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Genomics In The Journals: Nov 3, 2011

NEW YORK (GenomeWeb News) – Two Nature Genetics studies by Chinese-led research teams describe genome-wide association studies used to uncover schizophrenia risk variants in the Han Chinese population.

In the first of these, investigators from China and several other countries tracked down schizophrenia-associated variants through a GWAS involving 3,750 cases and 6,468 controls from three northern, central, and southern Han Chinese cohorts genotyped on Affymetrix SNP 6.0 arrays. The team then did replication studies involving more than 8,900 additional Han Chinese individuals with or without schizophrenia as well as a meta-analysis of data from all of the groups, identifying genome-wide significant schizophrenia-associated SNPs on chromosomes 1 and 8.

"Several promising candidate genes are implicated in these two regions, making it difficult to determine precisely which genes contain the causative variants," researchers wrote. "Nevertheless, the identification of these new common genetic risk variants that predispose individuals to schizophrenia is an encouraging first step in a process that has the potential to translate into improved methods for the prediction and treatment of disease."

Meanwhile, researchers from Peking University and elsewhere did a two-stage GWAS, first looking at 746 Han Chinese schizophrenia cases and 1,599 controls genotyped on Illumina Human610-Quad BeadChip arrays and then verifying potential associations in another 4,027 cases and 5,603 controls from the same population. That search led to two schizophrenia susceptibility loci: one on chromosome 11 and another in a chromosome 6 major histocompatibility complex region that has previously been associated with schizophrenia in Europeans. Based on their analyses, researchers suspect distinct variants at the MHC locus may influence schizophrenia risk in Han Chinese and European populations, though they say more fine mapping of the region is needed to be sure.

In Nature Neuroscience, an Emory University-led team used chromatin immunoprecipitation sequencing and other methods to look at 5-hydroxymethylcytosine (5-hmC) patterns in two regions of the mouse brain during three stages of development or aging. From these mouse experiments and follow-up analyses of human cerebellum samples, the researchers found evidence that 5-hmC, an epigenetically modified form of the cytosine nucleotide that's sometimes generated from 5-methylcytosine (5-mC), likely has its own role in gene regulation and is not merely a 5-mC bi-product.

"Our data tells us that 5-hmC is not just an intermediate state," senior author Peng Jin, a human genetics researcher at Emory University, said in a statement. "It looks like it has specific functions in stem cells and brain. 5-hmC may poise a gene to be turned on after being repressed."

Uppsala University researchers Pontus Skoglund and Mattias Jakobsson used Neandertal and Denisovan genome sequence data and genotyping data for more than 1,500 individuals assessed through HapMap3 or the Human Genome Diversity Project to look for signatures of archaic hominin ancestry in modern human populations. Their analyses, which was based on statistical analyses and simulations designed to account for serial founder effects during human population expansions, support the notion that Denisovan sequences are found not only in present-day populations in Oceania but also in East Asia, especially Southeast Asia. The findings appear in the early, online version of the Proceedings of the National Academy of Sciences.

Also in PNAS, American and Korean researchers outline the systems biology approach that they used to come up with a network for predicting gene functions in rice and other monocotyledonous plant species, including cereal crops and other grasses. The network, which they call RiceNet, was developed using more than two-dozen types of genetic data from rice, Caenorhabditis elegans, Arabidopsis thaliana, budding yeast, and humans. Though the proof-of-principle study demonstrated RiceNet's potential for finding genes involved in biotic stress response in rice and for predicting some maize gene functions, those involved in the study say the RiceNet has a range of applications in agricultural and biofuel-related research.

"With RiceNet, instead of working on one gene at a time based on data from a single experimental set, we can predict the function of entire networks of genes, as well as entire genetic pathways that regulate a particular biological process," co-corresponding author Pamela Ronald, a plant genetics researcher affiliated with the University of California at Davis and the US Department of Energy's Joint BioEnergy Institute, said in a statement.

An international team headed by investigators at the University of Copenhagen used ancient mitochondrial sequence data to complement archeological and climate information in an effort to understand how climate and humans may have influenced the massive mammalian extinctions that occurred during the Late Quaternary period, beginning about 50,000 years ago. As they report in Nature, the researchers concluded that a combination of factors likely spelled the end for some of the species, such as the woolly rhinoceros and woolly mammoths. Nevertheless, they did not find any obvious features that gave other species an edge in surviving the same circumstances.

"We find no genetic signature or any distinctive range dynamics distinguishing extinct from surviving species," senior author Eske Willerslev, director of the University of Copenhagen's Centre for GeoGenetics at the Natural History Museum, and co-authors wrote, "emphasizing the challenges associated with predicting future responses of extant mammals to climate and human-mediated habitat change."

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

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