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Video Game Provides Framework For Solving Genomic Sequence Alignment Problems

gene-puzzle-game

Over the past year our genetic understanding of diseases such as Alzheimer’s, diabetes and cancer has been accelerated by thousands of video gamers thanks to an online flash game called Phylo. Phylo is a video game created by Dr. Jérôme Waldispuhl of the McGill Centre for BioInformatics and collaborator Mathieu Blanchette. The game itself is a framework for solving the common problem of multiple sequence alignments in comparative genomics and leverages the visual problem solving skills of online gamers.

The Phylo website explains the background to game: Read more »

*This blog post was originally published at Medgadget*

Developing Priorities In The Field Of Genomics And Public Health

Text: 2012-2017 Priorities for Public Health Genomics Stakeholder Consultation|Priorities Conference Report|September 2011  In June 2011, the CDC Office of Public Health Genomics launched a community wide consultation process to develop priorities for the field of public health genomics in the next 5 years. This process was initiated as part of strategic visioning for integrating the emerging tools of genomics into practice and assuring the success of these new tools in improving population health. The process was conducted at a time of a widening gap between the rapid scientific advances in genomics and their impact on improving population health.   The University of Michigan Center for Public Health and Community Genomics and Genetic Alliance spearheaded an effort to seek, collate and synthesize advice and recommendations from numerous stakeholders and constituents. The effort culminated in a workshop conducted on September 14, 2011 in Bethesda, Maryland. The results of the consultation, discussions and deliberations are summarized in a report published by the University of Michigan. Highlights of the recommendations are summarized here but readers should consult the full report.  Some of the recommendations include:

To improve public health genomics education: Read more »

*This blog post was originally published at Genomics and Health Impact Blog*

Studies Find Consistent Molecular Architecture Of The Human Brain Across Individuals

Source: JNenad Sestan, MD, PhD, Yale University Department of Neurobiology and Kavli Institute for Neuroscience, via NIH

Human brains have a consistent molecular architecture despite all the other genetic differences across individuals and ethnicities, according to two studies that recorded when and where genes turn on and off in multiple brain regions throughout life.

Despite individual and ethnic genetic diversity, the human prefrontal cortex shows a consistent molecular architecture, as shown in this picture. The vertical span of color-coded areas is about the same, indicating that our brains all share the same tissue at a molecular level, despite distinct DNA differences on the horizontal axis. Each dot represents a comparison between two individuals.

The research appeared in the Journal Nature and was described by the National Institutes of Health in a press release.

The first study focused on Read more »

*This blog post was originally published at ACP Internist*

Do We Have Enough Information About The Whole Genome Sequence To Improve Medical Care?

cake with double helix decoration - text: One base pair at a time

The popular proverbial saying “you cannot have your cake and eat it too” implies that one cannot consume something and preserve it at the same time–in other words, we cannot have it both ways.  Well, for once, maybe we can have our cake–our whole genome sequence (WGS)–and eat it too. I believe having our WGS and consuming it in small bite sizes over a lifetime may be the only way to integrate it into medicine and public health.

Rapid advances in genomic sequencing technologies are making the possibility of reliable and affordable whole genome sequencing (WGS) a reality in the next few years. We all carry about 6 billion base pairs of DNA in each of our cells, with 5-10 million inherited variants that are different among us. This genetic variation along with environmental influences provides a blueprint for health throughout the life span, and is related to virtually every disease of public health significance. There is definite interest among the public and scientists about the personal utility of this information.  In a recent survey by Nature, attitudes towards genome sequencing were explored among a sample dominated by scientists and professionals from medicine and public health. Although only 18.2% of respondents had had their genome sequenced or analyzed, 2/3 of those who had not reported they would take the opportunity should it arise. Curiosity was reported as the main single factor influencing respondents.

Can this information be useful today in improving medical care and preventing disease?   Read more »

*This blog post was originally published at Genomics and Health Impact Blog*

Researchers Identify Gene Associated With Cold Sore Outbreaks

Image from Centers for Disease Control and Prevention/Dr. Hermann

Investigators identified a specific, previously obscure human gene associated with susceptibility to herpes simplex labialis (HSL), the common cold sore.

Cold sores affect 70% of the U.S. population. This study follows previous ones identifying a region of chromosome 21 as a base for genes possibly linked to cold sore outbreaks.

To narrow in further on the chromosome, this study used Read more »

*This blog post was originally published at ACP Internist*

Latest Interviews

IDEA Labs: Medical Students Take The Lead In Healthcare Innovation

It’s no secret that doctors are disappointed with the way that the U.S. healthcare system is evolving. Most feel helpless about improving their work conditions or solving technical problems in patient care. Fortunately one young medical student was undeterred by the mountain of disappointment carried by his senior clinician mentors…

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How To Be A Successful Patient: Young Doctors Offer Some Advice

I am proud to be a part of the American Resident Project an initiative that promotes the writing of medical students residents and new physicians as they explore ideas for transforming American health care delivery. I recently had the opportunity to interview three of the writing fellows about how to…

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Latest Book Reviews

Book Review: Is Empathy Learned By Faking It Till It’s Real?

I m often asked to do book reviews on my blog and I rarely agree to them. This is because it takes me a long time to read a book and then if I don t enjoy it I figure the author would rather me remain silent than publish my…

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The Spirit Of The Place: Samuel Shem’s New Book May Depress You

When I was in medical school I read Samuel Shem s House Of God as a right of passage. At the time I found it to be a cynical yet eerily accurate portrayal of the underbelly of academic medicine. I gained comfort from its gallows humor and it made me…

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Eat To Save Your Life: Another Half-True Diet Book

I am hesitant to review diet books because they are so often a tangled mess of fact and fiction. Teasing out their truth from falsehood is about as exhausting as delousing a long-haired elementary school student. However after being approached by the authors’ PR agency with the promise of a…

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