[This is a repost of an article that appeared on May 26, 2007. Since Iâ€™m knee-deep in final projects and exams, I thought Iâ€™d pull out a popular article from the archives. I hope you enjoy it (again)]:
In Part I and Part II of the â€œYou and the $1000 Genomeâ€ series we examined the history of the Archon X PRIZE for Genomics and the success of the International HapMap Project. Today weâ€™ll talk about some of the ethical issues associated with efficient and inexpensive genome sequencing. The value of whole genome sequencing will only be realized if individuals believe they have complete and legal control over their genetic information. I am greatly indebted to a thorough analysis of this issue by John A. Robertson at the University of Texas School of Law (â€The $1000 Genome: Ethical and Legal Issues in Whole Genome Sequencing of Individuals (pdf).â€ 2003 The American Journal of Bioethics 3(3):InFocus). Note that this analysis is not intended to constitute answers to any of the ethical questions – it is only meant to be part of the discourse.
[This is a repost of an article that appeared on May 24, 2007. Since Iâ€™m knee-deep in final projects and exams, I thought Iâ€™d pull out a popular article from the archives. I hope you enjoy it (again)]:
In Part I of the â€œYou and the $1000 Genomeâ€ series we examined the Archon X PRIZE for Genomics, a $10 million purse for the group that can sequence 100 genomes in 10 days for no more than $10,000/genome with an error rate below 0.001%. With todayâ€™s technology this goal is still a few years away.
But do we need an entire genomic sequence to obtain all the relevant medical information that our DNA contains? After all, 99.9% of my DNA is exactly the same as everyone elseâ€™s! Why sequence that 99.9% over and over and over if the results are the same every time? Wouldnâ€™t it be cheaper to just sequence and then decode the 0.1%?
A lot of people write me to ask me questions about genetic genealogy, and a few have asked if there are any books on the subject that might help them learn more about it.Â I thought I should provide a list of great reading material to help someone who might not have time to ask (but keep the questions coming!).
Great beginner books which are specifically about genealogy and DNA:
Trace Your Roots with DNA: Use Your DNA to Complete Your Family Tree by Megan Smolenyak and Ann Turner (Published October 7, 2004):
The Seven Daughters of Eve: The Science That Reveals Our Genetic Ancestry by Bryan Sykes (Published July 9, 2001):
How to Interpret Your DNA Test Results for Family History & Ancestry: Scientists Speak Out on Genealogy Joining Genetics by Anne Hart (Published December 2002):
The DNA-NEWBIE mailing list is a great resource for people who are new to genetic genealogy or genetic testing in general. The list provides a forum for questions while promoting education and the sharing of ideas. I primarily use the mailing list to follow current trends or concerns in the field of genetic genealogy so that I can share them here on the blog.
The recent deluge of media attention regarding J. Craig Venter’s diploid genome sequencing prompted one list-member to quote Dr. Edward Rubin: “It’s not clear whether it’ll be 10 years or 50 years, but in our lifetime, [individual DNA sequencing ] will happen.” The list-member goes on to say that it will probably not happen in his lifetime since he turns 75 next month.
The results of a Y-DNA test are either a string of plusses and minuses, or a series of numbers.The plusses and minuses are the result of a SNP (single-nucleotide polymorphism) test and denote the testeeâ€™s Haplogroup, while the string of numbers are the result of a STR (short tandem repeat) test and denote the testeeâ€™s haplotype.
To learn more oneâ€™s haplotype, or to compare it to otherâ€™s results, most people enter those results into a database such as Ysearch, Ybase, SMGF, YHRD, or the Y-STR Database.To do this, however, it is sometimes necessary to â€˜normalizeâ€™ the numbers.For instance, one testing company might find a result of 27 for DYS481 while another finds a result of 23 on the same individual.This is typically due to different sequencing primers used by each company to characterize each particular STR.
Welcome to edition #13 of the Gene Genie. There were many interesting and exciting submissions for this issue, so I hope you do a little exploring and learn something new about genes, personal genetics, and personalized medicine.
Splicing Genes.Letâ€™s start off with something fun.I donâ€™t know if weâ€™ll ever try to splice our genes with those from famous or successful people, but hereâ€™s at least one conversation that might result!
In the past decade, scientists have repeatedly referred to ‘Mitochondrial Eve‘, the (hypothesized) source of mtDNA for all humans alive today. She is believed to have lived approximately 140,000 years ago in Africa. There is also ‘Y-chromosomal Adam‘, the (hypothesized) source of every living man’s Y-DNA. He is also believed to have lived in Africa, but more recently, between 60,000 and 90,000 years ago. Thus, Mitochondrial Eve and Y-chromsomal Adam were not a couple – they were not the source of all human genetic material on the planet today. Instead, the terms refer to the founders of all the mtDNA and Y-DNA respectively.
For a wonderful description of some of the genetic behind Mitochondrial Eve and Y-chromsomal Adam, go to “The Questionable Authority“, a blog which is part of Scienceblogs. While you’re there, be sure to read the comments, where the discussion addresses the time disparity between the two DNA sources (140,000 years ago versus 60-90,000 years ago).
Â Â Â Â Â Â Â I was recently interviewed by Hsien at EyeonDNA.Â She asked some great questions about the field of genetic genealogy, and I hope youâ€™ll check it out.
Â Â Â Â Â Â Â Â Â I consider my new friendship with Hsien and other fellow bloggers to be one of the great successes of this blog, and I thank her for the opportunity to share my enthusiasm for genetic genealogy with her readers!
Often, at least at the current stage of genetic genealogy, DNA sequencing does not reveal enough information to identify a personâ€™s particular Y chromosome or mtDNA haplogroup.The example I will be using in this post is Haplogroup E.Haplogroup E split into E1, E2, and E3 about 28,000 years ago.Current tests offered by many sequencing companies are able to place a person in the general â€œEâ€ Haplogroup, but might be unable to determine exactly which subclade of E a person descends from.In such a situation, a â€œDeep SNPâ€ test can be used to fill in that information.
A SNP is single nucleotide polymorphism, or a change in the DNA sequence at a single nucleotide.For instance, the switch of a C for G, a cytosine for a guanine.You can see a chart of some of the most common SNPs tested for genetic genealogy here or here.The Deep SNP test (which can go by other names) analyzes a personâ€™s DNA, such as the Y chromosome, for the presence or lack of these mutation(s).