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Genomics In The Journals: Sep 8, 2011

NEW YORK (GenomeWeb News) – In Nature Genetics, an international group describes a role for the interleukin 7 receptor gene in a type of leukemia known as T-cell acute lymphoblastic leukemia. The team found gain-of-function mutations in exon 6 of the gene in seven percent of cases when they did targeted IL7R re-sequencing in 68 children diagnosed with T-ALL at a hospital in Brazil. Exon 6 mutations, which appear to contribute to leukemia development by promoting unchecked T-cell proliferation, also turned up in a dozen cases from the Netherlands and Germany when the team tested 133 children from these populations. The findings hint that it may be possible to treat some forms of the disease by targeting the signaling pathway found downstream of the receptor.

"Our observations allowed us to identify potential therapeutic weapons against these tumors," corresponding author João Barata, a cancer biology researcher at Portugal's Instituto de Medicina Molecular, said in a statement. "Although pediatric acute lymphoblastic leukemia is among the success stories in cancer therapy, improvements are still needed. We hope our findings will help further increase the efficacy and selectivity of already existing treatments."

American researchers used multi-locus DNA comparisons in three present-day populations from sub-Saharan Africa to find evidence of archaic admixture in populations on the African continent, findings they describe online in the Proceedings of the National Academy of Sciences. Scientists re-sequenced 61 non-coding regions of the genome per person in about 16 individuals from each of the three groups: the Mandenka, Biaka, and San populations. Using statistical methods to model human populations and evolution, the researchers detected three sites in the genome where sequences appear more similar to those predicted for extinct archaic hominins than to those in the rest of the human genome.

"We can simulate a model of hybridization between anatomically modern humans and some archaic form … [W]e can see what we would expect the pattern to look like if it did occur," first author Michael Hammer, an ecology and evolutionary biology researcher affiliated with the University of Arizona at Tucson and the Arizona Research Laboratories Division of Biotechnology, said in a statement. "We discovered three different genetic regions fit the criteria for being archaic DNA still present in the genomes of sub-Saharan Africans."

Also set to appear in PNAS this week, an international group led by investigators in Norway describes the integrated molecular method that it used to profile invasive breast cancer samples. The group relied on the "pathway recognition algorithm using data integration on genomic models" or PARADIGM method to bring together gene expression, copy number, microRNA, and DNA methylation information on about 110 breast tumors collected from the MicroMetastases Project cohort. In the process, they identified pathways and immune response patterns corresponding to tumor features and subtypes. Overall, the team reported, they gleaned the most predictive prognostic information by classifying patients based on copy number and gene expression patterns in the tumors.

In the American Journal of Human Genetics, researchers from Switzerland, Spain, and the Netherlands used linkage analysis and exome sequencing to detect mutations involved in a familial form of narcolepsy. The team did genotyping and linkage studies on 11 affected and 15 unaffected individuals from four generations of a Spanish family, coupled with exome sequencing on three family members with both narcolepsy and a related muscle weakness condition called cataplexy. The search led to a candidate locus on chromosome 6 where the researchers narrowed in on a missense mutation in MOG, a myelin oligodendrocyte glycoprotein gene previously linked to conditions ranging from multiple sclerosis to neuropsychiatric disorders.

"Gene-expression studies in major depression, bipolar disorder, schizophrenia, and multiple sclerosis indicate that genes expressed in oligodendrocytes are downregulated, supporting the hypothesis that problems with oligodendrocytes might cause neurodevelopmental disorders," co-corresponding author Mehdi Tafti, an integrative genomics and sleep researcher at the University of Lausanne, said in a statement. "The identification of a mutation in MOG, so far unique to our family, not only provides insight into the pathogenesis of narcolepsy but also highlights the role of myelin and oligodendrocytes in disease susceptibility in other complex neuropsychiatric disorders."

American, Norwegian, and German researchers relied on a combination of transcriptome and genome data to clarify the relationships between animals in the mollusc lineage — work that they describe in Nature. The team used the Roche 454 GS FLX and Titanium platforms to generate transcriptome data for 20 mollusc species from 18 mollusc operational taxonomic units. By combining this information with publicly available genome and expressed sequence tag data, the researchers put together the most complete phylogenomic picture yet of animals from the eight main mollusc lineages.

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

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