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In Print: Last Week's Microarray Papers of Note: Apr 30, 2013


Genetic markers associated with early cancer-specific mortality following prostatectomy.
Cancer. 2013 Apr 22. [Epub ahead of print]
Liu W, Xie C, Thomas C, et al.

This study sought to identify novel effectors and markers of localized but potentially life-threatening prostate cancer, by evaluating chromosomal copy number alterations in tumors from patients who underwent prostatectomy and correlating these with clinicopathologic features and outcome. CNAs in tumor DNA samples from 125 patients in the discovery cohort who underwent prostatectomy were assayed with high-resolution Affymetrix SNP 6.0 microarrays and then analyzed using the Genomic Identification of Significant Targets in Cancer algorithm. The assays revealed 20 significant regions of CNAs, four of them novel, and identified the target genes of four of the alterations.

Genomic arrays in chronic lymphocytic leukemia routine clinical practice: are we ready to substitute conventional cytogenetics and fluorescence in situ hybridization techniques?
Leuk Lymphoma. 2013 May; 54(5):986-95.
Puiggros A, Puigdecanet E, Salido M, et al.

The authors analyzed 70 patients with chronic lymphocytic leukemia using Affymetrix's Cytogenetics Whole-Genome 2.7M Array and CytoScan HD Array, CGC, and FISH with the classical CLL panel. Though they found that abnormality detection is higher when arrays are applied, one case with del(11q) and three with del(17p) were missed by genomic arrays due to their limited sensitivity. The authors concluded that the complete substitution of CGC and FISH by genomic arrays in routine laboratories could negatively affect the management of some patients harboring 11q or 17p deletions.

SNP genotyping in melons: genetic variation, population structure, and linkage disequilibrium.
Theor Appl Genet. 2013 May; 126(5):1285-303.
Esteras C, Formisano G, Roig C, et al.

The authors present the first validated design for a genotyping array with 768 SNPs that are evenly distributed throughout the melon genome. The customized Illumina GoldenGate assay was used to genotype a collection of 74 accessions, representing most of the botanical groups of the species. Of the assayed loci, 91 percent were successfully genotyped.

The Scan

Lung Cancer Response to Checkpoint Inhibitors Reflected in Circulating Tumor DNA

In non-small cell lung cancer patients, researchers find in JCO Precision Oncology that survival benefits after immune checkpoint blockade coincide with a dip in ctDNA levels.

Study Reviews Family, Provider Responses to Rapid Whole-Genome Sequencing Follow-up

Investigators identified in the European Journal of Human Genetics variable follow-up practices after rapid whole-genome sequencing.

BMI-Related Variants Show Age-Related Stability in UK Biobank Participants

Researchers followed body mass index variant stability with genomic structural equation modeling and genome-wide association studies of 40- to 72-year olds in PLOS Genetics.

Genome Sequences Reveal Range Mutations in Induced Pluripotent Stem Cells

Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.