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In Print: Last Week's Microarray Papers of Note: Dec 4, 2012

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The principal genetic determinants for nasopharyngeal carcinoma in China involve the HLA class I antigen recognition groove.

PLoS Genet. 2012 Nov 29 [Epub ahead of print]

Tang M, Lautenberger J, Gao X, et al.

The authors of this paper sought to resolve the major genetic influences for nasopharyngeal carcinoma incidence using a genome-wide association study. This project includes independent cohort replication and high-resolution molecular HLA class I gene typing including 4,055 study participants from the Guangxi Zhuang Autonomous Region and Guangdong province of southern China. Using Affymetrix SNP arrays, they were able to detect and replicate strong association signals involving SNPs, HLA alleles, and amino acid variants across the major histocompatibility complex-HLA-A, HLA –B, and HLA -C class I genes.


Haplotype-based profiling of subtle allelic imbalance with SNP arrays.

Genome Res. 2012 Nov 27. [Epub ahead of print]

Vattathil S, Scheet P.

The authors provide an approach that they claim offers an improvement for the detection of subtle allelic imbalance, or low proportions of cells harboring aberrant allelic ratio among nonaberrant cells, in unpaired tumor samples using SNP microarrays. In this paper, they demonstrate the method on real and simulated data from the CRL-2324 breast cancer cell line genotyped on the Illumina 370K array.


A parallel genome-wide mRNA and microRNA profiling of the frontal cortex of HIV patients with and without HIV-associated dementia shows the role of axon guidance and downstream pathways in HIV-mediated neurodegeneration.

BMC Genomics. 2012 Nov 28;13(1):677.

Zhou L, Pupo G, Gupta P, et al.

Parallel profiling of mRNA and miRNA of the frontal cortex autopsies from HIV positive patients with and without dementia was performed using the Illumina Human-6 BeadChip and Affymetrix version 1.0 miRNA array, respectively. The gene ontology and pathway analysis of the two data sets showed high concordance between miRNA and mRNAs, revealing significant interference with the host axon guidance and its downstream signalling pathways in HIV-associated dementia brains. Moreover, the differentially expressed miRNAs identified in this study targeted neurodegeneration-related pathways, implying their future potential in diagnosis, prognosis and possible therapies for HIV-mediated and possibly other neurodegenerative diseases.


Sensing immune responses with customized peptide microarrays.

Biointerphases. 2012 Dec;7(1-4):47.

Schirwitz C, Loeffler F, Felgenhauer T, et al.

The authors describe the laser printer-based synthesis of peptide microarrays and focus on an application involving the blood sera of tetanus immunized individuals, indicating the potential of peptide arrays to sense immune responses.


An evaluation of the applicability of microarrays for monitoring toxic algae in Irish coastal waters.

Environ Sci Pollut Res Int. 2012 Nov 27. [Epub ahead of print]

McCoy G, Touzet N, Fleming G, et al.

This study evaluated the applicability of microarrays to monitor harmful algae across a broad range of ecological niches and toxic species responsible for harmful algal events as part of the EU's Seventh Framework Program-funded Microarrays for the Detection of Toxic Algae project. Water samples were collected from a number of coastal sites around Ireland, including several that are used in the Irish National Phytoplankton and Biotoxin Monitoring Program. Ribosomal RNA was extracted from filtered field samples, labeled with a fluorescent dye, and hybridized to probes spotted in a microarray format on a glass slide. The fluorescent signal intensity of the hybridization to the 120 probes on the chip was analyzed and compared with actual field counts. There was a general agreement between cell counts and microarray signal.

The Scan

Review of Approval Process

Stat News reports the Department for Health and Human Services' Office of the Inspector General is to investigate FDA's approval of Biogen's Alzheimer's disease drug.

Not Quite Right

A new analysis has found hundreds of studies with incorrect nucleotide sequences reported in their methods, according to Nature News.

CRISPR and mRNA Together

Time magazine reports on the use of mRNA to deliver CRISPR machinery.

Nature Papers Present Smartphone Platform for DNA Diagnosis of Malaria, Mouse Lines for Epigenomic Editing

In Nature this week: a low-cost tool to detect infectious diseases like malaria, and more.