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In Print: Last Week's Microarray Papers of Note: Sep 4, 2012


Prognostic significance of promoter DNA methylation in patients with childhood neuroblastoma.

Clin Cancer Res. 2012 Aug 28. [Epub ahead of print]

Lau D, Hesson L, Norris M, et al.

The authors used a customized Illumina GoldenGate methylation assay to assess the methylation status of 96 CpG sites within 48 candidate genes in primary neuroblastoma tumors obtained from 131 children diagnosed in Australia. They found that hypermethylation of the genes FOLH1, MYOD1, and THBS1 remained "significant independent predictors of poorer clinical outcome."

Reliability of genomic prediction for German Holsteins using imputed genotypes from low-density chips.

J Dairy Sci. 2012 Sep;95(9):5403-11.

Segelke D, Chen J, Liu Z, et al.

According to the authors, the costs associated with Illumina's BovineSNP50 BeadChip are still too high to have all cows genotyped and genomically evaluated. The purpose of this study was to evaluate the accuracy of imputing genotypes from data derived from cheaper low-density chips, the Illumina Bovine3K BeadChip and BovineLD BeadChip. The authors reported that the 6K gave "markedly higher imputation accuracy and more accurate genomic prediction" than the 3K chip.

Identification of germline genomic copy number variation in familial pancreatic cancer.

Hum Genet. 2012 Sep;131(9):1481-94.

Al-Sukhni W, Joe S, Lionel A, et al.

A total of 120 familial pancreatic cancer cases and 1,194 controls were genotyped on the Affymetrix 500K array, and 36 cases and 2,357 controls were genotyped on the Affymetrix 6.0 array. A total of 93 non-redundant FPC-specific copy number variants were identified in 50 cases. The authors believe that further investigation in high-risk subjects may elucidate the role of one or more of these variants in genetic predisposition to pancreatic cancer.

Microarray and suppression subtractive hybridization analyses of gene expression in hybrid poplar (Populus alba × Populus tremula var. glandulosa) cell suspension cultures after exposure to NaCl.

Plant Physiol Biochem. 2012 Sep;58:151-8.

Bae EK, Lee H, Lee JS, et al.

The gene expression profiles of hybrid poplar (Populus alba × Populus tremula var. glandulosa) cells in suspension culture after exposure to salinity-induced stress were examined by constructing two suppression subtractive hybridization libraries. Between the two libraries, 542 unique SSH clones were selected for placement on a cDNA microarray. In total, 18 differentially expressed genes were identified with 4 and 12 genes being significantly differentially expressed two and 10 hours after the treatment, respectively.

A molecular signature for oncogenic BRAF in human colon cancer cells is revealed by microarray analysis.

Curr Cancer Drug Targets. 2012 Sep 1;12(7):873-98.

Joyce T, Oikonomou E, Kosmidou V, et al.

In this study, the authors report a molecular profile for a BRAF oncogenic mutation BRAFV600E in colon cancer using an Illumina 45,000-gene microarray.

Probe mapping across multiple microarray platforms.

Brief Bioinform. 2012 Sep;13(5):547-54.

Allen JD, Wang S, Chen M, et al.

The authors compared different approaches to map probes across seven platforms from different vendors: the U95A, U133A and U133 Plus 2.0 GeneChips from Affymetrix; the HT-12 v1, HT-12 v2, and HT-12 v3 BeadChips from Illumina; and the 4112A array from Agilent. They used a data set consisting of 56 lung cancer cell line samples to evaluate the consistency of expression measurement across platforms using the different approaches.

Microarray-based transcriptome of Listeria monocytogenes adapted to sublethal concentrations of acetic acid, lactic acid, and hydrochloric acid.

Can J Microbiol. 2012 Sep;58(9):1112-23.

Tessema GT, Møretrø T, Snipen L, et al.

The authors of this study used microarrays to observe the transcriptional responses of L. monocytogenes toward food-related acidulants.

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