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Lessons Learned From a Genetic Genealogy Quiz

30 April 2008 – 3:00 am

On April 9th, 2008, I posted a quiz about genetic genealogy here on the blog. (If you haven’t taken the quiz yet, it is available here; it only requires a few minutes and might make the following analysis more clear and personally relevant). I created and posted this quiz because I thought it was a fun way to interact with my readers, and because I thought it was educational material to share with others.

As readers began to take the quiz, I realized that there was valuable information contained with the results. The following is an analysis of those results with a few preliminary conclusions. As I proceed, don’t feel bad about missing any of these questions, since this isn’t meant to be a critique of any single individual (especially since individual responses were not recorded). I merely hope to share the results as a whole in an effort to help inform and educate. The quiz was, and still is, meant to be fun.

Additionally, this analysis is also not meant to be a negative critique of genetic genealogy. There are MANY benefits to genetic genealogy testing, when it is used correctly. It can break (and has, many times, broken) through brick walls, validate traditional genealogical research, and confirm or deny a genetic relationship between two individuals in a relevant genealogical timeframe. As one of the correct answers in the quiz stated, genetic genealogy “is the forefront of science, and I get to play along.”

Results
As of today, the quiz has been completed a total of 375 times. Most of the questions were easily answered, ranging from 80% correctly answered (”We all came from Africa, so why bother with a genetic genealogy test?” - Correct answer: Many things have happened in the last 100,000 years) to 97% correctly answered (”Genetic genealogy is a scam, created by big business to capitalize on consumer ignorance” - Correct answer: False). For some of these, the incorrect answers were probably a result of the ‘fun’ element I added to the quiz, such as creative (but less-correct) answers. Each question, however, had an answer that I considered to be the “best” answer.

Prior Research Required?
Only two of the questions had correct answer rates below 80%, and perhaps not surprisingly the questions were directly related. The most problematic question in the quiz, with a correct answer rate of just 46%, was the following: “I can sign up for a genetic genealogy test without doing any prior research.” The answers were:

  • A1. True - heck, I’ve been doing genealogy for years.
  • A2. True - after all, I saw it on TV.
  • A3. False - no way! (correct)
  • A4. Why would I have to research genetic genealogy?

Although the service I used did not track which answers were selected, I have a feeling that many individuals chose “A1″ rather than the correct answer of “A3″, under the assumption that experience with genealogy prepares an individual for genetic genealogy. However, the fact that a genealogist has been doing research for years does not mean that they should undergo genetic testing without prior research. The other incorrect answers, “A2″ and “A4″ are also problematic in that they suggest that either (1) TV reporting/coverage provides enough background information to fully inform an individual about genetic testing, or (2) that no research is needed for genetic genealogy.

Health Information Revealed?
The need for research before genetic testing is evident from the second-most frequently missed question, with 26% answering incorrectly, which states: “The results of a genetic genealogy test might reveal health information about me.” The answers were:

  • A1. True! (correct)
  • A2. False!
  • A3. My DNA knows exactly how much I weigh.
  • A4. Genetics has nothing to do with my health information.

Again, I am uncertain which incorrect answers were chosen, but “A2″ and “A4″ are essentially the same answer and suggest that there is no connection between a genetic genealogy test and genetic disease or health. “A3″ is one of the ‘other’ elements I mentioned in the introduction (and my sorry attempt at humor!).

A total of 1 out of 4 individuals was unaware that a genetic genealogy test can reveal medical information. I have previously highlighted this problem here at TGG, and I included it in both my eBooks (see the sidebar). Many people are unaware, for example, that a Y-DNA test, provided by some of the major genetic genealogy testing firms, can reveal male sterility. Additionally, a full mtDNA sequence can reveal any one of a number of metabolic or other genetic disorders. Although the percentage of these results is extremely low and I don’t think this should discourage people from genetic genealogy, I do believe that people MUST be aware of the possibilities BEFORE swabbing their cheeks.

Conclusions
Today I received the following comment: “This quiz fails to distinguish between facts - you can get a test done without doing any research - and values - you should do some research first. Poor.” I have to admit that receiving this comment stung a little, but then I realized that the author of this comment served to perfectly reinforce the results of the quiz. A genetic genealogy test is a genetic test. Although it is not meant to detect genetic disease or reveal other secrets contained within the genome (such as adoption and illegitimacy), it is fully capable of doing so. As with ANY type of genetic testing, the tested individual must be aware of the possible outcomes before consenting to the test. Educating individuals about the possible outcomes of genetic genealogy is just one of the goals of the Genetic Genealogist. I have a feeling that my regular readers were among those that answered these difficult questions correctly.

Thank you to everyone who took the quiz or wrote about it on their blog or newsletter. I hope you enjoyed taking it, and I hope you’ll consider taking future quizzes. To stay up-to-date on the latest in news and information about genetic genealogy and personal genomics, subscribe to my feed.

