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In Print: Oct 6, 2009

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Microarray Papers of Note Published in September 2009

Journal: American Journal of Clinical Pathology. 2009 Sep;132(3):349-60.

Title: Validation of the Agilent 244K oligonucleotide array-based comparative genomic hybridization platform for clinical cytogenetic diagnosis.

Authors: S Yu; D Bittel; N Kibiryeva; D Zwick; L Cooley

The authors present validation data for the Agilent Human Genome Microarray Kit 244K for use in clinical cytogenetic applications. The Agilent platform contains approximately 240,000 distinct 60-mer oligonucleotide probes spanning the human genome. Using the platform, the authors studied 45 previously characterized samples. Array analysis confirmed known aberrations in 43 samples and a normal result in two. The array analysis corrected one karyotype and clarified two additional cases. Array data from six patients with 22q11.2 deletion found an average of 2.56 megabases with a common 2.43-Mb deleted region. Approximately seven copy number variants ranging in size from 400 base pairs to 1.6 Mb were identified per sample.


Journal: Annals of Human Genetics. 2009 Sep;73(Pt 5):502-13.

Title: Combining microarray-based genomic selection (MGS) with the Illumina Genome Analyzer platform to sequence diploid target regions.

Authors: D Okou; A Locke; K Steinberg; K Hagen; P Athri; A Shetty; V Patel; M Zwick

The authors optimized microarray-based genomic selection for use with the Illumina Genome Analyzer. A set of 202 fragments contained within a 1.7 Mb genomic region on human chromosome X were selected and sequenced in 10 female HapMap samples generating a total of 2.4 gigabases of DNA sequence. The authors say the resulting data provide the first demonstration that targeted resequencing can generate quality sequence data that is necessary for human genetics research.


Journal: Biomacromolecules. 2009 Sep 14;10(9):2577-83.

Title: A new surface for immobilizing and maintaining the function of enzymes in a freeze-dried state.

Authors: N Nosworthy; D McKenzie; M Bilek

The authors describe a new surface produced by plasma treatment for immobilizing proteins in a dry state, suitable for use in microarray diagnostic services, biosensors, and chemical processing. Specifically, the authors produced plasma-modified polyethylene surfaces and tested them using horseradish peroxidase and catalase. The authors found the factors important for maintenance of surface attached enzyme stability were plasma immersion ion implantation treatment of the surface, freeze-drying with sucrose in the buffer solution, dry storage with desiccant, and maintenance of the freeze-dried protein at a reduced temperature.


Journal: Biometrics. 2009 Sep 17. [Epub ahead of print]

Title: Segmentation and estimation for SNP microarrays: a Bayesian multiple change-point approach.

Authors: Y Tai; M Kvale; J Witte

The authors propose a Bayesian multiple change-point model for the segmentation and estimation of SNP microarray data. According to the authors, segmentation concerns separating a chromosome into regions of equal copy number differences between the sample of interest and some reference, and involves the detection of locations of copy number difference changes. Estimation concerns determining true copy number for each segment. The authors say their approach not only gives posterior estimates for the parameters of interest, namely locations for copy number difference changes and true copy number estimates, but also provides useful confidence measures. In addition, the authors claim their algorithm can segment multiple samples simultaneously, and infer both common and rare CNVs across individuals.


Journal: BMC Bioinformatics. 2009 Sep 4;10:280.

Title: EDGE(3): a web-based solution for management and analysis of Agilent two color microarray experiments.

Authors: A Vollrath; A Smith; M Craven; C Bradfield

The authors developed EDGE(3) to support the storage, analysis, and sharing of Agilent microarray data. The software platform has two major functions. The first is to provide a workflow process for the generation of microarray data by a research laboratory or a microarray facility. The second is to store, analyze, and share microarray data in a manner that doesn't require complicated software. To satisfy this function, EDGE(3)'s user interface is a web browser that enables users to perform a number of bioinformatics-based analyses, collaborate between research groups through a user-based security model, and access the raw data files and quality control files generated by the software used to extract the signals from an array image.

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Journal: European Journal of Medical Genetics. 2009 Sep 15. [Epub ahead of print]

Title: Challenges for CNV interpretation in clinical molecular karyotyping: Lessons learned from a 1,001 sample experience.

