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In Print: Last Week's Microarray Papers of Note: Apr 23, 2013


Diagnosis of copy number variation by Illumina next-generation sequencing is comparable in performance to oligonucleotide array comparative genomic hybridization.
Genomics. 2013 Apr 15. [Epub ahead of print]
Hayes J, Tzika A, Thygesen H, et al.

Detection of copy number using the BlueGnome 8x60K oligonucleotide aCGH platform was compared with low resolution next-generation sequencing using the Illumina GA IIx on 39 patients referred to the Leeds Clinical Cytogenetics Laboratory with developmental delay and learning difficulties. Of the 39 patients analyzed, all 11 imbalances detected by array CGH were also detected by CNV-seq. In addition, CNV-seq reported one purported pathogenic copy number variant that was not detected by array CGH.

Conversion strategy using an expanded genetic alphabet to assay nucleic acids.
Anal Chem. 2013 Apr 17. [Epub ahead of print]
Yang Z, Durante M, Glushakova L, et al.

Methods to detect DNA and RNA, collectively referred to as xNA, are plagued by noise, false positives, and false negatives, especially with increasing levels of multiplexing in complex assay mixtures, according to the authors. To mitigate these problems, the authors converted xNA analyte sequences into sequences that incorporate the nonstandard nucleotides Z and P. The resulting improvements are assessed in an assay that inverts the standard Luminex xTAG architecture, placing a biotin on a primer, rather than on a triphosphate.

The genome-wide landscape of copy number variations in the MUSGEN study provides evidence for a founder effect in the isolated Finnish population.
Eur J Hum Genet. 2013 Apr 17. [Epub ahead of print]
Kanduri C, Ukkola-Vuoti L, Oikkonen J, et al.

The authors characterized the genome-wide architecture of copy number variations in 286 healthy, unrelated Finnish individuals belonging to the MUSGEN study, where molecular background underlying musical aptitude and related traits are studied. Using the Illumina HumanOmniExpress BeadChip, they identified 5,493 CNVs that were spread across 467 different cytogenetic regions, spanning a total size of 287.83 megabases. Merging the overlapping CNVs across samples resulted in 999 discrete copy number variable regions, of which about 7 percent were putatively novel.

The Scan

Study Finds Sorghum Genetic Loci Influencing Composition, Function of Human Gut Microbes

Focusing on microbes found in the human gut microbiome, researchers in Nature Communications identified 10 sorghum loci that appear to influence the microbial taxa or microbial metabolite features.

Treatment Costs May Not Coincide With R&D Investment, Study Suggests

Researchers in JAMA Network Open did not find an association between ultimate treatment costs and investments in a drug when they analyzed available data on 60 approved drugs.

Sleep-Related Variants Show Low Penetrance in Large Population Analysis

A limited number of variants had documented sleep effects in an investigation in PLOS Genetics of 10 genes with reported sleep ties in nearly 192,000 participants in four population studies.

Researchers Develop Polygenic Risk Scores for Dozens of Disease-Related Exposures

With genetic data from two large population cohorts and summary statistics from prior genome-wide association studies, researchers came up with 27 exposure polygenic risk scores in the American Journal of Human Genetics.