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In Print: Apr 14, 2009


Journal: Bioinformatics. 2009 Mar 15;25(6):751-7.
Title: Statistical methods of background correction for Illumina BeadArray data.
Authors: Y Xie; X Wang; M Story

Abstract: In this article, the authors consider the problem of background correction for BeadArray data. One distinct feature of BeadArrays is that for each array, the noise is controlled by over 1,000 bead types conjugated with non-specific oligonucleotide sequences. The authors extend a multi-array analysis background correction model to incorporate the information from negative control beads, and consider three commonly used approaches for parameter estimation, namely non-parametric estimation, maximum likelihood estimation, and Bayesian estimation. The proposed approaches, as well as the existing background correction methods, are compared through simulation studies and a data example. Specifically, the authors found that the maximum likelihood and Bayes methods seem to hold the most potential.

Journal: Biomacromolecules. 2009 Mar 30. [Epub ahead of print]
Title: Multifunctional polymer coatings for cell microarray applications.
Authors: M Kurkuri; C Driever; G Johnson; G McFarland; H Thissen; N Voelcker

Abstract: In this study, multifunctional polymer surface chemistries were developed for a cell microarray application with the aim of screening cellular interactions with surface immobilized factors. Coatings were prepared by the deposition of an allylamine plasma polymer pinning layer followed by the deposition of random copolymers of glycidyl methacrylate and poly(ethylene glycol) methacrylate. Coatings were characterized by X-ray photoelectron spectroscopy, infrared spectroscopy, ellipsometry, and contact angle measurements. A variety of proteins as well as synthetic polymers were printed onto copolymer-coated slides using a high-precision contact microarrayer. Printing conditions were optimized for a fluorescently labeled model protein in regard to the temperature, humidity, pin geometry, concentration, and pH of the printing solution. Finally, the suitability of the surface chemistry for the evaluation of cellular responses to surface immobilized factors in a microarray format was demonstrated using HeLa cells.

Journal: BMC Genetics. 2009 Mar 24;10(1):15. [Epub ahead of print]
Title: Copy number variation in African Americans.
Authors: J McElroy; M Nelson; S Caillier; J Oksenberg

Abstract: Employing a SNP platform with greater than 500,000 SNPs, a first-generation CNV map of the African American genome was generated using DNA from 385 healthy African American individuals, and compared to a sample of 435 healthy individuals who were not of African descent. A total of 1,362 CNVs were identified within African Americans, which included two CNV regions that were significantly different in frequency between the two populations. In addition, duplication was identified in 74 percent of DNAs derived from cell lines that was not present in any of the whole-blood derived DNAs.

Journal: BMC Genomics. 2009 Mar 5;10:98.
Title: SiPaGene: A new repository for instant online retrieval, sharing and meta-analyses of GeneChip expression data.
Authors: A Menssen; G Edinger; J Grün; U Haase; R Baumgrass; A Grützkau; A Radbruch; G Burmester; T Häupl

Abstract: The authors developed a database platform that can load preprocessed Affymetrix GeneChip expression data for immediate access to immunology, infection, inflammation, tissue regeneration, and cancer data. SiPaGene exploits the MAS5.0/GCOS pairwise comparison algorithm, and enables restricted access and user-specific sharing. It does not aim for a complete representation of all public arrays but for high-quality analysis with stepwise integration of reference signatures for detailed meta-analyses, the authors note.

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Journal: BMC Genomics. 2009 Mar 25;10:129.
Title: Detection of genomic deletions in rice using oligonucleotide microarrays.
Authors: M Bruce; A Hess; J Bai; R Mauleon; M Diaz; N Sugiyama; A Bordeos; G Wang; H Leung; J Leach

Abstract: The authors present a microarray-based approach to identify deleted genomic regions in rice mutants selected from a large collection generated by gamma ray or fast neutron treatment. The study focuses on the method’s potential as a reverse genetics tool through accumulation of hybridization data for a collection of deletion mutants harboring multiple genetic lesions. The paper demonstrates that hybridization of labeled genomic DNA directly onto the Affymetrix Rice GeneChip allows rapid localization of deleted regions in rice mutants. Deletions ranged in size from one gene model to approximately 500 kb and were predicted on all 12 rice chromosomes. The technique was used to identify a candidate gene responsible for a lesion mimic phenotype, and the positions of mutations in 14 mutants were aligned onto the rice pseudomolecules in a genome browser to allow for identification of untagged mutations.