Authors: K Buysse; B Chiaie; R Van Coster; B Loeys; A De Paepe; G Mortier; F Speleman; B Menten

The authors analyzed 1,001 patients using a large insert clone array and an oligonucleotide-based platform. In the studied cohort, the authors encountered several examples of causal imbalances that could have been interpreted as benign variants when relying on older technologies. Based on their experience, the authors suggest a decision tree that can be used as a guideline in clinical diagnostics. Using this workflow, they detected 106 clinically significant CNVs in 100 patients. Of these imbalances, 58 occurred de novo, 22 were inherited, and 26 were of unknown inheritance, they reported.


Journal: Genome Research. 2009 Sep;19(9):1616-21.

Title: Microarray-based multicycle-enrichment of genomic subsets for targeted next-generation sequencing.

Authors: D Summerer; H Wu; B Haase; Y Cheng; N Schracke; C Stähler; M Chee; P Stähler; M Beier

The authors report a strategy to multiply target enrichment performance and improve the coverage for desired target sequences by applying two iterative cycles of hybridization with microfluidic Geniom biochips. Using this strategy, they enriched and then sequenced the cancer-related genes BRCA1 and TP53 and a set of 1,000 individual dbSNP regions of 500 basepairs using Illumina's sequencing platform. The authors achieved overall enrichment factors of up to 1,062-fold and average coverage depths of 470-fold. According to the authors, analysis of SNP-calling accuracies after enrichment revealed concordance, with the reference sequence mirroring the previously reported performance of Illumina sequencing conducted without sequence enrichment.


Journal: Infection and Immunity. 2009 Sep 8. [Epub ahead of print]

Title: A genome-wide study of Pseudomonas aeruginosa outer membrane protein immunogenicity using self-assembling protein microarrays.

Authors: W Montor; J Huang; Y Hu; E Hainsworth; S Lynch; J Kronish; C Ordonez; T Logvinenko; S Lory; J Labaer

The authors report a comprehensive study of all 262 outer membrane and exported Pseudomonas aeruginosa PAO1 proteins, using nucleic acid programmable protein arrays. In this study, the authors were able to identify 12 proteins that trigger an adaptive immune response in cystic fibrosis and acutely infected patients, information about which bacterial proteins are actually recognized by the immune system in vivo, during the natural course of infection. The study also provides a list of potential candidates for the improvement of serological diagnostics and the development of vaccines.


Journal: Journal of Proteome Research. 2009 Sep 30. [Epub ahead of print]

Title: Carbohydrate cluster microarrays fabricated on 3-dimensional dendrimeric platforms for functional glycomics exploration.

Authors: X Zhou; C Turchi; D Wang

The authors describe a bioarray platform and methodology for the construction of carbohydrate cluster microarrays. The technology uses a three-dimensional poly(amidoamine) starburst dendrimer monolayer assembled on a glass surface that is functionalized with terminal aminooxy and hydrazide groups for site-specific coupling of carbohydrates. A wide range of saccharides, including monosaccharides, oligosaccharides, and polysaccharides of diverse structures are applicable for the 3D bioarray platform without prior chemical derivatization, according to the authors. The process of carbohydrate coupling is effectively accelerated by microwave radiation energy. The bioarray platform also presents sugar chains in defined orientation and cluster configurations, a quality that the authors claim is useful for exploration of the conformational diversity of sugar chains and their functional properties. According to the authors, sugar microarrays can be constructed using the methodology for glycan profiling of the Influenza hemagglutinins of H3N1 and H5N1.


Journal: Journal of Proteomics. 2009 Sep 22. [Epub ahead of print]

Title: Validation of serum protein profiles by a dual antibody array approach.

Authors: R Rimini; J Schwenk; M Sundberg; R Sjöberg; D Klevebring; M Gry; M Uhlén; P Nilsson

In this study, the authors describe the production of an antibody microarray to allow protein profiling of biotinylated human serum samples with reproducible sensitivity in the picomolar range. They describe a cross-platform strategy based on data concordance with a suspension bead array to interrogate the identical set of antibodies with the same cohort of serum samples. Comparative analysis enabled the authors to screen for high-performing antibodies, which displayed consistent results across the two platforms and targeted known serum components. Additionally, data processing methods such as sample referencing and normalization were evaluated for their effects on inter-platform agreement.

