Counting Chromosomes
A blog of random musings on genealogy, genetics, science, and history

It's a riddle that scores of websites will try to solve for you: which DNA test should you buy? But today's answer may surprise you.

Confused
An image I'll no doubt find many other uses for. Thank you to Robin Higgins, from Pixabay.

How much advertising money is spent trying to convince you one DNA test is better than another? How many websites and "experts" will break it down for you—usually starting with accuracy of ethnicity predictions—and tell you which test you should buy?

Truth is, the only rational response from someone truly informed about genetic genealogy will sound like a corporate consultant: "It depends." But there's a good reason for that. Our currently popular, over-the-counter autosomal DNA tests are remarkably similar in the lab; there really are only three major variants. Choosing a test is more about personal goals and objectives, portability, comparison and analysis tools, where other family members have already tested, and the list goes on.

I usually don't reply to public questions about which test to buy. If asked privately, I'll start with, "It depends," and then dive into the list of considerations. Today, though, the matter came up and I broke my own pattern. I provided an explicit answer about which test, for a first-time buyer, I would recommend right now. As in today.

My response has nothing to do with any of the usual suspects (e.g., ethnicity pie charts, eye color prediction), and I thought it might be worthwhile sharing it here.

The net message first: 1) My prognostication is that Whole Genome Sequencing (WGS) will completely supplant our current microarray genotyping tests for genealogy by 2022 or so. But I wouldn't wait for that to happen. Leading to, 2) If the funds are available, I would get an AncestryDNA test as soon as possible, then consider also taking a test from 23andMe, MyHeritage, Family Tree DNA, or Living DNA.

Why the urgency with Ancestry? Well, we're due for an AncestryDNA shake-up very, very soon.

It all has to do with those little microarray, microscope-slide-looking things that are programmed to attract our nucelotides to line-up in specific places so that a small part of our genome can be digitized.

Microarray

At issue is the "Intel" of DNA testing companies, a manufacturer called Illumina. Right now, we have about 29 million people who have taken direct-to-consumer autosomal DNA tests. Of those tests, roughly 20 million or so have been performed using Illumina's OmniExpress chip; the next largest chunk were done on Illumina's Global Screening Array, or GSA, chip; and a small percentage use a chip made by Illumina's only real competitor, Thermo Fisher Scientific.

With no fanfare, and a seemingly successful exfil/infil unbeknownst to many genealogists, Family Tree DNA switched from the OmniExpress to the GSA chip last April. And, ta dah!, the Family Tree DNA lab does the testing for MyHeritage...which means that MyHeritage switched chips at the same time.

AncestryDNA is the only testing provider, large or small, that still processes samples on the OmniExpress chip. Why? Illumina had intended to retire the chip long before now. In fact, when Living DNA first began planning its operational debut circa mid-2016 they were advised by Illumina that the OmniExpress chip would soon no longer be available, so they went with the GSA chip from the outset (subsequently, as of November 2018 Living DNA became the first, and so far only, tester to use the Thermo Fisher Scientific Affymetrix chip). And on 5 September 2017, Roberta Estes wrote on her blog that Illumina "has obsoleted their OmniExpress chip previously in use, forcing companies to utilize their new Global Screening Array (GSA) chip when their current chip supply runs out."

That didn't happen, but it also didn't mean that Illumina had changed its mind about retiring the chip. That retirement is happening now. We can speculate that the unprecedented (and unexpected) explosion in direct-to-consumer testing spurred by Ancestry's lederhosen-for-a-kilt advertisements persuaded Illumina to postpone the inevitable for a time. But while genealogy may not be quite a rounding error to Illumina's bottom line, it doesn't represent a large share of their earnings. For Q4 2018, Illumina booked $867 million in revenues; revenues for fiscal year 2018 were $3.33 billion. The entirety of their microarray chip business makes up about 12% to 14% of that, the genealogy market being only a portion of that percentage, and the OmniExpress chip a portion of that portion. Add to that some slippage in the growth rates of DNA test sales beginning around April 2018 (see the latest DNA database numbers and analysis from Leah Larkin). Manufacturing a microarray chip that it has "tooled down" and wants to retire is costing Illumina substantially more money and resources to continue to produce and support than does the newer GSA chip.

