Bug hunting »

An awful lot of microbes could reveal a great deal about the human body

THIS year teams of dedicated researchers working on the new Human Microbiome Project (HMP) began collecting faeces samples and swabs from the vagina, mouth, nose and skin of 250 volunteers. They are the modern equivalent of Victorian bug hunters, classifying new species in uncharted territory.

But rather than using nets and chloroform, their tools are the high-speed gene-sequencing machines developed for the Human Genome Project. And their task dwarfs the genome project: with perhaps 1,000 species under investigation, the number of bacterial genes could amount to 200,000, compared with 20,000 human ones. HMP is a $100m American project funded by the National Institutes of Health. Its aim is not only to classify the microbial inhabitants of humans, but also to identify where they live and what strains people have in common. ...

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Drugstore Shopping List: Aspirin, Shampoo, Paternity Test »

Through the miracle of DNA technology, a trip to the drugstore can sort out those nagging paternity questions that bubble up at the family picnic. A company called Identigene said today that its paternity test is now available over the counter at Rite Aid and Meijer drugstores around the country.

Identigene TestThe test, which costs $29.99 at the store plus another $119 for lab fees, is the similar to tests widely available online. The kit includes Q-tip-like swabs for the mother, child and alleged father. Rub the swab on the cheek, send it to Salt Lake City in a postage paid envelope, and a few days later get your results by mail, phone or Internet.

But don’t try and take the answer to the judge. For the answer to be legally binding, you’ve got to pay a few hundred bucks extra for a third party (or in this case, fourth party) to administer the tests and confirm that everybody is who they say they are.

The lab work on the store test is just as rigorous on this test as it is on a legally binding one, Identigene COO Douglas Fogg told the Health Blog. The results are certain to 99.99%, he said. “This test is pretty much black and white.”

Itentigene is owned by Sorenson Genomics. Fogg wouldn’t discuss how much money the privately held company makes on the tests, but he did say that more than 500,000 legally admissible paternity tests are conducted in this country every year.

Bonus Test: The test isn’t sold in New York, where state rules require a doctor’s prescription or a court order, the company said. But it’s not far to Jersey, where the test is available.

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Kitty and Fido: providing companionship, entertainment, and nasty bacteria? »

I've written about methicillin-resistant Staphylococcus aureus (MRSA) previously on this site. This is a pathogen that first came to our recognition almost 50 years ago, but has increased in prevalence in our hospitals over the last 20 years. In the last decade or so, it's also become more common in the community, spreading among individuals who have never had any hospital exposure. This includes, surprisingly enough, animals, both large and small. Studies have identified horses, cattle, and swine who were colonized with MRSA. Even pet animals can carry the bacterium, as a recent study exemplified:

A German woman repeatedly battled the same strain of drug-resistant superbug MRSA until her cat was tested and treated. It's one of the few documented cases of transmission of methicillin-resistant Staphylococcus aureus between a person and a cat. Nasal and other swabs from her husband and two children showed they carried the MRSA germ on skin but had no signs of infection.
We're typically closer to our pets than almost anyone else in our lives. We may sleep with them; we kiss them, or they lick our faces and hands--and they can also act as germy vectors. Again, a little handwashing can go a long way.

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Atlanta conference posts soon, I promise... »

It's been a busy 3 days here in Atlanta. My talk Tuesday was well-received, I have lots of new ideas for future projects, and I'll have posts on the conference itself starting, hopefully, this afternoon (last night was family time, so no posting). In the meantime, I'm writing up the manuscript for the study I presented and I thought I'd ask for some input with one small portion.

The study itself is a sampling of swine for bacterial carriage. On the first farm we headed out to (and by "we" I, of course, mean my trusty graduate student), we only had on hand as many swabs as we were going to use--no extras. Swine aren't always very cooperative, and one swab ended up getting contaminated .

So, how would you write this up? Of course in the end I'll have to go with something dry, academic and boring, but I'm sure y'all can come up with something much more creative...

Read the comments on this post...
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High school students uncover their past through their DNA »

Students at Soldan International High School are participating in an amazing experiment and breaking ground that most science teachers fear to tread.

Soldan students, along with hundreds of thousands of other people, are participating in the National Geographic's Genographic Project. Through this project, students send in cheek swabs, DNA is isolated from the cheek cells, and genetic markers are used to look at ancestry.

Read the rest of this post... | Read the comments on this post...
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10 DNA Testing Myths Busted »

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1. Genetic genealogy is only for hardcore genealogists.

Wrong! If you’ve ever wondered about the origins of your DNA, or about your direct paternal or maternal ancestral line, then genetic genealogy might be an interesting way to learn more. Although DNA testing of a single line, such as through an mtDNA test, will only examine one ancestor out of 1024 potential ancestors at 10 generations ago, this is a 100% improvement over 0 ancestors out of 1024. If you add your father’s Y-DNA, this is a 200% improvement. Now add your mother’s mtDNA, and so on. However, with this in mind, please note the next myth:

2. I’m going to send in my DNA sample and get back my entire family tree.

Sorry. DNA alone cannot tell a person who their great-grandmother was, or what Italian village their great-great grandfather came from. Genetic genealogy can be an informative and exciting addition to traditional research, and can sometimes be used to answer specific genealogical mysteries.

