Parallel genotyping of human SNPs using generic high-density oligonucleotide tag arrays.

PubWeight™: 2.79‹?› | Rank: Top 1%

🔗 View Article (PMC 310915)

Published in Genome Res on June 01, 2000


J B Fan1, X Chen, M K Halushka, A Berno, X Huang, T Ryder, R J Lipshutz, D J Lockhart, A Chakravarti

Author Affiliations

1: Affymetrix, Inc., California 95051 USA.

Associated clinical trials:

Family Blood Pressure Program - GenNet Network | NCT00005268

Articles citing this

Bayesian haplotype inference for multiple linked single-nucleotide polymorphisms. Am J Hum Genet (2001) 10.48

Parallel genotyping of over 10,000 SNPs using a one-primer assay on a high-density oligonucleotide array. Genome Res (2004) 5.59

Genome-wide association studies: contribution of genomics to understanding blood pressure and essential hypertension. Curr Hypertens Rep (2010) 2.03

SBE-TAGS: an array-based method for efficient single-nucleotide polymorphism genotyping. Proc Natl Acad Sci U S A (2000) 1.74

Validation and extension of an empirical Bayes method for SNP calling on Affymetrix microarrays. Genome Biol (2008) 1.61

Minisequencing on oligonucleotide microarrays: comparison of immobilisation chemistries. Nucleic Acids Res (2001) 1.52

Locked nucleic acid (LNA) single nucleotide polymorphism (SNP) genotype analysis and validation using real-time PCR. Nucleic Acids Res (2004) 1.52

Quantitative detection of single nucleotide polymorphisms for a pooled sample by a bioluminometric assay coupled with modified primer extension reactions (BAMPER). Nucleic Acids Res (2001) 1.46

Multiplex SNP genotyping in pooled DNA samples by a four-colour microarray system. Nucleic Acids Res (2002) 1.44

Silhouette scores for assessment of SNP genotype clusters. BMC Genomics (2005) 1.44

Demonstration of loss of heterozygosity by single-nucleotide polymorphism microarray analysis and alterations in strain morphology in Candida albicans strains during infection. Eukaryot Cell (2005) 1.42

Fabrication of DNA microarrays with poly(L-glutamic acid) monolayers on gold substrates for SPR imaging measurements. Langmuir (2009) 1.38

Genome-wide single-nucleotide polymorphism map for Candida albicans. Eukaryot Cell (2004) 1.31

High-density single-nucleotide polymorphism maps of the human genome. Genomics (2005) 1.27

Multiplexed SNP genotyping using the Qbead system: a quantum dot-encoded microsphere-based assay. Nucleic Acids Res (2003) 1.25

ProbeMaker: an extensible framework for design of sets of oligonucleotide probes. BMC Bioinformatics (2005) 1.23

DNA microarrays with PAMAM dendritic linker systems. Nucleic Acids Res (2002) 1.22

Cloning of the Arabidopsis RSF1 gene by using a mapping strategy based on high-density DNA arrays and denaturing high-performance liquid chromatography. Plant Cell (2000) 1.21

Single-nucleotide polymorphism genotyping by nanoparticle-enhanced surface plasmon resonance imaging measurements of surface ligation reactions. Anal Chem (2006) 1.20

Homogeneous assays for single-nucleotide polymorphism typing using AlphaScreen. Genome Res (2001) 1.14

Comparison of GenFlex Tag array and Pyrosequencing in SNP genotyping. J Mol Diagn (2003) 1.11

DNA microarrays in medical practice. BMJ (2001) 1.05

Fluorescence detection of single-nucleotide polymorphisms with a single, self-complementary, triple-stem DNA probe. Angew Chem Int Ed Engl (2009) 1.04

Rice molecular breeding laboratories in the genomics era: Current status and future considerations. Int J Plant Genomics (2008) 1.04

SNP typing by apyrase-mediated allele-specific primer extension on DNA microarrays. Nucleic Acids Res (2002) 1.02