By Blaine Bettinger | Posted in DNA for Newbies | Comments (0)

Kwäday Dän Ts’ìnchi - "Long-Ago Person Found"

27 April 2008 – 6:00 am

image Around the year 1700, a relatively healthy young hunter was walking along a glacier in land that would one day be British Columbia in Canada. He wore a robe of 95 animal skins, perhaps gopher or squirrel, stitched together with sinew, and carried a walking stick, iron-blade knife, and spear thrower. For some reason, the young man, aged 17 to 22, died on the glacier and was quickly incorporated into the ice. There he remained, frozen, for the next 300 years.

In August 1999, three hikers noticed a walking stick, fur, and bone lying on a melting glacier (60′ N 138′ W). The young hunter, renamed Kwäday Dän Ts’ìnchi in the Southern Tutchone language of the Champagne and Aishihik First Nations, was removed by scientists for analysis (see the NY Times article, and the Journal of Canadian Archaeology article). From an article in the Sydney Morning Herald:

[When scientists were led to the site], they found a torso with the left arm attached. The hand was mummified. The fingernails were missing. The head was missing, too. A few metres away lay the lower body, with thighs and muscle attached. They also found a wooden dart and walking stick, and pieces of fish and scales within the folds of the man’s robe.

Over the next two days the team members carefully lifted the remains. They collected a knife still in its sheath and a leather pouch. They found a woven hat, fragments of clothing and what was later described as the man’s “personal medicine bag”, which was considered sacred, even after more than five centuries. They did not open it.

In 2001, Kwäday Dän Ts’ìnchi’s remains were given back to the Champagne and Aishihik, and in July 2001 he was cremated in a closed ceremony and returned to the glacier. Kwäday Dän Ts’ìnchi’s skull was found in 2003 but was not removed from the site.

Discovery Continues

Even though Kwäday Dän Ts’ìnchi has been cremated, the analysis of his DNA, intestinal contents, and artifacts continues. This past weekend, at the Kwäday Dän Ts’ìnchi Symposium, researchers around the world presented the results of their research:

The conference brings together more than 30 researchers from fields as diverse as archeology, criminology and microbiology. They come from local universities, the Royal B.C. Museum, Vancouver General Hospital, first nations, and institutions as far afield as Indiana and Scotland.

Haplogroup A

One of the research projects involved sequencing of Kwäday Dän Ts’ìnchi’s mtDNA, which revealed that it belonged to Haplogroup A, with the polymorphisms 16111T, 16189C, 16223T, 16290T, 16319A, and 16362C. As part of the study, the researchers collected blood samples from 250 to 300 members of the Champagne and Aishihik First Nations to compare their mtDNA sequence to that of Kwäday Dän Ts’ìnchi’s (more info here and here). At the Symposium, the researchers revealed that 17 people had mtDNA that closely matched that of the subject, suggesting that they are close maternal relatives. 15 of those 17 people belong to the Wolf clan, also suggesting that Kwäday Dän Ts’ìnchi might have belonged to the Wolf clan himself (more info here).

This topic is of particular interest to me, since my mtDNA belongs to Haplogroup A and therefore I am also (very) distantly related to Kwäday Dän Ts’ìnchi. Last year I profiled the Qilakitsoq mummies in Greenland, all of whom belonged to Haplogroup A.

HT: Geneasofts

By Blaine Bettinger | Posted in Ancient DNA, DNA Articles, DNA in the News | Comments (5)

DNAPrint Genomics and a New Roots Television Video

26 April 2008 – 9:40 am

Megan Smolenyak Smolenyak recently wrote “I’m a Euro-Mutt!” about the results of her AncestrybyDNA EuropeanDNA 2.0 test (from DNAPrint Genomics). Megan found that the results of her test were both expected and surprising! From DNAPrint Genomics’ website:

DNAPrint® Genomics’ powerful new EuropeanDNA 2.0 product, further elucidates European sub-ancestry using 1,349 European Ancestry Informative Markers (SNP AIMs). This test reports a customer’s proportional basic continental European ancestry: Southeastern Europe (SEE - Armenian, Jewish, Italian and Greek), Iberian (IB -Spanish, Portuguese), Basque (BAS - Spanish/French Pyrenees border), Continental European (CE - German, Irish, English, Netherlands, French, Swiss and some Italian) and North Eastern European (NEE - Polish, Baltic, Swedish, Norwegian, Finnish, Russian) ancestry.

For the newbies, this test examines autosomal DNA, which is DNA other than the sex chromosomes and mtDNA. These types of tests will become much more popular as SNP testing and genomic sequencing become cheaper and more widespread.

Roots Television

Have you visited Roots Television lately? Don’t forget that the DNA Channel is available here at TGG (click the Roots Television - DNA Channel button above). Currently featured (under “DNA Testing”) is an interview with Rick Kittles, the co-founder of African Ancestry and a well-known name in the genetic genealogy field.