3. I would like to try genetic genealogy, but I’m terrified of needles.

Good news! Genetic genealogy firms don’t use blood samples to collect cells for DNA testing. Instead, these companies send swabs or other means to gently obtain cells from the cheek and saliva.

4. I would like to test my ancestor’s DNA, but they died years ago.

You don’t always need your ancestor’s DNA to get useful information from a genetic genealogy test. If you are male, you contain the Y-chromosome (Y-DNA) that was given to you by your father, who received it from his father, and so on. Both males and females have mitochondrial DNA (mtDNA), which was passed on to them by their mother, who received it from her mother, and so on. Everyone of us contains DNA (Y-DNA and/or mtDNA) from our ancestors that can be studied by genetic genealogy.

5. I want to test my mother’s father’s Y-DNA, but since he didn’t pass on his Y-chromosome to my mother, I’m out of luck.

Wrong! There is a very good chance that there is another source of that same Y-DNA. For instance, does your mother have a brother (your uncle) who inherited the Y-DNA from his father? Or does your mother’s father have a brother (your great-uncle) who would be willing to submit DNA for the test? Sometimes there might not be an obvious source of “lost” Y-DNA, or no one in the family is willing to take a DNA test. The secret to solving this problem is to do what every good genealogist does – use traditional genealogical research (paper records, census information, etc) to “trace the DNA”. Follow the line back while tracing descendants in order to find someone who is interested in learning more about their Y-DNA. This applies to finding a source of mtDNA as well.

6. Only men can submit DNA for genetic genealogy tests, since women do not have the Y-chromosome.

Wrong! Most genetic genealogy testing companies also offer mtDNA testing. Both men and women have mtDNA in their cells and can submit that DNA for testing. In addition, women can test their father’s, brother’s, or some other male relative’s Y-DNA to learn more about their paternal ancestral line, even though they did not inherit the Y-chromosome.

7. My genetic genealogy test will also reveal my propensity for diseases associated with the Y-chromosome and mtDNA.

Wrong, thank goodness. Most of the information obtained by genetic genealogy tests has no known medical relevancy, and these firms are not actively looking for medical information. It is important to note, however, that some medical information (such as infertility detected by DYS464 testing or other diseases detectable by a full mtDNA sequence) might inadvertently be revealed by a genetic genealogy test.

8. I don’t like the thought of a company having my DNA on file or my losing control over my DNA sample.

This is, of course, an understandable concern. However, most testing firms give a client two options: the DNA is either immediately destroyed once the tests are run, or it is securely stored for future testing. If the DNA is stored, the firm will typically destroy the DNA upon request. If the long-term storage of DNA is a concern, be sure to research the company’s policy before sending in a sample.

9. If my test reveals Native American ancestry, I plan to join a particular Native American affiliation group.

Although genetic genealogy can potentially reveal Native American ancestry (for instance, my mtDNA belongs to the Native American haplogroup A2), it is incredibly unlikely that this information will be sufficient to positively identify the specific source of the lineage (such as a tribe) or allow membership in a particular Native American affiliation.

10. My DNA is so boring that genetic genealogy would be a waste of time and money.

Very wrong! A person’s DNA is a very special possession – although everyone has DNA, everyone’s DNA is different (okay, except identical twins – if your identical twin has been tested, you should think twice about buying the same test!). As humans settled the world, Y-DNA and mtDNA spread and mixed randomly. As a result, it is impossible to guess with 100% assurance that a person’s Y-DNA or mtDNA belongs to a particular haplogroup (a related family of DNA sequences) without DNA testing.

BONUS MYTH: My genetic genealogy test says that my mtDNA belongs to Haplogroup A2. Juanita the Ice Maiden, a frozen mummy discovered in the Andes Mountains in Peru also has Haplogroup A2 mtDNA. Therefore, she must be my ancestor!

Unfortunately, although genetic genealogy can reveal that a person is RELATED to an ancient DNA source, it cannot prove that a person is a DESCENDANT of an ancient DNA source. For instance, perhaps you are descended from Juanita’s sister, or her 5th cousin. Thus, although Juanita might be your great-great-great-great…great-grandmother, she might instead be your great-great-great-great…great-aunt. And since Juanita died when she was just 12 to 14, it is unlikely she has any descendants.

If you understand the risks associated with genetic genealogy (such as the detection of non-paternal events and other risks) and are ready and willing to embrace the results to learn more about your genetic ancestry, then genetic genealogy might be for you. I recommend that you read archived posts here at The Genetic Genealogist, and do some online research through one of the many companies that offer genetic genealogy testing.

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