Journal: Chembiochem. 2009 Mar 23;10(5):877-88.
Title: Bacterial glycoprofiling by using random sequence peptide microarrays.
Authors: C Morales Betanzos; M Gonzalez-Moa; K Boltz; B Vander Werf; S Johnston; S Svarovsky

Abstract: The authors developed a high-throughput screening platform for identification of surface-immobilized peptides that specifically bind O-antigenic glycans of bacterial lipopolysaccharides. This method involves the screening of random-sequence peptide libraries in addressable high-density microarray format with the newly developed luminescent LPS-quantum dot micelles. Screening of LPS fractions from different serotypes of E. coli on a microarray consisting of 10,000 20-mer peptide features revealed minor differences, while comparison of LPS from E. coli and P. aeruginosa produced sets of highly specific peptides. While the main value of this approach lies in the ability to rapidly differentiate bacterial and possibly other complex glycans, the authors claim the peptides discovered can potentially be used off-array as antiendotoxic and antimicrobial lead compounds, and on-array/on-bead as diagnostic and affinity reagents.

Journal: Computational Methods and Programs in Biomedicine. 2009 Mar 9. [Epub ahead of print]
Title: A comparative study of individual and ensemble majority vote cDNA microarray image segmentation schemes, originating from a spot-adjustable based restoration framework.
Authors: A Daskalakis; D Glotsos; S Kostopoulos; D Cavouras; G Nikiforidis

Abstract: The aim of this study was to comparatively evaluate the performance of various segmentation algorithms, in conjunction with a noise reduction step, for the extraction of gene expression intensity in cDNA microarray images. Different segmentation algorithms, based on histogram and unsupervised classification methods, were employed either individually or in ensemble majority vote structures for separating spot images from background pixels. The performance of segmentation algorithms or ensemble structures was evaluated by assessing the validity and reproducibility of gene expression level extraction in simulated and real cDNA microarray images. By processing high-quality simulated images, the highest segmentation accuracy was achieved by an ensemble structure. Optimum performance in terms of processing time and segmentation precision for low-quality simulated and replicated real cDNA microarray images was attained by the Histogram Concavity algorithm.

Journal: Genetics in Medicine. 2009 Mar 10. [Epub ahead of print]
Title: Targeted comparative genomic hybridization array for the detection of single- and multiexon gene deletions and duplications.
Authors: M Tayeh; E Chin; V Miller; L Bean; B Coffee; M Hegde

Abstract: The authors have developed a high-resolution comparative genomic hybridization array to detect single- and multiexon deletions and duplications in a large set of genes on a single microarray, using a NimbleGen 385K array with an exon-centric design. They claim to have developed, validated, and implemented the arrays for detecting single- and multiexon deletions and duplication in autosomal and X-linked disease-associated genes. The authors conclude that the arrays can be adopted by clinical molecular diagnostic laboratories as an approach for the detection of single- and multiexon deletions or duplications, particularly in cases where direct sequencing fails to identify a mutation.

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Journal: Human Mutation. 2009 Mar;30(3):371-8.
Title: SNP array mapping of chromosome 20p deletions: genotypes, phenotypes, and copy number variation.
Authors: B Kamath; B Thiel; X Gai; L Conlin; P Munoz; J Glessner; D Clark; D Warthen; T Shaikh; E Mihci; D Piccoli; S Grant; H Hakonarson; I Krantz; N Spinner

Abstract: The authors studied 21 patients and five relatives with deletions of the short arm of chromosome 20 using the Illumina HumanHap550 SNP array to: a) more accurately determine the deletion sizes; b) identify and compare breakpoints; c) establish genotype/phenotype correlations; and d) investigate the use of the HumanHap550 platform for analysis of chromosome deletions. The authors identified 47 additional polymorphic genome-wide copy number variants, with up to 5 variants called per patient. Deletions of the short arm of chromosome 20 are associated with relatively mild and limited clinical anomalies. The use of SNP arrays, the authors argue, provides accurate high-resolution definition of genomic abnormalities.