A low-cost open-source SNP genotyping platform for association mapping applications. Genome Biol (2005) 1.00

MARA: a novel approach for highly multiplexed locus-specific SNP genotyping using high-density DNA oligonucleotide arrays. Nucleic Acids Res (2004) 1.00

SNP genotyping by multiplexed solid-phase amplification and fluorescent minisequencing. Genome Res (2001) 0.98

Region-specific detection of neuroblastoma loss of heterozygosity at multiple loci simultaneously using a SNP-based tag-array platform. Genome Res (2005) 0.95

Thermodynamically based DNA strand design. Nucleic Acids Res (2005) 0.93

New separation-free assay technique for SNPs using two-photon excitation fluorometry. Nucleic Acids Res (2004) 0.92

Clinical relevance of multiple single-nucleotide polymorphisms in Pneumocystis jirovecii Pneumonia: development of a multiplex PCR-single-base-extension methodology. J Clin Microbiol (2011) 0.90

DNA microarrays with stem-loop DNA probes: preparation and applications. Nucleic Acids Res (2001) 0.89

AccuTyping: new algorithms for automated analysis of data from high-throughput genotyping with oligonucleotide microarrays. Nucleic Acids Res (2006) 0.88

Genotyping on a thermal gradient DNA chip. Genome Res (2003) 0.88

Rapid detection of single nucleotide polymorphisms associated with spinal muscular atrophy by use of a reusable fibre-optic biosensor. Nucleic Acids Res (2004) 0.83

Comparison of PrASE and Pyrosequencing for SNP Genotyping. BMC Genomics (2006) 0.83

Applications of array technology: identification of molecular targets in bladder cancer. Br J Cancer (2003) 0.82

Effect of single nucleotide polymorphisms on Affymetrix match-mismatch probe pairs. Bioinformation (2008) 0.82

Detecting imbalanced expression of SNP alleles by minisequencing on microarrays. BMC Biotechnol (2004) 0.82

Genome-wide SNP discovery in walnut with an AGSNP pipeline updated for SNP discovery in allogamous organisms. BMC Genomics (2012) 0.81

DNA probes on beads arrayed in a capillary, 'Bead-array', exhibited high hybridization performance. Nucleic Acids Res (2002) 0.80

Diagnosis of HNF-1alpha mutations on a PNA zip-code microarray by single base extension. Nucleic Acids Res (2005) 0.80

Gene expression profiling: from microarrays to medicine. J Clin Immunol (2004) 0.80

Mind the dbGAP: the application of data mining to identify biological mechanisms. Mol Interv (2011) 0.79

Multiplex allele-specific amplification from whole blood for detecting multiple polymorphisms simultaneously. Genet Test Mol Biomarkers (2012) 0.79

Application of DNA array technology for diagnostic microbiology. Can J Infect Dis (2000) 0.79

High-throughput SNP genotyping. Comp Funct Genomics (2002) 0.79

Bench-to-bedside review: fulfilling promises of the Human Genome Project. Crit Care (2002) 0.78

Auto-validation of fluorescent primer extension genotyping assay using signal clustering and neural networks. BMC Bioinformatics (2004) 0.76

TAMGeS: a Three-array Method for Genotyping of SNPs by a dual-colour approach. BMC Genomics (2007) 0.75

Chemical gradient-mediated melting curve analysis for genotyping of SNPs. Electrophoresis (2009) 0.75

Screening the single nucleotide polymorphisms in patients with internal carotid artery stenosis by oligonucleotide-based custom DNA array. Bioinform Biol Insights (2009) 0.75

Familial clustering of mice consistent to known pedigrees enabled by the genome profiling (GP) method. Biophysics (Nagoya-shi) (2014) 0.75

EGNAS: an exhaustive DNA sequence design algorithm. BMC Bioinformatics (2012) 0.75

