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In Print: Last Week's Microarray Papers of Note: Aug 21, 2012


Mitochondrial diversity patterns and the Magdalenian resettlement of Europe: new insights from the edge of the Franco-Cantabrian refuge.

J Hum Genet. 2012 Aug 16. [Epub ahead of print]

Pardiñas AF, Roca A, Garcia-Vazquez E, et al.

As mitochondrial DNA is a kind of data that has been commonly used in human population genetics, the authors used SNP arrays to study the population dynamics of the Franco-Cantabrian glacial refuge, located in the northern Iberian peninsula and southwestern France.

Genome-wide somatic copy number alterations in low-grade PanINs and IPMNs from individuals with a family history of pancreatic cancer.

Clin Cancer Res. 2012 Aug 15;18(16):4303-12.

Hong SM, Vincent A, Kanda M, et al.

The authors used Illumina SNP arrays to conduct genome-wide copy number analysis in 60 benign neoplasms, including 58 mostly low-grade pancreatic intraepithelial neoplasias and intraductal papillary mucinous neoplasms, and two pancreatic neuroendocrine tumors, as well as matched normal tissues from 16 individuals with a family history of pancreatic cancer.

Synthesis of a library of fucosylated glycoclusters and determination of their binding toward Pseudomonas aeruginosa Lectin B (PA-IIL) using a DNA-based carbohydrate microarray.

Bioconjug Chem. 2012 Aug 15;23(8):1534-47.

Gerland B, Goudot A, Pourceau G, et al.

Sixteen fucosylated glycoclusters with antenna-like, linear, or crown-like spatial arrangements were synthesized using a combination of DNA solid-phase synthesis and alkyne azide 1,3-dipolar cycloaddition. Their binding properties toward PA-IIL were then evaluated with a DNA-directed immobilization carbohydrate microarray.

Comparative transcript profiling of gene expression between seedless Ponkan mandarin and its seedy wild type during floral organ development by suppression subtractive hybridization and cDNA microarray.

BMC Genomics. 2012 Aug 16;13(1):397.

Qiu WM, Zhu AD, Wang Y, et al.

An integrative strategy combining suppression subtractive hybridization library with cDNA microarray was employed to study the underlying mechanism of seedlessness of a Ponkan mandarin seedless mutant (Citrus reticulata Blanco).

DNA microarray fabricated on poly(acrylic acid) brushes-coated porous silicon by in situ rolling circle amplification.

Analyst. 2012 Aug 16. [Epub ahead of print]

Wang C, Jia XM, Jiang C, et al.

The authors describe the application of rolling circle amplification for multiplex detection of nucleic acid targets on oligonucleotide-conjugated polymer brushes covalently grown from porous silicon. A two-color DNA microarray was achieved via RCA of two kinds of circular DNA targets on one chip simultaneously.

Toxicogenetics-cytochrome P450 microarray analysis in forensic cases focusing on morphine/codeine and diazepam.

Int J Legal Med. 2012 Aug 17. [Epub ahead of print]

Andresen H, Augustin C, Streichert T.

The authors sought to determine whether genetic tests, such Roche's AmpliChip cytochrome P450 genotyping test, should be applied to forensic problems as a matter of routine. They conclude that "the overall relevance of toxicogenetics in forensic problems is moderate," though genotyping may provide "new insight" in some individual cases.

Unintended diagnosis of Von Hippel Lindau syndrome using array comparative genomic hybridization (CGH): counseling challenges arising from unexpected information.

J Genet Couns. 2012 Aug 16. [Epub ahead of print]

Hogan J, Turner A, Tucker K, et al.

The authors present a case where array CGH identified the cause of a proband's moderate mental retardation by the unanticipated discovery of a de novo deletion that included the VHL gene, the deletion or mutation of which leads to Von Hippel Lindau syndrome. As presymptomatic testing for VHL is usually offered after appropriate genetic counseling about the implications of this condition, the authors suggest that further understanding of the psychosocial effects of array CGH is needed in order for appropriate pre- and post-test counseling to be provided.

The Scan

Genetic Risk Factors for Hypertension Can Help Identify Those at Risk for Cardiovascular Disease

Genetically predicted high blood pressure risk is also associated with increased cardiovascular disease risk, a new JAMA Cardiology study says.

Circulating Tumor DNA Linked to Post-Treatment Relapse in Breast Cancer

Post-treatment detection of circulating tumor DNA may identify breast cancer patients who are more likely to relapse, a new JCO Precision Oncology study finds.

Genetics Influence Level of Depression Tied to Trauma Exposure, Study Finds

Researchers examine the interplay of trauma, genetics, and major depressive disorder in JAMA Psychiatry.

UCLA Team Reports Cost-Effective Liquid Biopsy Approach for Cancer Detection

The researchers report in Nature Communications that their liquid biopsy approach has high specificity in detecting all- and early-stage cancers.