Journal: Journal of Clinical Microbiology. 2009 Mar;47(3):743-50.
Title: Comparison of automated microarray detection with real-time PCR assays for detection of respiratory viruses in specimens obtained from children.
Authors: F Raymond; J Carbonneau; N Boucher; L Robitaille; S Boisvert; W Wu; G De Serres; G Boivin; J Corbeil

Abstract: The authors developed and compared two assays that allow the detection of up to 23 different respiratory viruses that frequently infect children. The first method consisted of single TaqMan quantitative real-time PCR assays in a 96-well-plate format. The second consisted of a multiplex PCR followed by primer extension and microarray hybridization in an integrated molecular diagnostic device, the Infiniti analyzer. These tests were used to identify viruses in 221 nasopharyngeal aspirates obtained from children hospitalized for respiratory tract infections. The two methods yielded concordant results for 94.1 percent of specimens, the authors write, and allow a thorough etiological assessment of respiratory viruses infecting children in hospital settings.

Journal: Journal of Molecular Diagnostics. 2009 Mar 26. [Epub ahead of print]
Title: Microarray-Based Comparative Genomic Hybridization Using Sex-Matched Reference DNA Provides Greater Sensitivity for Detection of Sex Chromosome Imbalances than Array-Comparative Genomic Hybridization with Sex-Mismatched Reference DNA.
Authors: S Yatsenko; C Shaw; Z Ou; A Pursley; A Patel; W Bi; S Cheung; J Lupski; A Chinault; A Beaudet

Abstract: The authors evaluated the ability of bacterial artificial chromosomes/P1-derived artificial and oligonucleotide array-CGH analyses to detect constitutional sex chromosome imbalances using sex-mismatched reference DNAs. Twenty-two samples with imbalances involving either the X or Y chromosome, including deletions, duplications, triplications, derivative or isodicentric chromosomes, and aneuploidy, were analyzed. Although concordant results were obtained for approximately one-half of the samples when using sex-mismatched and sex-matched reference DNAs, array-CGH analyses with sex-mismatched reference DNAs did not detect genomic imbalances that were detected using sex-matched reference DNAs in 6 of 22 patients, according to the paper. Small duplications and deletions of the X chromosome were most difficult to detect in female and male patients, respectively, when sex-mismatched reference DNAs were used. According to the authors, sex-matched reference DNAs in array-CGH analyses provides optimal sensitivity and enables an automated statistical evaluation for the detection of sex chromosome imbalances when compared with an experimental design using sex-mismatched reference DNAs.

Journal: Journal of Virological Methods. 2009 Mar;156(1-2):8-18.
Title: Development and evaluation of a generic tag array to detect and genotype noroviruses in water.
Authors: N Brinkman; G Fout

Noroviruses are the leading cause of nonbacterial gastroenteritis outbreaks in the United States, some of which are caused by the ingestion of contaminated water. Detection and genotypic characterization of noroviruses is commonly performed by RT-PCR followed by sequencing. However, sequencing of products amplified from environmental water samples is often hindered by the co-amplification of non-specific cDNA, according to the paper's abstract. To overcome this issue, the authors used a generic microarray to genotype noroviruses by probe hybridization. RT-PCR amplicons were used in a single-base extension reaction where genotype-specific probes were labeled and then hybridized to an Affymetrix GeneChip GenFlex Tag Array for detection. Using a standardized, multiplex SBE reaction, the authors genotyped representative strains through the identification of genotype-specific patterns of positive hybridization results. Additionally, the SBE-GenFlex array method was successful in the genotype identification of noroviruses seeded into tap and Ohio River water samples.

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Journal: Methods. 2009 Mar 9. [Epub ahead of print]
Title: Using ChIP-chip and ChIP-seq to study the regulation of gene expression: Genome-wide localization studies reveal widespread regulation of transcription elongation.
Authors: D Gilchrist; D Fargo; K Adelman

Abstract: The authors describe techniques for coupling ChIP-chip/ChIP-seq with genetic, chemical, and experimental manipulation to obtain mechanistic insight from genome-wide protein-DNA binding studies. The techniques were used to discern immature promoter-proximal Pol II from productively elongating Pol II, and infer a critical role for the transition between initiation and full elongation competence in regulating development and gene induction in response to environmental signals.