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Journal: Journal of Molecular Diagnostics. 2009 Sep 24. [Epub ahead of print]

Title: A new chromosome X exon-specific microarray platform for screening of patients with X-linked disorders.

Authors: S Bashiardes; L Kousoulidou; H van Bokhoven; H Ropers; J Chelly; C Moraine; A de Brouwer; H Van Esch; G Froyen; P Patsalis

This study used a chromosome X exon-specific array to screen 20 families, including a positive control, with suspected X-linked mental retardation in order to identify new causative X-linked mental retardation genes. The microarray used in the study contains 21,939 oligonucleotides covering 92.9 percent of all exons of all genes on chromosome X. Patient screening resulted in the successful identification of the blind positive control included in the sample of 20 families, and one of the remaining 19 families was found to carry a 1.78-kilobase deletion involving all exons of pseudogene BRAF2, the authors stated. Additionally, the BRAF2 deletion segregated in the family and was not found in 200 normal male samples, and no copy number variations were reported in this region.


Journal: Journal of the National Cancer Institute. 2009 Sep 2. [Epub ahead of print]

Title: Replication of prostate cancer risk loci in a Japanese case-control association study.

Authors: H Yamada; K Penney; H Takahashi; T Katoh; Y Yamano; M Yamakado; T Kimura; H Kuruma; Y Kamata; S Egawa; M Freedman

The authors of this paper evaluated the association of 23 single-nucleotide polymorphisms associated with prostate cancer risk and clinical covariates, including Gleason score, tumor aggressiveness, and age at diagnosis, in men of Japanese ancestry using unconditional logistic regression. They also used logistic regression to test the association between increasing numbers of independently associated risk alleles and the risk of prostate cancer, prostate cancer aggressiveness, and age at diagnosis. The researchers found that seven of the 23 SNPs were associated with prostate cancer risk. None of the seven SNPs was associated with Gleason score or aggressive disease. Two were associated with age at diagnosis. The authors also found that men with six or more risk alleles had a higher risk of prostate cancer than men with two or fewer risk alleles.


Journal: Journal of Veterinary Diagnostic Investigation. 2009 Sep;21(5):623-32.

Title: Detection and differentiation of four poultry diseases using asymmetric reverse transcription polymerase chain reaction in combination with oligonucleotide microarrays.

Authors: Q Tao; X Wang; H Bao; J Wu; L Shi; Y Li; C Qiao; S Yakovlevich; P Mikhaylovna; H Chen

The authors combined asymmetric RT-PCR and microarrays to distinguish four viruses, including avian influenza virus, Newcastle disease virus, infectious bronchitis virus, and infectious bursal disease virus, and hemagglutinin subtypes H5, H7, and H9, and neuraminidase subtypes N1 and N2 of AIV. According to the authors, the AIV matrix protein, HA and NA genes, IBV nucleoprotein gene, NDV NP gene, and IBDV A fragment gene were cloned into plasmids. The genes were amplified from the positive recombinant plasmids, which included the inserted target genes by PCR. The PCR products were then purified and printed on the amino-modified slides as the probes. RNA was extracted from samples and labeled by asymmetric RT-PCR using Cy3-labeled primers. The labeled cDNA was hybridized to the probes immobilized on the glass slides. After hybridization, the microarrays were scanned, and the hybridization pattern agreed with the known location of each probe, the authors found.


Journal: Journal of Virological Methods. 2009 Sep;160(1-2):90-100.

Title: Microarray immunoassay for the detection of grapevine and tree fruit viruses.

Authors: I Abdullahi; M Rott

The authors developed an antibody microarray for the detection of plant viruses. Using the ELISA technique as a benchmark, the procedure was used to detect several grapevine and tree fruit viruses. In a direct labeling approach, arabis mosaic virus and grapevine fanleaf virus were detected after incubating the antibody array with alkaline phosphatase-conjugated viral extract. Indirect detection using a double or triple antibody sandwich format also resulted in good reaction signals, using either chromogenic or fluorescence dyes, the authors found. In a multiplex system, four grapevine viruses were detected without compromising sensitivity and specificity. Compared to ELISA, the authors said the antibody microarray system is similar with respect to sensitivity and specificity, and a high correlation was observed in regression analysis of virus concentration measurements.


