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In Print: Last Week's Microarray Papers of Note: Oct 14, 2014

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Reproducible, quantitative and flexible molecular sub-typing of clinical DLBCL samples using the NanoString nCounter system.
Clin Cancer Res. 2014 Oct 9. [Epub ahead of print]
Veldman-Jones M, et al.

The authors evaluated the NanoString nCounter gene expression system to address issues with current approaches for subtyping diffuse large B-cell lymphoma. They devised a scoring system using 145 genes from published datasets to categorize DLBCL samples and profiled biospies using NanoString, Affymetrix microarrays, and HTG Molecular's qNPA platform. The authors found that NanoString offered the "most flexibility and fewest limitations in regards to robust clinical tissue subtype characterization."


FISH for 22q11.2 deletion not cost-effective for infants with congenital heart disease with microarray.
Pediatr Cardiol. 2014 Oct 11. [Epub ahead of print]
Geddes G, et al.

The authors evaluated the yield of fluorescence in situ hybridization and microarray-based genetic testing in infants with congenital heart disease. The commonly encountered 22q11.2 deletion was abnormal in around 7 percent of patients using FISH, while SNP microarray testing identified the abnormality in 33 percent of patients. Based on the results, the authors suggested that a more directed approach of genetic screening with only microarray would have saved their institution approximately $101,200 on the 103 patients who were tested using both methods. Screening infants with congenital heart disease for 22q11.2 deletion with FISH resulted in a loss of approximately $32,000 per 100 patients at our institution, they wrote. According to the authors, institutions should develop microarray-based protocols for genetic screening in patients with congenital heart disease with the anticipation of adding lesion-specific single-gene testing as single-gene testing becomes routinely available.


Epigenome-wide association study for Parkinson's disease.
Neuromolecular Med. 2014 Oct 11. [Epub ahead of print]
Moore K, et al.

The authors used the Illumina Infinium HumanMethylation450K BeadChip to carry out a methylation-based EWAS on carefully phenotyped individuals with Parkinson's disease. Twenty genes with a sizable difference in methylation were identified between PD and controls, while 17 were identified that could distinguish Parkinson's disease cases where the patient reported anxiety from those cases where no anxiety was reported. Twelve significantly associated loci in PD were evaluated in an independent replicate population using Sequenom's EpiTYPER DNA methylation technology (which now belongs to Agena Bioscience) for 219 individuals with similar phenotypes to the cross-sectional case-control discovery design.

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