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In Print: Last Week's Microarray Papers of Note: Jul 10, 2012


GPR-Analyzer: a simple tool for quantitative analysis of hierarchical multispecies microarrays.
Dittami SM, Edvardsen B.
Environ Sci Pollut Res Int. 2012 Jul 6. [Epub ahead of print]

Microarray Detection of Toxic Algae, or MIDTAL, is an FP7-funded EU project. This paper suggests a protocol for the analysis of the MIDTAL-developed and other hierarchical multispecies arrays.

Cytogenetic and morphological analysis of early products of conception following hystero-embryoscopy from couples with recurrent pregnancy loss.
Robberecht C, Pexsters A, Deprest J, Fryns JP, D'Hooghe T, Vermeesch JR.
Prenat Diagn. 2012 Jul 4:1-10.

Products of conception from 51 couples with at least one previous miscarriage were collected by hystero-embryoscopy and the extracted DNA was analyzed by low resolution array comparative genomic hybridization and high resolution SNP arrays to detect aneuploidies, polyploidies, submicroscopic copy number variants or copy neutral loss of heterozygosity.

Characterizing the surface quality and droplet interface shape for microarray plates.
Schertzer MJ, Ahamed MJ, Ben-Mrad R, Lea P, Sullivan PE.
Langmuir. 2012 Jul 3;28(26):9961-6.

The variation in the surface quality of microarray plates was examined by measuring the contact angles of 480 droplets on five microarray plates.

Liposomal glyco-microarray for studying glycolipid-protein interactions.
Ma Y, Sobkiv I, Gruzdys V, Zhang H, Sun XL.
Anal Bioanal Chem. 2012 Jul;404(1):51-8.

The authors report on the fabrication of a liposomal glyco-microarray by using an azide-reactive liposome that carries synthetic and natural glycolipids via chemically selective and biocompatible liposome immobilization chemistry.

High-capacity and high-intensity DNA microarray spots using oxygen-plasma nanotextured polystyrene slides.
Tsougeni K, Koukouvinos G, Petrou PS, Tserepi A, Kakabakos SE, Gogolides E.
Anal Bioanal Chem. 2012 Jul;403(9):2757-64.

Commercially available polystyrene slides were plasma nanotextured through treatment in oxygen plasma discharges to create substrates with increased surface area for microarray applications.

Evaluation of 96 SNPs in 14 populations for worldwide individual identification.
Zeng Z, Wang L, Feng Q, Zhang L, Lee L, Wang L, Yue Y, Fang Y, Yang W, Qiu H, Dong Z.
J Forensic Sci. 2012 Jul;57(4):1031-1035.

The authors describe a new computational strategy for developing individual identification SNPs based on HapMap.

Genomic profiling by whole-genome single nucleotide polymorphism arrays in Wilms tumor and association with relapse.
Perotti D, Spreafico F, Torri F, Gamba B, D'Adamo P, Pizzamiglio S, Terenziani M, Catania S, Collini P, Nantron M, Pession A, Bianchi M, Indolfi P, D'Angelo P, Fossati-Bellani F, Verderio P, Macciardi F, Radice P; Associazione Italiana Ematologia Oncologia Pediatrica Wilms Tumor Working Group.
Genes Chromosomes Cancer. 2012 Jul;51(7):644-53.

The authors investigated 77 tumors using Illumina HumanCNV370-Quad BeadChips and compared their genomic profiles to detect copy number abnormalities and allelic ratio anomalies associated with a number of clinicopathological variables

Polymorphisms in the glial glutamate transporter SLC1A2 are associated with essential tremor.
Thier S, Lorenz D, Nothnagel M, Poremba C, Papengut F, Appenzeller S, Paschen S, Hofschulte F, Hussl AC, Hering S, Poewe W, Asmus F, Gasser T, Schöls L, Christensen K, Nebel A, Schreiber S, Klebe S, Deuschl G, Kuhlenbäumer G.
Neurology. 2012 Jul 3. [Epub ahead of print]

Using the Affymetrix Genome-Wide SNP Array 6.0, the authors conducted a two-stage GWAS in a total of 990 subjects and 1,537 control subjects from Europe to identify genetic variants associated with ET.

Genotype imputation for African Americans using data from HapMap Phase II versus 1000 Genomes Projects.
Sung YJ, Gu CC, Tiwari HK, Arnett DK, Broeckel U, Rao DC.
Genet Epidemiol. 2012 Jul;36(5):508-16.

The authors evaluated both 1000 Genome Project-based imputations and HapMap-based imputations using 23,707 SNPs from chromosomes 21 and 22 on Affymetrix SNP Array 6.0 genotyped for 1,075 HyperGEN African Americans.

The Scan

Alzheimer's Risk Gene Among Women

CNN reports that researchers have found that variants in MGMT contribute to Alzheimer's disease risk among women but not men.

Still Hanging Around

The Guardian writes that persistent pockets of SARS-CoV-2 in the body could contribute to long COVID.

Through a Little Spit

Enteric viruses like norovirus may also be transmitted through saliva, not just the fecal-oral route, according to New Scientist.

Nature Papers Present Method to Detect Full Transcriptome, Viruses Infecting Asgard Archaea, More

In Nature this week: VASA-seq approach to detect full transcriptome, analysis of viruses infecting Asgard archaea, and more.