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In Print: Last Week's Microarray Papers of Note : Aug 14, 2012


Cerebrospinal fluid APOE levels: an endophenotype for genetic studies for Alzheimer's disease.
Hum Mol Genet. 2012 Aug 7. [Epub ahead of print]
Cruchaga C, Kauwe JS, Nowotny P, et al.

The authors used Illumina BeadChips to test whether cerebrospinal fluid or plasma apolipoprotein E levels could be a useful endophenotype for Alzheimer's disease and to identify genetic variants associated with APOE levels.

The carbon starvation response of Aspergillus niger during submerged cultivation: insights from the transcriptome and secretome.
BMC Genomics. 2012 Aug 8;13(1):380. [Epub ahead of print]
Nitsche BM, Jørgensen TR, Akeroyd M, et al.

This study describes the physiological, morphological, and genome-wide transcriptional changes caused by prolonged carbon starvation during submerged batch cultivation of the filamentous fungus Aspergillus niger. The Affymetrix GeneChip platform was used to establish genome-wide transcriptional profiles for three selected time points during prolonged carbon starvation.

Enhanced stability of microRNA expression facilitates classification of FFPE tumour samples exhibiting near total mRNA degradation.
Br J Cancer. 2012 Aug 7;107(4):684-94.
Hall JS, Taylor J, Valentine HR, Irlam JJ, et al.

The authors used Affymetrix microRNA and exon arrays to explore factors predicting the success of mRNA expression profiling of formalin-fixed, paraffin-embedded material, and investigated an approach to overcome existing limitations.

Microarray expression analysis and identification of serum biomarkers for Niemann-Pick disease, type C1.
Hum Mol Genet. 2012 Aug 15;21(16):3632-46.
Cluzeau CV, Watkins-Chow DE, Fu R, et al.

In order to identify pathological mechanisms underlying Niemann-Pick disease type C and uncover potential biomarkers, the authors characterized liver gene expression changes in an Npc1 mouse model at six ages spanning the pathological progression of the disease.

Spot identification and quality control in cell-based microarrays.
ACS Comb Sci. 2012 Aug 13;14(8):471-7.
Bauer M, Kim K, Qiu Y, et al.

The authors introduce an automated approach to identify cell-based microarray spots and spot quality control. The approach was used to analyze the adhesion of murine cardiac side population cells on combinatorial arrays of extracellular matrix proteins.

Lectin microarrays differentiate carcinoma cells from reactive mesothelial cells in pleural effusions.
Cytotechnology. 2012 Aug 9. [Epub ahead of print]
Shi YQ, He Q, Zhao YJ, et al.

The aim of this study was to evaluate the diagnostic utility of lectin microarrays in pleural effusions of patients with lung cancer.

North African Jewish and non-Jewish populations form distinctive, orthogonal clusters.
Proc Natl Acad Sci U S A. 2012 Aug 6. [Epub ahead of print]
Campbell CL, Palamara PF, Dubrovsky M, et al.

The authors used arrays to conduct a genome-wide analysis of five North African Jewish groups and a comparison with other Jewish and non-Jewish groups. They demonstrated distinctive North African Jewish population clusters with proximity to other Jewish populations and variable degrees of Middle Eastern, European, and North African admixture.

Impact of genetic ancestry and socio-demographic status on the clinical expression of systemic lupus erythematosus in Amerindian-European populations.
Arthritis Rheum. 2012 Aug 8. [Epub ahead of print]
Sánchez E, Rasmussen A, Riba L, et al.

According to the authors of this study, Amerindian-Europeans, Asians, and African-Americans have excess morbidity from SLE and higher prevalence of lupus nephritis than Caucasians. They used Illumina arrays to analyze the relationship between genetic ancestry and socio-demographic characteristics and clinical features in a large cohort of Amerindian-European SLE patients.

The Scan

Study Tracks Responses in Patients Pursuing Polygenic Risk Score Profiling

Using interviews, researchers in the European Journal of Human Genetics qualitatively assess individuals' motivations for, and experiences with, direct-to-consumer polygenic risk score testing.

EHR Quality Improvement Study Detects Demographic-Related Deficiencies in Cancer Family History Data

In a retrospective analysis in JAMA Network Open, researchers find that sex, ethnicity, language, and other features coincide with the quality of cancer family history information in a patient's record.

Inflammatory Bowel Disease Linked to Gut Microbiome Community Structure Gradient in Meta-Analysis

Bringing together data from prior studies, researchers in Genome Biology track down microbial taxa and a population structure gradient with ties to ulcerative colitis or Crohn's disease.

Ancient Greek Army Ancestry Highlights Mercenary Role in Historical Migrations

By profiling genomic patterns in 5th century samples from in and around Himera, researchers saw diverse ancestry in Greek army representatives in the region, as they report in PNAS.