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In Print: Apr 5, 2011

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Microarray Papers of Note Published March 2011

Journal: American Journal of Human Genetics. 2011 Mar 11;88(3):317-32.

Title: Population-genetic properties of differentiated human copy-number polymorphisms.

Authors: Campbell C, et al.

The authors developed a method based on single-channel intensity data and benchmarked against copy numbers determined from sequencing read depth to successfully obtain copy number polymorphism genotypes for 1,495 CNPs from 487 human DNA samples of diverse ethnic backgrounds. Their approach relied on a microarray containing CNPs in segmental duplication-rich regions and insertions of sequences not represented in the reference genome assembly or on standard SNP microarray platforms. They claim that their microarray design allows CNPs to be rapidly tested for disease association.


Journal: Analytica Chimica Acta. 2011 Mar 18;689(2):234-42.

Title: Regenerable immuno-biochip for screening ochratoxin A in green coffee extract using an automated microarray chip reader with chemiluminescence detection.

Authors: Sauceda-Friebe J, et al.

Ochratoxin A can contaminate foodstuffs and, once formed, is difficult to remove. The authors of this paper synthesized an OTA conjugate functionalized with a water-soluble peptide for covalent immobilization on a glass biochip by means of contact spotting. The chip was used for OTA determination with an indirect competitive immunoassay format with flow-through reagent addition and chemiluminescence detection, carried out on the author's platform, the Munich Chip Reader. A buffer model and real green coffee extracts were used for this purpose. At the present, the authors wrote, covalent conjugate immobilization supports 20 assay-regeneration cycles of the chip surface.


Journal: Analytical Chemistry. 2011 Mar 31. [Epub ahead of print]

Title: Enhanced colorimetric detection on porous microarrays using in situ substrate production.

Authors: Le Goff G, et al.

The authors report a new technique for the enhanced colorimetric detection of multiplexed hybridization onto porous membrane-based microarrays. The approach combines the use of horseradish peroxidase as a label together with a chromogen substrate and a local production of the hydrogen peroxide required for substrate oxidation. The method was successfully applied to the multiplex detection of SNPs in complex PCR samples.


Journal: Applications in Environmental Microbiology. 2011 Mar;77(6):2071-80.

Title: Microarray analysis and barcoded pyrosequencing provide consistent microbial profiles depending on the source of human intestinal samples.

Authors: van den Bogert B, et al.

In this study, barcoded pyrosequencing and phylogenetic microarray analysis were compared and contrasted for analysis of the bacterial composition in three fecal and three small intestinal samples from human individuals. Microbial profiles obtained by pyrosequencing and phylogenetic microarray analysis correlated strongly for fecal and ileal lumen samples but were less concordant for ileostomy effluent. The authors concluded that equivalent biological conclusions were obtained by high-throughput profiling of microbial communities, independent of technology or primer choice.


Journal: Applied Microbiology and Biotechnology. 2011 Mar;89(6):1979-90.

Title: Development of a single base extension-tag microarray for the detection of pathogenic Vibrio species in seafood.

Authors: Chen W, et al.

In this study, a single base extension-tag array was created to detect the seven leading seafood-borne pathogens, including Vibrio parahaemolyticus, Vibrio cholera, Vibrio vulnificus, Vibrio mimicus, Vibrio alginolyticus, Vibrio anguillarum, and Vibrio harveyi. Application of the DNA microarray methodology to 55 naturally contaminated seafood samples from shrimp, fish, and oysters revealed the presence of V. parahaemolyticus at 50.9 percent and V. alginolyticus at 32.7 percent. This corresponds with traditional assays (microbiological and biochemical tests).


Journal: Atherosclerosis. 2011 Mar 2. [Epub ahead of print]

Title: Array-based resequencing for mutations causing familial hypercholesterolemia.

Authors: Chiou K, et al.

The authors designed a custom DNA resequencing array to detect mutations on all 3 known familial hypercholesterolemia -causing genes - LDL receptor (LDLR), apolipoprotein B (APOB), and proprotein convertase subtilisin/kexin type 9 gene (PCSK9), as well as 290 known insertion/deletion mutations on LDLR. They verified FH array performance by analyzing 35 previously sequenced subjects and blindly screening 125 FH patients. The average microarray call rate was 98.45 percent and the agreement between microarray and capillary sequencing was 99.99 percent.