By Blaine Bettinger | Posted in DNA Companies | Comments (0)

Human mtDNA Diversity Before Migration Out of Africa

25 April 2008 – 1:00 am

image Yesterday, a very interesting paper was published in the American Journal of Human Genetics by the Genographic Project Consortium entitled “The Dawn of Human Matrilineal Diversity.” The results of the study, which examined the 624 mtDNA genomes from sub-saharan Haplogroup L lineages, suggests that humanity once split into two small groups with one group in eastern Africa and the other in southern Africa, and that humanity bottlenecked into a relatively small number of individuals (as few as 2,000 based on results from a previous study). Note, as always, that these are hypotheses based upon the results of this and other studies, and will require further research to support or refute.

Two mtDNA Branches

The human mtDNA tree has two main branches, the L0 branch which includes individuals concentrated in southern and eastern Africa, and the L1′2′3′4′5′6′ branch (aka the L1′5 branch), which includes the entire remainder of humanity including non-Africans (see the figure to the left). Based upon the analysis of the 624 genomes, the researchers hypothesized that the L0 and L1′5 branches diverged into two small populations around 140,000 to 210,000 years ago, with one group settling in eastern Africa (the L1′5 branch) and the other settling in southern Africa (the L0 branch). Interestingly, the results also suggest that there was little to no intermingling of these branches for the next 50,000 to 100,000 years!

The L0 branch comprises 60% of the Khoisan people (two ethnic groups named the Khoi and the San) of Southern Africa. The L1′5 branch comprises all other branches of the mtDNA tree, which includes the N and M matrilines that eventually spread out from Africa.

Population Bottleneck

The results of the study also suggest that humanity was once comprised of a relatively small number of individuals (as few as 2,000, according to another study cited by the researchers). This was suggested because there are very few matrilineal lineages present today that split during the first 100,000 years of our species’ history, likely because they they died out or never developed in the first place. If there had been many more individuals alive at that time (with descendants alive today), scientists would expect to see more different types of lineages in Africa. This is what happened during the second 100,000 years of human history, with as many as 40 different matrilines at the time that humans left Africa to spread to the remainder of the world. As many of us know now, there is a multitude of current matrilines because of our enormous population explosion in the past few thousand years. Note, however, that this hypothesis may change if researchers suddenly discover large amounts of new matrilines present in Africa which split from the main line in the first 100,000 years.

An article in the Economist did a very good job of making the article understandable. Here is a quote from this terrific article in the Economist, which I suggest you read for yourself:

Comparing Khoi and San DNA with that of other Africans shows that the first big split in Homo sapiens happened shortly after the species emerged, 200,000 years ago. Most people now alive are on one side of that split. Most bushmen are on the other. The consortium’s analysis of which DNA “matrilines” are found where suggests that for much of its history the species was divided into two isolated populations, one in eastern Africa and one in the south of the continent, that were defined by this split. However, few other matrilineal splits from the first 100,000 years of the species’s history have survived to the present day.

This suggests the early human population was tiny (so the opportunities for new matrilines to evolve in the first place were limited) and reinforces the idea that Homo sapiens may have come close to extinction (eliminating some matrilines that did previously exist). Indeed, there may, at one point, have been as few as 2,000 people left to carry humanity forward.

This shrinkage coincides with a period of prolonged drought in eastern Africa, and was probably caused by it. The end of the drought, however, was followed by the appearance of many new matrilines that survive to the present day. The researchers estimate that by 60,000-70,000 years ago, the period when the exodus that populated the rest of the world happened, as many as 40 such groups were flourishing in Africa—though that migration involved only two of these groups.

For more information, check out the following sources:

By Blaine Bettinger | Posted in Ancient DNA, DNA Articles, DNA in the News | Comments (8)

GINA: An Update

24 April 2008 – 1:32 pm

1:25PM EST: Senator Olympia Snowe is currently on the floor of the Senate speaking about GINA (see it live on C-SPAN 2). And yes, I realize that live-blogging C-SPAN coverage is dangerously boring, but I can’t help myself!

3:00PM EST: I just received a press release from the Genetics & Public Policy Center that GINA passed the Senate 95-0:

The Senate today passed the Genetic Information Nondiscrimination Act (GINA), approving by unanimous consent of 95-0 an amended version of H.R. 493, which passed the House April 25, 2007 by a vote of 420-3. The House is expected to take up the measure again quickly before sending it to President Bush to sign the measure into law.

“After a very long wait, Americans can now be confident that their genetic information cannot be used by health insurers or employers in harmful or hurtful ways,” says Kathy Hudson, director of the Genetics and Public Policy Center, established at Johns Hopkins University by The Pew Charitable Trusts. “Our challenge now is to make sure that doctors and patients are aware of these new protections so that fear of discrimination never again stands in the way of a decision to take a genetic test that could save a life.”

The legislation, when signed, will fulfill the longstanding agreement among American citizens and politicians that protection from genetic discrimination should be clear and consistent, Hudson explains. Until now, individuals’ genetic information has been protected only by a largely untested patchwork of state and federal regulations. Ninety-two percent of Americans are concerned that results of a genetic test could be used in ways that are harmful to the person.

