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This Week in Genome Research: Feb 3, 2012

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In Genome Research this week, a team of Japanese investigators report their whole-exome sequencing of human pancreatic cancers and characterization of their genomic instability. The team sequenced the exomes of 15 pancreatic tumor cell lines and matched normal samples and identified 1,517 somatic mutations, 934 of which were validated by transcriptome sequencing. Overall, the team detected recurrent mutations in 56 genes, 41 of which have never been described before. "The diversity of the mutation rates was significantly correlated with the distinct MLH1 copy-number status," the authors write. "Exome-seq revealed intensive genomic instability in a cell line with MLH1 homozygous deletion, indicated by a dramatically elevated rate of somatic substitutions, small insertions/deletions (indels), as well as indels in microsatellites. Notably, we found that MLH1 expression was decreased by nearly half in cell lines with an allelic loss of MLH1." This data suggests that hemizygous MLH1 deletion plays a role in the development and progression of sporadic cancers, they add.

A team of researchers from the Netherlands and the US report their genome-scale analysis of aberrant DNA methylation in colorectal cancer, in Genome Research this week. The team performed comprehensive genome-scale DNA methylation profiling of 125 colorectal tumor samples and 29 adjacent normal tissue samples, and identified four DNA methylation-based subgroups of the disease. "Each subtype shows characteristic genetic and clinical features, indicating that they represent biologically distinct subgroups," the authors write. The found a CIMP-high subgroup that is strongly associated with MLH1 DNA hypermethylation and BRAFV600E mutation, and a CIMP-low subgroup enriched for KRAS mutations. Of the two non-CIMP tumors subtypes, one has a significantly higher frequency of TP53 mutations and frequent occurrence in the distal colon, while the other subgroup has a low frequency of both cancer-specific DNA hypermethylation and gene mutations.

Researchers at Helicos Biosciences describe a single-step capture and sequencing method for the detection of BRCA1 mutations. The team extracts whole-genome DNA, which is "acoustically sheared and loaded in a flow cell channel for single-molecule sequencing." As no gene isolation or amplification is needed, the sample prep costs are low, the authors write. "Additionally, this approach has applications for sequencing integration sites for gene therapy vectors, transposons, retroviruses, and other mobile DNA elements in a more facile manner than possible with other methods," they add.

Finally in Genome Research this week, researchers in Canada report on the prevalence of Fusobacterium nucleatum infection in human colorectal carcinoma. The team screened colorectal cancer samples and compared them to matched normal samples, and found an over-representation of F. nucleatum in the cancer samples. "F. nucleatum is an invasive anaerobe that has been linked previously to periodontitis and appendicitis, but not to cancer," the authors write. "Fusobacteria are rare constituents of the fecal microbiota, but have been cultured previously from biopsies of inflamed gut mucosa." The team also observed a positive association between F. nucleatum infection and lymph node metastasis.

The Scan

Unique Germline Variants Found Among Black Prostate Cancer Patients

Through an exome sequencing study appearing in JCO Precision Oncology, researchers have found unique pathogenic or likely pathogenic variants within a cohort of Black prostate cancer patients.

Analysis of Endogenous Parvoviral Elements Found Within Animal Genomes

Researchers at PLOS Biology have examined the coevolution of endogenous parvoviral elements and animal genomes to gain insight into using the viruses as gene therapy vectors.

Saliva Testing Can Reveal Mosaic CNVs Important in Intellectual Disability

An Australian team has compared the yield of chromosomal microarray testing of both blood and saliva samples for syndromic intellectual disability in the European Journal of Human Genetics.

Octopus Brain Complexity Linked to MicroRNA Expansions

Investigators saw microRNA gene expansions coinciding with complex brains when they analyzed certain cephalopod transcriptomes, as they report in Science Advances.