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Journal: Biomedical Microdevices. 2011 Mar 4. [Epub ahead of print]

Title: Development and characterization of a disposable plastic microarray printhead.

Authors: Griessner M, et al.

The authors of this study developed an 8-channel plastic microarray printhead. A combination of injection-molding and laser processing allowed them to produce cheap, customizable and disposable microarray printheads. The use of plastics minimizes the need for surface modifications required previously for proper printing results, the authors stated.


Journal: BMC Genomics. 2011 Mar 28;12(1):162. [Epub ahead of print]

Title: A cell spot microarray method for production of high density siRNA transfection microarrays.

Authors: Rantala J, et al.

In this paper, the authors describe a miniaturized cell spot microarray method, which they claim supports a transfection microarray technique for disparate RNAi analyses. The approach was tested with a panel of 92 adherent cell types, including primary human cells. They also demonstrated the method in the systematic screening of 492 GPCR coding genes for impact on growth and survival of cultured human prostate cancer cells. The authors claim the method enables the preparation of cell microarrays for gene-knockdown analyses.


Journal: Clinical Chemistry. 2011 Mar;57(3):518-21.

Title: Concordance study of 3 direct-to-consumer genetic-testing services.

Authors: Imai K, et al.

The authors evaluated three direct-to-consumer services and a genomics service that are based on microarray or solution genotyping with hydrolysis probes and compared the test results obtained for the same individual. The concordance rates between the services for SNP data were greater than 99.6 percent. However, there were some marked differences in the relative disease risks assigned by the DTC services. The authors suggested that the reason for this difference is that different SNPs were used to calculate risk for the same disease. The reference population also had an influence on the relative disease risk, they posited in the paper.


Journal: Human Reproduction. 2011 Mar 29. [Epub ahead of print]

Title: First births after preimplantation genetic diagnosis of structural chromosome abnormalities using comparative genomic hybridization and microarray analysis.

Authors: Alfarawati S, et al.

The authors explored the use of two comprehensive chromosome screening methods, conventional metaphase comparative genomic hybridization and array CGH, as alternatives for preimplantation genetic diagnosis of chromosome rearrangements. The study included 16 patients who underwent 20 cycles of PGD for a variety of chromosome rearrangements. Following the application of the techniques, the delivery rate per cycle was 21 percent. The authors note that the methods can enable the detection of abnormalities affecting chromosomes unrelated to the rearrangement, which may assist in the selection of viable embryos for transfer.


Journal: Journal of the American Chemical Society. 2011 Mar 30;133(12):4271-4273.

Title: Ultrasensitive DNA microarray biosensing via in situ RNA transcription-based amplification and nanoparticle-enhanced SPR imaging.

Authors: Sendroiu I, et al.

The authors describe a method where the specific sequence-dependent adsorption of a target single-stranded DNA template molecule onto an ssDNA-modified gold microarray is followed by the generation of multiple copies of ssRNA via in situ surface transcription by RNA polymerase. The RNA created on this generator element is then detected by specific adsorption onto a second adjacent detector element of ssDNA that is complementary to one end of the ssRNA transcript. SPR imaging is then used to detect the hybridization of cDNA-coated gold nanoparticles with the surface-bound RNA.


Journal: Journal of Infection in Developing Countries. 2011 Mar 2;5(2):94-105.

Title: Microarray analysis of virulence gene profiles in Salmonella serovars from food/food animal environment.

Authors: Zou W, et al.

The objective of this study was to demonstrate the use of a microarray platform to assay the virulence gene profiles in Salmonella and then use ArrayTrack software for data analysis. The authors' spotted array consisted of 69 selected Salmonella-specific virulence gene probes. Nearly 58 percent of the virulence-associated genes tested were present in all Salmonella strains tested. The authors recommended their method for evaluating the disease-causing potential of Salmonella in outbreak investigations by targeting a selective set of Salmonella-associated virulence genes.

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Journal: Molecular Psychiatry. 2011 March 1. [Epub ahead of print]

Title: Rare structural variation of synapse and neurotransmission genes in autism.

Authors: X Gai, et al.

