A general approach to single-nucleotide polymorphism discovery.

PubWeight™: 13.39‹?› | Rank: Top 0.1% | All-Time Top 10000

🔗 View Article (PMID 10581034)

Published in Nat Genet on December 01, 1999

Authors

G T Marth1, I Korf, M D Yandell, R T Yeh, Z Gu, H Zakeri, N O Stitziel, L Hillier, P Y Kwok, W R Gish

Author Affiliations

1: Washington University Department of Genetics and Genome Sequencing Center, St. Louis, Missouri, USA. gmarth@watson.wustl.edu

Articles citing this

(truncated to the top 100)

Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res (2008) 157.44

SNP detection for massively parallel whole-genome resequencing. Genome Res (2009) 15.96

Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding. Genome Res (2009) 15.15

Insights into social insects from the genome of the honeybee Apis mellifera. Nature (2006) 13.67

SNPdetector: a software tool for sensitive and accurate SNP detection. PLoS Comput Biol (2005) 10.04

A de novo paradigm for mental retardation. Nat Genet (2010) 8.57

Rapid whole-genome mutational profiling using next-generation sequencing technologies. Genome Res (2008) 8.01

novoSNP, a novel computational tool for sequence variation discovery. Genome Res (2005) 7.42

Genome assembly comparison identifies structural variants in the human genome. Nat Genet (2006) 6.93

SNP discovery via 454 transcriptome sequencing. Plant J (2007) 5.92

A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries. Genome Biol (2011) 5.11

A SNP discovery method to assess variant allele probability from next-generation resequencing data. Genome Res (2009) 4.78

A flexible and efficient template format for circular consensus sequencing and SNP detection. Nucleic Acids Res (2010) 4.48

Human diallelic insertion/deletion polymorphisms. Am J Hum Genet (2002) 4.44

The functional spectrum of low-frequency coding variation. Genome Biol (2011) 4.42

Single-nucleotide polymorphisms in soybean. Genetics (2003) 3.73

A soybean transcript map: gene distribution, haplotype and single-nucleotide polymorphism analysis. Genetics (2007) 3.54

Impacts of genetic bottlenecks on soybean genome diversity. Proc Natl Acad Sci U S A (2006) 3.23

SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines. BMC Genet (2002) 3.23

Sequence variations in the public human genome data reflect a bottlenecked population history. Proc Natl Acad Sci U S A (2002) 2.70

Survey of allelic expression using EST mining. Genome Res (2005) 2.67

An SNP resource for rice genetics and breeding based on subspecies indica and japonica genome alignments. Genome Res (2004) 2.56

A SNP resource for human chromosome 22: extracting dense clusters of SNPs from the genomic sequence. Genome Res (2001) 2.49

Development and evaluation of SoySNP50K, a high-density genotyping array for soybean. PLoS One (2013) 2.40

Efficient frequency-based de novo short-read clustering for error trimming in next-generation sequencing. Genome Res (2009) 2.36

Dissemination of scientific software with Galaxy ToolShed. Genome Biol (2014) 2.34

Computational and statistical approaches to analyzing variants identified by exome sequencing. Genome Biol (2011) 2.32

Sequencing studies in human genetics: design and interpretation. Nat Rev Genet (2013) 2.27

Gene discovery using massively parallel pyrosequencing to develop ESTs for the flesh fly Sarcophaga crassipalpis. BMC Genomics (2009) 2.21

Genetic and haplotypic structure in 14 European and African cattle breeds. Genetics (2007) 2.18

Inference of population genetic parameters in metagenomics: a clean look at messy data. Genome Res (2006) 2.17

A linkage map of the Atlantic salmon (Salmo salar) based on EST-derived SNP markers. BMC Genomics (2008) 2.07

Mining for single nucleotide polymorphisms and insertions/deletions in maize expressed sequence tag data. Plant Physiol (2003) 2.05

