People Who’ve Had Their Genomes Sequenced

by Dr. Hsien-Hsien Lei
Posted September 21, 2009 in DNA in General

Trying to compile a list of people who’ve had their genome sequenced and announced it publicly:

1. Craig Venter
2. James Watson
3. Stephen Quake
4. George Church
5. Marjolein Kriek
6. Hermann Hauser
7. Han Chinese
8. Seong-Jin Kim
9. Korean AK1
10. Yoruban African NA18507
11. 14 others sequenced by Complete Genomics
12. Unknown number sequenced by Knome
13. 6 genomes sequenced at high depth by the 1000 Genomes Project
14. 180 genomes sequenced at low coverage by the 1000 Genomes Project
15. Two acute myeloid leukemia patients

Know any I’ve missed?

Please see the comments for more links.

Sources: Technology Review, Nature 2009 Aug 20; 460(7258):1011-5

Last edited 22 September 2009

(8 comments)

DNA Auction: UK DNA Double Helix Coin

by Dr. Hsien-Hsien Lei
Posted January 24, 2008 in DNA on Auction

The £2 coin from the UK you see on the left was minted in 2003 to celebrate the 50th anniversary of James Watson and Francis Crick’s discovery of DNA’s double helix . It was designed by sculptor John Mills. This DNA coin is now available on e-Bay UK for a starting bid of £0.99. Auction ends on January 27, 2008 at 21:26 GMT.

(>> Start a discussion!)

Beijing Genomics Institute Sequences Fourth Human Genome in the World

by Dr. Hsien-Hsien Lei
Posted January 7, 2008 in DNA Around the World

Chinese scientists at the Beijing Genomics Institute (BGI) have completed the fourth human genome to be sequenced worldwide. The first two were James Watson and J. Craig Venter, the third was a researcher of Han Chinese descent in October 2007, and this fourth genome was a Chinese volunteer.

The Chinese-British collaborative BGI genome project, called The Yanhuang Project, aims to map the 100 Chinese genomes. It’s not clear whether all of them will be expected to be as generous as the Chinese volunteer who donated approximately 1.3 million US dollars to the project. (Note: Harvard’s Personal Genome Project will not be expecting their volunteers to donate anything except their DNA, tissue samples, and medical data.)

The Yanhuang Project has three phases:

1. To sequence a Chinese individual’s genome that serves as the reference.
2. To sequence at least 99 more individuals’ genomes to construct a Chinese genetic polymorphism map.
3. To study the results of the first two phases and apply the findings to medical science.

Researchers plan to use the Chinese genome database to “solve problems related to Chinese-specific genetic diseases*” as well as improve diagnosis, prediction, and therapy.

*What Chinese-specific genetic diseases might they be referring to? Unlike the Ashkenazi Jewish community, I was unaware of any hereditary diseases that disproportionately affected the Chinese population. Maybe I just don’t know because most of the studies conducted in China stay in China and aren’t even indexed in PubMed.

Tags: genetics, genes, dna, chinese, genome, genomics, diseases, illness, health

(4 comments)

Crazy Genetic Marketing Ideas

by Dr. Hsien-Hsien Lei
Posted December 14, 2007 in DNA Fun, DNA Products, DNA Testing

Less than three weeks until the start of 2008 and everyone’s making their final marketing push. Genetic services companies are not exempt.

Boston-based dating service, ScientificMatch.com , uses a “patent-pending technology” that analyzes DNA having to do with the immune system to find a match who:

• Smells good to you (but probably not to me)
• Has complementary genetic material to yours so you can produce healthier children (unless you feed them McDonald’s every day and smoke around them)
• Is so good in bed that you’ll wonder if a good sex life is in your DNA

Not to be topped by DNA-induced, euphoric love, the much maligned Genebase DNA Ancestry Project claims that Rudolph the Red Nose Reindeer has joined their online networking community where you can email, post photos and messages, and join his network. You can even send an electronic postcard that shows that human HVR-1 mtDNA is 65% similar to Reindeer mtDNA. I guess Genebase thinks going goofy will somehow boost their credibility.

deCODE Genetics thought stirring the pot would keep the spotlight on them too. This past week, they put out the word that Dr. James Watson has 16 times the number of African-origin gene than the average white European (see this post for background about Dr. James Watson’s comments about race and intelligence). John Hawks said it best :

I mean, what is the purpose really of spreading a news story that Watson may be 1/16 African, without adding the context of how common this degree of genetic mixture has been in American history in particular, and between populations generally? Why would a geneticist working with humans not realize the ethical problem?

