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Genomics In The Journals: Sep 12, 2013

NEW YORK (GenomeWeb News) – In Nature Genetics, an international team reported on findings from a genome sequencing study of the dog tapeworm Echinococcus granulosus.

The researchers used a combination of Roche 454 GS FLX and Illumina GA sequencing to tackle genomic DNA from cyst tissue of an E. granulosus strain known for infecting sheepdogs. With the sequences generated, they then put together a draft genome assembly spanning almost 152 million bases.

To that, they added transcriptome sequence data representing four stages of tapeworm development — information that helped in annotating the genome and uncovering 11,325 predicted protein-coding genes. By analyzing such sequences and comparing them with those from related worms, the team got a glimpse at the dog tapeworm's biology and interactions with its unfortunate hosts.

For instance, the study suggests a number of genes involved in lipid and amino synthesis have been jettisoned from the parasitic worm's genome. On the other hand, the dog tapeworm appears to have nabbed other sequences or expanded gene families coding for factors that help it grow, survive stressful situations, and joust with host immune responses.

Through sequence comparisons, investigators also narrowed in on potential treatment targets amongst a set of genes that appear to be specific to parasitic helminth worms.

"Our study provides insights into the biology, development, differentiation, evolution, and host interaction of E. granulosus," the Chinese- and Australian-led group noted, "and has identified a range of drug and vaccine targets that can facilitate the development of new intervention tools for hydatid [cyst-forming disease] treatment and control."

Earlier this year, an international team published a whole-genome sequencing analysis of not only E. granulosus, but also the fox tapeworm E. multilocularis, the pork tapeworm Taenia solium, and the rodent tapeworm Hymenolepis microstoma.

Infection with simian immunodeficiency virus, or SIV, can lead to pronounced changes in chimpanzees' gut microbiome communities, according to a study in Cell Host & Microbe.

Yale University's Howard Ochman and colleagues used 16S ribosomal RNA sequencing to track gut microbiome patterns in half a dozen chimps from Gombe National Park over nine years. Each of the animals initially tested negative for SIV infection and became SIV-positive over the course of the study.

Using sequence data generated from 49 fecal samples, the team saw discernible shifts in the composition of gut communities in each chimp before and after SIV infection. In particular, SIV infection appeared to upend previously stable gut communities in the chimps, leading to a wider range of microbes and a jump in representation by potential pathogens.

In the same issue of Cell Host & Microbe, researchers from the University of Colorado described results from a 16S rRNA sequencing study of human gut microbe communities in a few dozen individuals who were HIV-negative, newly infected with HIV-1, or who had had long term HIV-1 infections.

"HIV infection is associated with highly characteristic gut community changes," senior author Brent Palmer, with the University of Colorado Denver, and co-authors noted, "and antiretroviral therapy does not consistently restore the microbiota to an HIV-negative state."

Earlier this year, a University of California at San Francisco-led team reported on changes to the human gut microbiome that appear to correspond with progression from HIV to AIDS.

A New England Journal of Medicine study suggests metastatic colorectal cancer patients are more apt to see a survival boost from having an epidermal growth factor-targeting drug called panitumumab — marketed as Vectibix by Amgen — added to their treatment regimen when their tumors do not contain KRAS and NRAS gene mutations.

An international team looked at progression-free survival patterns, together with KRAS, NRAS, and BRAF mutation status, in metastatic colorectal cancer patients treated with oxaliplatin, fluorouracil, and leucovorin, known as FOLFOX4 treatment, either alone or in combination with panitumumab.

In more than 500 individuals whose tumors were RAS mutation-free, the addition of panitumumab to FOLFOX4 therapy was associated with a boost in progression-free survival time and overall survival compared to FOLFOX4 treatment on its own.

But similar to previous findings for individuals whose tumors contained mutations affecting exon 2, the Amgen-sponsored study indicated that individuals with other RAS mutations in their tumors tend to show poor response to treatments targeting EGFR.

Consequently, the study's authors noted, "[p]anitumumab plus oxaliplatin-containing regimens have no value in patients with metastatic colorectal cancer and mutated RAS."

"The benefit-risk profile of panitumumab-FOLFOX4 was improved by excluding patients with mutated RAS metastatic colorectal cancer tumors," they wrote. "Pooled trials or meta-analyses of anti-EGFR therapy are needed to confirm these findings."

University of Washington Genome Sciences researcher Evan Eichler and colleagues used whole-exome sequence data from the Simons Simplex Collection to look at the extent to which small copy number changes are present in coding regions of the genome in individuals with sporadic autism spectrum disorder — work that they described in the American Journal of Human Genetics.

With the help of a computational method called "Copy Number Inference From Exome Reads," or CoNIFER, the researchers rooted through exome sequence data for members of 411 ASD-affected families, each containing only one affected child. The approach unearthed roughly twice as many small, coding copy number changes as have been found from SNP array data, they noted.

In addition, the team found that children with ASD inherited more rare CNVs than their unaffected siblings. Such small CNVs were transmitted slightly more often from mothers than their fathers, both in children with and without ASD. But amongst children with ASD, these small, inherited CNVs were more common and affected a wider swath of genes.

An enhanced appreciation for the role that small inherited variants play in sporadic ASD cases is expected to bolster the general view of genes contributing to the condition, study authors noted, while improving ASD mutation models.

For their part, Eichler and his colleagues came up with a combined mutation model considering inherited and de novo CNVs, as well as de novo single-nucleotide variants, for instance, illustrating that each contributes to ASD risk independently.