20 November 2010

Family Tree DNA's 6th International Conference, part 2

Sunday, October 31, 201

ISOGG
met at 8:30 a.m. Katherine Borges, director of ISOGG, gave a presentation on the organization and its history. This non-profit society started in 2005 by a handful of people and without any funding. No dues are required and the only goal is to spread the word about Genetic Genealogy.

ISOGG recently developed the ISOGG wiki page and has many topics to assist researcher of all levels.

The ISOGG newsletter is distributed to about 4,400 members.

Several members staffed the booth last February at the Who Do You Think You Are? Conference in London, the largest genealogy convention in the world. Nearly 20,000 people attended that conference. Some administrators offered free DNA tests for anyone at the conference who was a male with the desired surname. At least five people received free tests. ISOGG will be manning a booth again this coming year. (February 25-27, 2011)

Dr. Bruce Walsh, Professor of Ecology and Evoluntionary Biology at the University of Arizona, presented The Math Behind Family Finder. Dr. Walsh uses the phrase “incorrectly ascertained paternity” instead of NPE (Non-parental event) which is more correct, actually.

He explained that one chromosome is contributed by each parent, but that chromosome is a combination of both of their parents. He states that autosomal DNA is sliced and diced, but the Y-chromosome does not recombine as there are never two copies in the cell. However, recombination of the X chromosome does occur because there are two copies. Since men have an X and a Y there is no recombination, but of course their X was a recombination of their mother’s two X chromosomes. The Mitochondrial DNA does not recombine, but is passed on as an identical block, except for random mutations.

Dr. Walsh also believes that the autosomal chips will have more than a million markers in 2-3 years. Current technology is about 500,000 markers.

The Family Finder test can reliably predict relationships for three generations (to the 3rd cousin level). However, fourth and fifth cousins are possible, but not as reliable. Each generation only gets 50% of the previous generations’ autosomal DNA. This means that that in only a few generations there is little to now autosomal DNA from the ancestors.

Bennett Greenspan, President and CEO of FTDNA, spoke on Reading Family Finder Results. He demonstrated how to use Family Finder test results to solve a 30-year mystery in his lineage. He used the chromosome browser portion of Family Finder to triangulate and determine whether a match is on the maternal or paternal side. Doing so does entail testing the correct level of family members. By testing close family members you can compare them with distant family members to see how where and how much the data overlaps. If you test a close on your paternal side and a close relative on your maternal side, you can compare a distant cousin to each and determine which side they are related.

He further explained that small block lengths (or centimorgans, aka cM) means that there is a more distant relationship even if the totally number of matching SNPs is large.

He clarified homozygosis and heterozygosis. Our DNA contains four chemical bases (adenine, cytosine, guanine, and thymine or ACGT). There are a pair of these bases at each location along the chromosome, but Family Finder cannot distinguish between them so you see two letters which are always given in alphabetical order. When looking at the raw data and comparing one person to another, the AA from one person matches an AT from another person and a TT matches an AT, but the AA does not match a TT. Therefore, if a person has the same chemical basis (i.e., AA or TT), this is called homozygous, and if the pair differ (i.e., AT) it is called heterozygous. If a person is heterozygous in an area they will tend to match more people, but if those people are homozygous, they will not match each other. That is, if you have an AT at a location and you match two people who are AA and TT, the people who are AA and TT will not match each other. This means you will have matches on your family Finder and those matches will not match each other if you are the one who heterozygous. These matches are usually on smaller segments of the DNA, but get everyone excited in that they are hoping that if everyone matched everyone, they could triangulate the lineages to more easily discover the common ancestor.

Bennett mentioned that the X-chromosome browser is being developed and may be available in March 2011.