Journal: Journal of Virological Methods. 2009 Sep;160(1-2):167-71.

Title: Serological microarray for detection of HSV-1, HSV-2, VZV, and CMV antibodies.

Authors: A Jääskeläinen; K Moilanen; S Bühler; M Lappalainen; O Vapalahti; A Vaheri; H Piiparinen

A microarray was designed and tested for the detection of IgG and IgM antibodies for Puumala hantavirus and IgG antibodies against four herpesviruses. Initially, a microarray platform was set up using an unrelated in-house antigen, PUUV recombinant nucleocapsid protein, to optimize the protocol for the detection of antibodies. Detection of the four herpesviruses was also set up in a microarray using the recombinant proteins of herpes simplex virus glycoprotein G1 and G2, varicella-zoster virus glycoprotein E, and cytomegalovirus pp150 phosphoprotein. The results of the PUUV panel were found to be in agreement with the PUUV IgG immunofluorescent assay and IgM enzyme immunoassay. Seropositive and negative clinical reference panels were tested for herpesviruses by the serological microarray, and the results were compared to those of individual EIAs used for standard diagnostic purposes. The authors found the serologic microarray for HSV, VZV and CMV antibody detection gave good specificities for IgG.

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Journal: Molecular Human Reproduction. 2009 Sep;15(9):563-8.

Title: Detection of novel copy number variants in uterine leiomyomas using high-resolution SNP arrays.

Authors: W Bowden; J Skorupski; E Kovanci; A Rajkovic

The authors employed a high-resolution SNP microarray on 16 randomly selected uterine leiomyomas and normal myometrium samples to detect submicroscopic chromosomal aberrations. The SNP array identified gene dosage changes in 56 percent of the fibroids, 25 percent of which had aberrations greater than 5 megabases, while 31 percent contained only submicroscopic copy number changes. Novel submicroscopic aberrations were identified on chromosomal segments 1q42.13, 11q13.1, and 13q12.13, and large, previously unreported deletions were detected on 15q11.2-q23, 17p-q21.31, and 22q12.2-q12.3. The authors believe their findings support the hypothesis that a fraction of ULs without visible cytogenetic changes harbor submicroscopic genomic rearrangements which may contribute to transformation of normal myometrial tissue into leiomyomas.


Journal: The Plant Journal. 2009 Sep;59(5):840-50.

Title: Genome-wide identification of small RNA targets based on target enrichment and microarray hybridizations.

Authors: J Franco-Zorrilla; F Del Toro; M Godoy; J Pérez-Pérez; I López-Vidriero; J Oliveros; G García-Casado; C Llave; R Solano

The authors report on a microarray-based methodology to identify target mRNAs of miRNAs and siRNAs at a genomic scale. Their strategy relies on RNA ligase-mediated amplification of 5' cDNA ends to isolate miRNA or siRNA cleavage products from biological samples. Cleaved transcripts are then subjected to T7 RNA polymerase-mediated amplification and microarray hybridizations. The authors said they applied the method and identified more than 100 putative miRNA or siRNA target mRNAs that had not been previously predicted by computational or microarray-based methods.


Journal: RNA. 2009 Sep 10. [Epub ahead of print]

Title: Quantitative miRNA expression analysis: Comparing microarrays with next-generation sequencing.

Authors: H Willenbrock; J Salomon; R Søkilde; K Barken; T Hansen; F Nielsen; S Møller; T Litman

Using synthetic RNA samples resembling human microRNA samples, the authors found that microarray expression measures correlate better with sample RNA content than expression measures obtained from sequencing data. The authors also argue that microarrays perform equivalently to second-generation sequencing in terms of reproducibility and relative ratio quantification.


Journal: Schizophrenia Research. 2009 Sep;113(2-3):268-72.

Title: Family-based association study of SELENBP1 in schizophrenia.

Authors: T Kanazawa; S Glatt; S Faraone; H Hwu; H Yoneda; M Tsuang

This study employed family-based association methods to a sample of more than 2,400 individuals, including 1,214 individuals affected by schizophrenia, of Han Chinese descent living in Taiwan. One of four haplotype-tagging SNPs and two different two-marker haplotypes showed nominally significant evidence for association with schizophrenia under an additive model, suggesting that genetic variation in the SELENBP1 gene may influence risk for the disorder.

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