5 Facts (and Caveats) About DNA Profiling

by Dr. Hsien-Hsien Lei
Posted October 24, 2007 in DNA and the Law, DNA in General

Reuters took the trouble to summarize five main facts about DNA profiling and I thought I’d comment on them.

DNA profiling was discovered in 1984 by geneticist Alec Jeffreys of Britain’s Leicester University, who first used it three years later to help solve the murders of Leicestershire schoolgirls Dawn Ashworth and Lynda Mann.

Sir Alec, a 2006 Great Briton, is actually credited with developing DNA fingerprinting specifically.

Here’s a very basic description of how DNA fingerprints were first created using restriction fragment length polymorphisms (RFLP):

1. Extract a sample of DNA from blood, hair, skin, cheek cells, etc.
2. Use polymerase chain reaction (PCR) to create more copies of the DNA to analyze.
3. Use restriction enzymes to cut the DNA strand at specific sequences, which will result in pieces of DNA of varying sizes. Since each person’s DNA unique, the enzymes will cut the DNA in different places and varying sizes of DNA pieces will result.
4. The small pieces of DNA will be passed through an agarose gel which separates them according to size.
5. Compare the DNA patterns created.

The technology makes use of the fact that small sections of DNA repeat themselves over and over in a way that is unique to each individual. The length of repeats can be measured at different locations to build up an individual’s profile.

There are actually different ways to create a DNA profile. The type of marker mentioned here is the short tandem repeat (STR). Another type of marker that can be used to create a genetic profile is the single nucleotide polymorphism(SNP).

Modern genetic tests typically look at 20 “marker” sections of DNA — 10 from the maternal and 10 from the paternal line. The chance of two strangers matching on all 20 is less than one in 1 billion. The chance of a match with a relative, though, is much higher and identical twins have identical profiles.

I’m not really sure what 20 markers this fact is referring to. Law enforcement relies on the Combined DNA Index System (CODIS) that creates DNA profiles from 13 core STR markers. Paternity tests examine as little as three markers to as many as 16. The genotypes at each of the markers would consist of data on two alleles – one from the mother and one from the father.

Scientists collect DNA direct from suspects, using a mouth swab, or from the scene of a crime, by gathering traces of blood, semen, hair or saliva. Crime scene samples are more difficult to analyze, since they may be very small and can contain the DNA of several people.

I don’t have much to say about this except that sometimes samples are just plain difficult to analyze whether or not it’s from a crime scene. It all depends on the sample from which the DNA is extracted and the informativeness of the markers being analyzed.

Governments around the world are building up DNA databases to match suspects with evidence. The United States has the largest database, with over 5 million profiles. But Britain has the highest proportion of people catalogued, with its 4 million records equal to more than 6 percent of the population.

As points of reference, Australia’s national DNA database has over 350,000 DNA samples while New York State has almost 250,000. You may also be interested in these previous posts about the UK national database:

• Be Fair – Add Your DNA to the Database
• Fake Names in the UK National DNA Database
• Police Want to Collect Abandoned DNA from Everyone

Tags: genetics, genes, dna, dna profiling, dna fingerprinting, crime

(1 comment)

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)

“Jacket Children” and DNA Testing in Jamaica

by Dr. Hsien-Hsien Lei
Posted October 23, 2007 in DNA Around the World, DNA Testing

A reader of the Jamaica Cleaner is proposing that everyone looking to be married in Jamaica undergo DNA testing first.

The Editor, Sir:

Based on the ‘jacket’ situation in Jamaica, DNA testing may become a way of life. If we do not know who our fathers are we may end up marrying our cousins, brothers, sisters, aunts, uncles, nieces, nephews and even our fathers.

Under these circumstances I would not recommend anyone get married without both partners doing DNA tests to see if they are blood-related. This is one situation where the women can’t blame the men for. Ladies if you have only one sex partner every nine months then you won’t have to worry about who the daddy is.

I am, etc.,

DAN VASSE

According to Out-of-Wedlock Births by Mark Abrahamson,

When people suspect that a Jamaican child’s social and biological fathers are not the same, but the child is publicly presented as the offspring of the social father, the child is called a “jacket” [emphasis added] in local gossip. The imagery implied is that a jacket child is something a husband “wears” to protect his honor.

