DNA Podcast: Genentech’s Joe McCracken

by Dr. Hsien-Hsien Lei
Posted June 30, 2007 in DNA Podcasts and Videos, Personalities with DNA

This podcast from last year is of Genentech Vice President of Business Development Joe McCracken speaking for the Stanford Entrepreneurial Thought Leaders lecture series.

Joe McCracken, VP of Business Development at Genentech, walks through the founding and growth phase of the company. In particular, Joe describes the culture at Genentech which is credited for consistent ground breaking R&D and the resulting financial success.

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Tags: genetics, genes, dna, genentech, genome, genomics, joe mccracken, podcast

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South Africa’s DNA Project Launches Website

by Dr. Hsien-Hsien Lei
Posted June 30, 2007 in DNA Around the World, DNA and the Law

South Africa has a National DNA Criminal Intelligence Database that only stores samples collected from crime scenes and suspects. There is no “convicted offender database” such as the ones in the US and UK that additionally hold DNA from people who’ve been charged with a crime, convicted criminals, current prisoners, parolees, people on probation, and registered sex offenders. The reason given for the reluctance of South African law enforcement to collect DNA from convicted offenders is the “assault” experienced by a convicted offender when blood is drawn. Of course, now that it’s possible to collect DNA from a cheek swab or other less invasive means, this should no longer be a concern.

 According to the South African DNA Project, which launched its website earlier this month, DNA profiling in South Africa has been hampered by:

• Insufficient DNA profiling equipment
• Lack of funding
• Embargos on processing crime stains and DNA profiles without a suspect
• Inadequate laboratory capacity
• Outdated information systems
• Overwhelming caseloads
• Lack of training

The DNA Project was established in 2004 after the murders of John Lynch and Leigh Matthews. Since then, the DNA Project has sought to raise funds, educate the public, increase awareness of forensic science, change legislation, and otherwise encourage the Forensic Science Labs. The DNA Project website is an excellent resource for anyone interested in the use of DNA in law enforcement. May they achieve their objectives to use DNA for solving crimes as well as deterring them.

Tags: south africa, dna project, john lynch, leigh matthews, genetics, genes, dna, forensics, forensic science, crime

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DNA Quote of the Day: Dr. Terri Beaty

by Dr. Hsien-Hsien Lei
Posted June 29, 2007 in DNA Quotes and Excerpts

The Spring 2007 issue of Johns Hopkins Public Health Magazine features The Genetic Journey: What’s Next? It was lovely to see all those familiar faces of professors who spent so much time with me during my graduate school days. I’ll be featuring their quotes over the weeks starting with Dr. Terri Beaty, one of my advisors in genetic epidemiology.

I think genetics has been oversold somewhat. Now that you can genotype 100,000 SNPs at a time or 500,000… How are you going to digest that much data? And when you’re doing a million tests, how many times are you going to be wrong? People get carried away. They say, ‘Well, gee, if we can find a gene for Huntington’s disease or cystic fibrosis, can we find a gene for alcoholism or cynicism?’ But they’re not that simple, you know? We are still working on the mechanism so we can understand it. A lot of diseases have become a little more clear, but not perfectly clear.

Perhaps now you can see where part of my attitude comes from!

Tags: genetics, genes, dna, epidemiology, genome, genomics, biotechnology, biotech, terri beaty, johns hopkins bloomberg school of public health

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First Results from The Genographic Project Mitochondrial DNA Database

by Dr. Hsien-Hsien Lei
Posted June 29, 2007 in DNA and Genealogy

Following up on yesterday’s discussion of the sale (or biopiracy) of Amerindian DNA for research purposes, National Geographic’s Genographic Project has published the first results from an analysis of their mitochondrial DNA (mtDNA) database in PLoS Genetics. The database is made up of almost 80,000 genotypes and is the largest standardized human mtDNA database ever collected – most from from participants like Jason at The Personal Genome, who purchased kits in the US and Western Europe. Samples collected from indigenous populations are in a separate database and will be published later.

