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Genomics In The Journals: Dec 29, 2011

NEW YORK (GenomeWeb News) – Researchers from the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University and elsewhere conducted whole-genome and whole-exome sequencing to identify mutations in the ATM gene that may increase the hereditary risk for pancreatic cancer.

The researchers, who published their work online in Cancer Research this week, found ATM mutations in two kindreds with familial pancreatic cancer. Using the Illumina GAIIx, the investigators found ATM mutations in four of 166 patients with pancreatic cancer compared to no deleterious mutations in 190 spouse controls.

"Our results have important implications for the management of patients in affected families and illustrate the power of genome-wide sequencing to identify the basis of familial cancer syndromes," the authors of the study concluded.


An international team of researchers led by Lavinia Paternoster at the University of Bristol and Medical Research Council Centre for Causal Analyses in Translational Epidemiology conducted a large-scale genome-wide association study of atopic dermatitis, unveiling two newly identified risk loci associated with the condition.

Their study, published in Nature Genetics this week, of 11,025 atopic dermatitis cases and 40,398 controls found genome-wide significance for rs479844 upstream of OVOL1 and rs2164983 near ACTL9 — both of which are near genes previously implicated in epidermal proliferation and differentiation — as well as rs2897442 in KIF3A within the cytokine cluster in 5q31.1.

"Our results are consistent with the hypothesis that atopic dermatitis is caused by both epidermal barrier abnormalities and immunological features," the researchers concluded. "Further studies are needed to identify the causal variants at the associated loci and to understand the mechanisms through which they confer risk for atopic dermatitis."


An international research team led by Erhan Yalcindag of Université de Montpellier in France has analyzed Plasmodium falciparum isolates in South America and concluded that two clusters from African sources introduced the parasite to the continent. The researchers obtained 577 moninfected isolates from 24 localities in 17 countries — nine from Africa, four from South America, one from the Middle East, and three from Asia. They conducted phylogenetic analyses and used Approximate Bayesian Computation methods to determine that the likely introduction of P. falciparum, which causes malaria, came during the transatlantic slave trade.

"Our study confirms an African origin of P. falciparum in the New World," the study authors wrote in this week's issue of the Proceedings of the National Academy of Sciences. "In addition, because our study now encompasses much of the distribution range of P. falciparum in South America, it provides a far more detailed picture of the genetic structure of the parasite in this continent, and hence of its colonization history."


Also in PNAS this week, researchers from Brigham and Women's Hospital in Boston and Harvard Medical School and elsewhere constructed a genome-wide, high-resolution copy number variants map for the zebrafish. The map comprises 6,080 CNV elements and encompasses 14.6 percent of the zebrafish reference genome culled from 80 zebrafish genomes. According to the study authors, this amount of CNVs is four times that previously observed in other vertebrates, including humans.

"Our data indicate not only a high degree of strain substructuring but also an increased level of variation between individual fish within a strain," the study authors wrote. "These high levels of variation within zebrafish strains potentially could confound studies intended for translation to human diseases."


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

The Scan

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Researchers in PLOS Biology explore M. tuberculosis resistance with a combination of sequencing and assays looking at the minimum inhibitory concentrations of 13 drugs.

Mendelian Disease Genes Prioritized Using Tissue-Specific Expression Clues

Mendelian gene candidates could be flagged for further functional analyses based on tissue-specific transcriptome and proteome profiles, a new Journal of Human Genetics paper says.

Single-Cell Sequencing Points to Embryo Mosaicism

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