted OUT of Investigative Genetic Genealogy (IGG) by default.

Regular matching consent and IGG matching consent have been separated during onboarding.

Biobanking Separate Consent

Another consent change is to have your sample biobanked. FamilyTreeDNA has always maintained your sample for “roughly 25 years.” You could always ask to have your sample destroyed, but going forward, you will be asked initially if you want your sample to be retained (biobanked.) It’s still free.

Remember, if someone declines the biobanking option, their DNA will be disposed of after testing. They can’t order upgrades without submitting a new sample. Neither can their family after they’re gone. I ordered my mother’s Family Finder test many years after she had gone on to meet our ancestors – and I’m incredibly grateful every single day.

MyHeritage Tree Integration

An exciting change coming next year is tree integration with MyHeritage.

And no, before any rumors get started, FAMILYTREEDNA IS NOT MERGING WITH MYHERITAGE. It’s a beneficial marriage of convenience for both parties.

In essence, one of the primary focuses of MyHeritage is trees, and they do that very well. FamilyTreeDNA is focused on DNA testing and their existing trees have had issues for years. MyHeritage trees are excellent, support pedigree collapse, provide search capabilities that are NOT case sensitive, SmartMatching, and much more.

If you don’t have a MyHeritage account, creating one is free, and you will be able to either port your existing FamilyTreeDNA tree, or begin one there. If you’re already a MyHeritage member, FamilyTreeDNA and MyHeritage are planning together for a smooth integration for you. More detailed information will be forthcoming as the integration progressed and is released to customers.

You’ll be able to connect multiple kits to your tree at MyHeritage, just like you can at FamilyTreeDNA today, which enables family matching, aka bucketing.

You can also have an unlimited number of different trees at MyHeritage on the same account. You’re not limited to one.

After you link your initial FamilyTreeDNA kit to the proper person in your MyHeritage tree, you’ll be able to relink any currently linked kits.

MyHeritage will NOT receive any DNA information or match information from FamilyTreeDNA, and yes, you’ll be able to use the same tree independently at MyHeritage for their DNA matching.

You’ll still be able to view your matches’ trees, except it will actually be the MyHeritage tree that will be opened at FamilyTreeDNA in a new tab.

To the best of my knowledge, this is a win-win-win, and customers of both companies aren’t losing anything.

One concern is that some FamilyTreeDNA testers have passed away and cannot transition their tree, so a view-only copy of their tree will remain at FamilyTreeDNA so that their matches can still see their tree.

Big Y Infrastructure

Katy mentioned that internal discussions are taking place to see what changes could be made to improve things like matching and test processing times.

No changes are planned for SNP or STR coverage, but discussions are taking place about a potential update to the Telomere to Telomere (T2T) reference. No promises about if or when this might occur. The last part of the human genome to be fully sequenced, the T2T reference model includes the notoriously messy and unreliable region of the Y chromosome with many repeats, duplications, gaps, and deletions. Some data from this region is probably salvageable but has previously been omitted due to the inherent problems.

I’m not sure this shouldn’t be in the next section, the Wishlist.

Wishlist

There are lots of good things on the Wishlist – all of which I’d love.

I’d have difficulty prioritizing, but I’d really appreciate some Family Finder features in addition to the items already discussed. I’d also like to see some GAP (administrator) tool updates.

Which items do you want to see most?

Katy said that FamilyTreeDNA is NOT planning to offer a Whole Genome Sequencing (WGS) test anytime soon. So, if you’re holding your breath, please don’t. Based on what Katy did say, WGS is very clearly not a consideration in 2024 and I don’t expect to see it in 2025 either unless something changes drastically in terms of technology AND pricing.

