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Short Reads: Mar 10, 2009


ABI, TGen Collaborate to Sequence Human Disease Samples Using SOLiD

Applied Biosystems, a business of Life Technologies, said this week that it has formed a strategic alliance with the Translational Genomics Research Institute to sequence human disease samples on SOLiD sequencers.

Under the agreement, a team of researchers from TGen and ABI will use the SOLiD 3 system to analyze thousands of patient samples. The goal is to increase researchers' understanding of the genetics behind various complex diseases and medical conditions and hasten the translation of such research into new diagnostic and other clinical tools.

The team plans to use five SOLiD 3 systems to create a pipeline for resequencing samples from individuals with diseases such as cancer, autoimmune disorders, and neurological conditions. The researchers also plan to co-develop a SOLiD bioinformatics analysis and visualization pipeline, including software tools for sequencing data analysis.

TGen President and Scientific Director Jeff Trent will be among the principal investigators partnering with ABI scientists. The effort will reportedly involve six projects aimed at comprehensively characterizing the genetic and molecular changes underlying disease in clinical cohorts of individuals with each condition.

NCGR Installs Kognitio's Database to Manage Sequencing Data

The National Center for Genome Resources said this week that it has deployed an analytical database made by UK bioinformatics firm Kognitio to handle its sequencing data.

Santa Fe, NM-based NCGR will use the company's WX2 system to support its genomic research data management capabilities.

"We realized that we needed a new database solution to increase the flexibility and the performance for our future plans," NCGR Program Leader Ernest Retzel said in a statement.

"The pace of data generation is exploding, and over the next twelve months we expect the amount of data that we need to analyze will expand at a rate of ten-fold or more," NCGR's database architect, Kathy Myers, added.

Type 1 Diabetes 454 Resequencing Study Finds Protective Variants

By resequencing a handful of candidate genes from genome-wide association studies, University of Cambridge and Roche 454 researchers have identified four rare variants and one common variant in an antiviral gene called IFIH1 that protect against type 1 diabetes, or T1D. Since the variants appear to curb the gene's activity, the team proposes that functional IFIH1 may contribute to T1D.

The team used 454 sequencing to re-sequence exons and splice sites of 10 GWAS candidate genes in nearly 500 individuals with T1D and as many control individuals. They identified four rare variants that lowered T1D risk, which they subsequently validated in more than 30,000 individuals, including more than 3,000 families. One common variant also showed independent association with T1D. The research appeared online in Science last week.

"Our goal was not only to discover new rare variants but also to test their association with T1D in the same experiment, comparing allele frequency in DNA pools of patients and controls," the authors explained.

The researchers first confirmed previous associations between common SNPs and T1D before focusing on the rare variants. Of these rare SNPs, the two that were most strongly associated with T1D fell in a gene called IFIH1.

IFIH1 codes for a cytoplasmic protein that recognizes RNA viruses called picornaviruses and participates in the production of interferons in response to these viruses. Intriguingly, prior studies have shown that individuals who are newly diagnosed with T1D are more likely to carry enteroviruses — a group of picornaviruses including coxsackie viruses, polioviruses, and echoviruses — than individuals in the general population.

Altogether, the researchers reported that four rare IFIH1 variants and one common variant were independently associated with T1D. The four rare protective variants all appear to inactivate or otherwise mute IFIH1 activity, either by truncating the gene, altering its splicing, or affecting a highly conserved amino acid. That, in turn, suggests that the common form of IFIH1 may contribute to T1D.

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Barcelona Genomics Center Buys Genomatix Analyzer

A Barcelona biomedical research center focused on genomic studies has bought a Genomatix Genome Analyzer for use in its disease and epigenetics studies, Genomatix said last week.

The GGA provides downstream tools and databases for deep biological analysis of mapped data that comes from next-generation sequencers, Genomatix said.

The Centre for Genomic Regulation in Barcelona will use the GGA to study the molecular mechanisms underlying breast cancer. It also will use the GGA for a second research program focused on identifying the mechanisms by which the genome is silenced through chromatin modification and small regulatory RNA, said Ramin Shiekhattar, group leader of the center's Gene Regulation Program, in a statement.

The CRG was created by the Catalan government's Department of Universities, Research and Information Society, the Catalan Department of Health, Pompeu Fabra University, and the Spanish Ministry of Education and Science.

LabCorp Collaborates with Duke in Operating Biorepository

LabCorp said last week that it has struck a collaborative agreement with Duke University covering operations at its biorepository in Kannapolis, NC.

The collaboration will focus on the operations of the facility and management of the samples deposited by Duke University, and by LabCorp's clients and its collaborators.

The company said that when the biorepository opens later this year it will hold up to 10 million samples and will offer a high-security storage environment and on-site nucleic acid and sample preparation capabilities. The facility will be closely linked to Duke University, the David H. Murdock Core Laboratory Building at the North Carolina Research Campus, and LabCorp's network of routine and esoteric laboratories for discovery and commercial testing.

DNAPrint Genomics Goes Bust

Genetic testing company DNAPrint Genomics has shut down its operations, according to a notice on its website.

The Sarasota, Fla.-based firm shut down operations sometime during the past month. Its most recent filing with the US Securities and Exchange Commission was on Feb. 9, in which it announced that its President and CEO Richard Gabriel had resigned from the firm, as well as its subsidiaries Ellipsis Biotherapeutics and Trace Genetics.

The cash-strapped firm, which had been trading on the Pink Sheets, had inked a deal a year ago to be acquired by Nanobac Pharmaceuticals. However, the deal fell apart after Nanobac was unable to raise additional funds before a deadline on March 31, 2008.

The Scan

Study Examines Insights Gained by Adjunct Trio RNA Sequencing in Complex Pediatric Disease Cases

Researchers in AJHG explore the diagnostic utility of adding parent-child RNA-seq to genome sequencing in dozens of families with complex, undiagnosed genetic disease.

Clinical Genomic Lab Survey Looks at Workforce Needs

Investigators use a survey approach in Genetics in Medicine Open to assess technologist applications, retention, and workforce gaps at molecular genetics and clinical cytogenetics labs in the US.

Study Considers Gene Regulatory Features Available by Sequence-Based Modeling

Investigators in Genome Biology set sequence-based models against observational and perturbation assay data, finding distal enhancer models lag behind promoter predictions.

Genetic Testing Approach Explores Origins of Blastocyst Aneuploidy

Investigators in AJHG distinguish between aneuploidy events related to meiotic missegregation in haploid cells and those involving post-zygotic mitotic errors and mosaicism.