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This Week in Nucleic Acids Research: Nov 26, 2014

A team from Japan characterized more than two dozen lung adenocarcinoma cell lines using a combination of whole-genome sequencing, RNA sequencing, bisulfite sequencing, and chromatin immunoprecipitation sequencing to look at everything from somatic mutation patterns and transcriptional profiles to methylation and histone marks. In the 26 lung adenocarcinoma cell lines, the researchers identified hundreds of coding and splice site mutations, along with thousands of methylation or histone mark changes and more than 13,500 alterations affecting apparent regulatory regions. "Unexpectedly, we found that the aberrant expression was associated with various causative events," they write, "which are characteristically gene-dependent."

For another Nucleic Acids Research study, investigators from the European Molecular Biology Laboratory and elsewhere explain how they used proteomic, transcriptomic, and experimental biochemical data to augment their annotation of the genome of Chaetomium thermophilum, a thermophilic, filamentous fungus that's sometimes used as a model in structural biology studies. By incorporating these additional sources of information, the team was able to tweak gene annotation, revising thousands of gene profiles, uncovering previously undetected genes, and predicting function for some genes that were poorly characterized in the past.

A China-led team introduces an online, open-access database called DoGSD that contains SNPs found in the canidae family. The site currently houses roughly 19 million SNPs identified in dozens of domesticated dog and grey wolf genomes through published and unpublished genotyping and whole-genome sequencing studies. The variant collection includes information found in 34 indigenous Chinese dog genomes, the study's authors note, "which represent a key phase in dog domestication" not found in prior dog SNP databases. "We will keep up with whole-genome SNP data releases and update DoGSD in a timely manner with new released data from population studies of dogs and wolves either by our own research groups or from publicly available resources," they write.

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.