Moreover, scientists can now in good conscience tell patients and research participants that their genetic information is protected against misuse by health insurers and employers. Linking gene variants to health outcomes often requires studies involving large numbers of people, but scientists report that potential subjects are deterred by the fear that their information could be used against them by employers or insurers. In a survey of more than 4000 people conducted earlier this year, for example, the Center found that when considering whether or not to participate in genetics research, 93 percent of respondents said it was important that it be “illegal for insurers or employers to get my information.”

In addition to impeding research that would help to bring about the much-heralded era of personalized medicine, the threat of discrimination affects individual patients who could benefit from genetic testing have sometimes foregone it out of concern over possible repercussions. When people opt not to be tested, they lose the opportunity to seek monitoring and preventive care to avoid conditions for which they are at higher risk. Passage of GINA means that Americans will no longer have to make the trade-off between genetic privacy and appropriate health care.

The Senate unanimously passed versions of GINA in 2003 and 2005, but in both years the bill stalled in committee in the House. Last year, however, the House passed the measure quickly and today, the Senate for a third time expressed its commitment to nondiscrimination.

By Blaine Bettinger | Posted in DNA for Newbies | Comments (0)

Finally, GINA Gets Her Day

24 April 2008 – 3:00 am

iStock_000005432570XSmall On April 27, 2007, I wrote “GINA: A Primer“, which was an introduction to the Genetic Nondiscrimination Act. Today, nearly a year later, the bill will most likely be voted on and passed by the Senate, the last step before being handed over to President Bush to sign into law (which he has indicated that he will do). As I wrote last April:

“GINA aims to protect individuals in a variety of different areas. The legislation would prohibit access to genetic information by insurance companies and would prohibit insurance companies from discriminating against an applicant based on genetic information, the refusal to submit genetic information, or for have been genetically tested in the past. Additionally, the Act would prohibit employers from using or collecting genetic information to make employment decisions. The Act also establishes a Genetic Nondiscrimination Study Commission that is charged with reviewing new developments in the field of genetics and advising Congress.”

This bill is considered by many to be an important first step in providing protections against the misuse of recent and future developments in genetic sequencing and analysis technology.

There is a great deal of information about today’s vote:

There is also some very recent information from the Center for American Progress entitled “Genetic Nondiscrimination: Policy Considerations in the Age of Genetic Medicine” (full pdf report here).  The Center (which I am not familiar with) also has a recent interview with a genetic counselor: “It’s All in the Genes (Or Is It?)”

Stay tuned!

By Blaine Bettinger | Posted in DNA in the News | Comments (6)

Genetic Genealogy, Public Databases, and Criminals

23 April 2008 – 12:00 am

The Washington Post has an article entitled “From DNA of Family, a Tool to Make Arrests” about using DNA obtained from family members to search DNA databases or identify relatives as criminals. Here is a summary of the issue from a recent Columbia Law review article available here (pdf):

For years, law enforcement personnel have compared DNA found at crime scenes with that of a convicted offender. Recently, a new technique has
begun to focus on the genetic similarity of biological relatives. Now, if a crime scene sample partially matches the DNA profile of a previous offender, law enforcement can investigate and possibly arrest that person’s family members. This process is called familial DNA testing and will significantly increase the amount of genetic information contained in the FBI’s Combined DNA Index System (CODIS), which consolidates local, state, and federal DNA databanks into a uniform body of data.

Hank T. Greely, a law professor at Stanford, is mentioned late in the article. Mr. Greely is an expert on this topic and has written a number of articles including “Family Ties: The Use of DNA Offender Databases to Catch Offenders’ Kin” (34 J.L. Med. & Ethics 248, 250–51 (2006)). Mr. Greely has argued, as have others, that this type of testing will disproportionately affect minorities such as African Americans because every year “more than 40 percent of people convicted of felonies in the United States are African American.” As Greely points out in the Washington Post article:

“If the national database were used for familial searching, he said, and assuming that on average each person whose profile in the database has five first-degree relatives, authorities would be “putting under surveillance” roughly a third of the African American population, compared with about 7.5 percent of the European American population, he said.”

Genetic Genealogy Testing on Suspect DNA

At the current stage of technology, comparing the results of a genetic genealogy test using DNA obtained from a suspected criminal to public databases such as Y-search or mitosearch would be of limited value. There is a remote possibility that an exact match might be found (as so many of us that are searching for exact matches can attest to), but it is unclear how useful that information would be, or if it would even be admissible evidence in a trial. With user-annotated data in most public databases, there is little direct or reliable evidence that any DNA sequence is actually associated with a user or a surname. This is, of course, a problem that even hobbyist genetic genealogists face with public databases.

It should be noted, however, that autosomal genetic genealogy has already been adopted for use in criminal investigations. DNAPrint Genomics offers DNAWitness, a product that offers autosomal analysis similar to their Ancestry by DNA service. From two recent press releases about DNAWitness (pdf):

DNAWitness™ derives the percentage of European, East Asian, Native American, and Sub- Saharan African markers in a person’s DNA. This ratio for an individual is termed BioGeographical Ancestry (BGA), representing general characteristics that can be matched with a searchable database containing information and photographs collected from samples around the world, leading to more accurate identifications of potential of criminal suspects.