FYI, here are a few reasons why mtDNA is so useful in genetic anthropology and genealogy:

• It’s uniparental, inherited only from the mother
• It has a nonrecombining mode of inheritance.
• It has a high mutation rate compared to that of the nuclear genome

If I’m not mistaken, however, the Genographic Project only analyzed mtDNA in female participants even though men also inherit mtDNA from their mothers. Can anyone tell me why?

More on the Genographic Project results from Blaine at The Genetic Genealogist.

Update: Here are Blaine’s thoughts on why the mtDNA tests were only offered to women.
Continue reading…

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Amerindian DNA Sells for 55 Dollars

by Dr. Hsien-Hsien Lei
Posted June 28, 2007 in DNA Around the World, DNA in General

Going once. Going twice. Sold! DNA for $55.*

The Karitiana Indians of the Amazon feel as if part of their heritage has been auctioned off by researchers who misled them. They first gave their blood in the 1970’s after making contact with “the outside world.” In 1996, they again gave samples of their blood in exchange for medicine, which the Karitiana Indians claim they never received. Similar to the American Indians who were studied to investigate the relationship between the MAOA gene, childhood sexual abuse, and alcoholism, Amazonian Indians live in closed communities where their lifestyle, living environment, and disease inheritance patterns make it easier to conduct genetic studies.

But the extent to which their genetic data would be used was not clear to the Karitiana Indians when they donated their blood. To their shock and anger, they recently discovered that their DNA is now being sold via the Coriell Institute for Medical Research which is funded by the US National Institutes of Health and other givernment agencies. You can obtain a listing of 25 cell cultures from the Karitiana Indian people with details such as race, age, gender, and disease status. A 1.0 ml cell culture costs $85 while 0.05 mg of DNA costs $55.

The situation is not as sinister as it seems, however. The Corielle Institute sells specimens only to scientists who sign an assurance form agreeing to guidelines that specify:

1. That the biomaterials will be used in compliance with all regulations protecting human subjects.
2. That the biomaterials or any products derived from them will not be commercialized.
3. That the biomaterials will not be distributed to a third party (that the researcher will not “share” with a colleague) without authorization by the Coriell Institute for Medical Research as agent for the National Institute of General Medical Sciences.

The Karitiana Indians are not satisfied and along with other Amerindian groups, they claim that selling or using their DNA in unapproved ways is biopiracy. For example, many indigenous groups have expressed their distrust of the National Geographic’s Genographic Project, including the Maori of New Zealand and Alaska natives who want National Geographic to stop “sucking indigenous blood.”

Continue reading…

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Eye on DNA Links – June 28, 2007

by Dr. Hsien-Hsien Lei
Posted June 28, 2007 in DNA and Disease, Eye on DNA Headlines, Genetic Engineering

• William Saletan examines transgenic animals and concludes that they’re the future of medicine.*
• The CHD7 gene is the first gene to be linked to idiopathic scoliosis.
• DNA tests on a tooth identifies Queen Hatshepsut’s mummy whose ingrate of a son tried to wipe out all traces of her after her death in 1482 BC.
• Finally, I can stop seeing Eddie Murphy pop up in my news scans for genetics, genes, and DNA. Murphy’s paternity test came up positive, pointing to him as the father of Angel Iris Murphy Brown whose mother is ex-Spice Girl Mel B. (You were wondering when I was going to slip this tidbit in, right?)
• Dr. David Altshuler of Harvard Medical School talks to MedPage Today about the genetics of diabetes (video).

*Update: Speaking of transgenic animals, here’s a naturally occurring zorse – zebra father, horse mother.

Tags: genetics, genes, dna, diabetes, mummies, queen hatshepsut, idiopathic scoliosis, transgenic animals

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Reconstructing the Prehistoric DNA of Neanderthals

by Dr. Hsien-Hsien Lei
Posted June 27, 2007 in DNA in General

Have we taken a step closer to Jurassic Park? That’s what I thought when I first saw the headline announcing that “researchers may remake Neanderthal DNA.” Unfortunately (or fortunately?), my imagination has misled me once again.