A research group led by investigators at The Children's Hospital of Philadelphia reported that rare, inherited copy number variants associated with autism often fall in pathways involved in brain communication and other processes that seem to be consistent with autism-associated behaviors and phenotypes. The team used Illumina Infinium II Human-Hap550 BeadChips to track down CNVs in families affected by autism spectrum disorders and compared these to copy number patterns in thousands of unaffected individuals. In this paper, they reported evidence that autism-specific copy number changes affect genes in pathways related to synaptic function, neurotransmission, and other processes.


Journal: Nature Genetics. 2011 Mar 6;43(4):345-9.

Title: Genome-wide association identifies a susceptibility locus for coronary artery disease in the Chinese Han population.

Authors: Wang F, et al.

The study’s authors tested samples from 230 cases and 230 controls from populations in Beijing and in China's Hubei province that were genotyped at Genentech and CapitalBio using Affymetrix Human SNP 5.0 arrays. From the nearly three-dozen SNPs identified in the first stage of the study, they narrowed in on nine suspect variants. After subsequent analysis, they identified a single chromosome 6 SNP called rs6903956 which they believe to be implicated in coronary artery disease — a finding the team ultimately replicated in another group of 2,668 coronary artery disease cases and 3,917 controls.


Journal: Nature Genetics. 2011 Mar 13;43(4):329-332.

Title: Genome-wide association study identifies 12 new susceptibility loci for primary biliary cirrhosis.

Authors: Mells G, et al.

To identify additional loci related to primary biliary cirrhosis, the authors of this study carried out a genome-wide association study using 1,840 cases from the UK PBC Consortium and 5,163 UK population controls as part of the Wellcome Trust Case Control Consortium. They followed up 28 loci in an additional UK cohort of 620 PBC cases and 2,514 population controls and identified 12 new susceptibility loci and replicated all previously associated loci. New candidate genes include STAT4, DENND1B, CD80, IL7R, CXCR5, TNFRSF1A, CLEC16A and NFKB1.


Journal: Proceedings of the National Academy of Sciences. 2011 Mar 8;108(10):4057-62.

Title: Two developmental modules establish 3D beak-shape variation in Darwin's finches.

Authors: Mallarino R, et al.

The authors studied a group of Darwin's finch species with different beak shapes. They found that TGFβIIr, β-catenin, and Dickkopf-3, the top candidate genes from a cDNA microarray screen, are differentially expressed in the developing premaxillary bone of embryos of species with different beak shapes. Functional experiments demonstrated that these molecules form a regulatory network governing the morphology of the premaxillary bone. This differs from the network controlling the prenasal cartilage, but has the same species-specific domains of expression. These results offer potential mechanisms that may explain how the tightly coupled depth and width dimensions can evolve independently, the authors stated.


Journal: PLoS One. 2011 Mar 22;6(3):e14777.

Title: Investigation of parameters that affect the success rate of microarray-based allele-specific hybridization assays.

Authors: Poulsen L, et al.

The authors of this paper developed a method for the genetic analysis of 42 Phenylketonuria-associated mutations in the phenylalanine hydroxylase gene. Custom-made microarrays with different lengths of complementary probe sequences and spacers were hybridized with pooled PCR products of 12 exons from each of 38 individual patient DNA samples. The data were then used to assess which parameters play significant roles in assay development.


Journal: Proteomics. 2011 Mar 3. [Epub ahead of print]

Title: Design of recombinant antibody microarrays for membrane protein profiling of cell lysates and tissue extracts.

Authors: Dexlin-Mellby L, et al.

The authors of this paper developed a human recombinant antibody microarray for membrane proteins targeting crude cell lysates and tissue extracts. The array has been optimized for all key technological parameters and the investigators successfully developed a setup for extracting, labeling, and analyzing non-fractionated membrane proteomes under non-denaturing conditions, they stated. The platform was also extended and shown to be compatible with simultaneous profiling of both membrane proteins and water-soluble proteins.

The Scan

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Participation Analysis

A new study finds that women tend to participate less at scientific meetings but that some changes can lead to increased involvement, the Guardian reports.

Right Whales' Decline

A research study plans to use genetic analysis to gain insight into population decline among North American right whales, according to CBC.

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In Science this week: pair of mutations in one gene uncovered in brothers with short stature and immunodeficiency, and more.