QualitySNP: a pipeline for detecting single nucleotide polymorphisms and insertions/deletions in EST data from diploid and polyploid species. BMC Bioinformatics (2006) 2.03

New explicit expressions for relative frequencies of single-nucleotide polymorphisms with application to statistical inference on population growth. Genetics (2003) 1.97

Genomic analyses of the microsporidian Nosema ceranae, an emergent pathogen of honey bees. PLoS Pathog (2009) 1.97

Annotation-based genome-wide SNP discovery in the large and complex Aegilops tauschii genome using next-generation sequencing without a reference genome sequence. BMC Genomics (2011) 1.88

Transcriptome sequencing and comparative analysis of cucumber flowers with different sex types. BMC Genomics (2010) 1.88

High-throughput SNP discovery and assay development in common bean. BMC Genomics (2010) 1.79

Population genetic inference from personal genome data: impact of ancestry and admixture on human genomic variation. Am J Hum Genet (2012) 1.75

Mu transposon insertion sites and meiotic recombination events co-localize with epigenetic marks for open chromatin across the maize genome. PLoS Genet (2009) 1.70

Scan of human genome reveals no new Loci under ancient balancing selection. Genetics (2006) 1.68

NRAS mutation is the sole recurrent somatic mutation in large congenital melanocytic nevi. J Invest Dermatol (2013) 1.63

Exome sequencing in an admixed isolated population indicates NFXL1 variants confer a risk for specific language impairment. PLoS Genet (2015) 1.55

Snipping polymorphisms from large EST collections in barley (Hordeum vulgare L.). Mol Genet Genomics (2003) 1.49

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

Single nucleotide polymorphisms associated with rat expressed sequences. Genome Res (2004) 1.43

SNPServer: a real-time SNP discovery tool. Nucleic Acids Res (2005) 1.42

Automated SNP detection from a large collection of white spruce expressed sequences: contributing factors and approaches for the categorization of SNPs. BMC Genomics (2006) 1.41

Genome-wide association studies in cancer--current and future directions. Carcinogenesis (2009) 1.39

Development of genomic resources for Citrus clementina: characterization of three deep-coverage BAC libraries and analysis of 46,000 BAC end sequences. BMC Genomics (2008) 1.38

Efficient high-throughput resequencing of genomic DNA. Genome Res (2003) 1.37

Population genomic inferences from sparse high-throughput sequencing of two populations of Drosophila melanogaster. Genome Biol Evol (2009) 1.36

Assessment of linkage disequilibrium in potato genome with single nucleotide polymorphism markers. Genetics (2006) 1.36

AutoSNPdb: an annotated single nucleotide polymorphism database for crop plants. Nucleic Acids Res (2008) 1.35

From RNA-seq to large-scale genotyping - genomics resources for rye (Secale cereale L.). BMC Plant Biol (2011) 1.35

Sympatric ecological speciation meets pyrosequencing: sampling the transcriptome of the apple maggot Rhagoletis pomonella. BMC Genomics (2009) 1.34

PurityEst: estimating purity of human tumor samples using next-generation sequencing data. Bioinformatics (2012) 1.33

Error and error mitigation in low-coverage genome assemblies. PLoS One (2011) 1.31

Association genetics of wood physical traits in the conifer white spruce and relationships with gene expression. Genetics (2011) 1.30

A garter snake transcriptome: pyrosequencing, de novo assembly, and sex-specific differences. BMC Genomics (2010) 1.29

Application of machine learning in SNP discovery. BMC Bioinformatics (2006) 1.28

Gene mapping in the wild with SNPs: guidelines and future directions. Genetica (2008) 1.27

Genomic resources for Myzus persicae: EST sequencing, SNP identification, and microarray design. BMC Genomics (2007) 1.26

Next generation sequencing has lower sequence coverage and poorer SNP-detection capability in the regulatory regions. Sci Rep (2011) 1.25

A DOC2 protein identified by mutational profiling is essential for apicomplexan parasite exocytosis. Science (2012) 1.24

