Author Archives: Cyndy

All I Want for Christmas Is a Personal Genome Sequence.

Santa's giftAll I Want for Christmas Is a Personal Genome Sequence.   If cialis order that seems like too much to ask from Santa, then I just want to say up front that I am not asking for my scientific thesis own genome sequence, only my husband’s. Not more that 7 or 8 years ago this type of “present” would have cost upwards of $3 billion.

It’s hard to believe that it can now be free. That’s because we signed him up as a volunteer for the Personal Genome Project, or PGP. So we will have to wait and see if Santa delivers – and it looks like it may not be this Christmas!

This all began several months ago when Mary and I attended a lecture series in Boston celebrating the retirement of Temple Smith (of the Smith-Waterman algorithm).

Mary highlighted this meeting on the blog here.

Among the distinguished list of speakers was George Church, a Harvard Medical School genetics professor, and a founder of PGP. After hearing him speak in detail about this project I thought how neat it would be to volunteer. They are aiming to enroll 100,000 volunteers now. The PGP website provides a nice outline of the volunteering process, and also presents the data for the 10 volunteers who have already gone through the entire process (including George Church and several other prominent local professors, i.e. the PGP-10). You can look through all of the information that the PGP-10 volunteers have provided by viewing their public profiles on the PGP website. So much detail is there – vital signs, medications, entire medical history, age, major traits, ancestry, and more. Upon viewing all of these details I decided I was not quite brave enough to volunteer yet (particularly after seeing the enlarged facial pictures of the volunteers from a variety of angles), yet my husband jumped at the prospect. I am altruistic, but it just seemed that this would be a good thing for him to try first.

So we began the PGP enrollment process several months ago. This is not an easy or quick process at all. There are a ton of consent/disclaimer-type forms, very involved medical and family history questions to answer, and general trait profiles. In addition, there are a series of tests that you must take (and pass) in order to prove that you are familiar with the process that is going to take place, as well as to demonstrate a basic knowledge of genetics. And let me just say that a Ph.D. in molecular biology didn’t seem to be enough to breeze through their “basic” tests. Eventually we did pass. And they do provide study guides so you really need to just swallow your ego – the phraseology and questioning is very unusual on their tests. They also have a neat testing method that certainly wasn’t around when I was in graduate school. You can keep resubmitting your answers until they are correct. They don’t tell you which answers are wrong, only that you didn’t get the entire test right, but with some patience anyone can pass all of the individual tests (there may have been about 10). We then continued on to another series of forms, tests and waiting periods. Currently, we are in one of the several 2-4 week waiting periods, and could still be rejected at any point. It would be quite frustrating to be rejected now because it really is a reasonable amount of work to enroll in this.

My main concern now is that the folks at PGP will reject my husband on the basis of him being a rather boring genetic specimen. They freely admit to giving preference to older individuals, people with an exome already, “under-represented categories”, and those with known common or rare genetic conditions. Check out the eligibility/selection criteria. :( The most exciting – and only – genetic issues we could come up with for him were allergies and eczema. And his demographic (early forties, white male) probably won’t help either. I imagine that to be one of the most highly populated groups of applicants. My only hope is that his 100% Italian heritage may add some genetic interest, but we shall see.

For any of you who would like to read more about this, George Church just published an article in Newsweek entitled The Genome Generation, the case for having your genes sequenced. In it he really makes a strong case for having your genome sequenced, as well as for being totally open with all of your medical and genetic background information. Probably volunteers are pouring into PGP now. My favorite part of this article is his quote that the message is not “Here’s your destiny. Get used to it! Instead it’s here’s your destiny and you can do something about it.”

What a Christmas present a genome sequence would be…maybe next year.

Merry Christmas and Happy New Year to all of you!

Happy Memorial Day (and gardening) to you this weekend!

Summer is rapidly approaching and I’m so looking forward to a nice long Memorial Day weekend with outdoor cookouts and plenty of time for gardening. Those of us New Englanders that have endured a long, hard winter really natural viagra alteratives appreciate ending our hibernation and spending time outside in the spring and summer. Gardening is one of my favorite activities, and in this region we are strongly advised to wait until Memorial Day to do the majority of our planting. But after hearing that one of my colleagues had just come down with poison ivy, I began to wonder why these plants so often get in the way of enjoying our short season of outdoor life.

Poison ivy, oak and sumac have always been a very annoying part of growing up in New England. They are plants that I never had too many fond thoughts of. Yet, I never really knew much at all about them – other than the itchy, irritating red rash they cause – that is. I decided to do a little digging, reasoning that they must have some redeeming, or at least interesting, biological qualities. After all, it seems that they are only protecting themselves against all of us herbivores. They can’t exactly run away from us, so they have to keep us at bay some how. Their defense mechanism seems quite clever actually.