Dr. Charmaine Royal’s, the lead author of the ASHG (American Society of Human Genetics) white paper entitled Inferring Genetic Ancestry: Opportunities, Challenges, and Implications. She is an Associate Research Professor in the Institute for Genome Sciences and Policy and the Department of African and African American Studies at Duke University. She stated that the reference populations in commercial databases are usually proprietary and pretty much unverifiable by other researchers. Therefore, a prediction by one company may be at odds with another and there is no way of understanding which information is correct since the databases are not public. She believes the term ancestry has multi definitions, that consumers and researchers are interested in genetic ancestry for a variety of reasons; that knowledge about human genetic diversity is incomplete; that various tools for assessing genetic and genomic ancestry, but provide limited information on origins of one’s ancestors; and that interpretation of individual DNA ancestry estimates by both scientists and consumers is sometimes unclear. There was more, but these seem to be general statements that assume the genetic genealogists in the group (some of which are scientists) do not understand that genetic diversity is incomplete; that limited information is provided, and there is a limit to information on origins. Let alone genetics, that is so in genealogy! All of this is on-going with only some of it easily predicted.

She was concerned that some people testing will not be prepared for the results or will become very concerned and emotional with unexpected results. Everyone in that room is beyond those issues and administrators do explain the possibilities of testing to customers…at least, those I know.

Members of the conference as well as Dr. Royal do agree that some companies are making poor predictions based on incomplete research. This hurts everyone and gives a bad name to companies who sell directly to consumers. She stated that the Food and Drug Administration doesn’t have enough time to do its current job, so she didn’t believe that they would place regulations on DTC (Direct To Consumer) testing.

She closed with some picky remarks regarding the Family Tree DNA website, stating that it is “one of best.” (As I have not seen one better, I beg her to show me THE best!) She called for a search engine which appears to be something that has been considered. There were minor wording changes she proposed to clarify information to customers who may have little knowledge of the subject.

I have a difficult time with someone standing in judgment of genetic testing when that person has not tested her genome. She seems to have no knowledge of how it does help genealogy and has helped many people find not only their ancestors, but their biological parents.

Elliott Greenspan in his presentation IT Roadmap gave us the future of Information Technology at FTDNA. He stated that they process about 1 terabyte per hour for customer support and analysis. By next year he forecasts that they will be processing 3.8 Petabytes (A Petabyte is one million Gigabytes). Mine boggling!

A new Gedcom viewer as well as new web pages for administrators, termed GAP 2.0, have been implemented. (GAP stands for Group Administrator Pages). GAP 2.1 will be available Spring 2011. These new pages give administrators much more flexibility in manipulating the information in a project.

Among other things there will be 110 markers available for testing on the Y-chromosome.

Thomas Krahn, Technical Laboratory Manager of Family Tree DNA’s Genomics Research Center in Houston, in his Walk through the Y Update, explained that this is a research program to find new SNPs on the Y-chromosome. At the cost of $750 per sample, they have processed 178 samples so far. In order to get this test now, you must be approved (i.e., be from an unusual haplogroup), and you must know the paternal county of origin. Ninety-six of the participants did not find a new SNP in their DNA, but 137 previously undocumented Y-SNP markers were found for G2, J1, Q, I, and R. Many “private” SNPs have been found at the family or genealogy level.

FTDNA has purchased the expensive “next generation” 454 sequencer which will allow a nearly full sequence of the Y.


Dr. Krahn suggested that one should do the Deep Clade test before doing the Walk Through the Y.

Dr. Krahn gave these SNP locations for various haplogroups:
1. The Irish Type III SNP is R-L226
2. L140 and L141 defines major branches in the G2 haplogroup
3. L222 is fond among Arab J1 groups
4. L161 is a significant branch downstream from I-M423
5. L245 defines a major branch downstream of Q-M378
6. L257 is the fourth largest branch below R-U106 and next to R-L8, R-L1 and R-U198

At the end of his presentation, Dr. Krahn raffled 18 mouse pads printed with the Yq11 Palindromic Region. I was a lucky recipient!

Again, there was a closing Panel for Questions and Answers.

Each participant received a new version of the Y-DNA Phylogenetic Tree.

With the 6th Annual International Family Tree DNA Conference at a close, everyone dispersed and many chattering about plans to attend the Who Do You Think You Are? Conference in London at the end of February.


Photos of Dr. Walsh and Dr. Krahn, courtesy of Family Tree DNA
Thanks to David Pitts for sharing his notes.

Emily
copyright November 2011

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