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In Print: Last Month's Microarray Papers of Note: Dec 20, 2011


Microarray Papers of Note Published November 2011

Journal: Analytical and Bioanalytical Chemistry. 2011 Nov;401(8):2549-59.

Title: Fast DNA and protein microarray tests for the diagnosis of hepatitis C virus infection on a single platform.

Authors: Ember S, et al.

The authors developed a DNA microarray test to detect hepatitis C virus RNA and a protein microarray to detect human anti-HCV antibodies on a single platform. The protein microarray exhibited an analytical sensitivity comparable to that of commercial systems and similar results were obtained with the DNA array using a universal probe that covered all different HCV genotypes. The authors were also able to reduce the assay time after PCR from 150 minutes to 16 minutes without any loss of sensitivity.

Journal: BMC Medical Genomics. 2011 Nov 28;4:81.

Title: Estimates of array and pool-construction variance for planning efficient DNA-pooling genome wide association studies.

Authors: Earp M, et al.

The authors of this study set out to control the variance in allele frequency estimation when DNAs are pooled in a genome-wide association study, with the aim of conducting a well-powered pool-based GWAS. They based their analysis on 27 DNA pools ranging in size from 74 to 446 individual samples, genotyped on a collective total of 128 Illumina BeadArrays. They concluded that, relative to array variance, pool-construction variance is of less importance in reducing the variance in allele frequency estimation from DNA pools, though it may be more important than previously thought.

Journal: BMC Genomics. 2011 Nov 14;12(1):557.

Title: Global assessment of genomic variation in cattle by genome resequencing and high-throughput genotyping.

Authors: Zhan B, et al.

The authors report the integration of the whole-genome sequence of a single Holstein Friesian bull with data from SNP and comparative genomic hybridization array technologies to determine a spectrum of genomic variation. The performance of resequencing SNP detection was assessed by combining SNPs that were identified to be either in identity by descent or in copy number variation with results from SNP array genotyping. The authors believe that given a moderate level of sequencing coverage, an ensemble of platforms and tools can be applied together to maximize the accurate detection of sequence and structural variants.

Journal: BMC Medical Genomics. 2011 Nov 23;4(1):79. [Epub ahead of print]

Title: miRNA signature associated with outcome of gastric cancer patients following chemotherapy.

Authors: Kim C, et al.

In order to identify miRNA signatures for gastric cancer and for predicting clinical resistance to cisplatin/fluorouracil chemotherapy, miRNA analysis was performed using an Agilent Technologies-manufactured custom array to survey endoscopic biopsy samples. A miRNA signature distinguishing gastric cancer from normal stomach epithelium was identified, as was a chemoreresistance miRNA expression signature that is correlated with time-to-progression after CF therapy.

Journal: British Journal of Haematology. 2011 Nov 25 [Epub ahead of print]

Title: Integrated DNA copy number and methylation profiling of lymphoid neoplasms using a single array.

Authors: Kwee I, et al.

The authors report that the Illumina Infinium Methylation assay, although not originally designed for copy number profiling, is able to estimate copy number changes. They compared these profiles to those obtained with a standard technique in a series of diffuse large B-cell lymphomas and found that the profiles showed a "high degree of consensus."

Journal: Development and Psychopathology. 2011 Nov 29:1-13. [Epub ahead of print]

Title: Differential patterns of whole-genome DNA methylation in institutionalized children and children raised by their biological parents.

Authors: Naumova O, et al.

The authors examined differential methylation among 14 children raised since birth in institutional care and 14 comparison children raised by their biological parents. Analysis of whole-genome methylation patterns was performed using the Infinium HumanMethylation27 BeadChip assay. The authors found that patterns of differential methylation seen in nonhuman species with altered maternal care are also characteristic of children who experience early maternal separation.

Journal: Experimental Parasitology. 2011 Nov;129(3):221-6.

Title: Glycan microarray profiling of parasite infection sera identifies the LDNF glycan as a potential antigen for serodiagnosis of trichinellosis.

Authors: Aranzamendi C, et al.

The authors set out to identify synthetic glycan antigens that could be used for serodiagnosis of parasitic infections. Using a glycan array containing more than 250 different glycan antigens, they identified GalNAcβ1-4(Fucα1-3)GlcNAc-R (LDNF) as a glycan antigen that is recognized by antibodies from Trichinella-infected individuals. They subsequently synthesized a neoglycoconjugate, consisting of five LDNF molecules covalently coupled to bovine serum albumin, and used this neoglycoconjugate as an antigen to develop a highly sensitive total-Ig enzyme-linked immunosorbant assay for serological screening of trichinellosis.

