Parallel Genotyping of Over 10,000 SNPs Using a One-Primer Assay on a High-Density Oligonucleotide Array

Matsuzaki, Hajime; Loi, Halina; Dong, Shoulian; Tsai, Ya Yu; Fang, Joy; Law, Jane; Di, Xiaojun; Liu, Wei Min; Yang, Guang; Li, Guoying; Huang, Jing; Kennedy, Giulia C.; Ryder, Thomas B.; Marcus, Gregory A.; Walsh, P. Sean; Shriver, Mark D.; Puck, Jennifer M.; Jones, Keith; Mei, Rui

doi:10.1101/gr.2014904

Cited by 282 publications

(224 citation statements)

References 33 publications

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“…SNP genotypes were obtained by following the Affymetrix protocol for the GeneChip Mapping 10K Xba Array. 37 In brief, 250 ng of genomic DNA taken from peripheral blood was digested with the Xba1 restriction enzyme into fragments. This step is followed by ligation to Xba adaptors that place no restriction on fragment size.…”

Section: Snp Genotypingmentioning

confidence: 99%

A high-density SNP genome-wide linkage scan in a large autism extended pedigree

et al. 2008

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We performed a high-density, single nucleotide polymorphism (SNP), genome-wide scan on a six-generation pedigree from Utah with seven affected males, diagnosed with autism spectrum disorder. Using a two-stage linkage design, we first performed a nonparametric analysis on the entire genome using a 10K SNP chip to identify potential regions of interest. To confirm potentially interesting regions, we eliminated SNPs in high linkage disequilibrium (LD) using a principal components analysis (PCA) method and repeated the linkage results. Three regions met genome-wide significance criteria after controlling for LD: 3q13.2-q13.31 (nonparametric linkage (NPL), 5.58), 3q26.31-q27.3 (NPL, 4.85) and 20q11.21-q13.12 (NPL, 5.56). Two regions met suggestive criteria for significance 7p14.1-p11.22 (NPL, 3.18) and 9p24.3 (NPL, 3.44). All five chromosomal regions are consistent with other published findings. Haplotype sharing results showed that five of the affected subjects shared more than a single chromosomal region of interest with other affected subjects. Although no common autism susceptibility genes were found for all seven autism cases, these results suggest that multiple genetic loci within these regions may contribute to the autism phenotype in this family, and further followup of these chromosomal regions is warranted.

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Section: Snp Genotypingmentioning

confidence: 99%

A high-density SNP genome-wide linkage scan in a large autism extended pedigree

et al. 2008

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“…Manufacturers like Affymetrix use a photolithography strategy to synthesize the oligo directly on the chip, producing 25mer oligonucleotides [15,51]. This technique allows strict control over number, concentration and spacing of each probe, enabling the production of high density microarray (500 k unique 25mer, each contained in an 18 lm 2 spot; [34]). …”

Section: Nucleic Acid Sequence Based Amplification (Nasba)mentioning

confidence: 99%

Potentials and limitations of molecular diagnostic methods in food safety

Lauri

Mariani

2008

Genes Nutr

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Molecular methods allow the detection of pathogen nucleic acids (DNA and RNA) and, therefore, the detection of contamination in food is carried out with high selectivity and rapidity. In the last 2 decades molecular methods have accompanied traditional diagnostic methods in routine pathogen detection, and might replace them in the upcoming future. In this review the implementation in diagnostics of four of the most used molecular techniques (PCR, NASBA, microarray, LDR) are described and compared, highlighting advantages and limitations of each of them. Drawbacks of molecular methods with regard to traditional ones and the difficulties encountered in pathogen detection from food or clinical specimen are also discussed. Moreover, criteria for the choice of the target sequence for a secure detection and classification of pathogens and possible developments in molecular diagnostics are also proposed.

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“…Genotyping was carried out using Affymetrix GeneChip 10K Human Mapping Arrays [Kennedy et al, 2003;Matsuzaki et al, 2004]. Briefly, the method consisted of a one-primer amplification assay performed on genomic DNA in which sequence complexity had been reduced by restriction enzyme digestion with XbaI.…”

Section: Genotypingmentioning

confidence: 99%

“…The markers in the Affymetrix panel were selected from SNPs previously validated by the SNP Consortium and for their genome-wide coverage [Kennedy et al, 2003;Matsuzaki et al, 2004]. Each SNP had a relatively high heterozygosity (40.25) in three population groups, and the SNPs were selected without consideration for proximity to genes.…”

Section: Snp Selectionmentioning

confidence: 99%

Localization of breast cancer susceptibility loci by genome‐wide SNP linkage disequilibrium mapping

Ellis

Kirchhoff

Mitra

et al. 2005

Genetic Epidemiology

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We studied the feasibility of a novel approach to localize breast cancer susceptibility genes, using a low-density genomewide panel of single-nucleotide polymorphisms and taking advantage of large regions of linkage disequilibrium (LD) flanking Jewish disease genes in high-risk cases. With Affymetrix GeneChip arrays, we genotyped 8,576 polymorphisms in three sets of Ashkenazi Jewish breast cancer cases: a ''validation'' set of 27 breast cancer cases, all of whom carried the BRCA2*6174delT founder mutation; a ''field'' set of 19 breast cancer cases from male breast cancer kindreds, which simulated conditions for finding new genes; and a ''test'' set of 57 probands from breast cancer kindreds (4 or more cases/ kindred), in which mutations in BRCA1 and BRCA2 had been excluded. To identify associations, we compared the frequency of genotypes and haplotypes in cases vs. controls by the Fisher's exact test and a maximum likelihood ratio test. In the ''validation'' set, we demonstrated the presence of a region of linkage disequilibrium on BRCA2*6174delT chromosomes that spanned over 5 million bases. In the ''field'' set, we showed that this large region of linkage disequilibrium flanking BRCA2 was detectable despite the presence of heterogeneity in the sample set. Finally, in the ''test'' set, at least three regions of interest emerged that could contain novel breast cancer genes, one of which had been identified previously by linkage analysis. While these results demonstrate the feasibility of genome-wide association strategies, further application of this approach will critically depend on optimizing the density and distribution of SNPs and the size and type of study design. Genet. Epidemiol. 30:48-61, 2006. r 2005 Wiley-Liss, Inc.

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Parallel Genotyping of Over 10,000 SNPs Using a One-Primer Assay on a High-Density Oligonucleotide Array

Cited by 282 publications

References 33 publications

A high-density SNP genome-wide linkage scan in a large autism extended pedigree

A high-density SNP genome-wide linkage scan in a large autism extended pedigree

Potentials and limitations of molecular diagnostic methods in food safety

Localization of breast cancer susceptibility loci by genome‐wide SNP linkage disequilibrium mapping

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