Journal: Nucleic Acids Research. 2009 Mar 18. [Epub ahead of print]
Title: Microarray labeling extension values: laboratory signatures for Affymetrix GeneChips.
Authors: Y Lee; C Chen; C Tsai; C Tsai; A Chao; T Wang

Abstract: Interlaboratory comparison of microarray data, even when using the same platform, imposes several challenges to scientists. RNA quality, RNA labeling efficiency, hybridization procedures and data-mining tools can all contribute variations in each laboratory. In Affymetrix GeneChips, between 11 and 20 different 25-mer oligonucleotides are used to measure the level of each transcript. Here, the authors report that labeling extension values, which are correlation coefficients between probe intensities and probe positions, are highly correlated with the gene expression levels on eukaryotic Affymetrix microarray data. By analyzing LEVs and GEVs in the publicly available 2,414 cel files of 20 Affymetrix microarray types covering 13 species, the authors found that correlations between LEVs and GEVs only exist in eukaryotic RNAs, but not in prokaryotic ones. The authors concluded that LEVs provide a new filtering parameter for microarray analysis of gene expression and may improve the inter- and intralaboratory comparability of Affymetrix GeneChips data.

Journal: Proceedings of the National Academy of Sciences. 2009 Mar 24;106(12):4840-5.
Title: GeoChip-based analysis of metabolic diversity of microbial communities at the Juan de Fuca Ridge hydrothermal vent.
Authors: F Wang; H Zhou; J Meng; X Peng; L Jiang; P Sun; C Zhang; J Van Nostrand; Y Deng; Z He; L Wu; J Zhou; X Xiao

Abstract: In this study, a GeoChip-based, high-throughput metagenomics technology revealed dramatic differences in microbial metabolic functions in a newly grown protochimney at the Juan de Fuca Ridge deep-sea hydrothermal vent. The numbers of functional genes differed based on location within the chimney, suggesting a rapid change in the microbial community composition during its growth. In addition, genes involved in methanogenesis, aerobic and anaerobic methane oxidation, nitrification, denitrification, sulfate reduction, degradation of complex carbon substrates, and metal resistance were also detected.

Journal: RNA. 2009 Mar;15(3):493-501.
Title: Impact of normalization on miRNA microarray expression profiling.
Authors: S Pradervand; J Weber; J Thomas; M Bueno; P Wirapati; K Lefort; G Dotto; K Harshman

Abstract: This study investigates the impact of normalization on data generated with the Agilent miRNA array platform. The authors have developed a method to select nonchanging miRNAs or invariants, and use them to compute linear regression normalization coefficients or variance-stabilizing normalization (VSN) parameters. They compared the invariants normalization to normalization by scaling, quantile, and VSN with default parameters as well as to no normalization using samples with strong differential expression of miRNAs and samples where only a few miRNAs are affected. All normalization methods performed better than no normalization, according to the paper. Normalization procedures based on the set of invariants and quantile were the most robust over all experimental conditions tested. The authors claim their method can be applied to other data sets including those from one-color miRNA microarray platforms, focused gene-expression arrays, and gene-expression analysis using quantitative PCR.

The Scan

And a Fourth?

A fourth dose of the Pfizer-BioNTech SARS-CoV-2 vaccine in an Israeli study increased antibody levels but did not prevent Omicron variant infections, according to the Financial Times.

For Better Science Software

A virtual institute funded by former Google CEO Eric Schmidt's philanthropy aims to lure software engineers to academia, Science reports.

Recommendation Explanations

The New York Times writes that the US Centers for Disease Control and Prevention is straining to both make and explain decisions based on limited information.

Genome Research Papers on De Novo Mutation Rates, Polyploid Genotyping, Oncogene Epigenomic Translocation

In Genome Research this week: de novo mutations rates in hemoglobin subunits, analysis of variant calling methods for polyploid plants, and more.