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In Print: Last Week's Microarray Papers of Note: Oct 16, 2012


High-resolution genomic profiling of chronic lymphocytic leukemia reveals new recurrent genomic alterations.
Blood. 2012 Oct 9. [Epub ahead of print]
Edelmann J, Holzmann K, Miller F, et al.

To identify genomic alterations in chronic lymphocytic leukemia, the authors performed SNP array analysis using Affymetrix 6.0 chips on 353 samples from untreated patients. Based on paired-sample analysis, a mean of 1.8 copy number alterations per case were identified and about 60 percent of cases carried no CNAs other than those detected by fluorescence in situ hybridization analysis.

Analysis of copy number variations in brain DNA from patients with schizophrenia and other psychiatric disorders.
Biol Psychiatry. 2012 Oct 15;72(8):651-4.
Ye T, Lipska B, Tao R, et al.

The authors used genotyping arrays to search for evidence of previously reported recurrent copy number variants and enriched genome-wide CNV burden in DNA from 600 brains, including 441 individuals with various psychiatric diagnoses. The analysis confirmed the presence of certain recurrent CNVs in the brain DNA of a small percentage of patients with psychiatric diagnoses.

Genome position specific priors for genomic prediction.
BMC Genomics. 2012 Oct 10;13(1):543.
Brøndum R, Su G, Lund M, et al.

This paper describes an approach to share information across populations for genomic predictions, allowing information to be captured even where the phase of SNP alleles and casual mutation alleles are reversed across populations, or the actual casual mutation is different between the populations but affects the same gene. Proportions of a four-distribution mixture for SNP effects in segments of fixed size along the genome are derived from one population and set as location-specific prior proportions of distributions of SNP effects for the target population. The model was tested using dairy cattle populations of different breeds: 540 Australian Jersey bulls, 2,297 Australian Holstein bulls and 5,214 Nordic Holstein bulls. The traits studied were protein, fat, and milk yield. The genotypic data was generated using Illumina arrays.

Microarray analysis reveals abnormal chromosomal complements in over 70 percent of 14 normally developing human embryos.
Hum Reprod. 2012 Oct 9. [Epub ahead of print]
Mertzanidou A, Wilton L, Cheng J, et al.

The authors of this study set out to determine aneuploidy rates and incidence of mosaicism in good-quality human preimplantation embryos. They performed array comparative genomic hybridization on nine embryos from 14 young in vitro fertilization patients. They found that good quality embryos exhibited high rates of aneuploidy, leading them to suggest further research on the origin and significance of chromosomal abnormalities in human preimplantation embryos.

A HaloTag-based small molecule microarray screening methodology with increased sensitivity and multiplex capabilities.
ACS Chem Biol. 2012 Oct 11. [Epub ahead of print]
Noblin D, Page C, Tae H, et al.

The authors modified a small-molecule microarray screening methodology by fusing target proteins to the HaloTag protein. This allowed them to covalently prelabel fusion proteins with fluorophores, leading to increased assay sensitivity and an ability to conduct multiplex screens.

Rapid characterization of candidate biomarkers for pancreatic cancer using cell microarrays (CMAs).
J Proteome Res. 2012 Oct 11. [Epub ahead of print]
Kim M, Kuppireddy S, Sakamuri S, et al.

The authors constructed a cell microarray containing a panel of 40 pancreatic cancer cell lines. To establish proof of principle, they performed immunocytochemical labeling of an epithelial cell adhesion molecule, a molecule generally expressed in the epithelium, on the pancreatic cancer CMA. In addition, selected molecules that had been previously shown to be differentially expressed in pancreatic cancer in the literature were validated.

Signal amplification of microarray-based immunoassay by optimization of nanoliposome formulations.
Anal Biochem. 2012 Oct 15;429(2):142-7.
Ruktanonchai U, Nuchuchua O, Charlermroj R, et al.

The authors evaluated two different liposome formations and several preparation methods to optimize encapsulation and signal-enhancing efficacy for enzyme-linked immunosorbent assay and antibody arrays. The signal amplification by liposome encapsulation was demonstrated through a detection for foodborne pathogenic Listeria.

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