Articles cited by this

The future of genetic studies of complex human diseases. Science (1996) 64.76

Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science (1999) 36.25

High density synthetic oligonucleotide arrays. Nat Genet (1999) 29.99

Genome-wide expression monitoring in Saccharomyces cerevisiae. Nat Biotechnol (1997) 27.78

Characterization of single-nucleotide polymorphisms in coding regions of human genes. Nat Genet (1999) 24.24

Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science (1998) 18.23

Patterns of single-nucleotide polymorphisms in candidate genes for blood-pressure homeostasis. Nat Genet (1999) 17.09

Analysis of any point mutation in DNA. The amplification refractory mutation system (ARMS). Nucleic Acids Res (1989) 15.35

Accessing genetic information with high-density DNA arrays. Science (1996) 13.89

Variations on a theme: cataloging human DNA sequence variation. Science (1997) 10.49

New goals for the U.S. Human Genome Project: 1998-2003. Science (1998) 8.30

Direct allelic variation scanning of the yeast genome. Science (1998) 5.90

Quantitative phenotypic analysis of yeast deletion mutants using a highly parallel molecular bar-coding strategy. Nat Genet (1996) 5.77

Population genetics--making sense out of sequence. Nat Genet (1999) 5.28

Genomic profiling of drug sensitivities via induced haploinsufficiency. Nat Genet (1999) 5.06

Polymorphism identification and quantitative detection of genomic DNA by invasive cleavage of oligonucleotide probes. Nat Biotechnol (1999) 3.01

A primer-guided nucleotide incorporation assay in the genotyping of apolipoprotein E. Genomics (1990) 2.95

Minisequencing: a specific tool for DNA analysis and diagnostics on oligonucleotide arrays. Genome Res (1997) 2.90

Genetic Bit Analysis: a solid phase method for typing single nucleotide polymorphisms. Nucleic Acids Res (1994) 2.79

Identification of individuals by analysis of biallelic DNA markers, using PCR and solid-phase minisequencing. Am J Hum Genet (1993) 2.46

Single nucleotide primer extension to detect genetic diseases: experimental application to hemophilia B (factor IX) and cystic fibrosis genes. Proc Natl Acad Sci U S A (1991) 2.21

Single-well genotyping of diallelic sequence variations by a two-color ELISA-based oligonucleotide ligation assay. Nucleic Acids Res (1996) 1.93

Template-directed dye-terminator incorporation (TDI) assay: a homogeneous DNA diagnostic method based on fluorescence resonance energy transfer. Nucleic Acids Res (1997) 1.86

Allele frequency distributions in pooled DNA samples: applications to mapping complex disease genes. Genome Res (1998) 1.81

Fluorescence energy transfer detection as a homogeneous DNA diagnostic method. Proc Natl Acad Sci U S A (1997) 1.71

A homogeneous, ligase-mediated DNA diagnostic test. Genome Res (1998) 1.38

Solid-phase minisequencing as a tool to detect DNA polymorphism. Methods Mol Biol (1998) 1.26

Direct haplotype determination by double ARMS: specificity, sensitivity and genetic applications. Nucleic Acids Res (1991) 1.22

Nested genetic bit analysis (N-GBA) for mutation detection in the p53 tumor suppressor gene. Nucleic Acids Res (1997) 1.22

Array-based multiplex analysis of candidate genes reveals two independent and additive genetic risk factors for myocardial infarction in the Finnish population. Hum Mol Genet (1998) 1.09

Two color hybridization analysis using high density oligonucleotide arrays and energy transfer dyes. Nucleic Acids Res (1998) 1.05

Testing the feasibility of DNA typing for human identification by PCR and an oligonucleotide ligation assay. Am J Hum Genet (1996) 0.97

Articles by these authors

Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science (1999) 36.25

Identification of the cystic fibrosis gene: genetic analysis. Science (1989) 33.61

High density synthetic oligonucleotide arrays. Nat Genet (1999) 29.99

Genome-wide expression monitoring in Saccharomyces cerevisiae. Nat Biotechnol (1997) 27.78

