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Microfluidic Advancements
White AK, VanInsberghe M, Petriv OI, et al. (2011). High-throughput microfluidic single-cell RT-qPCR. PNAS. Epub: doi 10.1073/pnas.1019446108.

Adam White and his colleagues present a fully integrated microfluidic platform capable of high-precision RT-qPCR. The platform can measure gene expression from hundred of single cells per run by executing all the steps of single-cell processing, including cell capture, cell lysis, reverse transcription, and quantitative PCR. The authors apply this platform to 3,300 single-cell measurements of miRNA expression in K562 cells, co-regulation of an miRNA, and SNV detection in breast cancer cells. They write that "the core functionality established here provides the foundation from which a variety of on-chip single-cell transcription analyses will be developed."

Sequencing Carcinomas
Stransky N, Egloff AM, Tward AD, et al. (2011). The mutational landscape of head and neck squamous cell carcinoma. Science. Epub: doi 10.1126/science.1208130.

Nicolas Stransky et al. present their analysis of whole-exome sequencing data for 74 tumor-normal head and neck squamous cell carcinoma sample pairs. The researchers say that most tumor samples "exhibited a mutational profile consistent with tobacco exposure," and report their detection of human papillomavirus by sequencing DNA from infected tumors. The team uncovered several known HNSCC-associated genes in addition to others not previously implicated in the disease. Stransky et al. say their "results indicate the ability of large-scale sequencing to reveal fundamental tumorigenic mechanisms."

Cucumber Resource
Wóycicki R, Witkowicz J, Gawronski P, et al. (2011). The genome sequence of the north European cucumber (Cucumis sativus L.) unravels evolutionary adaptation mechanisms in plants. PLoS One. Epub: doi 10.1371/journal.pone.0022728.

Here the authors present a draft genome sequence for Cucumis sativus, or cucumber, of the north-European Borszczagowski cultivar along with their comparative genomics study involving a previously reported C. sativus genome, Arabidopsis thaliana, Populus trichocarpa, and Oryza sativa. The researchers say that the "cucumber genomes show extensive chromosomal rearrangements, distinct differences in quantity of the particular genes ... as well as in distributions of abscisic acid-, dehydration-, and ethylene-responsive cis-regulatory elements in promoters of orthologous group of genes, which lead to the specific adaptation features."

Lymphoma Mutations
Morin RD, Mendez-Lago M, Mungall AJ, et al. (2011). Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma. Nature. Epub: doi 10.1038/nature10351.

To identify genes with mutations in non-Hodgkin lymphomas, Morin and his collaborators sequenced tumor and matched normal DNA from 13 diffuse large B-cell lymphoma cases and one follicular lymphoma case. The team "analyzed RNA-seq data from these and another 113 NHLs to identify genes with candidate mutations, and then resequenced tumor and matched normal DNA from these cases to confirm 109 genes with multiple somatic mutations." Morin et al. report that genes with roles in histone modification were frequent targets of somatic mutation and their analysis could point to a previously unrecognized disruption of chromatin biology in lymphomagenesis.

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.