High-throughput SNP genotyping in the highly heterozygous genome of Eucalyptus: assay success, polymorphism and transferability across species. BMC Plant Biol (2011) 1.20

A pipeline for high throughput detection and mapping of SNPs from EST databases. Mol Breed (2010) 1.20

High-throughput genetic mapping of mutants via quantitative single nucleotide polymorphism typing. Genetics (2009) 1.19

Identification and characterisation of novel SNP markers in Atlantic cod: evidence for directional selection. BMC Genet (2008) 1.19

A cSNP map and database for human chromosome 21. Genome Res (2001) 1.15

Analysis of expressed sequence tags generated from full-length enriched cDNA libraries of melon. BMC Genomics (2011) 1.13

Chondrodysplasia and abnormal joint development associated with mutations in IMPAD1, encoding the Golgi-resident nucleotide phosphatase, gPAPP. Am J Hum Genet (2011) 1.12

In vitro vs in silico detected SNPs for the development of a genotyping array: what can we learn from a non-model species? PLoS One (2010) 1.11

A comparative genomics strategy for targeted discovery of single-nucleotide polymorphisms and conserved-noncoding sequences in orphan crops. Plant Physiol (2006) 1.10

Whole-exome sequencing of DNA from peripheral blood mononuclear cells (PBMC) and EBV-transformed lymphocytes from the same donor. BMC Genomics (2011) 1.08

Whole-genome resequencing of two elite sires for the detection of haplotypes under selection in dairy cattle. Proc Natl Acad Sci U S A (2012) 1.08

Dengue Virus Evolution under a Host-Targeted Antiviral. J Virol (2015) 1.05

A toolkit for rapid gene mapping in the nematode Caenorhabditis briggsae. BMC Genomics (2010) 1.04

A transcriptome map of perennial ryegrass (Lolium perenne L.). BMC Genomics (2012) 1.03

Mining for single nucleotide polymorphisms in pig genome sequence data. BMC Genomics (2009) 1.02

SNP-PHAGE--High throughput SNP discovery pipeline. BMC Bioinformatics (2006) 0.99

Genome-wide discovery of DNA polymorphism in Brassica rapa. Mol Genet Genomics (2009) 0.98

PineSAP--sequence alignment and SNP identification pipeline. Bioinformatics (2009) 0.97

Performance comparison of SNP detection tools with illumina exome sequencing data--an assessment using both family pedigree information and sample-matched SNP array data. Nucleic Acids Res (2014) 0.97

Statistical mutation calling from sequenced overlapping DNA pools in TILLING experiments. BMC Bioinformatics (2011) 0.97

Mapping genes for resistance to Verticillium albo-atrum in tetraploid and diploid potato populations using haplotype association tests and genetic linkage analysis. Mol Genet Genomics (2004) 0.96

Evaluation of an integrated clinical workflow for targeted next-generation sequencing of low-quality tumor DNA using a 51-gene enrichment panel. BMC Med Genomics (2014) 0.95

Comparative genomics of grasses promises a bountiful harvest. Plant Physiol (2009) 0.95

Novel tools for conservation genomics: comparing two high-throughput approaches for SNP discovery in the transcriptome of the European hake. PLoS One (2011) 0.95

SNP discovery using Next Generation Transcriptomic Sequencing in Atlantic herring (Clupea harengus). PLoS One (2012) 0.95

HaploSNPer: a web-based allele and SNP detection tool. BMC Genet (2008) 0.94

A method for finding single-nucleotide polymorphisms with allele frequencies in sequences of deep coverage. BMC Bioinformatics (2005) 0.94

Comparative analysis of the transcriptome in tissues secreting purple and white nacre in the pearl mussel Hyriopsis cumingii. PLoS One (2013) 0.94

Transcriptome sequencing and annotation for the Jamaican fruit bat (Artibeus jamaicensis). PLoS One (2012) 0.94