A genome-wide transcriptional analysis of the mitotic cell cycle. Mol Cell (1998) 19.67

Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science (1998) 18.23

Patterns of single-nucleotide polymorphisms in candidate genes for blood-pressure homeostasis. Nat Genet (1999) 17.09

TRANSFAC: an integrated system for gene expression regulation. Nucleic Acids Res (2000) 15.70

Accessing genetic information with high-density DNA arrays. Science (1996) 13.89

The TRANSFAC system on gene expression regulation. Nucleic Acids Res (2001) 13.63

Functional and genomic analyses reveal an essential coordination between the unfolded protein response and ER-associated degradation. Cell (2000) 13.44

Comparative analyses of multi-species sequences from targeted genomic regions. Nature (2003) 13.31

The integrin alpha v beta 6 binds and activates latent TGF beta 1: a mechanism for regulating pulmonary inflammation and fibrosis. Cell (1999) 11.59

Mutation detection and single-molecule counting using isothermal rolling-circle amplification. Nat Genet (1998) 9.84

ER stress induces cleavage of membrane-bound ATF6 by the same proteases that process SREBPs. Mol Cell (2000) 9.13

Mitotic misregulation and human aging. Science (2000) 8.47

New goals for the U.S. Human Genome Project: 1998-2003. Science (1998) 8.30

Nonuniform recombination within the human beta-globin gene cluster. Am J Hum Genet (1984) 7.97

DNA duplication associated with Charcot-Marie-Tooth disease type 1A. Cell (1991) 7.93

Replication dynamics of the yeast genome. Science (2001) 7.56

A DNA polymorphism discovery resource for research on human genetic variation. Genome Res (1998) 7.44

RAGE and amyloid-beta peptide neurotoxicity in Alzheimer's disease. Nature (1996) 7.04

B7-DC, a new dendritic cell molecule with potent costimulatory properties for T cells. J Exp Med (2001) 6.97

Expanding the TRANSFAC database towards an expert system of regulatory molecular mechanisms. Nucleic Acids Res (1999) 6.70

A genome-wide search for human non-insulin-dependent (type 2) diabetes genes reveals a major susceptibility locus on chromosome 2. Nat Genet (1996) 6.58

Natural engineering principles of electron tunnelling in biological oxidation-reduction. Nature (1999) 6.38

RNA expression analysis using a 30 base pair resolution Escherichia coli genome array. Nat Biotechnol (2000) 6.36

Revealing the maximum strength in nanotwinned copper. Science (2009) 6.27

Direct allelic variation scanning of the yeast genome. Science (1998) 5.90

Transcriptional regulation and function during the human cell cycle. Nat Genet (2001) 5.89

Analysis of gene expression profiles in normal and neoplastic ovarian tissue samples identifies candidate molecular markers of epithelial ovarian cancer. Proc Natl Acad Sci U S A (2001) 5.57

Stroke incidence among white, black, and Hispanic residents of an urban community: the Northern Manhattan Stroke Study. Am J Epidemiol (1998) 5.54

Mutations in the hepatocyte nuclear factor-1alpha gene in maturity-onset diabetes of the young (MODY3) Nature (1996) 5.32

High-throughput variation detection and genotyping using microarrays. Genome Res (2001) 5.24

Mechanisms of fatty acid-induced inhibition of glucose uptake. J Clin Invest (1994) 5.12

Exploring the DNA-binding specificities of zinc fingers with DNA microarrays. Proc Natl Acad Sci U S A (2001) 5.08

Regional and strain-specific gene expression mapping in the adult mouse brain. Proc Natl Acad Sci U S A (2000) 5.01

Gene delivery to skeletal muscle results in sustained expression and systemic delivery of a therapeutic protein. Proc Natl Acad Sci U S A (1996) 4.76

A hierarchical network of interreceptor interactions determines signal transduction by Neu differentiation factor/neuregulin and epidermal growth factor. Mol Cell Biol (1996) 4.47