Personally, I’m pretty worn out after the excitement of the past few weeks and months. Great advances have been made in the field of personal genomics but we’re still taking things step-by-step. What may seem to have happened overnight is actually the culmination of years of hard work. And as 2007 draws to a close, we have more years of hard work ahead of us.

Tags: genetics, genes, dna, personal genomics, genomics, genebase, dna ancestry project, decode genetics, scientific match, dating

(7 comments)

Personal Genome Sequencing Company Knome Launches

by Dr. Hsien-Hsien Lei
Posted November 29, 2007 in DNA Testing

Hope you’ve been saving your pennies because starting today, you can order your entire genomic sequence from Knome. Please see Eye on DNA’s interview with Knome CEO Jorge Conde is due to be published this week (he promised!) but until then. Here you can feast your eyes on the press release!

HUMAN WHOLE-GENOME SEQUENCING HITS COMMERCIAL MARKET
20 individuals to be among first in history to be fully sequenced

CAMBRIDGE, Massachusetts – Nov. 27, 2007 – Knome, a personal genomics company, today announced the launch of the first commercial whole-genome sequencing and analysis service for individuals.

“In 2003, the Human Genome Project completed a 12-year effort to sequence the first human genome at a cost of $3 billion. Only very recently have costs come down to a level where it is now feasible for private individuals to be sequenced and analyzed. We expect this evolution to quickly usher in a new era in personalized medicine,” said Dr. George Church, PhD, a cofounder of the firm and Professor of Genetics at Harvard Medical School.

First to know, first to benefit
Knome today opens enrollment for its first sequencing flight. Because the sequencing and analysis process is both labor and computationally intensive, initial capacity is expected to be limited to approximately 20 clients.

“To date, Craig Venter and James Watson are the only named individuals to have their genome sequenced. Our first 20 clients will have a historic opportunity to help pioneer the emerging field of personal genomics. They will be among the first to know and the first to benefit from the latest advances in our rapidly developing understanding of the human genome,” said Jorge Conde, the firm’s CEO.

Building the gold standard
Whole-genome sequencing decodes the 6 billion bits of information that make up an individual’s genome. Unlike existing genome scanning or “SNP chip” technologies that provide useful but limited information on approximately 20 conditions, whole-genome sequencing allows for the analysis of up to 2,000 common and rare conditions, and over 20,000 genes – numbers that are rapidly growing.

“Whole-genome sequencing is the endgame,” according to Mr. Conde. “It will enable us to look at nearly 100% of your genetic code compared to the less than 0.02% currently available on SNP chips. This is the approach that most fully reveals what our genomes can tell us about ourselves.”

Pricing for Knome’s service will start at $350,000, including whole-genome sequencing and a comprehensive analysis from a team of leading geneticists, clinicians and bioinformaticians. This team will also provide continued support and counseling.

“Knome’s goal is to establish the gold standard in personal genomic services for individuals. We are bringing our clients the latest sequencing technology, Knome’s proprietary analytic engine and security solutions, and access to top genomic scientists and medical professionals,” said Conde. “Analytics, privacy and on-going client service are as important to us as the actual sequencing.”

Core to the fundamental principles of the company, clients will retain full ownership of their personal genome and have the ability to anonymously share all or portions of their genome with researchers and other medical professionals.

Continue reading…

(6 comments)

Eye on DNA Headlines for 13 November 2007

by Dr. Hsien-Hsien Lei
Posted November 13, 2007 in Eye on DNA Headlines

• Doctor Anonymous hosts Grand Rounds – Volume 4 Number 8 from Tucson, Arizona. Dang. Those cacti are huge!

• Sonia Smith of Slate included some of my comments in a round-up of blogs discussing the Sunday New York Times article regarding genetics, race, and prejudice. Also don’t miss this thoughtful comment from Eye on DNA reader Scott. Here’s an excerpt:

  The most frustrating part of this is that the data do not actually support these beliefs. The IQ data from the continent [Africa] is of terrible quality, such Malloy in his defence of James Watson was forced to resort to measures of schooling to shore up his conclusions. (A hint: African schools for the most part do not do a good job of teaching their students: if Malloy had ever been in one, he might have realised that.) But in this gene-crazy age, any explanation that invokes genetics and biology will automatically be privileged over one that invokes environmental effects, even at the New York Times.

