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In Print: Last Week's Microarray Papers of Note: Apr 8, 2014


Genome-wide analysis of CNV (copy number variation) and their associations with narcolepsy in a Japanese population.
J Hum Genet. 2014 Apr 3. [Epub ahead of print]
Yamasaki M, et al.

The authors sought to investigate any possible association between rare and large CNVs and human narcolepsy. They used array data and a CNV detection software application called PennCNV-Affy to detect CNVs in 426 Japanese narcoleptic patients and 562 healthy individuals. They identified a risk association between multiple rare and large CNVs and the pathogenesis of narcolepsy.

Analytical method evaluation and discovery of variation within maize varieties in the context of food safety: transcript profiling and metabolomics.
J Agric Food Chem. 2014 Apr 2;62(13):2997-3009.
Zeng W, et al.

To assess the potential regulatory use of microarrays, proteomics, and metabolomics in agricultural biotechnology, the authors carried out microarray and metabolomic studies of three different tissues from 11 conventional maize varieties. Both microarray and metabolomic technologies proved to be reproducible and the authors concluded they can be used to detect plant-to-plant and variety-to-variety differences. At the same time, they cautioned that unknown genomic sequences differing between maize varieties might hinder the application of microarrays.

Association between upper digestive tract microbiota and cancer-predisposing states in the esophagus and stomach.
Cancer Epidemiol Biomarkers Prev. 2014 Apr 3. [Epub ahead of print]
Yu G, et al.

The authors used a human oral microbe identification microarray to test for the presence of 272 bacterial species in 333 upper digestive tract samples from a Chinese cancer screening cohort.
Lower microbial richness in the upper digestive tract was independently associated with both cancer-predisposing states in the esophagus and stomach.

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.