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


Identification of 23 new prostate cancer susceptibility loci using the iCOGS custom genotyping array.
Nat Genet. 2013 Apr;45(4):385-91.
Eeles R, Olama A, Benlloch S, et al.

To identify common prostate cancer susceptibility alleles, we genotyped 211,155 SNPs on a custom Illumina array in blood DNA from 25,074 prostate cancer cases and 24,272 controls from the international PRACTICAL Consortium. Twenty-three new prostate cancer susceptibility loci were identified at genome-wide significance. The authors believe their results will facilitate population risk stratification for clinical studies (see related story, this issue).

Large-scale genotyping identifies 41 new loci associated with breast cancer risk.
Nat Genet. 2013 Apr;45(4):353-61.
Michailidou K, Hall P, Gonzalez-Neira A, et al.

The authors report a meta-analysis of nine genome-wide association studies, including 10,052 breast cancer cases and 12,575 controls of European ancestry, from which they selected 29,807 SNPs for further genotyping in 45,290 cases and 41,880 controls of European ancestry from 41 studies in the Breast Cancer Association Consortium using a custom Illumina iSelect genotyping array. They identified SNPs at 41 new breast cancer susceptibility loci at genome-wide significance, and state that additional analyses suggest that more than 1,000 additional loci are involved in breast cancer susceptibility (see related story, this issue).

Global increases in both common and rare copy number load associated with autism.
Hum Mol Genet. 2013 Mar 27. [Epub ahead of print]
Girirajan S, Johnson R, Tassone F, et al.

The authors assessed 516 individuals with autism or typical development from the population-based Childhood Autism Risks from Genetics and Environment study using a custom targeted DNA microarray. They also carried out a separate study of five highly dynamic, hotspots associated with autism or developmental delay syndromes using a finely-tiled array platform in 142 children matched for gender and ethnicity. In both studies, a significant increase in the number of base pairs of duplication, but not deletion, was associated with autism.

Prenatal diagnosis of chromosomal abnormalities in fetuses with abnormal cardiac ultrasound findings: evaluation of chromosomal microarray-based analysis.
Ultrasound Obstet Gynecol. 2013 Apr;41(4):375-82.
Mademont-Soler I, Morales C, Soler A, et al.

The authors carried out retrospective analysis of 276 different 22q11.2 deletion syndrome cases diagnosed between January 2009 and December 2011 among fetuses with abnormal cardiac ultrasound findings. Chromosomal microarray analysis was performed in 51 of the fetuses with such findings, normal karyotype and negative or no 22q11.2 deletion syndrome study, and in the only fetus with a heart defect and an apparently balanced de novo chromosomal rearrangement. The authors found that the detection rate of pathogenic copy number variants by CMA was 2 percent greater than conventional cytogenetics, and suggest that CMA could be a "good alternative to karyotyping in these pregnancies."