• DNA Network member Thomas Goetz of Epidemix attended the Annual Burrill Personalized Medicine Meeting yesterday. My boss, Ryan Phelan of DNA Direct, will be a panel member at today’s session: Patient-centric Medicine – PM from the Patient’s Point of View. I was also honored to contribute to the Burrill Personalized Medicine Report that was distributed to meeting attendees; I wrote on the intersection of consumer genomics and personalized medicine.
• Barry Starr of the QUEST Community Science Blog has more on “gay genes” and says Bobby is more likely to be gay than Greg. So weird because I was trying desperately to remember the middle brother’s name in The Brady Bunch yesterday and had to look it up (it’s Peter played by Christopher Knight).
• I’ve talked mice, dogs, tigers, mules, and other wildlife before so why not mention wild pigs? DNA fingerprinting is being used to identify wild pigs that have been illegally moved from one region of Western Australia to another for “recreational purposes.” I’m assuming that means hunting but you just never know nowadays….

Tags: genetics, genes, dna, personalized medicine, gay genes

(2 comments)

DNA, Race, and Intelligence in The New York Times

by Dr. Hsien-Hsien Lei
Posted November 11, 2007 in DNA in General

Much excitement over at Gene Expression today over a New York Times article by Amy Harmon looking at genetic differences between races – In DNA Era, New Worries About Prejudice.

Jason Malloy was quoted with respect to his defense of James Watson’s comments about blacks last month. He writes of the NY Times article:

Nothing quite like this article has ever really appeared in the press. The underlying message is that the biological information environment is changing rapidly and if we don’t start opening up the tightly monitored public forum for it right now, we are endangering our ability to handle its potential revelations with any sort of real preparedness or rationality. We, as a civilization, can’t just keep silencing and punishing everyone who broaches these topics in a way that challenges our hopes and visions about human equality. The result is to shut down the discussion completely and disarm ourselves to ideas that are most likely – to some degree – correct.

Sure, I’d like to talk but how do I and everybody else go about becoming better educated on the issue first? The average person likely assumes that genes don’t play a huge role in differences between individuals simply because we’re constantly being told that our DNA is more than 99% the same. So what does it mean when we’re told that there are significant genetic differences between races and that these differences influence our physical appearance, susceptibility to disease, intelligence, etc.?

Here’s what I can say about the influence of genetics on intelligence and performance in everyday life – I don’t even think about it. Last week, one of the mothers at my son’s UK school, who’s from Afghanistan and doesn’t speak English well, asked me to explain one of the kids’ homework problems to her. She said neither she nor her husband could figure out what the teacher was asking for so her son wasn’t going to be turning in his homework on time. Do you think genetics figures into this situation much?

Maybe on a big picture level but day-to-day, children’s success today and in the future comes down to having parents who are fluent (or at least semi-fluent) in the local language and organized enough to plan ahead so that they’d know if they had a question about the homework and anything else that’s going on in school. There is no doubt that my son has an advantage when it comes to having motivated parents

What’s important to remember in the discussion about genetics and intelligence is that our genes carry us a certain distance but our environment–the people we come into contact with and the resources that are available to us–is also critically important in determining our future. A person with Albert Einstein’s genes born and raised by Bushmen is going to be very different than his twin born and raised in 21st century Manhattan. Transforming the infrastructure in African countries into a replica of the United States’ will improve people’s living conditions dramatically but there will still be unique differences brought about by differences in the citizens and the locale. It’s actually a relief to think that no matter how many McDonald’s and Starbucks pepper the globe, each place and its people retain their own identity. People are different from one another, but not always in a bad way.

HT: Renata McGriff of CareTALK

Tags: genetics, genes, dna, amy harmon, race, intelligence, iq, jason malloy

(59 comments)

Breaking DNA News: James Watson Resigns

by Dr. Hsien-Hsien Lei
Posted October 25, 2007 in Personalities with DNA

About an hour ago, USA Today published excerpts from an email Dr. James Watson sent directly to them announcing his resignation from Cold Spring Harbor Laboratory:

This morning I have conveyed to the Trustees of the Cold Spring Harbor Laboratory my desire to retire immediately from my position as its Chancellor, as well as from my position on its Board, on which I have served for the past 43 years. Closer now to 80 than 79, the passing on of my remaining vestiges of leadership is more than overdue. The circumstances in which this transfer is occurring, however, are not those which I could ever have anticipated or desired.

This week’s events focus me ever more intensely on the moral values passed on to me by my father, whose Watson surname marks his long ago Scots-Irish Appalachian heritage; and by my mother, whose father, Lauchlin Mitchell, came from Glasgow and whose mother, Lizzie Gleason, had parents from Tipperary. To my great advantage, their lives were guided by a faith in reason; an honest application of its messages; and for social justice, especially the need for those on top to help care for the less fortunate. As an educator, I have always striven to see that the fruits of the American Dream are available to all. I have been much blessed.

More about the debacle:

• DNA Auction: African-American Sisters’ Copy of Avoid Boring People by James Watson
• Nobody Likes James Watson

Update: The full letter is available at GenomeWeb.

