Results 1 to 10 of about 80,665 (254)

Optimizing copy number variation analysis using genome-wide short sequence oligonucleotide arrays [PDF]

Nucleic Acids Research, 2010
The detection of copy number variants (CNV) by array-based platforms provides valuable insight into understanding human diversity. However, suboptimal study design and data processing negatively affect CNV assessment. We quantitatively evaluate their impact when short-sequence oligonucleotide arrays are applied (Affymetrix Genome-Wide Human SNP Array 6.
D. A. Oldridge, S. Banerjee, S. R. Setlur, A. Sboner, Demichelis, Francesca   +4 more
openaire   +7 more sources

Enhanced high density oligonucleotide array-based sequence analysis using modified nucleoside triphosphates [PDF]

Nucleic Acids Research, 1998
Pairs of high density oligonucleotide arrays (DNA chips) consisting of >96 000 oligonucleotides were designed to screen the entire 5.53 kb coding region of the hereditary breast and ovarian cancer BRCA1 gene for all possible sequence changes in the homozygous and heterozygous states.
J G Hacia, Stephen A Woski, S P Fodor
exaly   +3 more sources

Analysis of oligonucleotide array experiments with repeated measures using mixed models

BMC Bioinformatics, 2004
Background Two or more factor mixed factorial experiments are becoming increasingly common in microarray data analysis. In this case study, the two factors are presence (Patients with Alzheimer's disease) or absence (Control) of the disease, and brain ...
Getchell Thomas V, Wood Constance L, Li Hao, Getchell Marilyn L, Stromberg Arnold J   +4 more
doaj   +3 more sources

Systematic validation and atomic force microscopy of non-covalent short oligonucleotide barcode microarrays. [PDF]

PLoS ONE, 2008
BACKGROUND: Molecular barcode arrays provide a powerful means to analyze cellular phenotypes in parallel through detection of short (20-60 base) unique sequence tags, or "barcodes", associated with each strain or clone in a collection.
Michael A Cook, Chi-Kin Chan, Paul Jorgensen, Troy Ketela, Daniel So, Mike Tyers, Chi-Yip Ho   +6 more
doaj   +2 more sources

Experimental optimization of probe length to increase the sequence specificity of high-density oligonucleotide microarrays [PDF]

BMC Genomics, 2007
Background High-density oligonucleotide arrays are widely used for analysis of genome-wide expression and genetic variation. Affymetrix GeneChips – common high-density oligonucleotide arrays – contain perfect match (PM) and mismatch (MM) probes generated
Kashiwagi Akiko, Furusawa Chikara, Ono Naoaki, Suzuki Shingo, Yomo Tetsuya   +4 more
doaj   +2 more sources

Strong position-dependent effects of sequence mismatches on signal ratios measured using long oligonucleotide microarrays [PDF]

BMC Genomics, 2008
Background Microarrays are an important and widely used tool. Applications include capturing genomic DNA for high-throughput sequencing in addition to the traditional monitoring of gene expression and identifying DNA copy number variations.
Hulme Helen, Kemp Stephen J, Noyes Harry A, Rennie Catriona, Brass Andy, Hoyle David C   +5 more
doaj   +2 more sources

Effective primer design for genotype and subtype detection of highly divergent viruses in large scale genome datasets [PDF]

BMC Bioinformatics
Identification of microorganisms in a biological sample is a crucial step in diagnostics, pathogen screening, biomedical research, evolutionary studies, agriculture, and biological threat assessment.
Burak Demiralay, Tolga Can
doaj   +2 more sources

Light-generated oligonucleotide arrays for rapid DNA sequence analysis. [PDF]

Proceedings of the National Academy of Sciences, 1994
In many areas of molecular biology there is a need to rapidly extract and analyze genetic information; however, current technologies for DNA sequence analysis are slow and labor intensive. We report here how modern photolithographic techniques can be used to facilitate sequence analysis by generating miniaturized arrays of densely packed ...
A C, Pease, D, Solas, E J, Sullivan, M T, Cronin, C P, Holmes, S P, Fodor   +5 more
openaire   +2 more sources

Sequencing analysis of HPV-other type on an HPV DNA chip [PDF]

Obstetrics & Gynecology Science, 2018
ObjectivesTo identify the specific human papillomavirus (HPV) genotypes from HPV-other type on an HPV DNA chip test by sequencing.MethodsAmong 13,600 women undergoing a routine gynecology examination including Pap smear and/or HPV test by DNA chip test ...
Min-Jeong Kim, Jin Ju Kim, Sunmie Kim
doaj   +1 more source

Rapid p53 sequence analysis in primary lung cancer using an oligonucleotide probe array [PDF]

Proceedings of the National Academy of Sciences, 1999
The p53 gene was sequenced in 100 primary human lung cancers by using direct dideoxynucleotide cycle sequencing and compared with sequence analysis by using the p53 GeneChip assay. Differences in sequence analysis between the two techniques were further evaluated to determine the accuracy and limitations of each method.
S A, Ahrendt, S, Halachmi, J T, Chow, L, Wu, N, Halachmi, S C, Yang, S, Wehage, J, Jen, D, Sidransky   +8 more
openaire   +2 more sources