Software Surfeit

October 2011

By Matthew Dublin

It's no easy task to sort through all of the currently available comparative genome analysis software tools, and to find the perfect one for the job.

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Video Spotlight

A Conversation with the American Museum of Natural History's George Amato

The American Museum of Natural History's George Amato, director of the museum's Sackler Institute for Comparative Genomics, discusses conservation and "landscape" genetics, his PLoS One paper on the use of DNA barcoding to detect illegal bushmeat in New York-area airports, and more.

May 22, 2012

Shashikant Kulkarni at ACMG

BioArray News editor Justin Petrone sat down with Shashikant Kulkarni, an associate professor at Washington University School of Medicine at St. Louis, to discuss chromosomal microarrary analysis in the clinic, SNP arrays versus CGH platforms for post-natal testing, and more.

May 16, 2012

Miragen Therapeutics' Eva van Rooij

Miragen Therapeutics' Eva van Rooij discusses microRNA-based therapeutics, the challenges associated with chronic microRNA knockdown, therapeutic microRNA antagonists, and more.

May 08, 2012

A Conversation with CeGaT's Saskia Biskup

In this video, Julia Karow, Editor of Clinical Sequencing News, interviews Saskia Biskup, CEO of the Center for Genomics and Transcriptomics, or CeGaT, at the company's headquarters in Tübingen, Germany.

May 02, 2012
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.
Blog

New Program Powers Population Diversity Research

Cornell University researchers have released an easy-to-use, platform-independent program for analyzing microbial datasets.

May 23, 2012

This Week in the Journal of Clinical Pathology

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

May 23, 2012

NCATS Skeptics

NIH should leave drug discovery to the professionals, says one former Pfizer exec.

May 23, 2012

This Week in Genome Biology

In Genome Biology this week: role of distal gene regulatory DNA sequences in an oncogenic transcriptional program, and more.

May 23, 2012
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.

Vermillion said this week that President and CEO Gail Page will be leaving the company by September and the firm has begun the process to find her successor. Page also has resigned her seat on the board of directors, and effective immediately Vermillion amended its bylaws to eliminate the vacant seat, reducing its board from seven to six members.

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.
Upcoming Events

Conferences, Meetings & Deadlines

The iMedicine & Mobile Life Sciences World Summit
May 16-17 / Boston
Arrowhead Publishers

New Perspectives on Immunity to Infection
May 19-22 / Heidelberg, Germany
EMBL

TIDES: Oligonucleotides and Peptide Technology & Product Development
Applications of Nucleic Acids Technologies in Molecular Diagnostics, Oligonucleotide Therapeutics Discovery, and Peptide Discovery and Development
May 20-23 / Las Vegas
IBC Life Sciences

Microtubules: Structure, Regulation and Functions
May 23-26 / Heidelberg, Germany
EMBL

Evidence for Clinical Utility of Molecular Diagnostics in Oncology: A Workshop
May 24 / Washington, DC
Institute of Medicine

Abstract & Registration Deadlines

more

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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