Law enforcement officers use DNAWitness™ 2.5 to determine genetic ancestry from DNA samples obtained from crime scenes, narrowing the potential suspect pool to a more focused group of likely candidates. The test enables law enforcement agencies to reduce both the cost and time needed to apprehend suspects. Current forensic DNA products in the market act like a fingerprint and can only be used to match DNA specimens.

The Future

As sequencing becomes cheaper and the complexities of the genome are more completely understood, the future of using DNA samples from crimes scenes will likely be very different. In addition to comparing DNA to sample databases, officials might be able to estimate the suspect’s height, weight, hair color, skin color, eye color, handedness, age, and so forth. It will be interesting to see what the future holds.

HT: M.E.B.

By Blaine Bettinger | Posted in DNA in the News | Comments (7)

The Spring 2008 Issue of the Journal of Genetic Genealogy

22 April 2008 – 3:00 am

Yesterday the Spring 2008 Issue of the Journal of Genetic Genealogy was published online. As always, the journal and every article is completely FREE. Here is a listing of the articles in the current issue:

  • Editor’s Corner - A New Y Tree by Whit Athey
  • ‘Satiable Curiosity - Y-Chromosome and mtDNA Information from deCODEMe by Ann Turner
  • Genetic Structure of an Isolated Sub-Tribe of the Adi People of Arunachal Pradesh State in Northeast India: Isonymy Analysis and Selective Neutrality of Surname Distribution in Adi Panggi by Suvendu Maji and T. S. Vasulu
  • The Subclades of mtDNA Haplogroup J and Proposed Motifs for Assigning Control-Region Sequences into these Clades by Jim Logan
  • A New Subclade of Y Haplogroup J2b by T. Whit Athey and Bonnie E. Schrack
  • Where Did European Men Come From by Kalevi Wiik
By Blaine Bettinger | Posted in DNA Articles | Comments (0)

Tracing a 500-Year-Old Founder Mutation Using Genetic Genealogy

21 April 2008 – 3:00 am

image In January I wrote about a study that traced a mutation in a single colon cancer gene to 1630. Today, researchers announced that a founder mutation in another gene, MSH2, has been traced to roughly 500 years ago (”Origins and Prevalence of the American Founder Mutation of MSH2” (pdf)).

MSH2 is a mismatch repair gene, and mutations in the gene results in Lynch syndrome, also known as hereditary nonpolypsis colorectal cancer. Lynch syndrome accounts for 2.8% of all colon cancers in the Western world, with 4,500 cases a year in the U.S. One specific mutation in MSH2, the deletion of exons 1 through 6, was named the American Founder Mutation (AFM) and was identified in nine families. Previously, research had suggested that the mutation in the MSH2 gene had been brought to Pennsylvania by German immigrants in the early 1700’s.

AFM More Prevalent Than Previously Thought

Upon further examination, researchers identified 32 new families who carried the AFM. Using extensive genealogical research that tracked the families as far back as the 18th century, 27 of the 41 AFM families were coalesced into seven extended pedigrees. These pedigrees are all available as WorldConnect databases. Unfortunately, the identification of 32 new families suggests that Lynch syndrome is far more prevalent than previously thought.

The AFM Arose About 500 Years Ago

Software used by the researchers predicted that this mutation arose about 500 years ago (with a 95% confidence interval of 425 to 625 years ago). Given that the seven extended pedigrees each had a common ancestor born between 1700 and the early 1800s, the researchers concluded that it was unlikely that there was a single common ancestor who arrived in the United States to link all the families. As a result, two hypotheses were asserted: either the AFM began with a common ancestor in Europe before the families emigrated to the New World, or, in light of the age of the mutation, it arose in a Native American population. Notably, despite efforts by the researchers, the specific MSH2 AFM has not yet been identified in Europe.

Genetic Genealogy Not Just for Entertainment

This study is another example of researchers using genetics and extensive genealogy research to identify the origins of disease-causing mutations. These studies do more than just attempt to identify a founder, which might be considered just entertainment. Rather, this research identifies genetic relatives who might be candidates for genetic screening and allows scientists to estimate the prevalence of certain mutations. Additionally, this study in particular identified three states (Ohio, Kentucky, and Texas) where the AFM is more prevalent. Luckily, there are some measures that affected individuals can take to minimize the danger of the AFM.