While WGS prices have come down, those consumer tests are NOT scanned at the depth and quality required for advanced tests like the Big Y or even Family Finder. Normally consumer-grade WGS tests are scanned between 2 and 10 times, where the FamilyTreeDNA lab scans up to 30 times in order to obtain a quality read. 30X scans are in the same category as medical or clinical grade whole genome scans. Significantly higher quality scans mean significantly higher prices, too, so WGS isn’t ready for genealogy prime time yet.

Additionally, commercially available WGS tests are returned to the customer “as is,” and you’re left to extract the relevant SNPs and arrange them into files, or find someone else to do that. Not to mention, in order to preserve the integrity of their database, FamilyTreeDNA does not accept Y or mitochondrial DNA uploads.

Recently, I saw two WGS files with a 20-25% no-call rate for the autosomal SNPs required for the Family Finder test. Needless to say, that’s completely unacceptable. Some tools attempt to “fix” that mess by filling in the blanks in the format of either a 23andMe or Ancestry file so you can upload to vendors, but that means you’re receiving VERY unreliable matches.

The reason none of the major four vendors offer WGS testing for genealogists is because it’s not financially feasible nor technologically beneficial. The raw data file alone won’t fit on most home computers. WGS is just not soup yet, and it won’t be for the general consuming public, including relevant tools, for at least a few years.

I’ve had my whole genome sequenced, and trust me, I wish it were feasible now, but it just isn’t.

Suggestions Welcomed

Katy said that if you have suggestions for items NOT on the wishlist today to contact her through support.

I would add that if you wish to emphasize any specific feature or need above others, please send that feedback, politely, to support as well.

Katy ended by thanking the various teams and individuals whose joint efforts together produce the products we use and enjoy today.

Lab Update

Normally, DNA testing companies don’t provide lab updates, but this conference is focused on group project administrators, who are often the most dedicated to DNA testing.

A lab update has become a tradition over the years.

Linda Jones, Lab Manager, provided a lab update.

You may or may not know that the FamilyTreeDNA lab shifted gears and stepped up to handle Covid testing.

Supply-chain shortages interfered, but the lab ran 24×7 between 2020 and 2022.

Today, the lab continues to make improvements to processes with the goal of delivering the highest quality results in a timely manner.

On Monday, after the conference, attendees could sign up for a lab tour. You might say we are a rather geeky bunch and really enjoy the science behind the scenes.

Q&A and Thank You

At the end of the conference, the FamilyTreeDNA management team answered questions from attendees.

Left to right, Daniel Au, CTO; Linda Jones, Lab Manager; Katy Rowe-Schurwanz, Product Manager; Clayton Conder, VP Marketing; Goran Runfeldt, Head of R&D; and Andrew Gefre, Development Manager. Not pictured, Jeremy Balkin, Support Manager; Kelly Jenkins, VP of Operations; and Janine Cloud, Group Projects Manager. Janine is also responsible for conferences and events, without whom there would have been no 2023 FamilyTreeDNA conference. Janine, I can’t thank you enough!

A huge thanks to all of these people and many others, including the presenters, CSRs,  IT, and other FamilyTreeDNA team members for their support during the conference, enabling us to enjoy the conference and replenish the well of knowledge.

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News: Nebula Genomics Whole Genome, MyHeritage Photos Go Viral & Upcoming Publication Schedule

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“It never rains but it pours.”

Let’s just say I’m a tad bit overwhelmed right now for numerous reasons. Never, ever even whisper to yourself, “what else could go wrong?” Because you know what happens next, right!

Right now, I need to focus on what needs to be done for RootsTech and on some unexpected matters.

Translated, this means that my blog article publication schedule is slipping, and here’s what to expect.

There won’t be any 52 Ancestors articles for at least two weeks, and perhaps a tad longer. There’s a lot of research and prep that goes into each one, and I just don’t have the cycles right now.

I will *try* to get my regular technical article out this week. I did have a couple queued before RootsTech, but they aren’t finalized. Fingers crossed.

