Up at 5AM: The 5AM Solutions Blog

Genomic Research: Whose Data Is It? What's Important?

Posted on Thu, Dec 15, 2011 @ 06:00 AM

Admittedly, I am a bit behind in my journals, so I only recently read articles in Nature entitled Secrets of the Human Genome Disclosed and Genomes on Prescription. The first article was about geneticist Ghoulson Lyon, who presented a research study at a conference on a family suffering from an unknown, apparently genetic, disease. He was trying to find genetic variants associated with the disease, which caused some male children in the family to die before they reached their first birthday.

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Tags: genomics tools, genomic data, genetic testing, human genome, genetic mutation

Designing Assays: The Oligo Craftsman vs. The Primer Jockey

Posted on Thu, Dec 08, 2011 @ 06:00 AM

I have been designing assays for some time now. Starting with a few oligos in graduate school, I kicked up my PCR primer design experience out of school when I went to work for a genome center. Then there was my first blunder--ordering a few hundred dollars worth of primers with the reverse primers in the wrong orientation. I broke the news to my boss, resignation letter in hand (it hadn’t occurred to me that we probably spent more than that in one week just on pizza). Later in my career, the stress level went up a few orders of magnitude when I had to design tens of thousands of probes for SNP genotyping panels. That’s when I developed my addiction to TUMS® and came to the realization that my reward for a job well done was invisibility. With assay design, people only look for you when something’s wrong.

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Tags: genomics tools, bioinformatics, assay design, assay design tools, oligo design, assay design methodologies, bioinformatic resources, probe database, nucleic assay data

Three Neat Things About Family Health

Posted on Thu, Nov 17, 2011 @ 06:00 AM

Next week is Thanksgiving (already?). My family is descending on my house to enjoy time together, veggies, pie, and Tofurky (that’s how we roll). The country’s Surgeon General, Regina Benjamin, will mark the day as the seventh annual “National Family Health History Day,” to encourage all American families to learn more about their family health history.

Here are three reasons why it’s useful to know your family health history:

1. Because we all know that diseases can “run in the family”

Most of us are marginally aware that family history can play a role in many common diseases, such as heart disease, diabetes, and some cancers. Some of us think about our grandfather's heart attack before we eat that cheesesteak. And we've all completed the form at doctor’s offices - the chart where you put check marks to link diseases with your family members. The reason doctors collect this information is because it gives them a quick glimpse into the disease history within our families, which they then use to consider our risk of developing certain diseases. 

Every day, the family history is used by physicians to assess disease risk, determine whether screening is required, and help us understand our risks of passing diseases to our own children. It’s valuable information, worth collecting.

And knowing our history can help us change our habits. In my case, my grandfather’s early death from heart disease and my mother’s high cholesterol were factors in my decision to become a vegetarian. Knowing the truth about the family’s health is often enough to compel many people to change smoking, drinking, diet, and exercise habits.

2. Because it’s proven that family history is the best predictor of disease risk

The concept of a disease “running in the family” is real. A study last year found that a family health history is better at predicting disease risk than genomic screening: http://abcnews.go.com/Health/Wellness/family-history-predictor-disease-risk-genomic-screening/story?id=12055615

In his book The Language of Life, geneticist (and HHS head) Francis Collins writes that “family health history turns out to be the strongest of all currently measurable risk factors for many common conditions, incorporating as it does information about both hereditary and shared environment…Surely the kind of information you and your doctor should know and incorporate into your own health care.”

The bit about “shared environment” is especially key – not only do we share genes with our family, but we tend to live with or near our families (at least some of them). So regardless of whether a disease’s cause is hereditary or environmental, the history can tell us a lot.

3. Because it’s easy

Whether by jotting down a note that Aunt Edna died of breast cancer, or using more sophisticated paper or web-based tools to collect your family health history, or going all the way with personal genetic services like 23andMe, many people now are taking their health information into their own hands, assembling, recording, and saving their family health history for the benefit of their own health and that of their family members. Because it’s easy, and because it makes sense.

While you’re chowing down next Thursday, expressing thanks for all you have and are, take a couple of minutes to gather your family’s health history. It’s a simple way to understand the story of your own health.

Here are some ways and means to do so:

Happy Thanksgiving from 5AM--Share stories, thoughts and comments, on family history or Tofurkey, by commenting below.

-Leslie Power, 5AM Solutions

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Tags: electronic health records, genomics tools, health IT, family health history

Python, R, and Other Open Source Goodies for Science

Posted on Thu, Aug 25, 2011 @ 06:00 AM

Earlier this summer, I drove down to the Southeast Linux Fest in Spartanburg, South Carolina. One of the talks that stood out to me was given by Heather Holl, bioinformaticist and Slackware Linux team member. She talked about the open source tools she uses most in her work in equine genomics. I was especially impressed at how she used standard, open source Linux command-line tools to get her job done.

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Tags: Python, R, open source, genomics tools

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