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

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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

Purnell Choppin Dies

Purnell Choppin, a virologist who led the Howard Hughes Medical Institute, has died at 91, according to the Washington Post.

Effectiveness May Decline, Data From Israel Suggests

The New York Times reports that new Israeli data suggests a decline in Pfizer-BioNTech SARS-CoV-2 vaccine effectiveness against Delta variant infection, though protection against severe disease remains high.

To See Future Risk

Slate looks into the use of polygenic risk scores in embryo screening.

PLOS Papers on Methicillin-Resistant Staphylococcus, Bone Marrow Smear Sequencing, More

In PLOS this week: genomic analysis of methicillin-resistant Staphylococcus pseudintermedius, archived bone marrow sequencing, and more.