[KerryOdair]

Well until the Y is fully sequenced this seems to be a significant article for finding new snp's that people match.

PRESS RELEASE
Nov. 3, 2010, 8:00 a.m. EDT
Affymetrix to Provide Data Set of Millions of Genotypes to 1000 Genomes Project
These Variants Will Empower Future Genotyping Studies and Genetic Characterizations of Human Disease and Health

In addition, Affymetrix will release a larger data set of approximately 5 million variants on its website, www.Affymetrix.com, before the end of 2010. The new data includes approximately 3 million human SNPs discovered by the 1000 Genomes Project that were not found in the HapMap Project or the NCBI's Single Nucleotide Polymorphism Database (dbSNP, release 130). This information, which was generated by Affymetrix using the Axiom(TM) Genotyping Solution, will allow scientists to create customized Axiom Genotyping Arrays containing 50,000 to as many as 2.6 million markers. The entire Axiom Genomic Database provides an extensive selection of ready-to-use variants for custom array designs and enables an unprecedented level of success in assay conversion.

http://www.marketwatch.com/story/affymetrix-to-provide-data-set-of-millions-of-genotypes-to-1000-genomes-project-2010-11-03?reflink=MW_news_stmp

[Joann]

no accusations of infringement

According to the NY Times:

In its brief to the appellate court, Myriad argued that the plaintiffs did not have standing to sue because Myriad was not accusing them of infringement.

See page 20 (internal document number) of Myriad appellate brief:

http://www.cap.org/apps/docs/statline/pdf/myriad.pdf

So right now, there is no indication from Myriad that there will be such infringement accusations made in the future....

.......But I mainly wanted to point out the crowd source capabilities that you had elucidated in a prior published SEQanswers post.

[ECO]

Maybe not ECO...

See comments at Forbes, Oct 11, 2010--Rober Langreth
http://blogs.forbes.com/robertlangre...iads-monopoly/

Which part "maybe not"...helping with the analysis or being late to the party.

Not sure how I see Myriad's inevitable wave of lawsuits would effect this type of community analysis.

[Joann]

Crowd-source gene analysis circa Oct. 11, 2010

This is very cool and inspiring. I wonder if the collective we could volunteer to help with this dataset. We have enough experts in assembly, annotation, SNP discovery, etc, that 4 human genomes (better yet a family) could be a very interesting data set.

I'll have to think on it a little more, but I would love to collaborate with her and her family to open up the dataset to SEQanswers users. Perhaps I could secure or fund a donation of some compute resources for the product.

Thanks for posting it Kerry!

edit: Looks like we'd be a little late to the party...

Maybe not ECO...

See comments at Forbes, Oct 11, 2010--Rober Langreth

http://blogs.forbes.com/robertlangreth/2010/10/11/do-it-yourself-gene-testing-threatens-myriads-monopoly/

[KerryOdair]

Familytreedna Administrators conference:

October 31, 2010 Walk Through the Y Paper by Thomas Krahn in Houston Texas. Possible enrichment strategy for Y chromosome. We are getting closer but we are not there yet. Waiting for someone to take the next big step.

http://www.dna-fingerprint.com/static/FTDNA-Conference-2010-WalkThroughY.pdf

2009 paper and prototype testing using our E-M35 project members for Walk Through the Y.

http://www.dna-fingerprint.com/static/FTDNA-Conference-2009-WalkThroughY.pdf

[krobison]

Blogger Luke Jostins apparently did the Y-chromosome analysis -- you might contact him to get more info.

[KerryOdair]

The 1000 Genomes Project Consortium

The 1000 Genomes has published information on its pilot project. Lots of good information on this at the links below. Mutation rate discoveries could be the most interesting part of this new information. I was surprised at how much supplemental information was released in the publication. The Y Chromosome information is still lacking for what I would like to see. Baby steps I guess at this point. Even with the pilot project a tremendous amount of data involved.

http://www.nature.com/nature/journal/v467/n7319/full/nature09534.html

http://johnhawks.net/weblog/reviews/genomics/variation/1000-genomes-2010.html

http://www.nih.gov/news/health/oct2010/nhgri-27.htm

http://dienekes.blogspot.com/

[Joann]

Within the context of whole genome sequencing, living relatives' approval is rather close to irrelevant. Furthermore, consent documents should never be used as a technical band-aid. The ethical budens should shift from relying on such consent documents to gated whole genome databases in order for research-relevant sections to be made consistently available from general genome databases. Quite frankly, the rules and order established by paper archivists (and in particular medical records archivists) already go a long way in serving as a model protocol. Sections of gene-centric, identity markers and ancestry markers can be bioinfomatically extracted from the whole genome data of a given individual volunteer (or group) and viewed in the context of a study or search.

