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In Print: Last Week's Microarray Papers of Note: Dec 18, 2012


Prenatal diagnosis of de novo partial trisomy 18p and partial monosomy 18q recurrent in a family with fatal aortic coarctation.
Gene. 2012 Dec 8. [Epub ahead of print]
Hu H, Hao J, Yao H, et al.

This paper describes a chromosomal breakpoint that may be responsible for aortic coarctation, a life-threatening heart defect. The authors used array comparative genomic hybridization to study two male fetuses with the condition. The analysis suggested a de novo 17.7 megabase deletion of chromosome 18q21.33 and a de novo 12.4 megabase duplication of chromosome 18p11.21 at the telomeric end of chromosome 18.

Comprehensive DNA methylation analysis of peripheral blood cells derived from patients with first-episode schizophrenia.
J Hum Genet. 2012 Dec 13. [Epub ahead of print]
Nishioka M, Bundo M, Koike S, et al.

The authors investigated the methylation profiles of DNA in peripheral blood cells from 18 patients with first-episode schizophrenia and from 15 normal controls using the Illumina Infinium HumanMethylation27 BeadChip array. They found that differentially methylated CpG sites, which were particularly abundant within CpG islands, were enriched in genes related to the nuclear lumen, to transcription factor binding, and to nucleotide binding. They also observed differential methylation of the promoters of HTR1E and COMTD1, which are functionally related to genes found to be differentially methylated in schizophrenia patients in previous studies.

Investigation of transferability of BovineSNP50 BeadChip from cattle to water buffalo for genome wide association study.
Mol Biol Rep. 2012 Dec 12. [Epub ahead of print]
Wu J, Song L, Wu F, et al.

The authors used genome-wide Illumina BovineSNP50 BeadChips to analyze 91 DNA samples from three breeds of water buffalo to demonstrate the genetic divergence between cattle and water buffalo through a SNP transferability study at the whole-genome level, and performed association analysis of functional traits in water buffalo as well. Seventy-six percent of bovine SNPs were found in the water buffalo genome, but 93 percent were with only one allele, and 935 SNPs were identified to be polymorphic and useful for association analysis in water buffalo. The authors concluded that the genome sequences of water buffalo and cattle share a high level of homology but the polymorphic status of the bovine SNPs varied between these two species.

Is chemically dispersed oil more toxic to Atlantic cod (Gadus morhua) larvae than mechanically dispersed oil? A transcriptional evaluation.
BMC Genomics. 2012 Dec 14;13(1):702.
Olsvik P, Lie K, Nordtug T, et al.

The authors exposed Atlantic cod larvae to chemically and mechanically dispersed oil for four days during the first-feeding stage of development, and collected larvae at 14 days post hatch for transcriptional analysis. A genome-wide microarray was used to screen for effects and to assess whether molecular responses to chemically and mechanically dispersed oil were similar, given the same exposure to oil with and without the addition of a chemical dispersant. Based on the subsequent analysis, they concluded that dispersants do not appear to add to the magnitude of transcriptional responses of oil compounds but rather appear to lower or modify the transcriptional effect on cod larvae.

Monitoring piroplasms infection in three cattle farms in Minorca (Balearic Islands, Spain) with previous history of clinical piroplasmosis.
Vet Parasitol. 2012 Dec 21;190(3-4):318-25.
Ros-García A, García-Pérez AL, Verdera J, et al.

Bovine piroplasmosis are tick-borne protozoan diseases caused by parasites of the genera Theileria and Babesia. Three Friesian cattle farms with previous history of clinical piroplasmosis were selected in Minorca. Blood samples were collected from eight to 11 animals every two months throughout a year and a multiplex DNA bead-based suspension array based on the Luminex xMAP technology was used to monitor for the presence of piroplasms. According to the authors, the study confirmed the endemic situation for piroplasm infection in the region and detected the presence of a large number of chronic asymptomatic carriers.

The Scan

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.

Researchers Retrace Key Mutations in Reassorted H1N1 Swine Flu Virus With Avian-Like Features

Mutations in the acidic polymerase-coding gene boost the pathogenicity and transmissibility of Eurasian avian-like H1N1 swine influenza viruses, a PNAS paper finds.

Genome Sequences Reveal Evolutionary History of South America's Canids

An analysis in PNAS of South American canid species' genomes offers a look at their evolutionary history, as well as their relationships and adaptations.

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.