Photo: “A second grade boy at the Christiana Primary School [in Jamaica] waves and flashes a brilliant smile while our team builds a new shelter nearby.” ~ Jake Brewer

Tags: jacket child, jamaica, out of wedlock births, babies, genetics, genes, dna, dna testing, paternity

(4 comments)

Eye on DNA Headlines for 23 October 2007

by Dr. Hsien-Hsien Lei
Posted October 23, 2007 in Eye on DNA Headlines

• Dr. Christian Sinclair at Pallimed: A Hospice & Palliative Medicine Blog hosts Grand Rounds Vol 4, No 5. My podcast interview with Kathy Flake about genetic testing for Huntington’s disease was one of only 15 that were included which “best reflected the variety of ways prognosis plays a role in medical care.”
• A twin study has shown that 41% to 48% of a person’s predisposition towards a particular food group–fruit and vegetables, alcohol, fried meat and potatoes, and low-fat products or low in meat, fish and poultry–is influenced by genetics. A couple of weeks ago, I attended a school lunch tasting and was really impressed at the variety of food they served. Although I tried most of everything and liked it, I can’t say the same about the other parents. Interestingly, these were the same parents whose children didn’t much like school lunch.

  I hope my son is as flexible as my husband and me when it comes to world cuisine. Being willing to try new, different, and strange foods makes life so much easier. Having been business expats for almost 10 years, I can safely say that you’ll be more successful in any country if you’re willing to try local cuisine. /end tangent

• Pedro Beltrao has penned an imaginative science fiction story that anyone interested in personal genomics should read – The Fortune Cookie Genome.
• The Women’s Bioethics Blog looks at DNA Testing Without Consent on historic or popular figures, such as Albert Einstein, Abraham Lincoln, Arnold Schwarzenegger, and Britney Spears.
• Tell your US senators to support the Genetic Information Nondiscrimination Act (GINA)! You can find sample letters and lists of senators who’ve cosponsored GINA over at Genetic Alliance.

Tags: genetic information nondiscrimination act, gina, genetic alliance, britney spears, science fiction, genetics, genes, dna, grand rounds

(>> Start a discussion!)

Geeky DNA T-Shirts: DNA Built for a Hostile World

by Dr. Hsien-Hsien Lei
Posted October 23, 2007 in Geeky DNA T-shirts

Today’s DNA tee from Descente, an athletic apparel company, is really stylin’. Even if you aren’t a freerider (mountain biker), you’ll look cool wearing this DNA t-shirt.

Tags: freeriding, freeride, freerider, mountain biking, bike, t-shirt, tees, genetics, genes, dna

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The United States Genetic Diagnostics Market

by Dr. Hsien-Hsien Lei
Posted October 22, 2007 in DNA Testing

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On one of my ramblings around the Web today, I came across this set of slides on genetic diagnostics technologies at SlideShare that was part of talks given at Canada’s MaRS Venture Group. The information is a little dated (March 2006 with 2005 data) but there are still many valid points.

Three types of genetic diagnostic applications are defined:

• Phamacogenomic testing – $95 million market value
• Prenatal newborn testing – $335 million market value
• Predisposition and diagnostic testing – $100 million market value

I expect these figures will skyrocket within a few years.

Some of the challenges listed:

• Healthcare providers are not adequately educated
• Healthcare conservatism
• FDA approval

Some of their recommendations:

• Clinician education
• Direct to consumer advertising (or maybe not?!)
• Promote anti-discrimination legislation (such as GINA, the Genetic Information Nondiscrimination Act)

Tags: genetics, genes, dna, MaRS, personalized medicine, pharmacogenomics, genetic testing, dna tests

(5 comments)

HPV DNA Test for Cervical Cancer

by Dr. Hsien-Hsien Lei
Posted October 22, 2007 in DNA Testing

Two recent studies have shown that the human papillomavirus (HPV) DNA test is more accurate than the traditional Pap smear for cervical cancer.

