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Short Reads: Oct 30, 2009


The US Department of Agriculture awarded $11 million to four research universities to study plant genomics and ways to improve the nutrition and health values of important crops. Grantees include North Dakota State University, the University of Minnesota, Michigan State University, and the University of California, Davis. The Coordinated Agricultural Project awards will fund applied plant genomics research and education on using genomics to inform breeding of crops such as tomato, potato, barley, soybean, and trees.

Samuel Levy joined Scripps Health's genomic medicine program as director of genomic sciences. Levy was previously director and professor in human genomics at the J. Craig Venter Institute and a senior scientist at Celera. At Scripps, he will direct the human genome sequencing research at the Scripps Translational Sciences Institute.

The Joint Genome Institute is in the process of hiring about 20 new staffers who will help analyze the growing amount of data it is generating through its sequencing activities. The institute, run by the Department of Energy, currently has a workforce that includes about 250 full-time equivalent employees.

The Sequenom board of directors terminated the employment of Harry Stylli, the company's president and CEO, as well as Elizabeth Dragon, who was senior vice president of R&D. The decision came on the heels of an investigation into the mishandling of R&D test data and results from the firm's Down syndrome test. Board Chairman Harry Hixson will serve as interim CEO while fellow board member Ronald Lindsay steps in temporarily to head up R&D.

Kaiser Permanente and the University of California, San Francisco, won a two-year, $24.8 million stimulus grant from NIH to use information and biospecimens from 100,000 of Kaiser Permanente's members in a large-scale study of how genetic and environmental interactions affect human health. UCSF's Institute for Human Genetics will perform the genotyping.

The Translational Genomics Research Institute plans to boost its workforce in the coming year by some 35 new workers directly related to its commercialization activities. The institute currently has a staff of about 300 people.

Xenomics, which announced that it will change its name to TrovaGene, chose Bruce Huebner as its CEO. Huebner was previously EVP and COO at Gen-Probe, and president and COO at Nanogen.

Biologists Lin He and Beth Shapiro were both awardees of the MacArthur Foundation's 2009 Fellows program, also known as "Genius Awards." He is a molecular biologist at the University of California, Berkeley, who has studied the role of microRNAs in cancer development. Shapiro is an evolutionary biologist at Pennsylvania State University who studies the genomes of extinct or threatened animals.

St. Louis-based Orion Genomics signed a multi-year collaboration and license agreement with Novartis Pharma's molecular diagnostics unit aimed at discovering epigenetic markers related to a range of diseases. The program will involve mapping DNA methylation across the genome using Orion's MethylScope Technology.

Kelly Frazer is the founding chief of the Division of Genome Information Sciences of the Department of Pediatrics at the University of California, San Diego, School of Medicine. Frazer was formerly at the Scripps Research Institute and before that at Perlegen Sciences.

David Haussler and James Kent won the 2009 Curt Stern Award from the American Society of Human Genetics in recognition of their development of the University of California Santa Cruz Genome Browser.

Nobel season was upon us this fall, and the systems biology community did well. The Nobel Prize for Medicine was awarded to Elizabeth Blackburn, Carol Greider, and Jack Szostack for their discovery of how chromosomes are protected by telomeres and the enzyme telomerase. Meantime, the chemistry award went to Venkatraman Ramakrishnan, Thomas Steitz, and Ada Yonath, who independently used X-ray crystallography to study the structure of the ribosome and how it translates nucleic acids into proteins.

Helicos BioSciences and Pacific Biosciences reported winning stimulus funding in the form of GO grants as part of NHGRI's $1,000 Genome program. Helicos won a two-year, $2.9 million grant, while PacBio received nearly $2 million in funding from NIH and NHGRI to further develop its real-time, single-molecule sequencing system.

Thermo Fisher Scientific announced plans to close two facilities and lay off about 480 people. The company will close a manufacturing plant in Dubuque, Iowa, by September 2010 and will cut the 350 jobs at the facility over coming year. It also will shutter a medical device production facility in Nashua, NH, by June 2010, resulting in around 130 layoffs.

The Scan

Lung Cancer Response to Checkpoint Inhibitors Reflected in Circulating Tumor DNA

In non-small cell lung cancer patients, researchers find in JCO Precision Oncology that survival benefits after immune checkpoint blockade coincide with a dip in ctDNA levels.

Study Reviews Family, Provider Responses to Rapid Whole-Genome Sequencing Follow-up

Investigators identified in the European Journal of Human Genetics variable follow-up practices after rapid whole-genome sequencing.

BMI-Related Variants Show Age-Related Stability in UK Biobank Participants

Researchers followed body mass index variant stability with genomic structural equation modeling and genome-wide association studies of 40- to 72-year olds in PLOS Genetics.

Genome Sequences Reveal Range Mutations in Induced Pluripotent Stem Cells

Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.