Journal: Genetics, Selection, Evolution. 2011 Nov 28;43(1):40. [Epub ahead of print]

Title: Accuracies of genomic breeding values in American Angus beef cattle using K-means clustering for cross-validation.

Authors: Saatchi M, et al.

The objective of this study was to estimate marker effects to derive prediction equations for direct genomic values for 16 routinely recorded traits of American Angus beef cattle and quantify corresponding accuracies of prediction. Deregressed estimated breeding values were used as observations in a weighted analysis to derive direct genomic values for 3,570 sires genotyped using the Illumina BovineSNP50 BeadChip. The authors concluded that genomic estimates of genetic merit can be produced in beef cattle at a young age but argued that the recurrent inclusion of genotyped sires in retraining analyses will be necessary to routinely produce for the industry the direct genomic values with the highest accuracy.

Journal: Genomics. 2011 Nov 3. [Epub ahead of print]

Title: Maternal gametic transmission of translocations or inversions of human chromosome 11p15.5 results in regional DNA hypermethylation and downregulation of CDKN1C expression.

Authors: Smith A, et al.

A high-resolution Roche NimbleGen custom microarray was designed representing all non-repetitive sequences in the telomeric 33 megabase of the short arm of human chromosome 11 containing p15.5, which is associated with Beckwith-Wiedemann syndrome. DNA methylation microarray analysis revealed a gain of DNA methylation in the translocation and inversion patients. BWS patients that inherited a maternal translocation or inversion also demonstrated reduced expression of the growth-suppressing imprinted gene CDKN1C. The authors determined that translocations and inversions on chromosome 11p15.5 alter regional DNA methylation patterns and imprinted gene expression in chromosomal imbalances.

Journal: Human Molecular Genetics. 2011 Nov 15;20(22):4360-70.

Title: Use of array CGH to detect exonic copy number variants throughout the genome in autism families detects a novel deletion in TMLHE.

Authors: Celestino-Soper P, et al.

The authors performed array comparative genomic hybridization using a custom Agilent Technologies-made, million-marker oligonucleotide array intended to cover 197,332 unique exons in RefSeq genes. The study group included 99 trios from the Simons Simplex Collection. The analysis identified and validated 55 potentially pathogenic CNVs, categorized as de novo autosomal heterozygous, inherited homozygous autosomal, complex autosomal, and hemizygous deletions on the X chromosome of probands.

Journal: Journal of Dairy Science. 2011 Nov 29. [Epub ahead of print]

Title: Performance of bovine high-density genotyping platforms in Holsteins and Jerseys.

Authors: Rincon L, et al.

The authors compared the performance of the Illumina High-Density Bovine BeadChip Array and the Affymetrix Axiom Genome-Wide BOS 1 Array using samples from 16 dairy cattle: 10 Holsteins and 6 Jerseys. They determined that both the Affymetrix BOS 1 and Illumina BovineHD genotyping platforms are "well designed and provide high-quality genotypes and similar coverage of informative SNPs." They also found that the combined use of both platforms "significantly improved coverage over either platform alone and decreased the gap size between SNP, providing a valuable tool for fine mapping quantitative trait loci and multibreed animal evaluation."

Journal: Journal of Human Genetics. 2011 Nov 3. [Epub ahead of print]

Title: Genome-wide association study of copy number variation identified gremlin1 as a candidate gene for lean body mass.

Authors: Hai R, et al.

The authors used Affymetrix SNP 6.0 arrays to genotype copy number variants in 1,627 Chinese individuals. They identified a CNV that is associated with lean body mass variation at the genome-wide significance level, CNV2073, which is located at chromosome 15q13.3. As the nearest gene, gremlin1, plays a role in the regulation of skeletal muscle formation and repair, the authors suggest that gremlin1 is a potentially important gene for LBM variation.

Journal: Mammalian Genome. 2011 Nov 22. [Epub ahead of print]

Title: Genome-wide association studies for multiple diseases of the German Shepherd dog.

Authors: Tsai K, et al.

