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In the Journals: April 1, 2011


A Little Human
Longo MS, O'Neill MJ, O'Neill RJ. (2011). Abundant human DNA contamination identified in non-primate genome databases. PLoS One. Epub: doi 10.1371/journal.pone.0016410.

Mark Longo, Michael O'Neill, and Rachel O'Neill report that many databases storing DNA sequences, genome assemblies, and trace archive reads are contaminated with human DNA. The researchers screened 2,749 non-primate public databases from NCBI, Ensembl, JGI, and UCSC using the primate-specific AluY as their query sequence. As a result of that search, they found that 492 databases have human DNA contaminants. "The level of contamination found in these databases is significant and worrisome," the authors write, especially as researchers increasingly rely on them for re-sequencing projects. "This study points to a need for more rigorous pre-sequencing protocols and laboratory standards," the authors add.

A New Gene for Schizophrenia
Vacic V, McCarthy S, Malhotra D, et al. (2011). Duplications of the neuropeptide receptor gene VIPR2 confer significant risk for schizophrenia. Nature. Epub: doi 10.1038/nature09884.

Vladimir Vacic and his colleagues searched for novel genes involved in schizophrenia by conducting a two-stage genome-wide scan for copy number variants. From this, they report that copy number gains at chromosome 7q36.3 were significantly associated with schizophrenia. These results implicate involvement of the gene VIPR2, which encodes a vasoactive intestinal peptide receptor. That receptor binds another protein to activate cyclic AMP signaling, which has previously been associated with schizophrenia. "Our results support the hypothesis that the pathogenesis of schizophrenia — in some patients — involves the dysregulation of cellular processes," the researchers write.

Rare Autism Variants
Gai X, Xie HM, Perin JC, et al. (2011). Rare structural variation of synapse and neurotransmission genes in autism. Molecular Psychiatry. Epub: doi 10.1038/mp.2011.10.

Xiaowu Gai and his colleagues hypothesize that rare structural variants in genes related to neurological pathways add up to a significant portion of autism spectrum disorder risk. In a modified case-control CNV study, they compared 631 children with autism and their parents to a control set of 1,775 children and found a number of genes — some that are already known to be involved in autism and some novel ones — that were enriched for CNVs, including some associated with brain communication pathways. The researchers say that these results support the theory that autism spectrum disorders are highly heterogeneous.

Organizing Meningitis
Budroni S, Siena E, Dunning Hotopp JC, et al. (2011). Neisseria meningitidis is structured in clades associated with restriction modification systems that modulate homologous recombination. PNAS. Epub: doi 10.1073/pnas.101975110.

The researchers analyzed 15 previously unpublished and five publicly available Neisseria meningitidis genomes to determine genomic variation patterns among Neisseria populations. They report that N. meningitidis has evolved into phylogenetic clades, each of which has "a unique set of restriction modification systems that results in a differential -barrier to genetic transfer and accounts for the observed structuring of the population of Nm genotypes." This, the researchers add, may affect a given lineage's virulence.

The Scan

New Study Investigates Genomics of Fanconi Anemia Repair Pathway in Cancer

A Rockefeller University team reports in Nature that FA repair deficiency leads to structural variants that can contribute to genomic instability.

Study Reveals Potential Sex-Specific Role for Noncoding RNA in Depression

A long, noncoding RNA called FEDORA appears to be a sex-specific regulator of major depressive disorder, affecting more women, researchers report in Science Advances.

New mRNA Vaccines Offer Hope for Fighting Malaria

A George Washington University-led team has developed mRNA vaccines for malaria that appear to provide protection in mice, as they report in NPJ Vaccines.

Unique Germline Variants Found Among Black Prostate Cancer Patients

Through an exome sequencing study appearing in JCO Precision Oncology, researchers have found unique pathogenic or likely pathogenic variants within a cohort of Black prostate cancer patients.