A quick check in Wikipedia revealed that poison ivy is a member of the Anacardiaceae family of flowering plants. To my surprise cashew and pistachio plants are also members of this same family. Apparently not all members of this plant family are skin irritants at least! The reaction you get from poison ivy is due to contact with urushiol, a very potent oil found in the sap. In fact, only about 1 nanogram is needed to cause a rash (as little as ¼ of an ounce is said to be necessary to cause a rash on every person on earth). The rash, or Toxicodendron dermatitis, is a result of the immune system’s delayed hypersensitivity response – i.e., the reaction may take hours or days to develop. Interestingly, about 20% of the population is not allergic to urushiol. They can wander through poison ivy indefinitely and have no problems (the genetic variations responsible for this trait are certain to be an interesting topic for future work in the genomics and immunology fields). Another surprising fact was that many animals don’t have any type of allergic reaction to urushiol. Deer, goats, horses and cattle are fine with these poisonous plants. In fact, one of the suggested ways to get rid of poison ivy is to get a goat. This seems to be another very interesting genetics of immunity issue – how and why do some animals manage to not only evade these plants, but thrive on them. As more complete genomes are resolved the genes, SNPs, or genetic variations in general, will be uncovered and we should all be enlightened.

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Tugging at the public’s heart strings-and wallets!

kids runningAfter the mad rush of the holiday season, I found a little time to catch up on reading, and stumbled across an astounding article in the NYtimes: New Genetic Test Asks Which Sport a Child was Born to Play, by Juliet Macur.

A company called ATLAS (Athletic Talent Laboratory Analysis System) is offering a genetic test for kids which they claim will determine if your child is likely to be a super-athlete.  Furthermore, they say it can tell you what type of a super-athlete your child may become, i.e., a sprinter or a weightlifter, so that you can begin preparations and training sessions for your child as early as one year old.

This test is based on genotyping for an isoform of the muscle protein actinin, ACTN3.

Actinins are an important family of actin-binding proteins.

Well, since I am a mom of a seven year old and a scientist that has spent more than fifteen years doing basic muscle research, this really caught my attention. My first thoughts were that this was morally appalling and scientifically impossible. All that I had learned and studied about muscle had led me to believe that muscles just don’t work that way.

No doubt that the actinins are crucial to muscle function, but I thought that one muscle protein couldn’t do all of that. My off-the-cuff guess would be that at least 200 genes would contribute to such traits, and probably half would encode non-muscle proteins (genes related to drive, metabolism and many other factors would seem likely to be involved equally here). I wondered if I had missed some major development in the muscle field while enjoying motherhood, Continue reading

On lab techniques for studying genetic variation, a review


Our emphasis at OpenHelix is to provide training on how to use specific genomics online tools and databases that you need for your research. We are sometimes asked, though, generic cialis 10mg for some more theoretical aspects of the research such the understanding the methodologies of SNP analysis or sequence alignment. So to help answer these questions here on the OpenHelix blog, we will be offering occasional links and reviews of videos and other instructional material on the web for these more theoretical aspects of genomics research. The OpenHelix Blog is pleased to welcome Cyndy Perrealt-Micale as a regular contributor for this feature.

Karen Moleke Talk

For those of you interested in the latest developments in laboratory techniques available to study genetic variability, there is a great lecture available by Karen Mohlke of the University of North Carolina. No background knowledge is needed to understand the topics discussed here.

Dr. Mohlke effectively reviews and explains all the major types of genetic variations, and the theory behind the latest methods used to study them.

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Summary of webinar “CNVs vs. SNPs: Understanding Human Structural Variation in Disease”

NHGRI CNV image Do you still believe that monozygotic, or identical, twins online canadian pharmacy are really genetically identical?

Or that we are all 99.9% genetically similar to each other? Well I certainly did, and boy was I wrong!

It turns out that CNVs (Copy Number Variations) are causing the “facts” some of us learned in Molecular Biology 101 to be rewritten. If you, like me, thought that what you learned years ago was still true, then there is a great webinar you may want to watch. It is brought to you by Science/AAAS, and it features three prominent experts in genetic variability, Drs. Charles Lee, Lars Feuk and Alexandra Blakemore.

The moderator is Dr. Sean Sanders, who is the Commercial Editor of Science. Even those of you that are up to speed on the current research can find many interesting facts and learn about the new techniques used to study CNVs, or just genetic variability in general. It turns out that CNVs are much more prevalent than was previously thought. You hear so much about SNPs that it seems like they are the source of genetic variability that we should be most concerned about, but CNVs are catching up real fast. This new field is rapidly advancing because of major technology breakthroughs.

All of the panelists present a short talk highlighting the prevalence, importance and experimental limitations of studying CNVs and their role in normal human variability, as well as in disease. They present some of their own data and discuss the future direction of this young field. This is followed by a very interesting question and answer session where they allowed listeners to email their questions. It may even turn out that CNVs are the reason that your personality, IQ, height and weight differ from your colleagues, friends and family. So not only is this an exciting new field, but it is certainly one we can all relate to! Continue reading