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Last Week's Microarray Papers of Note


Impact of genetic ancestry and sociodemographic status on the clinical expression of systemic lupus erythematosus in American Indian-European populations.

Arthritis Rheum. 2012 Nov;64(11):3687-94.

Sánchez E, Rasmussen A, Riba L, et al.

The aim of this study was to analyze the relationship between genetic ancestry and sociodemographic characteristics and clinical features in a large cohort of American Indian-European systemic lupus erythematosus patients. Genotyping of 253 continental ancestry-informative markers was performed on the Illumina platform. The average American Indian genetic ancestry of 2,116 SLE patients was 40.7 percent. The authors found that American Indian genetic ancestry conferred increased risks of renal involvement and early age at onset of SLE. American Indian ancestry also protected against photosensitivity, oral ulcers, and serositis after adjustment for age, sex, and age at onset. However, age and sex had stronger effects than genetic ancestry on malar rash, discoid rash, arthritis, and neurologic involvement. In general, the authors stated, American Indian genetic ancestry correlates with lower sociodemographic status and increases the risk of developing renal involvement and SLE at an earlier age.

Genome-wide association study (GWAS) of resistance to head smut in maize.

Plant Sci. 2012 Nov;196:125-31.

Wang M, Yan J, Zhao J, et al.

According to the authors, head smut, caused by the fungus Sphacelotheca reiliana (Kühn) Clint, is a global disease in maize, leading to quality and yield loss each year. They conducted a genome-wide association study of head smut resistance using the Illumina MaizeSNP50 array. Out of 45,868 SNPs in a panel of 144 inbred lines, 18 novel candidate genes were associated with head smut resistance in maize. The authors classified these candidate genes into three groups: resistance genes, disease response genes, and other genes with possible plant disease resistance functions.

Rapid characterization of candidate biomarkers for pancreatic cancer using cell microarrays.

J Proteome Res. 2012 Nov 2;11(11):5556-63.

Kim M, Kuppireddy S, Sakamuri S, et al.

The authors constructed a cell microarray containing a panel of 40 pancreatic cancer cell lines available from American Type Culture Collection in addition to those available at Johns Hopkins University. As proof of principle, they performed immunocytochemical labeling of an epithelial cell adhesion molecule, a molecule generally expressed in the epithelium, on the pancreatic cancer CMA. They believe the array could be a "useful resource for rapid screening of molecules of interest" and suggest that CMAs "can become a universal standard platform in cancer research."

Concordance among gene expression-based predictors for ER-positive breast cancer treated with adjuvant tamoxifen.

Ann Oncol. 2012 Nov;23(11):2866-73.

Prat A, Parker J, Fan C, et al.

The authors evaluated the ability of six clinically relevant genomic signatures, including the PAM50, OncotypeDX, and MammaPrint signatures, to predict relapse in patients with ER+ breast cancer tumors treated with adjuvant tamoxifen only. They determined that established genomic signatures were successful in outcome predictions in ER+ breast cancer and provided statistically independent information. From a clinical perspective, they argued that multiple signatures combined together most accurately predicted outcome, but a common finding was that each signature identified a subset of luminal A patients with node-negative disease who might be considered suitable candidates for adjuvant endocrine therapy alone.

Variability in the distribution of genes encoding virulence factors and putative extracellular proteins of Streptococcus pyogenes in India, a region with high streptococcal disease burden, and implication for development of a regional multisubunit vaccine.

Clin Vaccine Immunol. 2012 Nov;19(11):1818-25.

Sagar V, Bergmann R, Nerlich A, et al.

This study sought to identify streptococcal antigens suitable for a region-specific vaccine in India. The authors performed epidemiological analysis to identify the conserved antigens among Indian isolates and then validated the identified antigens by serological analysis. Virulence profiling of the North and South Indian S. pyogenes isolates with a custom-designed streptococcal virulence microarray identified seven conserved putative vaccine candidates.

Clinical significance of genetic aberrations in secondary acute myeloid leukemia.

Am J Hematol. 2012 Nov;87(11):1010-6.

Milosevic J, Puda A, Malcovati L, et al.

The study aimed to identify genetic lesions associated with secondary acute myeloid leukemia in comparison with AML arising de novo and to assess their impact on patients' overall survival. High-resolution genotyping and loss of heterozygosity mapping was performed on DNA samples from 86 sAML and 117 dnAML patients, using Affymetrix Genome-Wide Human SNP 6.0 arrays. The resulting data suggested that distinct genetic lesions drive leukemogenesis in sAML, that high karyotype complexity of sAML patients does not influence overall survival, and that somatic mutations in the TP53 gene are the only independent adverse prognostic factor in sAML.

ColoGuideEx: a robust gene classifier specific for stage II colorectal cancer prognosis.

Gut. 2012 Nov;61(11):1560-7.

Agesen T, Sveen A, Merok M, et al.

An optimal 13-gene expression classifier for prediction of relapse among patients with stage II colorectal cancer was developed using Affymetrix exon microarrays to screen Norwegian patients treated according to current standard protocols. Its predictive value was successfully validated for patients with stage II CRC in a second Norwegian CRC series collected two decades previously.

BioArray News spoke with the researchers about the new signature earlier this year (BAN 3/13/2012).

The Scan

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.

Circulating Tumor DNA Linked to Post-Treatment Relapse in Breast Cancer

Post-treatment detection of circulating tumor DNA may identify breast cancer patients who are more likely to relapse, a new JCO Precision Oncology study finds.

Genetics Influence Level of Depression Tied to Trauma Exposure, Study Finds

Researchers examine the interplay of trauma, genetics, and major depressive disorder in JAMA Psychiatry.

UCLA Team Reports Cost-Effective Liquid Biopsy Approach for Cancer Detection

The researchers report in Nature Communications that their liquid biopsy approach has high specificity in detecting all- and early-stage cancers.