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In Print: Last Week's Microarray Papers of Note: Aug 7, 2012


Pretreatment dietary intake is associated with tumor suppressor DNA methylation in head and neck squamous cell carcinomas.
Epigenetics. 2012 Aug 1;7(8).
Colacino JA, Arthur AE, Dolinoy DC, et al.

The goal of this study was to describe the association between pretreatment diet and head and neck cancer tumor DNA methylation. Information on usual pretreatment food and nutrient intake was estimated via a food frequency questionnaire for 49 HNC cases and tumor DNA methylation patterns were assessed using the Illumina GoldenGate Methylation Cancer Panel.

Germline copy number variants are not associated with globally acquired copy number changes in familial breast tumors.
Breast Cancer Res Treat. 2012 Aug;134(3):1005-1011.
Walker LC, Krause L, et al.

By comparing germline CNVs and tumor-specific CNVs in matched breast tumor and normal tissue using data from the Illumina Human CNV370-Duo BeadChip, the authors claim to provide evidence that germline CNVs do not tend to act as a foundation on which larger chromosome copy number aberrations develop in tumor cells.

Chromosome 2p15p16.1 microdeletion syndrome: 2.5 Mb deletion in a patient with renal anomalies, intractable seizures and a choledochal cyst.
Eur J Med Genet. 2012 Aug;55(8-9):485-9.
Hucthagowder V, Liu TC, Paciorkowski AR, et al.

Using the Affymetrix SNP 6.0 array, the authors identified a de novo interstitial deletion on the short arm of chromosome 2, spanning approximately 2.5 Mb in the cytogenetic band position 2p15p16.1, in a female infant with characteristic features of 2p15p16.1 deletion syndrome including severe developmental delay, congenital microcephaly, intractable epilepsy, and renal anomalies, as well as a congenital choledochal cyst that has not been previously reported in other patients with this cytogenetic defect.

Identification of circulating fetal cell markers by microarray analysis.
Prenat Diagn. 2012 Aug;32(8):742-51.
Brinch M, Hatt L, Singh R, et al.

The objective of the study was to identify specific fetal cell markers from fetal cells found in the maternal blood circulation at the end of the first trimester. The expression pattern of a subset of expressed genes was compared between fetal cells and maternal blood cells using stem cell microarray analysis.

Integrative comparative analyses of transcript and metabolite profiles from pepper and tomato ripening and development stages uncovers species-specific patterns of network regulatory behavior.
Plant Physiol. 2012 Aug;159(4):1713-29.
Osorio S, Alba R, Nikoloski Z, et al.

The authors conducted combined gas chromatography-mass spectrometry and heterologous microarray hybridization assays in tomato and pepper fruits across development and ripening.

Characterization of antimicrobial resistance and virulence genotypes of Enterococcus faecalis recovered from a pork processing plant.
J Food Prot. 2012 Aug;75(8):1486-91.
Aslam M, Diarra MS, Masson L.

The authors of this study designed a microarray to assess the antimicrobial resistance and virulence genotypes of Enterococcus faecalis isolated from samples obtained from a commercial pork processing plant.

Spot identification and quality control in cell-based microarrays.
ACS Comb Sci. 2012 Aug 1. [Epub ahead of print]
Bauer M, Kim K, Qiu Y, et al.

This work introduces an automated approach to identify cell-based microarray spots and spot quality control. The approach was used to analyze the adhesion of murine cardiac side population cells on combinatorial arrays of extracellular matrix proteins.

Regions of homozygosity identified by SNP microarray analysis aid in the diagnosis of autosomal recessive disease and incidentally detect parental blood relationships.
Genet Med. 2012 Aug 2. [Epub ahead of print]
Sund KL, Zimmerman SL, Thomas C, et al.

The purpose of this study was to document the ability of SNP microarrays to identify copy-neutral regions of homozygosity, demonstrate clinical utility of regions of homozygosity, and discuss the ethical and legal implications when regions of homozygosity are associated with a parental blood relationship.

The Scan

Genes Linked to White-Tailed Jackrabbits' Winter Coat Color Change

Climate change, the researchers noted in Science, may lead to camouflage mismatch and increase predation of white-tailed jackrabbits.

Adenine Base Editor Targets SCID Mutation in New Study

Researchers from the University of California, Los Angeles, report in Cell that adenine base editing was able to produce functional T lymphocytes in a model of severe combined immune deficiency.

Researchers Find Gene Affecting Alkaline Sensitivity in Plants

Researchers from the Chinese Academy of Science have found a locus affecting alkaline-salinity sensitivity, which could aid in efforts to improve crop productivity, as they report in Science.

International Team Proposes Checklist for Returning Genomic Research Results

Researchers in the European Journal of Human Genetics present a checklist to guide the return of genomic research results to study participants.