Bottom line: the OmniExpress chip is going away. Completely. AncestryDNA will be (is currently being?) forced to make a very significant decision, and they really have only the two choices: switch to Illumina's GSA chip, or join Living DNA and go with Thermo Fisher Scientific. Either way, I believe the change will be made before the end of this year, if not by the fourth quarter.

Okay. So why is this a big deal to us? Both tests are accurate, both tests provide good, solid data.

'Woj' is the nickname coined by her students decades ago, but monikers others have given her include 'The Godmother of Silicon Valley' and 'the Real Mother of Dragons'

Esther Wojcicki
Esther Wojcicki, the mother other mothers are reading to see how to raise remarkable children

With eternal gratitude, a very happy Mother's Day wish to all the mothers out there. Because, after all, without you we wouldn't have any mitochondrial DNA...and, well, we wouldn't be here at all.

This short post, though, is about a mother I've never met, but wish I had. And, yes, there's a genetic genealogy connection beyond mtDNA donation.

Esther Wojcicki (pronounced, roughly, wuu-CHIT-skee), the eldest of three children, was born Esther Denise Hochman in New York City. The family moved to California after her birth, and Esther received baccalaureates in both English and Political Science from UC Berkeley, and from the same school secondary teaching credentials and an M.A. in Journalism. She also holds an advanced degree in French and French History from the Sorbonne, Paris, and an M.A. in Educational Technology from San Jose State University.

She says that journalism has always been in her blood, but the reason she became a teacher was because it was too far for her to drive from her home—with husband Stanley Wojcicki, professor of physics at Stanford University, and her three children—in Palo Alto to San Francisco to be a reporter. Esther thought, "If I can't be a journalist, why not just teach journalism?"

She began teaching at Palo Alto High School in 1984, where she founded the Media Arts programs at Palo Alto High School, taught and mentored many of Silicon Valley's brightest including Steve Jobs' daughter, Lisa Brennan-Jobs, and helped launch the Google Teachers Academy. The journalism program at Palo Alto High has grown to become one of the largest such high school programs in America. In 1990, Esther was named Northern California Journalism teacher of the year, and in 2002 was named California Teacher of the Year.

Wojcicki family
An idyllic portrait of the Wojcicki family

She was awarded the Gold Key by Columbia Scholastic Press Association in 2009; she's on the Board of Trustees of the Developmental Studies Center and on the Board of Governors of the Alliance for Excellent Education; she is Chairman of the Board of Learning Matters; she's Chief Learning Officer for Explore Planet3, an exploration based science platform for middle school students. She is on the board of the Newseum in Washington, D.C. and the Freedom Forum; is the founder of the Journalistic Learning Initiative at the University of Oregon; is the founder of the Moonshots in Education Movement; and she has an honorary doctorate from Palo Alto University.

That's an impressive resume. But none of it is what Esther is known for best. What she's best known for is being a mother. Esther has three daughters. They are, alas, a brood of disappointing underachievers, but you may have heard of them anyway:

  • Susan Wojcicki has been the CEO of YouTube since 2014; she was involved in the founding of Google, becoming Google's first marketing manager in 1999. She started her first business at age 11, selling "spice ropes" door-to-door.
     
  • Janet Wojcicki, PhD, MPH, is a Fulbright-winning anthropologist, Assistant Professor of Pediatrics and researcher at the University of California School of Medicine. She has over 60 peer-reviewed research publication credits.
     
  • Anne Wojcicki is the co-founder and CEO of personal genomics company 23andMe; her alma mater is Yale University and she was a researcher in molecular biology at the National Institutes of Health and the University of California, San Diego (and an irresistible bit of Anne trivia: she was a competitive ice skater and played on the Yale varsity women's ice hockey team).

There is only one thing genealogically special about the X chromosome in relation to males: the inheritance pattern. The important distinction is that, in males, the X is "naturally phased."

Human X chromosome

Q: I've been told that if two men share a match on the X chromosome, that special conditions apply. That because they're both male and because they can only have gotten their X chromosome from their mothers, that the match means more than matches on other chromosomes do. I've seen matching that indicate a very small amount of shared DNA on the X chromosome, for two males only, can be used as confirmation of the relationship and no other DNA information is needed. That just doesn't sound right to me, and I wanted to get your thoughts.

