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In Print: Last Week's Microarray Papers of Note: Oct 2, 2012


Comprehensive molecular portraits of human breast tumors.
Nature. 2012 Sep 23. [Epub ahead of print]
Louis, Koboldt D, Fulton R, et al.

The authors of this study analyzed primary breast cancers by genomic DNA copy number arrays, DNA methylation, exome sequencing, messenger RNA arrays, microRNA sequencing and reverse-phase protein arrays. In the paper, they report that their ability to integrate information across platforms provided insights into previously defined gene expression subtypes and demonstrated the existence of four main breast cancer classes when combining data from five platforms, each of which shows significant molecular heterogeneity.

Genome-wide significant association between a 'negative mood delusions' dimension in bipolar disorder and genetic variation on chromosome 3q26.1.
Transl Psychiatry. 2012 Sep 25;2:e165.
Meier S, Mattheisen M, Vassos E, et al.

The authors performed a genome-wide association study of factor dimensions in 927 clinically well-characterized bipolar disorder patients of German ancestry. One variant, rs9875793, was significantly associated with the dimension 'negative mood delusions,' such as delusions of poverty, delusions of guilt, and nihilistic delusions.

Density variant glycan microarray for evaluating cross-linking of mucin-like glycoconjugates by lectins.
J Am Chem Soc. 2012 Sep 26;134(38):15732-42.
Godula K, Bertozzi C.

In this study, the authors employed a microarray platform consisting of synthetic glycopolymers that emulate natural mucins arrayed at different surface densities to evaluate how glycan valency and spatial separation affect the preferential binding mode of a particular lectin. Assay results suggested that glycopolymer microarrays can reveal discrete higher-order binding preferences beyond the recognition of individual glycan epitopes.

A HaloTag-based small molecule microarray screening methodology with increased sensitivity and multiplex capabilities.
ACS Chem Biol. 2012 Sep 26. [Epub ahead of print]
Noblin D, Page C, Tae H, et al.

The authors modified current small molecule microarray screening. By fusing target proteins to the HaloTag protein, they were able to covalently pre-label fusion proteins with fluorophores, leading to increased assay sensitivity and an ability to conduct multiplex screens.

Application of array comparative genomic hybridization in 102 patients with epilepsy and additional neurodevelopmental disorders.
Am J Med Genet B Neuropsychiatr Genet. 2012 Oct;159B(7):760-71.
Bartnik M, Szczepanik E, Derwińska K, et al.

The authors applied whole-genome exon-targeted oligonucleotide array comparative genomic hybridization to a cohort of 102 patients with various types of epilepsy with or without additional neurodevelopmental abnormalities. Chromosomal microarray analysis revealed 24 non-polymorphic CNVs in 23 patients, among which 10 CNVs are known to be clinically relevant, two were newly identified pathogenic genetic loci, and 12 were of unknown clinical significance. The authors suggested that the clinical application of array CGH should be extended to patients with unexplained epilepsies.

Comprehensive oligonucleotide array-comparative genomic hybridization analysis: new insights into the molecular pathology of the DMD gene.
Eur J Hum Genet. 2012 Oct;20(10):1096-100.
Ishmukhametova A, Khau Van Kien P, Méchin D, et al.

The authors report on the effectiveness of a custom-designed oligonucleotide-based comparative genomic hybridization microarray to interrogate copy number across the entire 2.2-megabase genomic region of the DMD gene and its applicability in diagnosis. Using the array, they were able to detect a series of 42 previously characterized large rearrangements of various size, localization and type, and known intronic CNVs and insertions/deletions. The technique also succeeded in identifying a small duplication of only 191 basepairs in one patient previously negative for DMD mutation.

The Scan

UK Pilot Study Suggests Digital Pathway May Expand BRCA Testing in Breast Cancer

A randomized pilot study in the Journal of Medical Genetics points to similar outcomes for breast cancer patients receiving germline BRCA testing through fully digital or partially digital testing pathways.

Survey Sees Genetic Literacy on the Rise, Though Further Education Needed

Survey participants appear to have higher genetic familiarity, knowledge, and skills compared to 2013, though 'room for improvement' remains, an AJHG paper finds.

Study Reveals Molecular, Clinical Features in Colorectal Cancer Cases Involving Multiple Primary Tumors

Researchers compare mismatch repair, microsatellite instability, and tumor mutation burden patterns in synchronous multiple- or single primary colorectal cancers.

FarGen Phase One Sequences Exomes of Nearly 500 From Faroe Islands

The analysis in the European Journal of Human Genetics finds few rare variants and limited geographic structure among Faroese individuals.