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In Print: Last Week's Microarray Papers of Note: Jan 22, 2013


Cost-effective genome-wide estimation of allele frequencies from pooled DNA in Atlantic salmon (Salmo salar L.).

BMC Genomics. 2013 Jan 16;14(1):12.

Ozerov M, Vasemägi A, Wennevik V, et al.

The authors tested the effectiveness of DNA pooling to obtain accurate allele frequency estimates for Atlantic salmon populations using an Illumina SNP chip. In total, 56 Atlantic salmon DNA pools from 14 populations were analyzed on an array containing probes for 5,568 SNP markers, 3,928 of which were bi-allelic. After applying multiple quality control filters, they obtained allele frequency estimates for 3,631 bi-allelic loci, observing high concordance between allele frequency estimates derived from individual genotyping and DNA pools. The authors believe that even relatively small DNA pools can provide accurate allele frequency estimates for a given sample.

Identification of rare recurrent copy number variants in high-risk autism families and their prevalence in a large ASD population.

PLOS ONE. 2013 Jan 14. [Epub ahead of print]

Matsunami N, Hadley D, Hensel C, et al.

To determine if large autism spectrum disorder families harbor high-impact copy number variantss that may have broader impact in the general ASD population, the authors used the Affymetrix SNP Array 6.0 to identify 153 putative autism-specific CNVs present in 55 individuals with ASD from nine multiplex ASD pedigrees. Then, to evaluate the actual prevalence of these CNVs as well as 185 CNVs reportedly associated with ASD from published studies, they designed a custom Illumina array and used it to interrogate the variants in 3,000 ASD cases and 6,000 controls. Ultimately, they confirmed the association of 31 of 185 published ASD-associated CNVs in a dataset with odds ratios greater than 2.0, suggesting they may be of clinical relevance in the evaluation of children with ASDs.

BioArray News spoke with Michael Paul, CEO of Lineagen, which participated in this study, last week (BAN 1/15/2013).

Polymer adhesive surface as flexible generic platform for multiplexed assays biochip production.

Biosens Bioelectron. 2013 Jan 15;39(1):37-43.

Mandon C, Berthuy O, Corgier B, et al.

The authors present a new microarray concept based on adhesive surfaces. They claimed to have produced 384- and 1,536-well plates modified with 100 and 25 spots per well, respectively. Such in-well densities were possible due to the fabrication process, which implies first the deposition of the microarray on a flat adhesive surface and then its assembly with bottomless 384- or 1,536-well plates. The concept has also been applied to various applications such as oligonucleotide detection, localized cell culture onto spotted adhesion proteins, and immobilization of peptide or active antibodies for immunoassays.

High-throughput SNP-based authentication of human cell lines.

Int J Cancer. 2013 Jan 15;132(2):308-14.

Castro F, Dirks W, Fähnrich S, et al.

To combat the use of false cell lines, the authors developed a Luminex-based, 24-plex SNP profiling assay, called multiplex cell authentication, for determining authentication of human cell lines. MCA was evaluated by analyzing a collection of 436 human cell lines from the German Collection of Microorganisms and Cell Cultures, previously characterized by eight-loci STR profiling. By analyzing mismatch repair-deficient cell lines, evidence was obtained for a higher robustness of the MCA compared to STR profiling. The authors argue that MCA could complement routine cell line authentication and replace the standard authentication STR technique in case of microsatellite instability cell lines.

Mosaic copy number variation in schizophrenia.

Eur J Hum Genet. 2013 Jan 16. [Epub ahead of print]

Ruderfer D, Chambert K, Moran J, et al.
On behalf of the International Schizophrenia Consortium, these authors used SNP genotyping arrays to study samples from schizophrenic patients for evidence of chromosomal anomalies. Data were processed using Birdsuite, analyzed with PLINK, and validated using custom Nanostring probes and quantitative PCR. Based on that analysis, the authors estimate chromosomal alterations in the schizophrenia population to be 0.42 percent, which was not significantly different from the 0.26 in controls. The authors concluded that chromosomal anomalies are present at low frequency in blood cells of both control and schizophrenia subjects.