A: Thanks for writing, and I've seen the same contention about the X chromosome in different places. I'm uncertain how that myth first started, but your impression—and discomfort with the claims—is well-founded.

Prove and Confirm

First, though, let's talk a moment about that word "confirmation." We do see it used in reference to genetic genealogy and, in my opinion, much too liberally so. The verb "confirm" has different meanings based on the circumstances or environment to which it's being applied, but let's look at what Google presents us at the top of its search results for the word:

General Definition of Confirm

Establish the truth or correctness of something previously believed or suspected; state with assurance that a report or fact is true.

In her indispensable book, Evidence Explained: Citing History Sources from Artifacts to Cyberspace, my genealogy totem spirit and guide, Elizabeth Shown Mills, defines "confirm" this way:

confirm: to test the accuracy of an assertion or conclusion by (a) consulting at least one other source that is both independently created and authoritative; and (b) finding agreement or compatibility between them.
     —Elizabeth Shown Mills

Note the conjunction and in Elizabeth's definition: for genealogy, both conditions a and b must be met, not either/or. Note also the phrase "independently created and authoritative."

Evidence Analysis Process

A digression—tangential though pertinent—but while I'm mentioning Evidence Explained I'd be remiss if I didn't call attention to the inside cover of the book, where Elizabeth gives us a simple and intuitive diagram of her Evidence Analysis Process Map. The image below (click to enlarge) is from her website, "QuickLesson 17: The Evidence Analysis Process Map". It isn't lengthy; I suggest it be in everyone's bookmarks list.

However, all genealogists, including applicants, need to make sound decisions about when DNA can or should be used, and any work products that incorporate it should meet the new standards and ethical provisions.
     —Richard G. Sayre, President, BCG

BCG
Founded in 1964 by leading American genealogists, BCG fosters public confidence in genealogy as a respected branch of history. Click the image above to visit the BCG website and learn more.

The following public press release is not yet published on the BCG website, bcgcertification.org, but I expect it will be tomorrow. I am posting it here—admittedly redundantly since it will be on the BCG website and all the genealogy blogs almost instantly—because I have a very brief tangential preface, and because this simply is big news.

Update: the BCG posted the press release on its website early Sunday morning, 28 October. You can view it at bcgcertification.org/standards-for-dna-evidence.

Many thanks to Blaine Bettinger for bringing this to our attention quickly on his Facebook Genetic Genealogy Tips & Techniques Group. Blaine has been working with and advising the BCG on this effort.

Virtually all of the more than 17 million direct-to-consumer autosomal DNA tests have been performed on microarray BeadChips made by Illumina. Living DNA opened their doors using the Illumina GSA chip, but are now the first major-tier DTC tester leaving Illumina.

Note: information updates obtained after this article was published are posted at the bottom of the page and we will attempt to add salient information as it becomes available.

Microarray

Living DNA announced yesterday, 22 October, that they are moving away from the Illumina GSA (Global Screening Array) genotyping array microchip they have used since the company opened, opting instead for an offering from Thermo Fisher Scientific under its Affymetrix brand, acquired by Thermo Fisher Scientific 31 March 2016. Living DNA is the first major direct-to-consumer (DTC) autosomal DNA testing company to cease using Illumina, and we can only make educated guesses at the reasons.

The industry has been watching closely for many months to see what the introduction of Illumina's GSA chip would mean to the genealogy marketplace.

People tend to hold overly favorable views of their abilities in many social and intellectual domains.... This overestimation occurs, in part, because people who are unskilled in these domains suffer a dual burden: Not only do these people reach erroneous conclusions and make unfortunate choices, but their incompetence robs them of the metacognitive ability to realize it.
     —David Dunning and Justin Kruger,
         Journal of Personality and Social Psychology,
        1999 Dec;77(6):1121-34

Dunning-Kruger Effect
Image courtesy of YLMSportScience

This will be somewhat of a departure in content: I have a serious point to make, then I need some cathartic comedy time. Welcome to the ride.

I'm sure most of you are familiar with the Dunning-Kruger Effect. Since its proposal as a theory in 1999, it's been borne out in multiple studies—more than 100 to date—across varying environments. In a nutshell, what it tells us is that we're not very good at evaluating our own levels of knowledge and skill. Illusory Superiority: we judge ourselves as being better than others to degrees that violate the laws of mathematics.