SNP profiles for 197 German Shepherd dogs were generated using the Affymetrix Canine SNP array in a genome-wide association study to identify loci associated with four diseases: pituitary dwarfism, degenerative myelopathy, congenital megaesophagus, and pancreatic acinar atrophy. They found loci on chromosomes 9 and 12 associated with the first three diseases. Results for PAA indicated "more complex genetic underpinnings" though, as several regions on multiple chromosomes reached genome-wide significance. The authors believe that that PAA may be governed by multiple loci with small effects, or it may be a heterogeneous disorder.

Journal: Optics Express. 2011 Nov 7;19(23):23327-40.

Title: Spatially selective photonic crystal enhanced fluorescence and application to background reduction for biomolecule detection assays.

Authors: Chaudhery V, et al.

The authors combined photonic crystal label-free biosensor imaging with photonic crystal enhanced fluorescence to selectively enhance the fluorescence emission from regions of the photonic crystal surface based upon the density of immobilized capture molecules. They argue that this capability improves the contrast of enhanced fluorescent images, and when applied to an antibody protein microarray, provides an advantage over conventional fluorescence microscopy.

Journal: PLoS One. 2011;6(11):e27341.

Title: A map of copy number variations in Chinese populations.

Authors: Lou H, et al.

The authors used Affymetrix's SNP 6.0 array to generate a CNV map of seven Chinese populations representing the country's major linguistic groups. They found that about 35 percent of CNV regions identified in minority ethnic groups are not shared by the Han Chinese population, indicating that the contribution of the minorities to the genetic architecture of the Chinese population should not be ignored. They also found that the SNP taggability of CNVs in Chinese populations was much lower than that in European populations, suggesting the necessity of a full characterization of CNVs in Chinese populations.

Journal: PLoS One. 2011;6(11):e27859.

Title: Genome-wide mapping of copy number variation in humans: comparative analysis of high resolution array platforms.

Authors: Haraksingh R, et al.

The authors quantitatively assessed the abilities of a dozen genome-wide CNV detection platforms to detect well-characterized sets of CNVs in the genome of HapMap CEU sample NA12878, and found "significant differences" in performance. The chips analyzed were Roche NimbleGen's 4.2M, 2.1M, and 3×720K whole-genome and CNV-focused arrays; Agilent Technologies' 1X1M CGH and High and 2×400K CNV, and SNP+CGH arrays; Illumina's Human Omni1Quad array; and Affymetrix's SNP 6.0 array. They found that sensitivity, total number, size range and breakpoint resolution of CNV calls were highest for CNV-focused arrays.

Journal: PLoS One. 2011;6(11):e27560.

Title: SNPs array karyotyping reveals a novel recurrent 20p13 amplification in primary myelofibrosis.

Authors: Visani G, et al.

The authors analyzed 20 primary myelofibrosis patients using the Affymetrix SNP Array 6.0 in order to identify recurrent genomic abnormalities. They observed a complex karyotype in all cases, detecting all the previously reported lesions and abnormalities while identifying several new cryptic lesions. In particular, they found a recurrent alteration involving cytoband 20p13 in 55 percent of patients and defined a minimal affected region, an amplification of 9,911 base-pair overlapping the SIRPB1 gene locus. By extending the analysis to the adjacent areas, the authors determined the cytoband was affected in 95 percent of cases.

Journal: Pediatric Critical Care Medicine. 2011 Nov;12(6):e427-32.

Title: 16q24.1 microdeletion in a premature newborn: usefulness of array-based comparative genomic hybridization in persistent pulmonary hypertension of the newborn.

Authors: Zufferey F, et al.

The authors report the case of a preterm male infant, born at 26 weeks of gestation with malformation and bilateral hydronephrosis. Though the infant's karyotype was normal, array-based comparative genomic hybridization analysis) showed an interstitial microdeletion encompassing the forkhead box gene cluster in 16q24.1. A final diagnosis of alveolar capillary dysplasia with misalignment of pulmonary veins was made.

Journal: Scientific Reports. 2011 Nov 24. [Epub ahead of print]

Title: Genetic variation and linkage disequilibrium in Bacillus anthracis.

Authors: Zwick M, et al.

The authors performed whole-genome amplification followed by hybridization of custom-designed resequencing arrays to resequence 303 kilobases of genomic sequence from a worldwide panel of 39 Bacillus anthracis strains. They discovered a total of 240 single nucleotide variants and showed that B. anthracis strains have an average of 2.25 differences per 10,000 bases in the region resequenced. According to the authors, these patterns of variation suggest there has been little if any historical recombination among B. anthracis strains since the origin of the pathogen.

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