Characterizing Ancylostoma caninum transcriptome and exploring nematode parasitic adaptation. BMC Genomics (2010) 0.93

SNP calling using genotype model selection on high-throughput sequencing data. Bioinformatics (2012) 0.92

INSIG1 influences obesity-related hypertriglyceridemia in humans. J Lipid Res (2009) 0.92

A novel approach to sequence validating protein expression clones with automated decision making. BMC Bioinformatics (2007) 0.91

PyroHMMsnp: an SNP caller for Ion Torrent and 454 sequencing data. Nucleic Acids Res (2013) 0.91

Articles by these authors

Initial sequencing and analysis of the human genome. Nature (2001) 212.86

The sequence of the human genome. Science (2001) 101.55

Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res (1998) 96.63

The genome sequence of Drosophila melanogaster. Science (2000) 74.32

A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature (2001) 42.18

Comparative genomics of the eukaryotes. Science (2000) 26.62

A physical map of the human genome. Nature (2001) 12.39

Rapid gene mapping in Caenorhabditis elegans using a high density polymorphism map. Nat Genet (2001) 9.54

Juxtaposed regions of extensive and minimal linkage disequilibrium in human Xq25 and Xq28. Nat Genet (2000) 5.65

Gene structure prediction and alternative splicing analysis using genomically aligned ESTs. Genome Res (2001) 5.38

The C. elegans genome sequencing project: a beginning. Nature (1992) 5.36

Enhanced fidelity of 3TC-selected mutant HIV-1 reverse transcriptase. Science (1996) 5.08

Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana. Nature (1999) 5.03

A survey of expressed genes in Caenorhabditis elegans. Nat Genet (1992) 4.63

Fluorescence polarization in homogeneous nucleic acid analysis. Genome Res (1999) 4.59

Surveying Saccharomyces genomes to identify functional elements by comparative DNA sequence analysis. Genome Res (2001) 4.22

Evolutionary analyses of the human genome. Nature (2001) 4.13

Prostate stem cell antigen: a cell surface marker overexpressed in prostate cancer. Proc Natl Acad Sci U S A (1998) 3.89

MaskerAid: a performance enhancement to RepeatMasker. Bioinformatics (2000) 3.66

Expression of bbc3, a pro-apoptotic BH3-only gene, is regulated by diverse cell death and survival signals. Proc Natl Acad Sci U S A (2001) 3.16

Ancient conserved regions in new gene sequences and the protein databases. Science (1993) 3.00

The same mutation that encodes low-level human immunodeficiency virus type 1 resistance to 2',3'-dideoxyinosine and 2',3'-dideoxycytidine confers high-level resistance to the (-) enantiomer of 2',3'-dideoxy-3'-thiacytidine. Antimicrob Agents Chemother (1993) 3.00

Changes in gene expression associated with developmental arrest and longevity in Caenorhabditis elegans. Genome Res (2001) 2.96

The syntenic relationship of the zebrafish and human genomes. Genome Res (2000) 2.68

Increasing the information content of STS-based genome maps: identifying polymorphisms in mapped STSs. Genomics (1996) 2.57

An encyclopedia of mouse genes. Nat Genet (1999) 2.48

The optimal measure of allelic association. Proc Natl Acad Sci U S A (2001) 2.41

Comparison of droplet digital PCR to real-time PCR for quantitative detection of cytomegalovirus. J Clin Microbiol (2012) 2.39

zA map for sequence analysis of the Arabidopsis thaliana genome. Nat Genet (1999) 2.39

Reading bits of genetic information: methods for single-nucleotide polymorphism analysis. Genome Res (1998) 2.38

Effects of alterations of primer-binding site sequences on human immunodeficiency virus type 1 replication. J Virol (1994) 2.37

In vivo nuclear transport kinetics in Saccharomyces cerevisiae: a role for heat shock protein 70 during targeting and translocation. J Cell Biol (1996) 2.33

