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In Print: Last Week's Microarray Papers of Note: Jun 25, 2013

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Genetic markers associated with early cancer-specific mortality following prostatectomy.
Cancer. 2013 Jul 1;119(13):2405-12.
Liu W, Xie C, Thomas C, et al.

Using Affymetrix 6.0 SNP microarrays, the authors were able to identify copy number alterations and genes that likely contribute to the pathogenesis of localized prostate cancer. They also suggested that patients whose tumors have acquired alterations of PTEN, MYC, or both, have an increased risk of early prostate cancer-specific mortality.


The use of miRNA microarrays for the analysis of cancer samples with global miRNA decrease.
RNA. 2013 Jul;19(7):876-88.
Wu D, Hu Y, Tong S, Williams B, et al.

To assess whether miRNA microarrays are suited or not to accurately detecting global miRNA decreases seen in cancers, the authors analyzed the miRNA profiles of samples with global miRNA decreases using Affymetrix miRNA microarrays following the inducible genetic deletion of Dicer1. Findings were validated in samples from patients with prostate cancer, where the combination of normal-exponential background correction with cyclic loess normalization and array weights correctly identified the greatest number of decreased miRNAs.


Neonatal levels of neurotrophic factors and risk of autism spectrum disorders.
Acta Psychiatr Scand. 2013 Jul;128(1):61-9.
Abdallah M, Mortensen E, Greaves-Lord K, et al.

The authors examined the levels of neurotrophic factors in dried blood spot samples of neonates diagnosed with autism spectrum disorders using Luminex technology. Results indicated that NTFs decreased during the neonatal period in ASD, leading the authors to suggest this may contribute to the pathophysiology of ASD through impairments of neuroplasticity.


Application of chromosomal microarray in the evaluation of abnormal prenatal findings.
Clin Genet. 2013 Jul;84(1):47-54.
Yatsenko S, Davis S, Hendrix N, et al.

The authors performed karyotype and array comparative genomic hybridization analyses on 177 prenatal samples. For 23 pregnancies, aCGH contributed important new information. In the paper, they also discuss the interpretation challenges associated with CNVs of unclear significance, incidental findings, and technical aspects.

The Scan

Expanded Genetic Testing Uncovers Hereditary Cancer Risk in Significant Subset of Cancer Patients

In Genome Medicine, researchers found pathogenic or likely pathogenic hereditary cancer risk variants in close to 17 percent of the 17,523 patients profiled with expanded germline genetic testing.

Mitochondrial Replacement Therapy Embryos Appear Largely Normal in Single-Cell 'Omics Analyses

Embryos produced with spindle transfer-based mitochondrial replacement had delayed demethylation, but typical aneuploidy and transcriptome features in a PLOS Biology study.

Cancer Patients Report Quality of Life Benefits for Immune Checkpoint Inhibitors

Immune checkpoint inhibitor immunotherapy was linked in JAMA Network Open to enhanced quality of life compared to other treatment types in cancer patients.

Researchers Compare WGS, Exome Sequencing-Based Mendelian Disease Diagnosis

Investigators find a diagnostic edge for whole-genome sequencing, while highlighting the cost advantages and improving diagnostic rate of exome sequencing in EJHG.