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In Print: Last Week's Microarray Papers of Note: Nov 13, 2012


Integration of genetics into a systems model of ECG traits using HumanCVD BeadChip.

Circ Cardiovasc Genet. 2012 Nov 8. [Epub ahead of print]

Gaunt T, Shah S, Nelson C, et al.

In this study, three population-based cohorts genotyped with the Illumina HumanCVD BeadChip and four quantitative electrocardiographic traits — PR interval, QRS axis, QRS duration, and QTc interval — were evaluated for SNP associations. Six gene regions contained SNPs associated with these traits, including SCN5A, CAV1-CAV2 locus, CDKN1A, NOS1AP, KCNH2, and KCNQ1. Expression QTL analyses of top associated SNPs were undertaken in human heart and aortic tissues. NOS1AP, SCN5A, IGFBP3, CYP2C9, and CAV1 showed evidence of differential allelic expression.

Gene profiling in partially resistant and susceptible near-isogenic tomatoes in response to late blight in the field.

Mol Plant Pathol. 2012 Nov 6. [Epub ahead of print]

Cai G, Restrepo S, Myers K, et al.

In order to better understand resistance to Phytophthora infestans in tomato, the authors compared the global gene expression of the susceptible tomato, M82, with its more resistant near-isogenic line, 6-2 (IL6-2), under field conditions using a microarray with more than 12,800 tomato expressed sequence tags. The two isolines had indistinguishable constitutive gene expressions prior to inoculation. However, a few genes were particularly prone to variation in both isolines in the absence of P.  infestans. Included among these genes were catalase, genes coding for pathogenesis-related proteins, endochitinase, and cytochrome P450.

Comparative transcriptome profiling in winter wheat grown under different agricultural practices.

J Agric Food Chem. 2012 Nov 7;60(44):10970-8.

Tenea G, Cordeiro Raposo F, Maquet A.

Comparative transcriptome profiling was conducted on winter wheat flag leaves of several cultivars growing in open fields under different agricultural production systems. Univariate and multivariate statistical analysis showed that the global wheat transcriptome is influenced by the agricultural system, indicating an approach for analytical verification of the production system of wheat at the farm level.

DNA microarray reveals that high proportions of human blastocysts from women of advanced maternal age are aneuploid and mosaic.

Biol Reprod. 2012 Nov 7. [Epub ahead of print]

Liu J, Wang W, Sun X, et al.

In this study, the authors used a microarray to examine aneuploid formation in human blastocysts produced in vitro and investigated the clinical outcome after transfer of euploid embryos. Transfer of array-screened blastocysts produced a pregnancy rate of 70 percent and an implantation rate of 64 percent. Additional microarray analysis indicated that high proportions of human blastocysts produced in vitro from women of advanced maternal age are aneuploid and mosaic.

Rapid aneusomy detection in products of conception using the KaryoLite BACs-on-Beads assay.

Prenat Diagn. 2012 Nov 8:1-7. [Epub ahead of print]

Paxton C, Brothman A, Geiersbach K.

The authors retrospectively tested 100 products of conception samples previously characterized by karyotype and microarray using PerkinElmer's KaryoLite BACs-on-Beads. They included samples extracted from either cultured or direct specimens from placental villi or fetal somatic tissue, with a variety of chromosomal abnormalities. TheKL-BoBs and microarray results were concordant for all cases of aneusomy.

High-throughput profiling of peptide-RNA interactions using peptide microarrays.

J Am Chem Soc. 2012 Nov 9. [Epub ahead of print]

Pai J, Yoon T, Kim N, et al.

The authors have developed a quantitative method that uses peptide microarrays to evaluate binding of hairpin RNAs to peptides. In this paper, they demonstrated the arrays' use in the high-throughput analysis of RNA-peptide interactions by profiling interactions between 111 peptides and six hairpin RNAs. The peptide microarrays were also employed to measure hundreds of dissociation constants of RNA-peptide complexes.

The Scan

UK Pilot Study Suggests Digital Pathway May Expand BRCA Testing in Breast Cancer

A randomized pilot study in the Journal of Medical Genetics points to similar outcomes for breast cancer patients receiving germline BRCA testing through fully digital or partially digital testing pathways.

Survey Sees Genetic Literacy on the Rise, Though Further Education Needed

Survey participants appear to have higher genetic familiarity, knowledge, and skills compared to 2013, though 'room for improvement' remains, an AJHG paper finds.

Study Reveals Molecular, Clinical Features in Colorectal Cancer Cases Involving Multiple Primary Tumors

Researchers compare mismatch repair, microsatellite instability, and tumor mutation burden patterns in synchronous multiple- or single primary colorectal cancers.

FarGen Phase One Sequences Exomes of Nearly 500 From Faroe Islands

The analysis in the European Journal of Human Genetics finds few rare variants and limited geographic structure among Faroese individuals.