[KerryOdair]

I don't think this version of informed consent is good enough. See one of my earliest remarks on this forum at the at the SeqAnswers thread:

DDBJ dealing with mass data produced by the second generation sequencer.

Nucleic Acids Res. 2008 Oct 16;

Authors: Sugawara H, Ikeo K, Fukuchi S, Gojobori T, Tateno Y


My comment focuses on these authors' stated concerns about individual genomes in public databases. While we are all products of evolution we are furthermore relatives of individual ancestors, not one generic "model organism". As you well know, Kerry, current genetic genealogy technique is already a very powerful trace back to deep ancestry. It crosses past many generations of our individual forebears, identifying them and linking them--and us--in detail not yet fully appreciated, in my opinion.

They suggest approval from relatives before entering into this consent form. How would you improve their comments? Or do you feel we cannot at this point in time put this information into public format?

[Joann]

not good enough

I don't think this version of informed consent is good enough. See one of my earliest remarks on this forum at the at the SeqAnswers thread:

DDBJ dealing with mass data produced by the second generation sequencer.

Nucleic Acids Res. 2008 Oct 16;

Authors: Sugawara H, Ikeo K, Fukuchi S, Gojobori T, Tateno Y


My comment focuses on these authors' stated concerns about individual genomes in public databases. While we are all products of evolution we are furthermore relatives of individual ancestors, not one generic "model organism". As you well know, Kerry, current genetic genealogy technique is already a very powerful trace back to deep ancestry. It crosses past many generations of our individual forebears, identifying them and linking them--and us--in detail not yet fully appreciated, in my opinion.

[KerryOdair]

Here is a link to the genomesunzipped consent form. It looks like a well thought out form for release of personalized genome information.

http://www.genomesunzipped.org/wp-content/uploads/2010/10/gnz_consent_phase2launch_101013.pdf

[KerryOdair]

What kind of consent problems do you forsee as a prelude to requesting individuals to grant the release their Y sequence data to a genealogy community?

This is another big question. However, I will start with ISOGG and Katherine Borges response as the Director of ISOGG. I will supply some other information and thoughts beyond the Y chromosome as well in the near future.


Katherine Borges is the Director of ISOGG, the International Society of Genetic Genealogy, a non-profit organization of over 7,000 members spread throughout the US and 60 other countries. She also serves as co-admin of the Portugal Project as well as several other surname Projects at FTDNA. Here is the essence of her statement before the FDA hearing earlier today:

"......Our (ISOGG's) mission is to promote and educate members and the general public about the use of DNA testing for genealogical and ancestry purposes. We are comprised of serious enthusiasts who represent an active core of the estimated one million people who have taken DTC (direct to consumer) tests for genealogy and ancestry purposes since their inception about ten years ago.

As the name of our society implies, our focus is primarily upon using DTC tests for genealogy, but a growing segment of our membership also use personal genome tests to trace health-related information within their families. However, testing for ancestry and anthropology is far and away the largest segment of the DTC genetic testing market. This clearly does not fall under FDA's area of responsibility. Our concern is that FDA should not attempt to expand its regulatory authority beyond its proper domain of medical applications, and it should assure that its actions in the medical area do not inadvertently impact the non-medical applications.

ISOGG is a dues-free society with no funding sources. The organization has no direct financial stake in any proposed regulation, and is not affiliated with or financially supported by the companies offering these tests. However, our members understand that they would bear the impact and resultant costs of any regulatory matrix imposed upon testing companies, first as taxpayers, and secondarily as consumers of the services they offer.

Our membership is not opposed to regulation that works to protect or help consumers where a clear need for legislation is evident and an agreed-upon national purpose is fulfilled. In 2008, we supported GINA, and many of our members wrote to their legislators to urge them to pass this important bill.

Additionally in 2008, ISOGG encouraged and facilitated the development of Y-chromosome nomenclature standards for Short Tandem Repeats or STRs by the National Institutes of Standards and Technology, and their subsequent adoption by the ancestral DNA companies and labs. These standards were published in the Fall edition of the free-access online Journal of Genetic Genealogy. This initiative for voluntary standards by a private organization is similar to the implementation of voluntary standards such as those of UL and NEMA in the electrical industry, and ANSI standards in many others.

The great majority of our ISOGG membership feels strongly that any expansion of FDA regulatory authority that would have the effect of preventing consumers from ordering DTC tests would be unwise and unnecessary. At a minimum, no action of that sort should be taken without credible, compelling scientific data to support such a move. Relevant studies of this nature and quality are currently being conducted.

