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Genomics In The Journals: Sep 22, 2011

NEW YORK (GenomeWeb News) – Members of the Psychiatric GWAS Consortium Bipolar Disorder Working Group report on a new bipolar disorder risk locus that they found in the chromosome 11 gene ODZ4 in Nature Genetics.

The large international consortium did a genome-wide association study involving 7,481 individuals with bipolar disorder and 9,250 unaffected controls. The researchers broke the cases and controls into several smaller groups before doing genotyping, imputing haplotypes, and looking for potential bipolar disease associations.

In the follow-up stages of the study, the team also did replication and meta-analyses that included another 4,496 cases and 42,422 controls. Along with several known risk loci, the search yielded a new bipolar risk locus in an intron of ODZ4.

A combined analysis between the bipolar samples and schizophrenia samples tested by the Schizophrenia Psychiatric GWAS Consortium also pointed to a shared risk locus for the conditions in the CACNA1C gene.

And as they reported in another Nature Genetics study, the schizophrenia-focused arm of the Psychiatric GWAS Consortium identified five new schizophrenia risk loci through a multi-stage GWAS meta-analysis involving tens of thousands of cases and controls. Among them: an association that fell in the intron of a gene coding for the microRNA MIR137 and schizophrenia-linked variants within predicted targets of the miRNA.

"The association near MIR137, associations in multiple predicted MIR137 targets and the known role of MIR137 in neuronal maturation and function together suggest an intriguing new insight into the pathogenesis of schizophrenia," members of the Schizophrenia Psychiatric GWAS Consortium wrote.

In Nature, researchers from Germany, Iran, and Canada describe the deep sequencing approach that they used to track down 50 new genes contributing to a group of cognitive disorders known as autosomal recessive intellectual disability.

The team did targeted sequencing in 136 consanguineous Iranian families that had been previously assessed by array-based methods and linkage analyses. By using custom oligonucleotide arrays to capture the exons of suspicious genes in areas detected by homozygosity mapping and then sequencing these exons, researchers found 50 genes not previously linked to cognitive disorders, along with new mutations in almost two-dozen known intellectual or neurological disability-related genes.

"We expect that these findings will have direct implications for the diagnosis and prevention of intellectual disability," co-corresponding author Hilger Ropers, a human molecular genetics researcher at the Max Planck Institute for Molecular Genetics, and co-authors wrote, "and perhaps also for autism, schizophrenia, and epilepsy, which often co-exist in intellectual disability patients and are frequently associated with mutations in the same genes."

An Australian research team used gene expression and other analyses to find clues about how pigeon parents make "milk," a nutrient-rich concoction produced by cells in the birds' crop that male and female pigeons use to feed their young.

When the researchers compared expression patterns in crop tissue from four "lactating" and four "non-lactating" birds that had been assessed using chicken microarrays, they found 639 genes that were down-regulated and 542 genes whose expression was bumped up during pigeon milk production. Among the genes that were up-regulated were some involved in melanocyte cell proliferation, antioxidant activity, cell signaling, immune function, and more. The findings appear in BMC Genomics.

An international team put together an improved mammalian phylogeny using a "molecular supermatrix" approach and relaxed molecular clock methods that allow for distinct rates of evolution, informed by fossil data, for members of different mammalian families. Using information on more than 35,600 bases of DNA sequence data representing 26 gene fragments and protein alignments comprised of around 11,000 amino acids, the group came up with a phylogeny that offers a refined view of relationships and divergence profiles for 164 mammalian species representing between 97 and 99 percent of known mammal families.

The study appears in Science Express.

"We were able to put together a diverse assemblage of fossil calibrations from different parts of the mammalian tree, and we used it in conjunction with molecular information to assemble the most robust time tree based on sequenced data that has been developed to date," co-corresponding author Mark Springer, a biologist at the University of California at Riverside, said in a statement. "Our phylogeny, underpinned by a large number of genes, sets the stage for us to understand how the different mammalian species are related to each other."

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