Treatment with a copper-zinc chelator markedly and rapidly inhibits beta-amyloid accumulation in Alzheimer's disease transgenic mice. Neuron (2001) 4.42

Cdc25 cell-cycle phosphatase as a target of c-myc. Nature (1996) 4.23

Automated construction of genetic linkage maps using an expert system (MultiMap): a human genome linkage map. Nat Genet (1994) 4.19

Infectivity, transmission, and pathology of human-isolated H7N9 influenza virus in ferrets and pigs. Science (2013) 4.17

Hirschsprung disease, associated syndromes and genetics: a review. J Med Genet (2007) 4.13

Affinity panning of a library of peptides displayed on bacteriophages reveals the binding specificity of BiP. Cell (1993) 3.93

Quantifying DNA-protein interactions by double-stranded DNA arrays. Nat Biotechnol (1999) 3.87

Simultaneous genotyping and species identification using hybridization pattern recognition analysis of generic Mycobacterium DNA arrays. Genome Res (1998) 3.85

Development of microsatellite markers and characterization of simple sequence length polymorphism (SSLP) in rice (Oryza sativa L.). Mol Gen Genet (1996) 3.75

CD8(+) T cells can block herpes simplex virus type 1 (HSV-1) reactivation from latency in sensory neurons. J Exp Med (2000) 3.62

Effects of p21(Cip1/Waf1) at both the G1/S and the G2/M cell cycle transitions: pRb is a critical determinant in blocking DNA replication and in preventing endoreduplication. Mol Cell Biol (1998) 3.61

The CBFbeta subunit is essential for CBFalpha2 (AML1) function in vivo. Cell (1996) 3.55

Quantitative interpretation of magnetization transfer. Magn Reson Med (1993) 3.55

Exploiting chemical libraries, structure, and genomics in the search for kinase inhibitors. Science (1998) 3.53

Global analysis of gene expression in pulmonary fibrosis reveals distinct programs regulating lung inflammation and fibrosis. Proc Natl Acad Sci U S A (2000) 3.47

A prognostic score for patients with lower risk myelodysplastic syndrome. Leukemia (2007) 3.45

Functionalized graphene sheets for polymer nanocomposites. Nat Nanotechnol (2008) 3.45

SVM-Prot: Web-based support vector machine software for functional classification of a protein from its primary sequence. Nucleic Acids Res (2003) 3.34

Depletion of murine CD4+ T lymphocytes prevents antigen-induced airway hyperreactivity and pulmonary eosinophilia. Am J Respir Cell Mol Biol (1994) 3.32

TGF-beta is a critical mediator of acute lung injury. J Clin Invest (2001) 3.29

ErbB-2 is a common auxiliary subunit of NDF and EGF receptors: implications for breast cancer. EMBO J (1996) 3.22

Smoking duration, intensity, and risk of Parkinson disease. Neurology (2010) 3.19

Basic fallacies in the formulation of the paternity index. Am J Hum Genet (1985) 3.18

'Seed' analysis of off-target siRNAs reveals an essential role of Mcl-1 in resistance to the small-molecule Bcl-2/Bcl-XL inhibitor ABT-737. Oncogene (2006) 3.10

Regulation of CSF1 promoter by the SWI/SNF-like BAF complex. Cell (2001) 3.10

Schizophrenia susceptibility loci on chromosomes 13q32 and 8p21. Nat Genet (1998) 3.00

Evidence for increased recombination near the human insulin gene: implication for disease association studies. Proc Natl Acad Sci U S A (1986) 2.96

Evolutionarily conserved sequences on human chromosome 21. Genome Res (2001) 2.95

Nucleotide sequence of the oncogene encoding the p21 transforming protein of Kirsten murine sarcoma virus. Science (1982) 2.94

Molecular evidence for a relationship between LINE-1 elements and X chromosome inactivation: the Lyon repeat hypothesis. Proc Natl Acad Sci U S A (2000) 2.94

