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In Brief This Week: Synthetic Genomics; BioTrove, GlaxoSmithKline; Caliper Life Sciences; Life Technologies; Decode Genetics; Genedata

NEW YORK (GenomeWeb News) – Synthetic Genomics and the Asiatic Centre for Genome Technology said this week that they had completed the first draft with 10X assembly of the jatropha genome. The partners used a combination of Sanger sequencing and next-generation sequencing to map the jatropha genome, which they said is around 400 million base pairs in size — similar to the size of the rice genome.

"Having the sequenced genome of jatropha will enable us to develop new, sustainable energy feedstocks that grow on marginal land or in more arid climates and that do not compete with agriculture for food production," Craig Venter, founder and CEO of SGI, said in a statement.

The partners had previously completed a draft of the oil palm genome.

BioTrove said this week that GlaxoSmithKline purchased two of the firm's RapidFire Mass Spectrometry systems for use in their R&D facilities in Pennsylvania and North Carolina. BioTrove said that GSK would use the system for "hit identification, compound profiling, and compound mechanism of action studies" in several therapeutic areas.

Caliper Life Sciences said that the Peter MacCallum Cancer Centre in Melbourne, Australia, is using the firm's Staccato automation system in its gene knockdown experiments.

Life Technologies this week announced the launch of the Applied Biosystems Genetic Conservation Laboratory, which is located at the headquarters of the Cheetah Conservation Fund in Otjiwarongo, Namibia. The lab is the result of a collaboration between the firm and the CCF. AB is providing genetic analysis systems and reagents for the genetic conservation program, which aims to ensure the long-term survival of the cheetah.

In a paper appearing in the online edition of Nature Genetics this week, researchers from Decode Genetics and its collaborators presented the discovery of SNP variations that influence the age of girls at menarche. The analysis included more than 300,000 SNPs across the genomes of more than 15,000 Icelandic women, and confirmed through genotypic analysis of some 10,000 Danish and Dutch women.

"[W]e have also been able to use them to confirm that overweight and obesity is linked to earlier AAM, and to suggest that later AAM contributes to greater height," Kari Stefansson, CEO of Decode and senior author on the paper, said in a statement. "The next step in this work is to look at how these and other new genetic factors linked to the timing of the reproductive cycle may be used to predict and prevent disease."

Genedata said that Asubio Pharma, a wholly owned subsidiary of Daiichi Sankyo, is using the Genedata Expressionist system to support compound profiling and biomarker discovery.

The Scan

Myotonic Dystrophy Repeat Detected in Family Genome Sequencing Analysis

While sequencing individuals from a multi-generation family, researchers identified a myotonic dystrophy type 2-related short tandem repeat in the European Journal of Human Genetics.

TB Resistance Insights Gleaned From Genome Sequence, Antimicrobial Response Assays

Researchers in PLOS Biology explore M. tuberculosis resistance with a combination of sequencing and assays looking at the minimum inhibitory concentrations of 13 drugs.

Mendelian Disease Genes Prioritized Using Tissue-Specific Expression Clues

Mendelian gene candidates could be flagged for further functional analyses based on tissue-specific transcriptome and proteome profiles, a new Journal of Human Genetics paper says.

Single-Cell Sequencing Points to Embryo Mosaicism

Mosaicism may affect preimplantation genetic tests for aneuploidy, a single-cell sequencing-based analysis of almost three dozen embryos in PLOS Genetics finds.