• The HPV DNA test detected 95% of cases in which participants had precancerous changes in the cervix
• The Pap test detected 55% of cases.
• The HPV DNA test had a false positive rate of 6%
• The Pap test had a false positive rate of 3%

When I first saw this news, I breathed a sigh of relief that perhaps sometime soon I would be able to skip regular pelvic exams and cervical cell sampling.

That would be wrong.

According to Lab Tests Online, the HPV DNA test still requires a sample of cells from the cervix. It is NOT a blood test. I emphasize this point because most of the news I’ve seen either got it wrong or didn’t clarify the testing procedure. For most people, DNA tests still mean a blood test even though DNA can be extracted from other samples, such as the ubiquitous cheek swab.

Currently, the HPV DNA test is used in combination with the traditional pap smear. However, recent studies have shown that HPV testing may be used alone and make it possible for women to prolong the time between exams.

One drawback to the HPV DNA test is cost; it is $90 compared to a $10 to $20 Pap test. Also, even girls vaccinated against HPV will need to be screened because there is more than one cancer causing strain not covered by the vaccine.

For more and a video news report, see CBS News.

Photo: HPV infection in squamous cells from Wellcome Images under Creative Commons

Tags: genetics, genes, dna, hpv, cervical cancer, human papillomavirus, pap smear, pap test, hpv dna test

(11 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

(41 comments)

DNA Video: Esther Dyson on the Personal Genome Project

by Dr. Hsien-Hsien Lei
Posted October 20, 2007 in DNA Podcasts and Videos

More hurrahs for Charlie Rose. He regularly features people involved in science and puts the shows on the Web for us all to watch even if we aren’t in the US and don’t have access to PBS.

via The Personal Genome

Tags: genetics, genes, dna, personal genome project, genomics, genome, esther dyson, charlie rose

(>> Start a discussion!)

Nobody Likes James Watson

by Dr. Hsien-Hsien Lei
Posted October 19, 2007 in Personalities with DNA

Yesterday, I briefly mentioned that Dr. James Watson, co-discoverer of the structure of DNA, was knee deep in kaka for saying that blacks have an inferior intelligence than “ours” (I wonder if Chinese people like me are included in that “our”). And although he has since apologized, that hasn’t stopped everyone from piling on.

Dr. Watson said in a statement to The Associated Press:

I cannot understand how I could have said what I am quoted as having said. There is no scientific basis for such a belief.

Other scorn since heaped on Dr. Watson:

• The board of Cold Spring Harbor Laboratory has suspended his administrative responsibilities.
• The London Science Museum has cancelled his talk that was part of the promotion of his new book, Avoid Boring People: Lessons from a Life in Science.
• Writer Bryan Appleyard who has interviewed Dr. Watson before is considering naming his own memoirs – Avoid James Watson. Bryan says:

  When I spoke to Watson we discussed the kind of choices that would be offered to people as a result of our genetic knowledge – for example, he thought the prenatal detection of homosexuality meant that most parents would abort any gay child. What effect would that have on society? He thought for a moment and then said, ‘Less ballet.’ This may be a harmless joke in the pub but, when you are a public figure with a tape recorder running, it’s just nasty. Watson is arrogant enough to think it doesn’t matter.

• Alex at Neatorama likens Dr. Watson to Montgomery Burns of The Simpsons and reminds us of some comments he made in February 2003.

  If you are really stupid, I would call that a disease. The lower 10 per cent who really have difficulty, even in elementary school, what’s the cause of it? A lot of people would like to say, ‘Well, poverty, things like that.’ It probably isn’t. So I’d like to get rid of that, to help the lower 10 per cent.

  People say it would be terrible if we made all girls pretty. I think it would be great.

• Razib at Gene Expression isn’t surprised by Watson’s comments.
• Roger Highfield of Telegraph thinks James Watson has Nobel Syndrome.

If you’d like to see Dr. James Watson in action, check out these videos:

• At Google
• At the Wellcome Trust

Emily Rooney of Greater Boston speaks with James Watson on October 3 about his book, Avoid Boring People.

Tags: genetics, genes, dna, james watson, racism, blacks, intelligence

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