Association between obesity and kidney disease: a systematic review and meta-analysis. Kidney Int (2007) 2.92

Estimating the prior probability of paternity from the results of exclusion tests. Forensic Sci Int (1984) 2.91

Similarity of DNA fingerprints due to chance and relatedness. Hum Hered (1993) 2.90

Mechanism of hypertriglyceridemia in human apolipoprotein (apo) CIII transgenic mice. Diminished very low density lipoprotein fractional catabolic rate associated with increased apo CIII and reduced apo E on the particles. J Clin Invest (1992) 2.80

An information-based sequence distance and its application to whole mitochondrial genome phylogeny. Bioinformatics (2001) 2.80

Testosterone dose-response relationships in healthy young men. Am J Physiol Endocrinol Metab (2001) 2.79

Dramatic aggregation of Alzheimer abeta by Cu(II) is induced by conditions representing physiological acidosis. J Biol Chem (1998) 2.78

Genetic mapping of autosomal dominant Charcot-Marie-Tooth disease in a large French-Acadian kindred: identification of new linked markers on chromosome 17. Am J Hum Genet (1990) 2.77

Filamentous growth of Candida albicans in response to physical environmental cues and its regulation by the unique CZF1 gene. Mol Microbiol (1999) 2.74

The forgotten serine. A critical role for Ser-2035.42 in ligand binding to and activation of the beta 2-adrenergic receptor. J Biol Chem (2000) 2.67

The fibronectin type III domain as a scaffold for novel binding proteins. J Mol Biol (1998) 2.65

Effects of fat on insulin-stimulated carbohydrate metabolism in normal men. J Clin Invest (1991) 2.65

Perceived discrimination and early substance abuse among American Indian children. J Health Soc Behav (2001) 2.60

Genetic evidence for the involvement of tau in progressive supranuclear palsy. Ann Neurol (1997) 2.60

Mutagenesis identifies new signals for beta-amyloid precursor protein endocytosis, turnover, and the generation of secreted fragments, including Abeta42. J Biol Chem (1999) 2.57

A proteolytic fragment from the central region of p53 has marked sequence-specific DNA-binding activity when generated from wild-type but not from oncogenic mutant p53 protein. Genes Dev (1993) 2.53

Connective tissue growth factor mediates transforming growth factor beta-induced collagen synthesis: down-regulation by cAMP. FASEB J (1999) 2.50

The common and distinct target genes of the p53 family transcription factors. Cell Mol Life Sci (2004) 2.47

Patterns of polymorphism and linkage disequilibrium suggest independent origins of the human growth hormone gene cluster. Proc Natl Acad Sci U S A (1984) 2.47

Agrobacterium-Mediated Transformation of Fusarium oxysporum: An Efficient Tool for Insertional Mutagenesis and Gene Transfer. Phytopathology (2001) 2.43

Genome-wide mapping with biallelic markers in Arabidopsis thaliana. Nat Genet (1999) 2.43

An intracellular protein that binds amyloid-beta peptide and mediates neurotoxicity in Alzheimer's disease. Nature (1997) 2.42

COP9 signalosome-specific phosphorylation targets p53 to degradation by the ubiquitin system. EMBO J (2001) 2.41

p63alpha and DeltaNp63alpha can induce cell cycle arrest and apoptosis and differentially regulate p53 target genes. Oncogene (2001) 2.40

Watching the growth of bulk grains during recrystallization of deformed metals. Science (2004) 2.38

Patterns of genetic variation in Mendelian and complex traits. Annu Rev Genomics Hum Genet (2000) 2.37

English language use as a risk factor for smoking initiation among Hispanic and Asian American adolescents: evidence for mediation by tobacco-related beliefs and social norms. Health Psychol (2000) 2.36

Structure of the trp RNA-binding attenuation protein, TRAP, bound to RNA. Nature (1999) 2.35

A genetic study of Hirschsprung disease. Am J Hum Genet (1990) 2.30