Tags: james watson, cold spring harbor, genetics, genes, dna

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DNA Auction: African-American Sisters’ Copy of Avoid Boring People by James Watson

by Dr. Hsien-Hsien Lei
Posted October 24, 2007 in DNA on Auction

On the day Dr. James Watson proclaimed that Africans had lower intelligence, African-American sisters Karah, Safiya, and Diana Cesar had him sign a copy of his book, Avoid Boring People. Now the sisters have put that signed copy up on eBay at a starting bid of $300. The auction ends on October 31st at 7:29 PDT.

Safiya, 17, a senior at Cold Spring Harbor High School:

He signed our book and we’re African-Americans. With all the hype still up, we thought it might be valuable to someone.

Twin sister Karah ina letter to Dr. Watson:

This incident has taught me a lesson that may not be in your book. No matter how venerable you are, you are still human.

James Watson apparently lives just 10 minutes from from the Cesar girls.

Tags: genetics, genes, dna, james watson, avoid boring people, ebay, auctions, book

(3 comments)

Gene Genie #18 with the PG Tips Chimp

by Dr. Hsien-Hsien Lei
Posted October 21, 2007 in DNA Podcasts and Videos, DNA in General

Welcome to Gene Genie #18 with the Personal Genomics (PG) Tips Chimp!

Grrlscientist at Living the Scientific Life examines the genetic link between SSRIs and suicidal ideation. (Editor’s note: Neuromark has begun developing two trials for the first genetic test to examine the markers–GRIK2 and GRIA3–that increase the risk of suicidal thoughts in people taking Celexa.)

Alvaro Fernandez of SharpBrains attended the 2007 Aspen Forum at which genetics and genomics featured prominently (see items 7 and 9).

Blaine Bettinger of The Genetic Genealogist goes all Shakespeare on us and asks: To Sequence or Not to Sequence – That is the Question. (In my poll about sequencing, 69 out of 100 respondents wanted to have their genome sequenced.)

John Fossella at Origins Genome Resources has a reminder that Dr. James Watson might find interesting – Having intelligence may have its limitations, but a thin corpus callosum is not thus handicapped.

Speaking of Dr. James Watson’s recent remarks on race and intelligence, Anasua at Gladly Beyond Any Distance explores the controversy in depth. And Jonathan Eisen at The Tree of Life wants to know whose genome should Roche/454 sequence to make up for selecting Watson’s? Harsh!

NOVA aired Ghost in Your Genes this past week about the epigenome. Wenchypoo at Wisdom from Wenchypoo’s Mental Wastebasket saw it and reminds us to think and act long-term because everything we do could have a physiological effect on our children and their children. Yvette at Six Impossible Things Before Breakfast also caught the program and thought that it was a little too advanced for the average viewer and didn’t care much for the title either.

With only two more months to go until 2008, Ramunas at Cancer Genetics has been busy tallying Exciting Discoveries of 2007 – Breast Cancer.

Walter at Highlight HEALTH also takes a closer look at breast cancer in Individual Genetics, Coffee Consumption, BRCA1 and Breast Cancer.

Mary Emma Allen of Alzheimer’s Notes ponders – Does Alzheimer’s Follow a Family Gene? And the answer, of course, is yes.

Professor of Classics Kristina Chew of Autism Vox delves into her area of expertise in Language Genetics: Knots and Finches. I loved her opening sentence:

Is language (like tying knots) unique to humans—is being able to talk and think in language part of being human?

My DNA Direct colleague, Trish Brown, who’s also VP of Clinical Affairs, has a new blog up at Revolution Health called Genes in Context. She tackles genetic testing and homosexuality in her first post. Welcome to the blogosphere, Trish!

Also new to the blogosphere is clinical geneticist, Matt Mealiffe, at DNA and You. He has a fascinating post about genetic voyeurism on TV in which a woman reveals the results of her BRCA test on camera shortly after learning them for the first time herself.

Matt also blogs at Cancer and Your Genes where he explains medicare and genetic testing for cancer risk. As if medicine is not complicated enough, the reimbursement model is ten times more so!

Keith Robison of Omics! Omics! has a real mash-up combining Harry Potter, Sherlock Holmes, Martha’s Vineyard & Science Magazine. Confused? So was I until I read his post.

Gene Genie founder Berci Mesko at ScienceRoll has rounded up some timeless resources for personalized medicine. Can anything on the Web truly be timeless? I know this science blogger isn’t….

Hope you enjoyed meeting the PG Tips Chimp and learning more about genetics, genomics, and health! The next issue of Gene Genie will be on November 4th at ScienceRoll.

Tags: pg tips chimp, genetics, genes, dna, gene genie, health, medicine, diseases

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