I will try to get at least a short RootsTech article out next week while I’m there. If I manage to do that, the photos will be uncropped and it will be “rough” and brief compared to my normal articles. Think of it as embedded reporting – I’m your correspondent on the ground:)

I do have a couple very interesting newsy items to share with you today.

Nebula Genomics Introduces 30X Whole Genome Sequence, Partners with Family Tree DNA

Nebula.png

I just received an e-mail from Nebula Genomics announcing that they are offering a whole genome 30X (30 scan coverage) sequence (WGS) for $299, plus a subscription to maintain access to updates in their research library. The idea is to sequence once and update your data forever, meaning that medical and other information will be at your fingertips as it becomes available. You can read their FAQ, here and the announcement here.

For this price, the DNA is sequenced in Hong Kong, not mainland China (a situation you can read about here,) but by BGI, renamed from Bejing Genomics Institute, a Chinese government-owned firm. This gives me significant pause due to the Chinese political regime and oppression of the Uighur population using genetic data. Nebula states that they are looking to move their processing onshore in the near future. I will be much more comfortable as soon as that happens.

However, there’s more news. Nebula has partnered with Family Tree DNA.

Hey, Family Tree DNA has a world-class lab, GenebyGene. Perhaps Nebula can move their processing there. I would even pay more to *NOT* send my DNA to a Chinese firm.

Nebula FTDNA.png

Beginning in Q2, you’ll be able to transfer at least some of your information from Nebula Genomics to Family Tree DNA’s Y and mitochondrial databases. This appears to be a direct company to company transfer, much easier than a download/upload, assures accuracy and provides enhanced security.

I don’t see details, and it’s not Q2 yet of course, but I would expect this transfer to function similar to others where the transfer and perhaps some basic tools are free, but for advanced tools, an unlock fee at Family Tree DNA would probably be required. I also don’t know if all data would be transferred, or what happens if you’ve already taken a lower level test, or if coverage isn’t sufficient. Lots to work out moving forward.

Unlike the other WGS products that I’ve considered, Nebula provides a genomic browser and available files for download. In other words, you don’t just receive your sequenced file on a disc and wonder what to do next, and how.

I do have questions about this new offering, but for the $299 price, anyone thinking about whole genome sequencing and is OK with BGI should consider Nebula, especially with the possibility of transferring Y and mitochondrial DNA directly.

As far as I’m concerned, whole genome sequencing become a viable option when:

  • It’s reasonably priced
  • The coverage is adequate, at least 30X
  • My data is secure (meaning not BGI or China)
  • I can easily transfer portions elsewhere (without having to use third party tools to extract the data) and utilize the Y, mitochondrial and autosomal files as uploads in other locations
  • The vendor provides tools or a subscription so I can reap continuing value

When Nebula processing moves onshore, or at least to a western-world lab, I’ll be all in!

My Heritage Colorized Photos Go Viral

I’m pleased to tell you that MyHeritage reports that people have colorized more than a million photos in the first 5 days since they first announced their new photo colorization tool. That means sharing with family and other people getting excited about genealogy.

I’m observing family members on social media realizing they have “long lost” pictures and sharing them when they see the new colorized photos posted. As genealogists, this is EXACTLY what we want to see.

Look at some of these amazing photos in the MyHeritage blog article, here.

Remember, if you’re not a MyHeritage subscriber, you can colorize 10 photos for free and then you can set up a free trial subscription account. When you colorize the photos, MyHeritage saves them beside the original in your MyHeritage account for you. I love this service.

If you’re having problems with older photos, try rescanning the original at the highest scan resolution possible.

I’ve also discovered that this tool doesn’t just colorize photos of people – but of buildings, landscapes and pets too. I’ve found the best results are with something that has a natural green, like leaves, because the software seems to calibrate itself by finding something it can identify.

Fluffy.png

Fluffy color.png

You’ll forgive me if I go and have a good cry now.

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Thank you so much.

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Whole Genome Sequencing – Is It Ready for Prime Time?

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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