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In Print: Last Week's Microarray Papers of Note: Oct 30, 2012


Identification of biomarkers to assess organ quality and predict posttransplantation outcomes.
Transplantation. 2012 Oct 27;94(8):851-858.
Scian M, Maluf D, Archer K, et al.

The authors examined the preimplantation transcriptome of 112 kidney transplant recipient samples from 100 deceased-donor kidneys by microarray profiling. Subject groups were segregated into high and low groups based on estimated glomerular filtration rate at a month after transplantation. Gene expression profiling identified higher expression of 160 probe sets (140 genes) in the GFR-low group, while expression of 37 probe sets was higher in the GFR-high group. Four genes — CCL5, CXCR4, ITGB2, and EGF — were selected based on fold change and P value and further validated using an independent set of samples. A random forest analysis identified three of these genes — CCL5, CXCR4, and ITGB2 — as important predictors of graft function after transplantation.

Matrix metalloproteinases and educational attainment in refractive error: evidence of gene-environment interactions in the Age-Related Eye Disease Study.
Ophthalmology. 2012 Oct 23. pii: S0161-6420(12)00741-5.
Wojciechowski R, Yee S, Simpson C, et al.

According to the authors, a previous study of Old Order Amish families showed an association of ocular refraction with markers proximal to matrix metalloproteinase genes MMP1 and MMP10 and intragenic to MMP2. A candidate gene replication study of association between refraction and SNPs within these genomic regions was conducted on 1,912 individuals using Illumina's HumanOmni2.5 BeadChip. The authors concluded that variants in MMP1 through MMP10 and MMP2 regions seem to affect population variation in ocular refraction in environmental conditions less favorable for myopia development.

Aberrant placenta gene expression pattern in bovine pregnancies established after transfer of cloned or in vitro produced embryos.
Physiol Genomics. 2012 Oct 23. [Epub ahead of print]
Salilew-Wondim D, Tesfaye D, Hossain M, et al.

The authors relied on a global transcriptome profile approach to identify dysregulated genes, molecular pathways, and molecular functional alterations in bovine placentas derived from somatic cell nuclear transfer and intravenous pyelogram pregnancies compared to their artificial counterparts at day 50 of gestation. Day 7 blastocysts derived from AI, IVP or SCNT were transferred to oestrus synchronized cows. The pregnant animals were then slaughtered at day 50 of the gestation and the placentas were then recovered and used for transcriptome analysis using Affymetrix GeneChip bovine genome arrays. The authors found that higher transcriptome dysregulation in the SCNT placenta followed by IVP reflects the degree of placental abnormality in SCNT and IVP pregnancies at day 50 of the gestation, which they claim "may have a profound effect" on subsequent fetal development and health of the offspring.

Identification of a CpG island methylator phenotype in adrenocortical carcinomas.
J Clin Endocrinol Metab. 2012 Oct 23. [Epub ahead of print]
Barreau O, Assié G, Wilmot-Roussel H, et al.

The authors set out to characterize the methylation in adrenocortical carcinomas at a whole-genome scale and to assess its clinical significance and its impact on gene expression. Methylation patterns of CpG islands in promoter regions of 51 adrenocortical carcinomas and 84 adenomas were studied using lllumina's Infinium HumanMethylation27 BeadChip and other methods. The authors found methylation to be higher in carcinomas than in adenomas. Hypermethylation was associated with a poor survival, leading the authors to conclude that hypermethylation is "important for silencing specific tumor suppressor genes."

Development, characterization and experimental validation of a cultivated sunflower (Helianthus annuus L.) gene expression oligonucleotide microarray.
PLoS One. 2012 Oct 26. [Epub ahead of print]
Fernandez O, Soria M, Blesa D, et al.

The goal of this study was the development and functional annotation of a comprehensive sunflower unigene collection and the design and validation of a custom sunflower oligonucleotide-based microarray. A large-scale EST curation, assembly and sequence annotation was performed using Blast2GO. The resulting Sunflower Unigen Resource was used to design an oligonucleotide-based Agilent microarray for cultivated sunflower. According to the authors the microarray includes a total of 42,326 features: 1,417 Agilent controls, 74 control probes for sunflower, and 40,169 different non-control probes. Microarray performance was validated using a model experiment examining the induction of senescence by water deficit.

The Scan

Genetic Tests Lead to Potential Prognostic Variants in Dutch Children With Dilated Cardiomyopathy

Researchers in Circulation: Genomic and Precision Medicine found that the presence of pathogenic or likely pathogenic variants was linked to increased risk of death and poorer outcomes in children with pediatric dilated cardiomyopathy.

Fragile X Syndrome Mutations Found With Comprehensive Testing Method

Researchers in Clinical Chemistry found fragile X syndrome expansions and other FMR1 mutations with ties to the intellectual disability condition using a long-range PCR and long-read sequencing approach.

Team Presents Strategy for Speedy Species Detection in Metagenomic Sequence Data

A computational approach presented in PLOS Computational Biology produced fewer false-positive species identifications in simulated and authentic metagenomic sequences.

Genetic Risk Factors for Hypertension Can Help Identify Those at Risk for Cardiovascular Disease

Genetically predicted high blood pressure risk is also associated with increased cardiovascular disease risk, a new JAMA Cardiology study says.