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In Print: Last Week's Microarray Papers of Note: Apr 9, 2013


Density matters: comparison of array platforms for detection of copy-number variation and copy-neutral abnormalities.
Genet Med. 2013 Apr 4. [Epub ahead of print]
Mason-Suares H, Kim W, Grimmett L, et al.

The authors compared the ability of three commercial array platforms of varying density and content sold by Affymetrix, Agilent Technologies, and Oxford Gene Technology to detect copy-number variation and absence of heterozygosity. In the paper, the authors reported that while all three chips reliably detected copy-number variation, mosaicism, and uniparental isodisomy, AOH detection "varied significantly." Additional experiments and analyses led the authors to conclude that Affy's CytoScan, the array containing the greatest SNP content of the trio, "is best for detecting AOH."

BioArray News spoke recently about the study with corresponding author Katie Rudd, a cytogenetics director at Emory Genetics Laboratory (see related story, this issue).

Genome-wide association study of pre-eclampsia detects novel maternal single nucleotide polymorphisms and copy-number variants in subsets of the Hyperglycemia and Adverse Pregnancy Outcome (HAPO) study cohort.
Ann Hum Genet. 2013 Apr 2. [Epub ahead of print]
Zhao L, Bracken M, Dewan A.

The authors carried out a genome-wide association study to identify maternal variants associated with pre-eclampsia using samples from mothers with Afro-Caribbean, Hispanic, and European ancestry. European ancestry subjects were genotyped on Illumina Human610-Quad and Afro-Caribbean and Hispanic subjects were genotyped on Illumina Human1M-Duo BeadChip microarrays. They identified SNPs and copy-number variable regions that they claim present "interesting candidate genetic variants for pre-eclampsia that warrant further replication and investigation."

Genome-wide linkage analysis is a powerful prenatal diagnostic tool in families with unknown genetic defects.
Eur J Hum Genet. 2013 Apr;21(4):367-72.
Arélin M, Schulze B, Müller-Myhsok B, et al.

The authors present a family with a severe recessive mental retardation syndrome, where the mother wished pregnancy termination to avoid delivering another affected child. Using an Affymetrix genotyping array, they were able to establish the disease haplotype. Without knowing the exact genetic defect, they excluded the condition in the fetus. The woman finally gave birth to a healthy baby. The authors suggest that genome-wide linkage analysis based on either SNP mapping or full-genome sequencing could be a useful tool in prenatal diagnosis of diseases.

The Scan

Study Tracks Off-Target Gene Edits Linked to Epigenetic Features

Using machine learning, researchers characterize in BMC Genomics the potential off-target effects of 19 computed or experimentally determined epigenetic features during CRISPR-Cas9 editing.

Coronary Artery Disease Risk Loci, Candidate Genes Identified in GWAS Meta-Analysis

A GWAS in Nature Genetics of nearly 1.4 million coronary artery disease cases and controls focused in on more than 200 candidate causal genes, including the cell motility-related myosin gene MYO9B.

Multiple Sclerosis Contributors Found in Proteome-Wide Association Study

With a combination of genome-wide association and brain proteome data, researchers in the Annals of Clinical and Translational Neurology tracked down dozens of potential multiple sclerosis risk proteins.

Quality Improvement Study Compares Molecular Tumor Boards, Central Consensus Recommendations

With 50 simulated cancer cases, researchers in JAMA Network Open compared molecular tumor board recommendations with central consensus plans at a dozen centers in Japan.