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In Print: Last Week's Microarray Papers of Note: Feb 5, 2013


A high-throughput SNP marker system for parental polymorphism screening, and diversity analysis in common bean (Phaseolus vulgaris L.).
Theor Appl Genet. 2013 Feb;126(2):535-48.
Blair M, Cortés A, Penmetsa R, et al.

The authors used a 768-marker, Illumina GoldenGate assay for common bean developed from conserved legume gene sequences to evaluate parental polymorphisms in a mini-core set of common bean accessions and to analyze genetic diversity in the crop. They found Illumina GoldenGate SNPs to provide equivalent evaluations as previous gene-based SNP markers, but with less fine distinctions than with previous microsatellite marker analysis. They also reported that the gene-based SNPs in the GoldenGate array had some use in structure analysis despite the low polymorphism.

Exome array analysis identifies new loci and low-frequency variants influencing insulin processing and secretion.
Nat Genet. 2013 Feb;45(2):197-201.
Huyghe J, Jackson A, Fogarty M, et al.

To examine low-frequency and rare nonsynonymous variants associated with insulin processing and secretion, the authors used the Illumina HumanExome Beadchip to analyze exome array data in 8,229 nondiabetic Finnish males. They identified low-frequency coding variants associated with fasting proinsulin concentrations at the SGSM2 and MADD GWAS loci and three new genes with low-frequency variants associated with fasting proinsulin or insulinogenic index: TBC1D30, KANK1, and PAM.

Investigation of transferability of BovineSNP50 BeadChip from cattle to water buffalo for genome wide association study.
Mol Biol Rep. 2013 Feb;40(2):743-50.
Wu J, Song L, Wu F, et al.

The authors used Illumina BovineSNP50 BeadChips to analyze 91 DNA samples from three breeds of water buffalo to demonstrate the genetic divergence between cattle and water buffalo through a large SNP transferability study at the whole-genome level, and performed association analysis of functional traits in water buffalo as well. They found that while the genome sequences of water buffalo and cattle share a high level of homology, the polymorphic status of the bovine SNPs varied between these two species.

High-resolution genomic analysis suggests the absence of recurrent genomic alterations other than SMARCB1 aberrations in atypical teratoid/rhabdoid tumors.
Genes Chromosomes Cancer. 2013 Feb;52(2):185-90.
Hasselblatt M, Isken S, Linge A, et al.

Atypical teratoid/rhabdoid tumor, or AT/RT, is a rare malignant pediatric brain tumor characterized by genetic alterations affecting the SMARCB1 locus in chromosome band 22q11.2. To identify potential additional genetic alterations, the authors performed high-resolution genome-wide analysis using Affymetrix's OncoScan FFPE Express on DNA isolated from 18 formalin-fixed paraffin-embedded archival samples, but found no recurrent mutations of other cancer-relevant genes. They concluded that there is an absence of recurrent genomic alterations other than SMARCB1 in AT/RT.

Development of a high density 600K SNP genotyping array for chicken.
BMC Genomics. 2013 Jan 28;14(1):59. [Epub ahead of print]
Kranis A, Gheyas A, Boschiero C, et al.

The authors report the development of a 600,000-marker Affymetrix Axiom HD genotyping array designed using SNPs segregating in a wide variety of chicken populations. They believe the array will find widespread usage both in research and commercial application such as in genomic selection, genome-wide association studies, selection signature analyses, fine mapping of QTLs, and detection of copy number variants.

BioArray News interviewed David Burt, a coauthor on the study and chair of comparative genomics at the Roslin Institute, about the chip while it was under development last year (BAN 1/24/2012).