Development of Ethnicity-Specific Reference for Interpreting Genome Data

In a study appearing in PLoS Genetics, a Stanford University-led team described the “ethnicity-specific” reference genome approach it used to analyze whole genome sequences from four members of a single family.

By incorporating estimated allele frequency data from the 1000 Genomes Project into the existing human reference genome, the researchers came up with three synthetic human genome references containing the major alleles identified in European, African, or East Asian populations — a strategy that’s intended to more accurately represent the genetic variation present in each of the major HapMap populations.

“There has been a large focus, at least in the genome-wide association study space, on Caucasian populations,” first author Frederick Dewey, a researcher at Stanford University’s Center for Inherited Cardiovascular Disease, told GenomeWeb Daily News. “What we hope to show is that ethnicity certainly matters — it begins at the point of genome assembly and carries all the way through variant interpretation and annotation.”

2011 Lasker Awards Announced

Nature Medicine: The 2011 Lasker Medical Research Awards
The Lasker Awards recognize science that profoundly transforms our thinking about key problems in biology and medicine. Every year, Nature Medicine has the privilege to publish commentaries written by the winners in celebration of the Award.    Read about the awards and the comments of the winners. 

Looking into the Future: The Dawn of Regenerative Medicine

George Church is thinking a lot about using regeneration as the key to treatments and keeping people healthy.  Induced pluripotent stem cells “is where I’m putting almost all of my chips these days, because it combines many of my interests — genomics, sequencing, epigenetics, synthetic biology, stem cells,” Church adds. While much of the work so far has been done in rodents, he says that it’ll be years, not decades, until it is tested in people. “The only way people are going to get this is through some brave soul,” Church says. “It will start with a sick person, and they will end up getting well, possibly more well than before they got sick.”   Read more in MIT’S Technology Review‘s Experimental Man.

Researchers Report on Sequencing, Analysis of 17 Mouse Genomes

 Researchers from the UK, US, and Germany reported in Nature that they have sequenced and compared the genomes of mice from 17 strains.

In the process, the researchers found some 56.7 million SNPs, nearly nine million small insertions and deletions, and hundreds of thousands of structural variants in mice. By bringing this information together with gene expression and other data, they were also able to track down hundreds of quantitative trait loci and variants contributing to tissue-specific gene expression.

Insulin Nasal Spray May Slow Alzheimer’s Disease

Intranasal insulin therapy may have beneficial effects on cognition and function among patients with Alzheimer’s disease, a pilot study suggested.

Patients who received 20 IU of intranasal insulin daily for four months had improvements on delayed story recall tests (P=0.02, Cohen f effect size=0.36), according to Suzanne Craft, PhD, of the Veterans Affairs Puget Sound Health Care System in Seattle, and colleagues.

And compared with placebo, baseline scores on the Dementia Severity Rating Scale were maintained over the study period in patients receiving either 20 IU or 40 IU of the insulin (P=0.01 for both, Cohen f = 0.38 for 20 IU and 0.41 for 40 IU), the researchers reported online in the Archives of Neurology.

Deep Comparison Reveals Similarities Between Pluripotent and Embryonic Stem Cells

Researchers at the University of Wisconsin, using a combination of techiques, conducted a rigorous analysis of  ESC’s and iPSC’s revealing significant and functionally related differences.   Their research also resulted in the establishment of a new online resource named SCOR for storing and searching data on pluripotency.   Read more in NATURE METHODS. 

Scripps’ Scientists Re-Engineer Antibiotic To Combat Vancomycin resistant SA

A team of scientists from The Scripps Research Institute has successfully reengineered an important antibiotic to kill the deadliest antibiotic-resistant bacteria. The compound could one day be used clinically to treat patients with life-threatening and highly resistant bacterial infections.

The synthesized compound, which was described in the Journal of the American Chemical Society, is an analogue of the well-known commercial antibiotic vancomycin.  The new analogue was prepared in an elegant total synthesis, a momentous achievement from a synthetic chemistry point of view.