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This Week in Genome Biology: Aug 29, 2012

Researchers led by Uppsala University's Matthew Webster present their study of copy-number variation in dogs in Genome Biology this week. Using high-density array CGH, they assayed CNVs in 50 purebred dogs from 17 breeds as well as three wolves and found 430 CNVs near 413 annotated genes. The researchers further write that the CNVs have a strong phylogenetic signal, though most are found in multiple breeds, and elevated GC content. "Our results suggest that many CNVs are generated by [non-allelic homologous recombination events] directed towards peaks of GC content, which is consistent with observations that these sequence features are also enriched in dog, but not human, recombination hotspots," they write. "Hence GC peaks may represent novel sites of elevated recombination and genome instability in dogs."

Also in Genome Biology, a Stanford University team reports on its screen of long, non-coding RNAs in a diverse set of cancer samples. Using a 3' End Sequencing for Expression Quantification, or 3SEQ, approach, the team examined known lncRNAs and other intergenic regions in 64 archival samples, which included adenocarcinomas, squamous cell carcinomas, and sarcomas from a variety of tissues. The team notes that a number of transcripts are differentially expressed in different tumor types, and one such transcript expressed in breast tissue was found to be correlated with low tumor grade and estrogen receptor expression and thus is a possible biomarker. "This study represents the first large survey of lncRNA expression across a diverse panel of primary human cancer samples and provides the research community with a valuable resource for cancer-expressed lncRNAs as well as a collection of novel transcripts expressed within cancers," it says.

Finally, the mouse ENCODE team writes in Genome Biology that it will be using the same experimental pipelines to annotate the mouse genome as the human ENCODE team used for its human genome work. "The laboratory mouse is a powerful tool for the investigation of human gene function and for dissecting the genetic and transcriptional regulatory circuits controlling development and homeostasis of mammals," the team adds. "The Mouse ENCODE Project aims to potentiate both the utility of the mouse as a model for regulatory genomics and the human ENCODE project effort to advance annotation of the human genome."

The Scan

UK Pilot Study Suggests Digital Pathway May Expand BRCA Testing in Breast Cancer

A randomized pilot study in the Journal of Medical Genetics points to similar outcomes for breast cancer patients receiving germline BRCA testing through fully digital or partially digital testing pathways.

Survey Sees Genetic Literacy on the Rise, Though Further Education Needed

Survey participants appear to have higher genetic familiarity, knowledge, and skills compared to 2013, though 'room for improvement' remains, an AJHG paper finds.

Study Reveals Molecular, Clinical Features in Colorectal Cancer Cases Involving Multiple Primary Tumors

Researchers compare mismatch repair, microsatellite instability, and tumor mutation burden patterns in synchronous multiple- or single primary colorectal cancers.

FarGen Phase One Sequences Exomes of Nearly 500 From Faroe Islands

The analysis in the European Journal of Human Genetics finds few rare variants and limited geographic structure among Faroese individuals.