For More Information:

ThinkGene - Inherited cancer mutation is widespread in America

The Columbus Dispatch - Study retraces colon-cancer link

By Blaine Bettinger | Posted in DNA Articles | Comments (6)

TGG Rated 9.0 at Blogged

20 April 2008 – 3:00 am

I recently received notification that The Genetic Genealogist has been rated a 9.0 at Blogged:

The Genetic Genealogist at Blogged

What is Blogged? From the website:

“Blogged.com is all about blog discovery. It’s a place for readers to discover interesting blogs and for authors to discover who their readers are. Blogged goes beyond being a traditional blog directory. We focus on providing tools for bloggers and readers alike. Through our database of over 200,000 blogs, readers can discover and explore new blogs. Through our user community, blog authors and their readers can communicate and interact directly with each other. Our blogs are reviewed, rated, and categorized by our editors, so you won’t have to experience the frustration of filtering through blogs that are either spam, outdated, or irrelevant. You’ll be able to find quality blogs that you would have unlikely found through a traditional blog search.”

By Blaine Bettinger | Posted in Miscellaneous | Comments (2)

From Forbes: "States Crack Down On Online Gene Tests"

18 April 2008 – 10:32 am

New York

Update: See the related story in GenomeWeb News (free sub. required).

Forbes.com published an article today entitled “States Crack Down On Online Gene Tests” that examines New York state’s response to the recent launch of direct-to-consumer (DTC) genetic testing services by companies such as 23andMe, deCODEme, SeqWright, and Navigenics, as well as the behind-the-scenes companies like Illumina and Affymetrix.

Unfortunately, the regulatory environment surrounding DTC genetic services is hazy at best. From the article:

“Over the last six months, New York State’s Department of Health has sent letters raising the specter of fines and jail time to six online gene-testing firms that offer consumers the ability to peer into their genome to assess their future risk of getting diseases such as cancer, heart disease and multiple sclerosis. Often, it turns out, the services offering these DNA deep-dives are doing so without the involvement of a doctor. That puts them on the wrong side of the law.”

Unclear Regulations

I’m still not convinced. I recently wrote an article that reviewed New York’s statutes and regulations regarding DTC testing, and it is far from clear. Additionally, there is almost an entire lack of case law to help interpret these statutes. Ultimately it is a question of statutory interpretation and legislative intent. What did the original drafters of these regulations intend the laws to do, or to protect? How should these laws be interpreted today? These are difficult questions without clear answers, and thus will be the subject of much debate in the near future.

P.S. - I am currently working to find a journal in which to publish my article, so stay tuned for my input on this very controversial topic!

By Blaine Bettinger | Posted in DNA Companies | Comments (8)

Essay Contest Reveals Misconceptions of High School Students in Genetics Content

16 April 2008 – 3:00 am

The American Society of Human Genetics announced a press release out today about a study of student essays submitted as entries in the National DNA Day Essay Contest in 2006 and 2007. The ASHG’s education staff examined 500 of the 2,443 essays and found that 55.6% of the essays contained at least one “obvious” misconception, and 20.2% contained two or more misconceptions.

At first glance I was a little concerned about mining these essays - notably submitted by eager students to win a contest - for this type of information, but then I concluded that the authors of the essays must have assumed that they were being evaluated based on the accuracy of their statements. Additionally, the ASHG took careful steps to preserve anonymity.

The panel concluded that “misconceptions about genetics remain prevalent in U.S. science classrooms”, and included information about using the findings to improve genetics education. I highly recommend reading the entire paper, available for free from the ASHG and Genetics: “Essay Contest Reveals Misconceptions of High School Students in Genetics Content.” From the press release:

“The misconception most frequently identified in the researchers’ analysis of student essays was broadly defined into the category of “genetic technologies” (17.2%), these responses displayed incomplete understanding of the complexity of scientific research, including biotechnology and genetic engineering. Another common theme identified in the analysis revealed that students did not fully understand concepts related to heredity and patterns of inheritance (14%); these essays reflected students’ belief that single genes are the cause of traits and inherited diseases. In actuality, even in cases of simple inheritance, multiple genetic and/or environmental factors often play a role in the expression of a trait or disease.”

The paper includes some interesting examples of misconceptions, such as the following quote from a student’s essay:

‘‘One study showed that chemical dependency skips a generation. This would make the gene for chemical dependency recessive. This means that if a psychiatric geneticist would make a Punnett square for two parents whose parents had chemical dependency, the Punnett square would say that 3 out of 4 of their children would be chemically dependant.’’

The authors of the study respond with: “Chemical dependency is a complex trait that cannot be explained by a simple, monohybrid Punnett square cross.”

Everyone remembers the “big B” “little b” Mendelian crosses of things like eye color in biology class. But in today’s world of genetics, teaching this simplistic view of genetics, especially in high school (which is really just a basic introduction to genetics) might be too confusing. What do you think?

By Blaine Bettinger | Posted in DNA Articles, DNA in the News | Comments (3)

ThinkGenealogy Presents "Are You Smarter than a Grade School Genealogist?"

14 April 2008 – 3:38 pm

ThinkGenealogy introduces episode 1 of “Are You Smarter than a Grade School Genealogist?“: “Match your genealogy knowledge against a grade schooler to determine: Are You Smarter than a Grade School Genealogist? In this episode, Nathan, a 4th grader from Arizona introduces DNA for the genealogist.” The episode is just over 4 minutes long and is a great introduction to genetic genealogy.

