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NIEHS, Perlegen, Children's Hospital of Philadelphia, Affymetrix, Gene Logic

NIEHS, Perlegen Publish SNP Database, Haplotype Map for 15 Mouse Strains
The National Institute of Environmental Health Sciences and Perlegen Sciences have published results from mouse genome-resequencing and genomic-analysis studies that can be used to link genes to environmental diseases, the National Institutes of Health said this week.
In the study, scientists at Perlegen used Affymetrix oligonucleotide arrays to resequence four wild-type and eleven “classical” mouse strains and identify 8.27 million SNPs across the 15 strains.
The NIH said the arrays queried around 1.49 billion of the 2.57 billion base pairs of the C57BL/6J mouse reference strain, and the resulting data was used to create the 41,000-segment haplotype map.
“These data allow researchers to compare the genetic makeup of one mouse strain to another, and perform the necessary genetic analyses to determine why some individuals might be more susceptible to disease than another,” David Schwartz, director of the NIEHS, said in a statement.
The results of the Mouse Genome Resequencing and SNP Discovery Project appear in the July 29 issue of Nature, while haplotype maps providing data from these studies are available on the NationalCenter for Biotechnology Information’s website and a site hosted by Perlegen.
Schwartz said the information will be “a valuable resource” for the National Toxicology Program, an interagency program based out of the NIEHS.
“We also hope that pharmaceutical companies developing new treatments for environmental diseases will find these data and this paper as a valuable resource,” Schwartz added.

CHOP to Use Affy's Human SNP Array 6.0 in Whole-Genome Studies
The Children's Hospital of Philadelphia will use Affymetrix’s newly released Genome-Wide Human SNP Array 6.0 in whole-genome studies aiming to identify genes responsible for cardiovascular, metabolic, and central nervous system disorders, Affy said last week.
CHOP researchers will initially run studies on DNA taken from 7,000 individuals and plan to increase the genome-wide studies with outside collaborators. Affy’s 6.0 SNP array, launched in May, measures 1.8 million markers for genetic variations.
Hakon Hakonarson, director of CHOP’s Center for Applied Genomics, said the Affy array allows researchers to genotype “more markers at a lower cost per sample,” and it increases the chance of finding genes that are linked to diseases or to adverse drug responses.
“The results from these projects will open the door to new genetic studies and help us extend current collaborations with other investigators around the world," Hakonarson said.
Financial terms of the agreement were not released.

Gene Logic Now 'Investigating Possibility' of Selling Genomics Arm; Q2 Revenue Rises and LossNarrows
Gene Logic is “investigating the possibility” of selling “all or parts” of its Genomics business, a slight change in tactics from “considering strategic alternatives” for the unit, which is the language it used as recently as April.
Two months before that, the firm said it may create “a spin-off entity with a retained equity position or other alternative structures to capture value for Gene Logic.”
Selling all or part of the Genomics business will "likely require” shareholder approval, Gene Logic said. The company has hired investment bank Aquilo Partners to consider its options.
Gene Logic made the disclosure in a statement reporting that second-quarter revenues rose 15 percent as R&D spending rose 8 percent and net losses narrowed 30 percent.
Total receipts for the three months ended June 30, which came almost entirely from its genomics services business, rose to $5.4 million from $4.7 million year over year.
R&D increased to $2.7 million from $2.5 million.
The company said net loss decreased to $7.9 million from $11.3 million in the year-ago period.
As of June 30, Gene Logic had $20.8 million in combined cash and equivalents and $15.8 million in marketable securities.

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Single-Cell Sequencing Points to Embryo Mosaicism

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