In making these statements I have in mind the role of the media and certain written academic opinions that over the past few years have sought to impact this issue. Sensationalistic media articles that relate anecdotal cases should not be used as a basis to regulate. Many of the articles I've read have been biased, reflecting the author's views without presenting voices from both sides of the issue. For example, just last week, a DC area reporter was looking for stories from consumers of DTC testing for an article to be published in anticipation of this meeting. He was contacted by several individuals who had positive testing experiences, but he did not follow up on these contacts. He told another consumer that he was specifically seeking negative experiences.

Even more seriously, we see a tendency towards a paternalistic attitude by certain groups in the medical professions who seek to limit access to medical information that is not directly under their control. Their arguments often express an extremely low opinion of the ability of people outside of their own professions to comprehend any genetic information or come to terms with its implications. Yet, we heard Col. Magill of Walter Reed state here yesterday that sometimes he sees a patient who knows more about a medical issue than he does, just from personal research. A mandated intermediary would impose yet another cost to consumers.

Additionally, over-regulation can even negatively impact participation in scientific studies. My own mother signed up to participate in Kaiser Permanente's genome study, but then backed out for the very reason that the results will not be returned to her. A barrier to access to one's own genetic information also seems contrary to the intent of HIPAA law, and to the new rules issued last week by the White House requiring health insurance companies to provide free coverage for screenings, laboratory tests and other preventative care.

The general view of ISOGG's members is that regulatory agencies should not stand between a consumer who wishes to collect data on their own genome, and labs that can provide that service. The genome of an individual consists fundamentally of information, and every individual in a free society has an absolute right to information about their own genome from a source of their choosing.

Our membership base consists of many MDs, PhDs, and other specialists who are willing to volunteer their time to assist with the development of industry standards, good practices, and advisory panels. These concepts could be developed in collaboration with federal agencies like NIST and the FTC. And FDA's regulatory requirements for DTCs could be met with something as simple as full and adequate disclosures of the limitations of the tests by the testing companies.

The result could be a happy medium to the benefit of consumers, the laboratories, the testing companies, the government and to taxpayers."


The full, edited, statement in final form will be filed with the records of the conference within the next two weeks. It will vary somewhat from the above.

[Joann]

There's always more questions

What kind of consent problems do you forsee as a prelude to requesting individuals to grant the release their Y sequence data to a genealogy community?

[KerryOdair]

Thanks Kerry. Now I would appreciate some futher comment from you on what this group's approach does or doesn't (will or won't) do for the genealogy special interest groups working with online data. For example, how accessible do you find the Y chromosome data?

Hello Joann,

These are big questions you have asked. I have not contacted these people directly as of yet but intend to do so. On the surface it looks like they are using autosomal data to compare at first with the ability to move on to sequenced data in the future. This would represent results from 23andme, DeCodeMe, and Familytreedna Family Finder results. This just came out on 10-11-10 about this site. Dienekes blog has already discussed and done some comparison of their data already. This can be found at the link below:

http://dienekes.blogspot.com/

We need some way to have a public repository of this information somewhere that everyone can use. Right now the data is being controlled by companies and academic institutions.

We have already established a collective of information from 23andMe and DeCodeMe tests in our community. It compares the data from their tests. The data can be downloaded from the zip file at the link below.

Adriano Asquecco files for 23andMe Data

Below are the links for all testing done with 23andMe by different haplogroups

http://www.webalice.it/asquecco/Y_DNA-Forums.zip

We have exhausted most of the new snp discoveries from this endeavor. We did not find as many new snp’s as we hoped due to the fact that the testing chips were designed with known snp’s. Testing chips can only test for known snp’s. We must move on to sequencing for complete data information. Autosomal data will only move us back 5 to 6 generations at best.

Currently today we use STR and SNP data. The largest STR public database is Ysearch which has its problems but it the best we have.

Link: http://www.ysearch.org/

Familytreedna has the largest selection for snp testing in the market place today. But this type of testing is difficult trying to establish a new snp placement in the Y tree. However, it is the best we have today. Many new L series snp’s have been established. Below is a link for a great utility looking at these new snp’s. It has the last 2008 release of the Y tree along with a draft tree which shows all the newly discovered snp’s. Using this utility you can click on the new snp and go directly to a Y mapper. There are a considerable number of haplogroup projects trying to find new snp’s in their particular haplogroup designation ours being the M35 project. This utility was developed by Thomas Krahn at Familytreedna. He also has a X mapper as well

http://ytree.ftdna.com/

http://xmap.ftdna.com/cgi-bin/gb2/gbrowse/hs_chrX/?

Well enough for this post maybe you will have some follow up questions. Hopefully I have answered your questions. I certainly do not have all the answers. My goal is to try and get the players together to make this Y Chromosome sequencing happen.

[Joann]

More questions

Thanks Kerry. Now I would appreciate some futher comment from you on what this group's approach does or doesn't (will or won't) do for the genealogy special interest groups working with online data. For example, how accessible do you find the Y chromosome data?