By Blaine Bettinger | Posted in DNA Articles | Comments (0)

Genetic Genealogy on TV - Meeting David Wilson

10 April 2008 – 11:17 am

MSNBC will air a documentary tomorrow evening about the journey of 28-year-old African American David Wilson as he discovers his genealogical roots. Wilson uses both traditional genealogical research as well as DNA testing to learn more about his ancestry. Along the way, Wilson meets another David Wilson, a white 62-year-old descendant of the slaveowners who owned the other’s ancestors. From the Meeting David Wilson website:

“Coinciding with the 40th anniversary of the assassination of civil rights leader Dr. Martin Luther King, Jr., MSNBC will premiere “Meeting David Wilson,” the remarkable and inspiring story of a young man’s reconciliation with his ancestors’ history as slaves. The world premiere of “Meeting David Wilson,” on April 11 at 9 p.m. ET will be hosted by “Today” Correspondent Tiki Barber and followed by a 90-minute live discussion of racial issues in America. The live event will be moderated by “NBC Nightly News” Anchor and Managing Editor Brian Williams and held at Howard University in Washington, D.C.”

The younger David Wilson also undergoes DNA testing in hopes to learn more about his ancestry:

“Curious to learn if they have more than a name in common, David tests his DNA. One of the results of this test identifies his African origins. Once this match is made, the lab provides him with a name and location of an African ethnic group and he travels back to Africa to complete his journey.”

To learn more, there is the official Meeting David Wilson Blog, an article on MSNBC, an interesting downloadable press kit (pdf) with a synopsis and pictures (pictures also available online here), other videos. And finally, here is the YouTube trailer:

HT: The Genealogue, and Megan’s Roots World.

By Blaine Bettinger | Posted in DNA in the News | Comments (2)

A Quiz - Test Your Genetic Genealogy Knowledge

9 April 2008 – 3:00 am

How much do you know about genetic genealogy testing? Take The Genetic Genealogist’s quiz!



By Blaine Bettinger | Posted in DNA for Newbies, Miscellaneous | Comments (15)

Navigenics Open For Business

8 April 2008 – 7:32 am

Navigenics, a genome scanning company, officially launches their genome service today - called the “Navigenics Health Compass”, with a cocktail reception in NYC tonight at 6:00PM. Thomas Goetz of Epidemix writes an article in Wired today about some of the differences between Navigenics and other large-scale genome scanning companies.

The launch is also mentioned in an exclusive interview at Genetics and Health with Navigenics’ medical director, Dr. Michael Nierenberg. This piece is the first article in a seven article series, including the future article 6, which discusses some of my favorite things: “Privacy, insurance, GINA, and ethics.” I’ll be sure to link to that article when it comes out. The launch is also discussed over at ScienceRoll.

For more information:

By Blaine Bettinger | Posted in DNA Companies, DNA in the News | Comments (5)

Genetic Testing Under the Microscope

7 April 2008 – 3:00 am

Genetic Testing Under the Microscope Genetic testing has once again come under the microscope, triggered by an article in the journal Science: “A Case Study of Personalized Medicine.”

In my opinion, adding to the conversation about genetic testing is always a good thing.

That being said, my biggest complaint with many of these articles (especially in the popular media) is that they tend to lump together every test that examines DNA. There are different types of genetic testing with different levels of quality control, interpretation, etc. The results, scientific background, and effects of tests offered by large-scale genome scanning companies, clinical entities, direct-to-consumer companies, and pharmacogenetic companies are not the same. When dealing with a readership that does not have a background in genetics (which is probably 99% of the readership), the media should take extra care to note these differences. Lumping every DNA test together does little to properly educate the public.

Also unclear from almost every article is how genetic genealogy fits into the conversation. Based on what I read online and in the media, I still get the impression that most people are either unaware of genetic genealogy, or fail to understand the (20+ years of) science behind it.

Here is a round-up of the discussion triggered by the article:

P.S. - another pet peeve is that the authors of these studies felt that public health is being threatened and wanted to educate the public, but submitted their article to a closed-access journal. A double-edged sword, I suppose; publish in a high-profile journal to attract attention, or risk less attention from publication in an open-access journal. This work was presumably funded by the Genetics and Public Policy Center, which in turn is funded by “The Pew Charitable Trusts, with research funding from the National Human Genome Research Institute and the U.S. Department of Veterans Affairs.” Thus it would appear that my tax dollars helped fund the work. I wish I could read it without paying $10 for access through Science.

By Blaine Bettinger | Posted in DNA in the News | Comments (7)

The 2010 Census

5 April 2008 – 9:32 am

At 12:01 on April 1, 2082, millions of genealogists around the solar system will be able to instantaneously download every image from the 2010 census into their neural storage chip, and within minutes these images will be linked to the ancestors in their 3D holographic family trees. Almost all of these genealogists will be able to find themselves in these census images and index.