The point of reconstructing a complete Neanderthal genome is to understand how they and modern humans diverged over 30,000 years ago. The plan would be to use DNA samples from more than one Neanderthal corpse. Being able to put together an accurate DNA sequence despite contamination and degradation caused by microorganisms is a technical achievement as well.

For more about the analysis of ancient DNA, read this excellent piece by Henry Nicholls in PLoS Biology: Ancient DNA Comes of Age.

In 1994, while Jurassic Park was still taking in millions of dollars at the box office, scientists claimed to have extracted and sequenced DNA from an 80-million-year-old dinosaur. When sceptical researchers took a look at the sequence, it turned out to be of human rather than dinosaur origin.

Oops. Guess I wasn’t the only one with Jurassic Park on the brain.

Tags: genetics, genes, dna, jurassic park, dinosaurs, ancient dna, neanderthal, prehistoric, genome, genomics

(5 comments)

DNA Video: James Watson at the Wellcome Trust

by Dr. Hsien-Hsien Lei
Posted June 27, 2007 in DNA Podcasts and Videos, Personalities with DNA

In case you haven’t had enough of Dr. James Watson lately, here he is in an interview at the launch of the Wellcome Collection last week.

Sandrine at Short Sharp Science has more about the museum exhibit itself.

Tags: genetics, genes, dna, james watson, wellcome collection, video, genome, genomics, human genome

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MAOA Gene, Childhood Sexual Abuse, and Alcoholism

by Dr. Hsien-Hsien Lei
Posted June 26, 2007 in DNA and Disease

We need gene therapy for a peaceful world. A world without fear, sadness, shame, anger, and hate. A world of equilibrium. A world of happy shiny shiny happy people.

Snap.

I’m out of it.

I didn’t know what else to think after reading about a recent study showing that girls with a particular variation of the monoamine oxidase A (MAOA) gene are more prone to developing alcoholism later in life after experiencing childhood sexual abuse. The MAOA gene that results in lower enzymatic activity has already been associated with behavior problems in “maltreated boys” and was also implicated in this study. No such association between the MAOA gene, alcoholism, and antisocial behavior were found in women who had not been abused.

Study participants were American Indian women who, as a group, are six times more likely to develop alcoholism and antisocial personality disorder than the average US woman. And, half of American Indian women report childhood sexual abuse as compared to 13% in the US population. Can it get any more depressing than this? And what are we supposed to do with results like these?

Clearly, my tongue-in-cheek suggestion of soul and mind-numbing gene therapy is totally inappropriate. But I ask you, so what if genes predispose abused women to alcoholism? We need to focus not on genes but on STOPPING CHILDHOOD SEXUAL ABUSE. Then, we can talk about alcoholism and anti-social behavior and perhaps targeting genes that increase a person’s susceptibility. But STOPPING CHILDHOOD SEXUAL ABUSE would go a long long way.

Continue reading…

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Eye on DNA Links June 26, 2007

by Dr. Hsien-Hsien Lei
Posted June 26, 2007 in DNA Podcasts and Videos, Eye on DNA Headlines

• An inspirational Grand Rounds is up at Wandering Visitor.
• Phillip Manning of Science Book News points to Frank Stephenson’s book, DNA: How the Biotech Revolution Is Changing the Way We Fight Disease.
• Steve Olson of The Atlantic considers genetic testing in Who’s Your Daddy? – The unintended consequences of genetic screening for disease. (The article is for subscribers only but you can email me for access.)
• Alisa Taylor of FirstScience.com explores the post-genomic era complete with “security keys” encoded with our genome.
• Science Friday talks about genetic genealogy. Click the button in the player below to listen.

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Tags: genetics, genes, dna, genetic genealogy, ancestry.com, sorenson genomics, genomics, genome, science

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