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Genomics In The Journals: Dec 20, 2012

NEW YORK (GenomeWeb News) – A genome-wide association study in Nature Genetics implicates a pair of new genetic variants in elevated liver cancer risk for individuals infected with hepatitis B virus.

Researchers from Fudan University, Wake Forest University, and other centers in the US and China tested almost 2,700 Chinese individuals with chronic HBV infection for the initial GWAS. After quality control steps, researchers were left with genotyping data for around 2,500 of the HBV-infected individuals, including 1,161 with hepatocellular carcinoma and 1,353 without. Through validation studies on thousands more HPV-positive liver cancer cases and controls from China, the team focused in on two significant hepatocellular carcinoma risk SNPs. One variant, which fell in the transcription factor-coding gene STAT4 on chromosome 2, was linked to lower-than-usual levels of that gene. The other variant turned up in a human leukocyte antigen locus on chromosome 6.


An international team headed by investigators at the US Department of Energy Joint Genome Institute, the HudsonAlpha Institute for Biotechnology, and the University of Georgia has sequenced, assembled, and started analyzing a high-quality genome for Gossypium raimondii, a diploid plant that resembles the D-genome of polyploid commercial cotton plant genomes.

As they reported Nature, the researchers compared the Gossypium raimondii data with gene, genome and/or transcriptome sequences from several related plants, such as G. longicalyx, G. herbaceum, and G. hirsutum, to retrace polyploidization events in the plants' lineage. The comparison also provided clues about the genetic profiles associated with cotton fiber production, which does not occur in G. raimondii.

"This cotton data will help accelerate the study of gene function, particularly cellulose biosynthesis, the understanding of which is fundamental to improved biofuels production," senior author Jeremy Schmutz, a HudsonAlpha researcher and head of JGI's plant program, said in a statement. "In addition, the unique structure of the cotton fiber makes it useful in bioremediation and accelerated cotton crop improvement also promises to improve water efficiency and reduce pesticide use."

Earlier this year researchers from the Chinese Academy of Agricultural Sciences, BGI-Shenzhen, Peking University, and the US Department of Agriculture's Agricultural Research Service presented findings from their own G. raimondii draft genome study in Nature Genetics.


A proteomic study in EMBO Molecular Medicine pointed to a set of urine-based markers for a tricky-to-diagnose condition called Kawasaki disease, characterized by blood vessel inflammation.

A Boston Children's Hospital-led team used mass spectrometry to assess urine samples from half a dozen children with Kawasaki disease, focusing on some 2,000 proteins. The investigators compared protein profiles in those samples with urine proteome data for six more children who were suspected of having Kawasaki syndrome but were ultimately diagnosed with another condition.

The analysis yielded several proteins present at relatively high levels in samples from Kawasaki disease patients. Two of these potential marker proteins — filamin C and meprin A — were subsequently found at elevated concentrations in blood and urine samples from hundreds of other children with Kawasaki disease, researchers reported. And their preliminary prospective study of more than 100 children suggested urine levels of the proteins helps distinguish between individuals with Kawasaki disease and those without.

If such results hold in the future, they explained, protein markers might serve as the basis for a non-invasive test for Kawasaki disease, which can cause dangerous complications such as coronary artery aneurisms if left untreated.


Two new studies in Science took a closer look at gene splicing — the ways in which transcribed precursor RNAs are sliced and diced to produce the various messenger RNAs that cells use to make proteins.

For the first of these, the University of Toronto's Benjamin Blencowe and his colleagues brought together high-throughput RNA sequence data representing multiple organs from humans and several other vertebrate species — information that made it possible to explore the nature and complexity of alternative splicing over the course of evolution within the vertebrate lineages considered.

Another team, led by Massachusetts Institute of Technology biologist and biological engineering researcher Christopher Burge, focused on gene splicing dynamics and regulation in mammals. There, researchers saw signs of both conserved mammalian exons and lineage-specific splicing when they parsed complementary DNA sequence data on nine tissue types from five vertebrate species (four mammals and a chicken).

"We find that while tissue-specific gene expression programs are largely conserved," the study's authors explained, "alternative splicing is well conserved in only a subset of tissues and is frequently lineage-specific."


Genomics In The Journals is a weekly feature pointing readers to select, recently published articles involving genomics and related research.