The first five months of 2018 we went from 12 million direct-to-consumer DNA testing kits sold to about 17 million, an average of 1 million new kits per month. The extrapolated growth trend may slow, but it's still within reason that we might see 10 million tests sold through the course of 2018.

DNA Testing Update
Graph by Antonio Regalado, Senior Editor, MIT Technology Review. Click image to view at full size.

New data are in, and business is positively booming. Antonio Regalado, Senior Editor for the MIT Technology Review, has been keeping tabs on testing trends since at least 2016, and he posted this updated chart August 6.

These numbers aren't yet affected by GDPR because they run through the month of May; GDPR went into effect May 25. The Golden State Killer genetic genealogy brouhaha surfaced last April, so the trend might also be blunted somewhat by new privacy concerns. Time will tell.

Market Research

If you follow genealogy and genetics news like I do, no doubt you have seen—multiple times over the past few weeks—notification of a market study from a company based, I believe, in India called Absolute Reports. The report is titled "2018-2025 Genealogy Products and Services Report on Global and United States Market, Status and Forecast, by Players, Types and Applications."

Sounds intriguing, doesn't it? It was published 22 June 2018; I first saw it advertised in July, and it is offered for the price of US$3,600 for a single-user license with the option to receive a limited, redacted preview. You can view a safe description of the study at Absolute Reports' website.

It remains unclear to me whether Absolute Reports is solely a reseller of externally prepared market reports, or whether they write any of the studies themselves. Regardless, the sample copy of this seven-year genealogy industry forecast that I received contained no attribution of authorship. In fact, section 15.4, "Author List," was redacted of all names or contact information. The only notice of copyright anywhere in the 79-page document (advertised as being 117 pages) is in section 15.3, "Disclaimer": "All trademarks, copyrights and other forms of intellectual property

The goal of the collaboration is to gather insights and discover novel drug targets driving disease progression and develop therapies for serious unmet medical needs based on those discoveries.
     —GlaxoSmithKline

GlaxoSmithKline
GlaxoSmithKline headquarters,
Brentford, London, UK

UK-headquartered Big Pharma company GlaxoSmithKline (GSK) has invested $300 million (£228 million) for an equity stake in direct-to-consumer DNA testing company 23andMe. The official GSK press release describes the investment as a "multi-year collaboration expected to identify novel drug targets, tackle new subsets of disease and enable rapid progression of clinical programmes."

The GSK press release highlights three primary goals of the collaboration; quoting:

  • Improve target selection to allow safer, more effective "precision" medicines to be discovered. Genetic data can significantly improve our understanding of diseases, their pathways and mechanisms, supporting the design and development of

Taking the two precedents cited by Ancestry.com in their motion of dismissal, it seems their platform is that neither natural phenomena nor abstract ideas are patentable unless there is a new, additional, inventive concept involved. Maybe we'll end up with the "do it on a computer" argument, and the "DNA is DNA" argument.

Court of Law
Invoking two Supreme Court precedents, Ancestry.com files for dismissal

This week, Ancestry.com responded to the lawsuit from 23andMe by filing a motion to dismiss with a California federal court. The filing indicated the 23andMe patent consisted of "abstract and non-inventive steps" of collecting two DNA samples and then comparing them to find a correlation based on phenomena that occur naturally. The U.S. Patent in play is number 8,463,554, titled "Finding Relatives in a Database," issued 11 June 2013.

The lawsuit was filed May 12 by 23andMe demanding, among other things, payment for damages and invalidation of the "Ancestry" trademark. An article at Law360 said, in part:

The European Parliament will now be able, in an open debate, to improve the text and defend freedom of expression ahead of the next elections.
     —Diego Naranjo, Senior Policy Advisor at EDRi

Next Steps from the EDRi
Infographic from EDRi, the European Digital Rights organization

I wrote recently about the sea of criticism mounting against the Orwellian proposal by the EU for a "Directive on Copyright in the Digital Single Market" (see "Will the Proposed EU Copyright Directive Irrevocably Damage the Internet?" and "Controversial Copyright Proposal Passes First Step in European Union Parliament"). Yesterday, July 5, Members of the European Parliament (MEP) voted by a slim margin of 318-278 to remove from its Committee on Legal Affairs (JURI) the mandate to negotiate with the EU Council the proposed copyright directive as it is currently written.