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Genomics in the Journals Jul 10, 2014

NEW YORK (GenomeWeb) – Researchers from China and the US used a combination of whole-exome sequencing and targeted gene sequencing to track down frequent mutations to the ErbB signaling pathway in gallbladder carcinoma tumors — work they highlighted in Nature Genetics.

The team started by doing exome sequencing on matched tumor and normal samples from 32 individuals with gallbladder carcinoma. From the nearly 1,500 somatic single nucleotide changes or small somatic insertions and deletions detected in the samples, the group narrowed in on a panel of genes for subsequent targeted sequencing in tumor samples from 51 more individuals with gallbladder carcinoma.

In nearly half of the tumors tested, the investigators identified mutations in the TP53 gene. Meanwhile, their pathway-focused analysis uncovered mutations to the ErbB signaling pathway in just over one-third of the gallbladder carcinoma cases. The ErbB signaling alterations were particularly common in individuals with poor outcomes, suggesting they may have prognostic potential.

As such, the study's authors argued that "patients harboring mutations in the ErbB pathway might benefit from targeted therapies presently available or in development."

A team from the Cincinnati Children's Hospital Medical Center, the Broad Institute, and elsewhere outlined intestinal gene expression and gut microbiome signatures that seem to coincide with the presence of Crohn's disease in children affected by the condition.

As they reported in the Journal of Clinical Investigation, the researchers did 16S ribosomal RNA gene sequencing and messenger RNA sequencing on ileal biopsy samples from 243 children who had Crohn's disease (with or without inflammation affecting the ileal portion of the small intestine), but who had not received treatment for their condition.

Similar methods were used to look at gut microbial community members and gene expression patterns in the ileum of 73 children with ulcerative colitis and in 43 controls not diagnosed with either form of inflammatory bowel disease.

From the RNA sequence data, investigators identified a set of differentially expressed genes characterizing pediatric Crohn's disease cases with ileal involvement. That signature — which included enhanced expression of proinflammatory cytokine and antimicrobial genes and a decline in levels of some nuclear receptor genes — was not present in controls or in individuals with ulcerative colitis.

Folding in the individual's gut microbiome information indicated that the children with Crohn's disease or ulcerative colitis typically have higher-than-usual Proteobacteria levels and an associated rise in ileal expression, while the Crohn's patients alone showed a decline in expression by a lipoprotein gene APOA1 and reduced Firmicutes bacteria levels.

In GigaScience, researchers from the US and China presented findings from a genome sequencing and analysis study of the Australian Parakeet, Melopsittacus undulatus, commonly known as the budgerigar, or "budgie."

Using genomic DNA from a male budgie named Mr. B, the group generated reads on Illumina, Pacific Biosciences, and Roche 454 sequence instruments that together covered the budgie's 1.2 billion base genome at an average depth of 300-fold.

Those sequence reads were combined into three different hybrid genome assemblies, including two assemblies (with 14-fold and 17-fold average coverage, respectively) that were annotated with the help of budgie transcript sequences and comparisons to bird and human genomes.

The two annotated genomes contained an estimated 15,470 and 16,204 protein-coding genes apiece — more modest gene sets than those described in birds such as the zebra finch and chicken.

The study's authors noted that they passed on raw reads produced for the study to those participating in a genome assembly competition called Assemblathon 2. The reads were also used to generate a billion base-plus de novo genome assembly that included single-molecule PacBio sequence reads.

"[T]his study shows that the budgerigar genomic resource we have generated has provided … valuable data and material for genome technology," they wrote, "and for further investigating complex behavioral traits at the genomics level."

A Nature Communications study outlined information gleaned from a draft genome and transcriptome sequence analysis of the Asian liver fluke, Opisthorchis viverrini. A team from Australia, China, Singapore, and elsewhere put together a 634.5 million base draft genome assembly using reads generated with DNA libraries representing more than two dozen adult O. viverrini flukes.

Along with repeat sequences, which made up more than 30 percent of the liver fluke genome, the researchers identified almost 16,400 predicted protein-coding genes using genome and transcriptome sequence data.

By comparing the genome with other fluke sequences and taking a closer look at Asian liver fluke-specific genes, the group started unraveling some of the biological features contributing to opisthorchiasis infections by O. viverrini flukes — a form of liver disease that can lead to a liver cancer known as cholangiocarcinoma.

For instance, findings from the analysis suggest that the fluke is adept at surviving in lipid-rich environments like those found in the human bile duct and can secrete proteins known for mediating cell proliferation patterns in its human host.