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In Print: Last Week's Microarray Papers of Note: Jan 2, 2013


Technical note: Characteristics and use of the Illumina BovineLD and GeneSeek Genomic Profiler low-density bead chips for genomic evaluation.
J Dairy Sci. 2012 Dec 19.
Wiggans G, Cooper T, Van Tassell C, et al.

This paper describes the similarities and differences between GeneSeek's Genomic Profiler BeadChip, or GGP, and Illumina's BovineLD Genotyping BeadChip, on which the GGP is based. Citing genotyping data on 82,510 animals, the authors state that their performance was similar. Both had similar SNP call rates, were highly effective in sex validation, and the rate of parent-progeny conflicts on a SNP basis was similar. However, they report that imputation accuracy was slightly higher for the GGP chip compared with the BovineLD chip because of its additional SNP content and that reliability for genomic evaluations using BovineLD and GGP genotypes was 3 percentage points higher than that for older Illumina Bovine3K genotypes.

A genome-wide association study identifies a gene network of ADAMTS genes in the predisposition to pediatric stroke.
Blood. 2012 Dec 20;120(26):5231-6.
Arning A, Hiersche M, Witten A , et al.

The authors report the results of the first GWAS on pediatric stroke using a large cohort of 270 family-based trios. The association study was performed using the Illumina 370 CNV SNP array and analyzed using the transmission disequilibrium test as implemented in PLINK. Based on subsequent analysis, the authors observed clustering of association signals in four genes belonging to one family of metalloproteinases at high and moderate significance levels.

Exome array analysis identifies new loci and low-frequency variants influencing insulin processing and secretion.
Nat Genet. 2012 Dec 23. [Epub ahead of print]
Huyghe J, Jackson A, Fogarty M, et al.

To examine low-frequency and rare nonsynonymous variants, the authors analyzed exome array data in 8,229 nondiabetic Finnish males using the Illumina HumanExome Beadchip. 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. In this paper, they also showed that the interpretation of single-variant and gene-based tests needs to consider the effects of noncoding SNPs both nearby and megabases away.

Identifying human-rhesus macaque gene orthologs using heterospecific SNP probes.
Genomics. 2013 Jan;101(1):30-7.
Kanthaswamy S, Ng J, Ross C, et al.

The authors genotyped a Chinese and an Indian-origin rhesus macaque using the Affymetrix Genome-Wide Human SNP Array 6.0 and cataloged 85,473 uniquely mapping heterospecific SNPs. The SNPs were assigned to rhesus chromosomes according to their probe sequence alignments as displayed in the human and rhesus reference sequences. The conserved gene order revealed by heterospecific SNP maps is in concordance with that of the published human and rhesus macaque genomes.

Different characteristics identified by single nucleotide polymorphism array analysis in leukemia suggest the need for different application strategies depending on disease category.
Genes Chromosomes Cancer. 2013 Jan;52(1):44-55.
Huh J, Jung C, Kim H, et al.

The purpose of this study was to evaluate the detection rate of chromosomal rearrangements in leukemia using SNP arrays in combination with metaphase cytogenetics, with the aim of proposing a practical approach for clinical karyotyping applications of SNP arrays. Affymetrix's Genome-Wide Human SNP Array 6.0 was applied in 469 patients with a variety of hematologic malignancies. The authors found that the combined use of the SNP array with conventional cytogenetics improved the detection rate in comparison with MC alone.

Estimates of penetrance for recurrent pathogenic copy-number variations.
Genet Med. 2012 Dec 20. [Epub ahead of print]
Rosenfeld J, Coe B, Eichler E, et al.

The authors sought to provide empiric estimates for the penetrance for some recurrent disease susceptibility loci. They conducted a Bayesian analysis based on the copy-number variation frequencies in control populations and their database of 48,000 postnatal microarray-based comparative genomic hybridization samples. They argue that this model could be used to provide more precise estimates for the chance of an abnormal phenotype for many copy-number variations encountered in the prenatal setting.

Nanobody-based chromatin immunoprecipitation/microarray analysis for genome-wide identification of transcription factor DNA binding sites.
Nucleic Acids Res. 2012 Dec 28. [Epub ahead of print]
Nguyen-Duc T, Peeters E, et al.

Nanobodies are single-domain antibody fragments derived from camelid heavy-chain antibodies. In this study, the authors applied a nanobody in chromatin immunoprecipitation followed by DNA microarray hybridization for genome-wide identification of DNA-protein interactions. The Lrp-like regulator Ss-LrpB, a well-studied transcription factor of the hyperthermophilic archaeon Sulfolobus solfataricus, was chosen for this proof-of-principle nanobody-assisted ChIP. Three distinct Ss-LrpB-specific nanobodies, each interacting with a different epitope, were generated for ChIP. Genome-wide ChIP-chip with one of these nanobodies identified the well-established Ss-LrpB binding sites and revealed several unknown target sequences. In addition, the authors report that the ChIP-chip profiles revealed auxiliary operator sites in the open reading frame of Ss-lrpB.

Fecal source tracking in water using a mitochondrial DNA microarray.
Water Res. 2013 Jan 1;47(1):16-30.
Vuong N, Villemur R, Payment P, et al.

A mitochondrial-based microarray called the MitoArray was developed for rapid identification of the presence of 28 animals and one family potentially implicated in fecal pollution in mixed activity watersheds. Validation study results confirmed that the mitochondrial microarray method could accurately detect the dominant animals present in water samples, emphasizing the potential for this methodology in the parallel scanning of a large variety of animals normally monitored in fecal source tracking, according to the authors.