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

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.

Tangent

In a recent and, as it proved to be, controversial post, I described that I have been an advocate of a formal method of accreditation for genetic genealogists. I'm afraid I described that position poorly, and also did not take into account the audience majority who have not been, in their careers, accustomed to the variety of professional, trade, compliance, and instructional certifications common in my business experience.

I am long overdue for a follow-up attempt to clarify my position, but I need to be clear: this is not that update, and the type of accreditation I was speaking of is unrelated to this announcement from BCG and its important press release about its new DNA standards. In my September post I intended to reference a type of specialty certification; for example, perhaps analogous to the American Board of Medical Specialties or their Focused Practice Designation program.

BCG's work is providing guidance and certification for genealogists. I can think of only two genealogists I've spoken with in the past year who do not believe DNA is now a vital element in evidentiary practice for genealogy. I was one of those who provided comment earlier this year to BCG regarding development of these new standards, knowing full well that the type of accreditation I've had in mind for a few years is beyond BCG's scope. They do not certify geneticists; they certify genealogists.

I want to thank BCG and all those who actively participated and advised on this effort. I consider this a very important development for the practice of genealogy. Even if you have no immediate interest in pursuing BCG certification, I believe the guidance offered is a benchmark for all genealogists. The new standards to be published in March 2019 will be included in a new edition of BCG's Genealogy Standards. I'm sure the current 50th Anniversary Edition of Genealogy Standards is already on your bookshelves.

For Immediate Release 27 October 2018

News Release, Board for Certification of Genealogists

Board for Certification of Genealogists Adopts Standards for DNA Evidence

On 21 October 2018, the Board for the Certification of Genealogists (BCG) approved five modified and seven new standards relating to the use of DNA evidence in genealogical work. BCG also updated the Genealogist's Code to address the protection of people who provide DNA samples.

The new measures are intended to assist the millions of family historians who now turn to genetic sources to establish kinships. The action followed a public comment period on proposed standards released by BCG earlier this year.

"BCG firmly believes the standards must evolve to incorporate this new type of evidence," according to BCG President Richard G. Sayre. "Associates, applicants, and the public should know BCG respects DNA evidence. It respects the complexity of the evidence and the corresponding need for professional standards. BCG does not expect use of DNA to be demonstrated in every application for certification. 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."

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. Living DNA launched 22 September 2016 selling its first test kits in the UK. It exclusively employed the GSA chip. As of September 2017, with its "v5" product, 23andMe had moved from the Illumina OmniExpress chip to the GSA chip, as well. The 800-pound gorilla in DTC genetic testing, AncestryDNA, continues to use the OmniExpress chip, as do large industry players Family Tree DNA and MyHeritage.

For genealogical matching, the wrench in the works has been that the OmniExpress and GSA chips—while both are testing over 665,000 of the approximately 10 million identified SNPs (single nucleotide polymorphisms; and to be precise, as many as 15 million SNPs may have been identified but only as many as 5 million have been used as yet in advanced genetics studies, so split the difference at 10 million) among the 3.2 billion base pairs of the human genome—look at only about 23% of the same SNPs. Almost 80% of the SNPs tested by each microarray product are unique and can't be directly compared.

SNP Venn Diagram
Venn Diagram displaying approximate in-common overlap of tested SNPs between the Illumina OmniExpress and GSA BeadChips

In other words, if you've taken a Living DNA test (or recent 23andMe test) and your cousin an AncestryDNA test, only one-fifth of the SNPs can be compared one-to-one. We were left with only two options: either omit the evaluation of non-tested SNPs (which reduces the genomic comparison to only about 135,000 total SNPs), or employ imputation algorithms—think of them as Wheel of Fortune math that use empirical probabilities to make best-guess determinations about missing DNA letters—to assume which nucleic acids would be at specific chromosomal loci, had those base pairs been tested.

If the goal is accuracy in genealogical matching, neither of those two options is exactly a stellar standout. Living DNA still has no production user-matching feature. Its Family Networks offering was announced last February at RootsTech but, eight months later, it is still in beta-only mode.

Not dissimilarly, GEDmatch introduced the Genesis Algorithm in late May 2017 as an intended matching accuracy enhancement in support of its mission to be testing-vendor neutral. This was begun as a beta test and deployed a second database, separate from the initial one some of us colloquially now call "Origin." While the Genesis database could accept raw data from GSA chip tests, the Origin database could not, and the two databases remained separate: kits in one could not be compared to kits in another. In what may be the longest public beta in the history of genealogy tools, the two GEDmatch databases are just now, 17 months later, beginning to share data.

This is in no way the fault of the GEDmatch developers; it's merely a testament to the difficulty of the task: attempting to work with the detailed correlation of two disparate sets of data. The verdict is still out as to the efficacy and accuracy of directly comparing GSA and OmniExpress results, and the Genesis side of GEDmatch is still labeled as a beta-mode product and requires a separate log-on account.

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.

In a plenary vote yesterday, 20 June 2018, the Legal Affairs Committee (JURI) of the European Union Parliament voted for a proposed copyright directive as presented, which includes measures to monitor, filter, and control—if not outright censor—uploads to the Worldwide Web. In an article titled "Will the Proposed EU Copyright Directive Irrevocably Damage the Internet?" I commented a few days ago on the highly controversial proposal for a "Directive on Copyright in the Digital Single Market," EU Interinstitutional File: 2016/0280 (COD).

EDRi Infographic
Infographic by the European Digital Rights (EDRi) organization, click image to view actual size

Considering the number of voices raised in opposition to the proposal, it is surprising to many that the current text passed without further alteration or amendment. In particular, Chapter 2, Article 13 (pages 56 through 60 of the 66-page proposal) is drawing dire warnings from many open-information notables. In essence, it will require that that providers of web services be responsible and liable for pre-screening everything people post online to make certain none of it potentially infringes on copyrighted material.

There is no such thing as an "international copyright" that will automatically protect an author's writings throughout the world. Protection against unauthorized use in a particular country depends on the national laws of that country. However, most countries offer protection to foreign works under certain conditions that have been greatly simplified by international copyright treaties and conventions.
     —the United States Copyright Office

Handcuffed at Keyboard

Just as we were all getting over the serious and painful surgery on May 25 that was enactment of the GDPR (General Data Protection Regulation), we have a new issue on the immediate horizon. Just three days from now, June 20-21, at the European Parliament meeting in Brussels, up for an initial vote on plenary approval is the controversial "Directive on Copyright in the Digital Single Market," EU Interinstitutional File: 2016/0280 (COD).

In particular, Chapter 2, Article 13 (pages 56 through 60 of the 66-page proposal) is drawing not only ire, but some dire warnings