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In Print: Last Week's Microarray Papers of Note: May 14, 2013

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Age dependence of tumor genetics in unfavorable neuroblastoma: arrayCGH profiles of 34 consecutive cases, using a Swedish 25-year neuroblastoma cohort for validation.
BMC Cancer. 2013 May 9;13(1):231.
Cetinkaya C, Martinsson T, Sandgren J, et al.

The authors used a 32K BAC whole-genome tiling path array and Affymetrix SNP array platforms to generate DNA copy number profiles for 34 consecutive high-risk or lethal outcome neuroblastomas. In addition, age and MYCN amplification, or MNA, status were retrieved for 112 unfavorable neuroblastomas of the Swedish Childhood Cancer Registry, representing a 25-year neuroblastoma cohort of Sweden, in order to validate the findings. They determined that MNA and segmental 11q loss define two major genetic variants of unfavorable neuroblastoma with differences in their pace of tumor evolution and in genomic integrity.


Assessment of a pharmacogenomic marker panel in a polypharmacy population identified from electronic medical records.
Pharmacogenomics. 2013 May;14(7):735-44.
Oetjens M, Denny J, Ritchie M, et al.

The authors genotyped 326 frequently medicated individuals of European descent on the ADME Core Panel to assess quality and performance of the assay. They also compared quality control metrics and determined the extent of direct and indirect marker overlap between the ADME Core Panel and the Illumina Omni1-Quad. Results: The authors found the quality of the ADME Core Panel data to be high, with exceptions in select copy number variants and markers in certain genes, most notably CYP2D6.


Fragile X screening: quantification of FMRP in dried blood spots by a Luminex immunoassay.
J Mol Diagn. 2013 May 6. [Epub ahead of print]
LaFauci G, Adayev T, Kascsak R, et al.

The authors claim to have developed a "rapid, highly sensitive method" for quantifying fragile X mental retardation protein from dried blood spots and lymphocytes. This assay uses two new antibodies, a bacterially expressed abbreviated FMRP standard, and the Luminex platform to quantify FMRP. In the paper, they demonstrate how the assay could distinguish between samples from males with fragile X full mutations and samples from normal males.

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Genome Research Papers on IPAFinder, Structural Variant Expression Effects, Single-Cell RNA-Seq Markers

In Genome Research this week: IPAFinder method to detect intronic polyadenylation, influence of structural variants on gene expression, and more.