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In Print: Last Week's Microarray Papers of Note: Sep 18, 2012


A genome-wide association study identifies five loci influencing facial morphology in Europeans
PLoS Genet. 2012 Sept 13. [Epub ahead of print]
Liu F, van der Lijn F, Schurmann C, et al.

The authors used SNP genotyping arrays to conduct a genome-wide association study for facial shape phenotypes in multiple discovery and replication cohorts, considering almost ten thousand individuals of European descent from several countries. They identified five independent genetic loci associated with different facial phenotypes, suggesting the involvement of five candidate genes — PRDM16, PAX3, TP63, C5orf50, and COL17A1 — in the determination of the human face.

Microarray, gene sequencing, and reverse transcriptase-polymerase chain reaction analyses of a cryptic PML-RARA translocation.
Cancer Genet. 2012 Sep 13. [Epub ahead of print]
Koshy J, Qian Y, Bhagwath G, et al.

Acute promyelocytic leukemia is a well-defined subtype of acute myeloid leukemia specifically characterized by the t(15;17)(q22;q12) translocation. The authors report an APL clone with a cryptic PML-RARA fusion that returned negative results by both karyotyping and fluorescence in situ hybridization, but returned positive results by RT-PCR analysis. The authors used Affymetrix's CytoScan HD to help resolve the discordance, revealing a 49-kilobase intragenic PML gene duplication.

Brain transcriptional and epigenetic associations with autism.
PLoS One. 2012;7(9):e44736.
Ginsberg M, Rubin R, Falcone T, et al.

To uncover important gene dysregulation in autism, the authors analyzed selected idiopathic autistic and control cerebellar and BA19 brain tissues using high-resolution, whole-genome gene expression and whole-genome DNA methylation microarrays. No changes in DNA methylation were identified in autistic brain but gene expression abnormalities in two areas of metabolism were apparent: down-regulation of genes of mitochondrial oxidative phosphorylation and of protein translation.

Gene-targeted analysis of copy number variants identifies three novel associations with coronary heart disease traits.
Circ Cardiovasc Genet. 2012 Sep 12. [Epub ahead of print]
Costelloe S, El-Sayed Moustafa J, Drenos F, et al.

The authors assessed the utility of the cnvHap algorithm for CNV detection. An Illumina custom chip including 722 SNPs covering 76 CHD-trait genes was employed and common CNVs were found to be significantly associated with CHD phenotypes in five genes.

Identification of unbalanced genome copy number abnormalities in patients with multiple myeloma by single-nucleotide polymorphism genotyping microarray analysis.
Int J Hematol. 2012 Sep 13. [Epub ahead of print]
Kamada Y, Sakata-Yanagimoto M, Sanada M, et al.

To obtain detailed information on genomic abnormalities related to pathogenesis or prognosis of multiple myeloma, the authors performed 250K SNP array analysis in 39 multiple myeloma patients and 11 cell lines, and identified an accumulation of deletions and uniparental disomies at 22q12.1.

Technical reproducibility of genotyping SNP arrays used in genome-wide association studies.
PLoS One. 2012;7(9):e44483.
Hong H, Xu L, Liu J, et al.

The authors of this paper assessed the reproducibility of Affymetrix and Illumina's genotyping platforms by analyzing four technical replicates from six individuals across five laboratories. Arrays with low quality data were detected when comparing genotyping data from technical replicates, but they could not be detected according to vendors' quality control suggestions. The authors concluded that incorporating some technical replicates for genotyping QC could improve the reliability of GWAS results.

The Scan

Ancient Greek Army Ancestry Highlights Mercenary Role in Historical Migrations

By profiling genomic patterns in 5th century samples from in and around Himera, researchers saw diverse ancestry in Greek army representatives in the region, as they report in PNAS.

Estonian Biobank Team Digs into Results Return Strategies, Experiences

Researchers in the European Journal of Human Genetics outline a procedure developed for individual return of results for the population biobank, along with participant experiences conveyed in survey data.

Rare Recessive Disease Insights Found in Individual Genomes

Researchers predict in Genome Medicine cross-population deletions and autosomal recessive disease impacts by analyzing recurrent nonallelic homologous recombination-related deletions.

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.