“[A]ffordable whole-genome sequencing is getting closer and closer every day (my prediction – which is based solely on my own educated guess – is that I will be able to sequence my entire genome for $1,000 or less by the end of 2009).”
It was pretty bold at the time, and I’ve since wondered if I was too optimistic, but now comes news that at least one other person agrees with my prediction.Â Harvard professor and genetics researcher George Church – also principal investigator for the Personal Genome Project (PGP) – stated at two conferences, one last week and one this week, that by mid-October of 2008, 36-fold coverage of the human genome will be available for $5,000.Â Church went on to say that the $1,000 human genome will be available by the end of 2009.
Welcome to the September 14, 2008 edition of Gene Genie!Â Bloggers have begun to pick up posting with the end of summer, and it seems like everyday there’s a bunch of new interesting posts about the human genome.
Yesterday I wrote about 23andMe’s decision to lower their price to $399 (down from $999) while adding more genealogically-relevant SNPs and partnering with Ancestry.com.Â Although I don’t have any further information about the new SNPs, I’ve seen a couple of interesting articles about the price drop around the blogosphere.
Aaron Rowe at Wired science writes “Human Genetics is Now a Viable Hobby.”Â He notes that the new price is “well within the reach of cash-strapped grad students, frugal genealogy buffs and other not-so-early adopters.”Â The comment thread is an interesting read as well.
See the new article at Seed Magazine “Inheriting Confucius,” which discusses efforts to generate a family tree containing the 2 million+ descendants of Confucius.
Kong De-Yong, a 77th(!) generation descendant of Confucius, has been compiling the tree for the last 10 years.Â Although the Committee is accepting submissions from women and other previously excluded groups, it is not accepting DNA contributions.Â According to the article, this “hints at the limits of Chinese engagement with the age of genomics, and demonstrates how high cultural stakes can constrain science.”Â Unfortunately, as the author of the article suggests, many people might be afraid of the results of such DNA testing: “Given the potential implications of genetic knowledge for long-presumed members of the [Confucius] family, they think it better not to know.”
Thomas Goetz has written another terrific article about genetic testing and the Personal Genome Project.Â This article, entitled “The Gene Collector,” appears in Wired Magazine.Â The article provides some new information about the PGP, including some of the incredibly detailed phenotype information that will be collected from the next 100,000 volunteers in the project.
The article also reveals the tenth and final participant of the “First 10″, the original 10 volunteers in the PGP.Â I wrote about the first nine volunteers in the PGP almost exactly one year ago and noted that the tenth participant had not yet released his or her name.Â The Wired article, however, mentions a number of participants including George Church, Esther Dyson, Rosalynn Gill, John Halamka, and Steven Pinker.Â Indeed, a check of the PGP website confirms that Steven Pinker is the last PGP volunteer to be identified.
Last week the genetic genealogy community lost one of its treasured members, Leo W. Little.
Leo’s passing was announced on the GENEALOGY-DNA mailing list on Sunday evening. Since then, many members of that mailing list, the ISOGG Yahoo Group, and the DNA- ANTHROGENEALOGY Yahoo Group have expressed their sympathy to Leo’s family and expressed their admiration for his work and contributions to the field of genetic genealogy.
Leo was the administrator of at least two DNA Projects, including the null439 DNA Project, and the Little DNA Project. The null439 group was begun by Leo after he helped characterize the “Little SNP” in 2002, a SNP that is also called “L1″ or “S26″. In 2005 Leo posted an email to the GENEALOGY-DNA that explained the discovery of the SNP, which defines the R1b1b2a1c Haplogroup in the new 2008 ISOGG Y-DNA Haplogroup Tree (previously known as R1b1c9a). The L1 SNP causes the primers used by Family Tree DNA to analyze Y-STR repeats at DYS439 to fail to anneal, and thus no result is recorded for that locus (i.e., it is “null”). The result is recorded as a default 12 with a blue asterisk. Here is Leo’s description from the null439 page:
Although the genome scanning services offered by companies such as 23andMe, deCODEme, and SeqWright have been front and center in the press the last few weeks, I’m sure that the following information will not be included in any of the reports.
Two different sources have concluded that the scanning service offered by 23andMe and deCODEme, who use different types of Illumina SNP Chips, are highly reproducible. In January 2008, Ann Turnercompared the results of testing at deCODEme and 23andMe, and concluded that of the 560,163 SNPs that overlapped and had a “call” (meaning there was a measurable result), they agreed on 560,128 and disagreed on 35. Ann wrote in January:
In all of [the disagreed calls], one company would make a homozygous call while the other company made a heterozygous call – there were no cases where they made a completely discordant call. All in all, I’d say that is pretty impressive.
A long-anticipated new version of the Y-Chromosome Tree will be released in the journal Genome Research tomorrow (Wednesday, April 2nd). In the paper, scientists from the University of Arizona and Stanford University use recent SNP data and research to reformulate the familiar Y-chromosome tree (see, for example, the current tree at ISOGG). Here is the full text of the press release.Â The paper should appear here as soon as it is made available by Genome Research tomorrow.
From the press release:
In an article published online today in Genome Research(www.genome.org), scientists have utilized recently described genetic variations on the part of the Y chromosome that does not undergo recombination to significantly update and refine the Y chromosome haplogroup tree. The print version of this work will appear in the May issue of GenomeResearch, accompanied by a special poster of the new tree.
The Scientific Studies/Papers Page at ISOGG – I’ve been meaning to share this one for a while. The page describes methods for obtaining and reading scientific papers about genetic genealogy (or any other scientific topic, for that matter). This is a helpful resource for anyone who is interested in learning more about the science behind genetic genealogy.
“In this study, a comprehensive overview of all available complete mitochondrial DNA (mtDNA) genomes of the four pan-American haplogroups A2, B2, C1, and D1 is provided by revising the information scattered throughout GenBank and the literature, and adding 14 novel mtDNA sequences. The phylogenies of haplogroups A2, B2, C1, and D1 reveal a large number of sub-haplogroups but suggest that the ancestral Beringian population(s) contributed only six (successful) founder haplotypes to these haplogroups.”