Q&A: Texas A&M's Raffaele Montuoro on Parallelizing Illumina's Genome Analysis Pipeline

June 04, 2010

Texas A&M's Raffaele Montuoro has developed a parallel version of Illumina's Genome Analysis Pipeline, called pGAP, which speeds up the analysis time by a factor of four.

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In this issue of BioInform

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Young Investigator Profile

Erin Carlson

Assistant Professor
Indiana University

Bacterial Pathogenesis

The Carlson lab researches the development and application of advanced chemical biology and systems biology technologies to both define the mechanisms of bacterial pathogenesis and identify potential therapeutic agents. They are pursuing the development of technologies for natural product discovery including innovative methods for compound isolation, screening, and diversification. In addition, they are also utilizing state of the art metabolomic and proteomic methods to map the biochemical pathways associated with bacterial pathogenesis and antibiotic resistance.
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New Program Powers Population Diversity Research

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This Week in the Journal of Clinical Pathology

In the Journal of Clinical Pathology this week: detecting hypermethylation in sputum samples, more.

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Papers of Note

Connection Between Epigenome, Selective Mutability, Evolution, and Human Disease
Li, Harris et al., PLoS Genetics
Researchers at the Baylor College of Medicine and elsewhere propose a "connection between the epigenome, selective mutability, evolution, and human disease" based on the findings of their study on associations of structural mutability with germline DNA methylation and with non-allelic homologous recombination mediated by low-copy repeats. "Combined evidence from four human sperm methylome maps, human genome evolution, structural polymorphisms in the human population, and previous genomic and disease studies consistently points to a strong association of germline hypomethylation and genomic instability," the Baylor-led team writes.

Genetic Data for Modern Genetic Breeds 'Have Yet to Shed Light on Dog Origins'
Larson, Karlsson et al., PNAS
A team led by researchers at the University of Durham investigate the value of modern genetic data to elucidate the origins of dog domestication by analyzing 49,024 autosomal SNPs in 19 wolves and 1,375 dogs, representing 35 breeds. The team reports having uncovered conflicting evidence when correlating the earliest archeological dogs with the geographic locations of 14 breeds thought to be ancient. "These genetically distinct ancient breeds only appear so because of their relative isolation, suggesting that studies of modern breeds have yet to shed light on dog origins," the authors write.
People on the Move

IntegenX has appointed David Smith to serve as its new COO. Smith most recently served as CFO of Thoratec, and previous to that was CFO at Chiron. He currently is chair of the audit committee and a director of OncoGenex Pharmaceuticals and previously was chair of the audit committee and a director of Perlegen Sciences.

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Genomic Health has appointed Richard Tompane as president of its new subsidiary InVitae, which will focus on developing next-generation-based sequencing diagnostics for genetic diseases. Tompane was previously president and CEO of Gemfire and has also served as an independent consultant.
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May 23-26 / Heidelberg, Germany
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Institute of Medicine

Abstract & Registration Deadlines

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Science
A study published in Science Translational Medicine suggests high-throughput sequencing is effective for finding post-treatment leukemia cells that can lead to patient relapse. Researchers used sequencing to test matched pre- and post-chemotherapy samples from 43 individuals with T-lineage acute lymphoblastic leukemia. They found that the sequencing method tracked down minimal residual disease in 25 of the cases tested, including several missed by flow cytometry.
Business
Agilent Technologies will spend $2.2 billion to acquire Danish diagnostics firm Dako. The deal marks a major push by Agilent into the diagnostics arena and provides the firm with Dako's portfolio of immunohistochemical cancer diagnostic tools and emerging companion diagnostics alliances as well as an entry into the $2.2 billion anatomic pathology market. Dako is expected to generate $373 million in revenues in fiscal 2013 with a $68 million operating profit.
Funding
The National Institute on Aging will provide up to $6 million in 2013 to support up to three projects undertaking whole exome and/or whole genome sequencing data analysis to identify genomic contributions to both the risk for and protection against Alzheimer's disease. The funding program is part of the Presidential Initiative on Alzheimer's Disease and is expected to fund between one and three awards with up to $2 million direct cost per award for fiscal year 2013.
Genome Technology Magazine
For this month's Q&A, Matthew Dublin speaks with McGill University's John Breitner about a European consortium that aims to develop molecular diagnostics for both Alzheimer's and Parkinson's disease. As part of the program, Breitner is developing standardized ways to describe patient samples as a first step in bringing innovations to the clinic. Breitner says that there are a number of biomarkers than can confirm or deny a presumptive diagnosis, but there is not yet a standard way to run tests based on such markers.

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Q&A: Texas A&M's Raffaele Montuoro on Parallelizing Illumina's Genome Analysis Pipeline

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