Okay, maybe it’s a little premature to guess about the use of a census that hasn’t even been enumerated yet, but as most genealogists know, census results are the backbone of the genealogical world. Only one census has been released since the advent of the internet. In 2002 the 1930 census was released, and the countdown to the April 2, 2012 release of the 1940 census has already begun.

The 2010 census is only 2 years away. Here is the planned schedule for the 2010 census:

  • March 2010 - Census questionnaires are mailed or delivered to households.
  • April - June 2010 - Census workers visit households that did not mail back a census questionnaire.
  • December 31, 2010 - U.S. population totals are due to the President.

On Thursday, it was announced that the government will not use handheld computers to collect information from Americans who fail to return their census forms (HT: GeneaSofts). Instead, census takers will use traditional pen and paper forms. It is estimated that this will increase the cost of the entire census to over $14 billion. That’s almost $47 per person!

Interestingly, however, the Census Bureau will still use GPS-enabled handheld computers to verify household locations in 2009, according to testimony from U.S. Secretary of Commerce Carlos M. Gutierrez on April 3rd. Wouldn’t it be great to have GPS coordinates associated with each census return?

Here is more information:

Genealogy law lesson of the day:

Why are census records held for 72 years (other than the obvious public policy reasons)? Because of 36 C.F.R. §1256.4 (a)(3), which states the following:

“NARA will not grant access to restricted census and survey records of the Bureau of the Census less than 72 years old containing data identifying individuals enumerated in population censuses in accordance with 44 U.S.C. 2108(b).”

44 U.S.C. 2108(b) simply states that agreements between the Census Bureau and the National Archives, such as the 72-year agreement, become law. As to why it is 72 years and not 10 or 100 years, supposedly 72 was chosen because it was the average lifespan of Americans when the agreement was made.

By Blaine Bettinger | Posted in Genealogy, Miscellaneous | Comments (4)

Abstract From the New Y-Chromosome Haplogroup Tree Article

2 April 2008 – 11:05 am

Here is the abstract of today’s Y-chromosome haplogroup tree paper in Genome Research, I’m still working to get a copy of the actual paper (unfortunately, it’s not open access at this time):

Markers on the non-recombining portion of the human Y chromosome continue to have applications in many fields including evolutionary biology, forensics, medical genetics, and genealogical reconstruction. In 2002, the Y Chromosome Consortium published a single parsimony tree showing the relationships among 153 haplogroups based on 243 binary markers and devised a standardized nomenclature system to name lineages nested within this tree. Here we present an extensively revised Y chromosome tree containing 311 distinct haplogroups, including two new major haplogroups (S and T), and incorporating approximately 600 binary markers. We describe major changes in the topology of the parsimony tree and provide names for new and rearranged lineages within the tree following the rules presented by the Y Chromosome Consortium in 2002. Several changes in the tree topology have important implications for studies of human ancestry. We also present demography-independent age estimates for 11 of the major clades in the new Y chromosome tree.

Karafet, T.M., Mendez, F.L., Meilerman, M.B., Underhill, P.A., Zegura, S.L., and Hammer, M.F. New binary polymorphisms reshape and increase resolution of the human Y-chromosomal haplogroup tree. Genome Res. doi:10.1101/gr.7172008.

By Blaine Bettinger | Posted in Uncategorized | Comments (7)

The New Y-Chromosome Tree to be Released Tomorrow

1 April 2008 – 7:37 pm

A long-anticipated new version of the Y-Chromosome Tree will be released in the journal Genome Research tomorrow (Wednesday, April 2nd). In the paper, scientists from the University of Arizona and Stanford University use recent SNP data and research to reformulate the familiar Y-chromosome tree (see, for example, the current tree at ISOGG). Here is the full text of the press release.  The paper should appear here as soon as it is made available by Genome Research tomorrow.

From the press release:

In an article published online today in Genome Research (www.genome.org), scientists have utilized recently described genetic variations on the part of the Y chromosome that does not undergo recombination to significantly update and refine the Y chromosome haplogroup tree. The print version of this work will appear in the May issue of Genome Research, accompanied by a special poster of the new tree.

Hammer’s group integrated more than 300 new markers into the tree, which allowed the resolution of many features that were not yet discernable, as well as the revision of previous arrangements.

Furthermore, Hammer explains that this work has resulted in the addition of two new major haplogroups, S and T, with novel insights into the ancestry of both. “Haplogroup T, the clade that Thomas Jefferson’s Y chromosome belongs to, has a Middle Eastern affinity, while haplogroup S is found in Indonesia and Oceania.”

Here is the full citation of tomorrow’s paper:

Karafet, T.M., Mendez, F.L., Meilerman, M.B., Underhill, P.A., Zegura, S.L., and Hammer, M.F. New binary polymorphisms reshape and increase resolution of the human Y-chromosomal haplogroup tree. Genome Res. doi:10.1101/gr.7172008.

By Blaine Bettinger | Posted in DNA Studies, DNA in the News | Comments (1)