Nature has a brand new web focus on personal genomics (as of November 5th, 2008).Â And best of all, most of the articles are entirely free to access, download, and read!Â From the site:
“As the number of human beings with their genomes fully sequenced ticks higher and direct-to-consumer gene profiling companies push the limits of what medical genetics can do, the once fantastical notion that any given human can walk into a doctor’s office with his or her genome on a hard drive looks more and more like a reality. Still the question remains to be answered: how do we use this wealth information? In this Nature web focus we proudly present the challenges this approaching reality poses for technology, the legal and ethical confines of research, and the ability of genomics to translate into clinical utility.”
Ötzi the Iceman is the popular name for a 5,000 year-old mummy discovered frozen in the ice of the Alps in 1991. Studies of the Iceman has revealed an immense amount of information about him, including details of his life, his death, and his culture.
Although Ötzi’s mtDNA has previously been studied, researchers had only examined short segments which suggested that his mtDNA belonged to Haplogroup K. A new paper in Current Biology (subscription only darn it) details Ötzi’s full mtDNA genome for the first time:
"Using a mixed sequencing procedure based on PCR amplification and 454 sequencing of pooled amplification products, we have retrieved the first complete mitochondrial-genome sequence of a prehistoric European. We have then compared it with 115 related extant lineages from mitochondrial haplogroup K. We found that the Iceman belonged to a branch of mitochondrial haplogroup K1 that has not yet been identified in modern European populations."
The latest issue of TIME Magazine lists the top 50 inventions of 2008, and the invention of the year is the Retail DNA Test.Â The article is mostly about the product currently offered by 23andMe.Â From the article:
As if there wasn’t enough to worry about during the genetic revolution, researchers have found a way to characterize redacted genetic sequences from whole-genome or large-scale sequencing.
Here’s how it works.Â Let’s say that Mr. X has had his genome sequenced, but doesn’t want to know the results of some genes known to influence the development or progression of Alzheimer’s Disease.Â So when he receives his genomic sequencing, these genes have been ‘redacted’, or removed from the data.Â This is exactly what James Watson decided to do when he received his data.
Characterizing Redacted Genes
However, researchers have characterized one of Watson’s redacted genes by examining the sequences surrounding the gene in question.Â Often, when we inherit a gene from our patents, we receive that gene as well as some of the surrounding genetic sequence.Â By examining the surrounding sequence, some insight into the redacted gene is gained.Â For example, if I gave you the quote “A penny _____ is a penny earned”, you can derive from the surrounding words that the missing word is “saved.”
This week I was quoted in the November issue of Wired Magazine about the use of autosomal DNA for genetic genealogy testing.
At “Adoptees use DNA to find surname,” Larry Moran at Sandwalk comments on my recent articles (here, here, and here) regarding the use of genetic genealogy (or genetic sequencing in general) test results to find unknown biological parents.Â Although Dr. Moran accuses me of being a “cheerleader” who is blind to any ethical concerns associated with using DNA to find biological parents, he obviously didn’t do his research!Â Less than a month ago I wrote this on the blog:
“For most people, being able to identify your own ancestors based on your own DNA poses few if any ethical dilemmas. However, what if your neighbor or your stalker or even law enforcement wants to use a sample of your DNA to identify your ancestors? Additionally, what if your living ancestor doesnâ€™t wish to be identified? Does the ancestor have that right, or is possible identification through genetic genealogy just one of the consequences of parenting a child anonymously or simply having sex with another person?”
Last week I wrote about using genetic genealogy databases to identify someone’s surname (see “DNA Could Reveal Your Surname, Of Course.”)Â The article discussed results from researcher Dr. Turi King which suggested that there is a 24% to 50% chance that two men who share the same surname share a common ancestor through that name, with chances increasing if the surname is rare.
Somehow I completely missed “Adoptees use DNA to find surname“, an article at BBC News this June.Â Men who were adopted as children are using genetic genealogy databases in an attempt to identify their biological surname.Â This is Dr. King’s research in motion.Â Family Tree DNA, for example, has a project for Adopted people that is over 2 years old, and has a success rate of more than 30%, thanks in large part to their database of over 130,000 records.Â From Bennett Greenspan:
New research from Mark Jobling’s lab at the University of Leicester suggests that Y-DNA can be used to determine a male’s surname.
I know, I know, this is obvious to anyone who is familiar with genetic genealogy.Â Just check out the many instances of this type of determination at ISOGG’s Success Stories website, for example.Â However, as you’ll see below, this research has resulted in some new and interesting information.
Dr. Turi King, who conducted the research, recruited over 2,500 men with roughly 500 different surnames to submit Y-DNA samples.Â The sample set included a group not sharing surnames as well as sets of men (between 2 and 180) who shared a surname (including recognized variants).Â She then typed 9 SNPs and 17 STRs.Â There’s much more information about this research at the Jobling lab’s website regarding this project.
This very interesting and insightful article aligns with my own premise, which I’ve stated previously, that receiving the results of a genetic genealogy test is only the beginning of the journey for any individual interested in their own identity or genealogy.
Based on her research in this area, Dr. Nelson writes about the complex interpretation of the results of genetic genealogy testing by African-Americans and black British.Â Rather than completely altering their preconceived biographical narratives based on the results of testing, many people struggle to mesh genetic results with these narratives.Â From the abstract:
The Personal Genome Project (PGP) was established to analyze and publicly share the genomes and personal information of up to 100,000 volunteers in order to advance understanding of “genetic and environmental contributions to human traits and to improve our ability to diagnose, treat, and prevent illness.”Â In the first phase of the PGP, ten volunteers (the “First 10″ – see information about the First 10 here on my blog and at the PGP website) have had their DNA analyzed and have given their personal information.
Last month, George Church, the PGP’s principal investigator, reported that the project expected to publish data about the First 10 on its website in mid- to late October.Â Church might have meant genotype (i.e. sequencing) information, since some information about phenotype, health history, and medication has already been posted on the PGP website.Â There is information about each of the 10 participants, although there is currently no active link to their genetic information:
“Complete Genomics will not begin its service until the second quarter of next year. By then, the cost of competing technologies will no doubt have fallen further. Just last week, Applied Biosystems, a leading manufacturer, said it expected that its newest machine would allow a human genome to be sequenced for $10,000, although that includes only the cost of consumable materials, not labor or the machinery.”