Comparison of deoxyoligonucleotide and tRNA(Lys-3) as primers in an endogenous human immunodeficiency virus-1 in vitro reverse transcription/template-switching reaction. J Biol Chem (1994) 2.28

Absence of cardiolipin in the crd1 null mutant results in decreased mitochondrial membrane potential and reduced mitochondrial function. J Biol Chem (2000) 2.26

Overlapping genomic sequences: a treasure trove of single-nucleotide polymorphisms. Genome Res (1998) 2.24

Single-nucleotide polymorphisms in the public domain: how useful are they? Nat Genet (2001) 2.24

PEGylated PLGA nanoparticles as protein carriers: synthesis, preparation and biodistribution in rats. J Control Release (2001) 2.15

Gene discovery by EST sequencing in Toxoplasma gondii reveals sequences restricted to the Apicomplexa. Genome Res (1998) 2.14

A BMP homolog acts as a dose-dependent regulator of body size and male tail patterning in Caenorhabditis elegans. Development (1999) 2.08

Identification and characterization of a p53 homologue in Drosophila melanogaster. Proc Natl Acad Sci U S A (2000) 2.04

AmpliTaq DNA polymerase, FS dye-terminator sequencing: analysis of peak height patterns. Biotechniques (1996) 2.02

The nucleotide sequence of Saccharomyces cerevisiae chromosome XII. Nature (1997) 1.89

Generation of drug-resistant variants of human immunodeficiency virus type 1 by in vitro passage in increasing concentrations of 2',3'-dideoxycytidine and 2',3'-dideoxy-3'-thiacytidine. Antimicrob Agents Chemother (1993) 1.86

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

Representation of cloned genomic sequences in two sequencing vectors: correlation of DNA sequence and subclone distribution. Nucleic Acids Res (1997) 1.78

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

Activation of c-myc gene expression by tumor-derived p53 mutants requires a discrete C-terminal domain. Mol Cell Biol (1998) 1.62

Universal SNP genotyping assay with fluorescence polarization detection. Biotechniques (2001) 1.62

Prostate stem cell antigen is overexpressed in human transitional cell carcinoma. Cancer Res (2001) 1.61

Efficient approach to unique single-nucleotide polymorphism discovery. Genome Res (1999) 1.59

Development of HIV-1 resistance to (-)2'-deoxy-3'-thiacytidine in patients with AIDS or advanced AIDS-related complex. AIDS (1995) 1.58

Expressed sequence tag analysis of the bradyzoite stage of Toxoplasma gondii: identification of developmentally regulated genes. Infect Immun (1998) 1.55

Automated sequence preprocessing in a large-scale sequencing environment. Genome Res (1998) 1.53

A trace display and editing program for data from fluorescence based sequencing machines. Nucleic Acids Res (1991) 1.50

Beta-adrenergic receptor polymorphisms and cardiac graft function in potential organ donors. Am J Transplant (2012) 1.49

Expressed sequence tags--ESTablishing bridges between genomes. Trends Genet (1998) 1.38

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

Linkage of a gene for familial hypobetalipoproteinemia to chromosome 3p21.1-22. Am J Hum Genet (2000) 1.37

Molecular basis of cystathionine beta-synthase deficiency in pyridoxine responsive and nonresponsive homocystinuria. Hum Mol Genet (1993) 1.34

Sequence assembly with CAFTOOLS. Genome Res (1998) 1.26

Peak height variations in automated sequencing of PCR products using Taq dye-terminator chemistry. Biotechniques (1995) 1.26

Single-step purification of recombinant wild-type and mutant HIV-1 reverse transcriptase. Protein Expr Purif (1996) 1.25

A high-density single-nucleotide polymorphism map of Xq25-q28. Genomics (2000) 1.24

Impact of hypertension on health-related quality of life in a population-based study in Shanghai, China. Public Health (2009) 1.23

Nuclear magnetic resonance solution structures of covalent aromatic amine-DNA adducts and their mutagenic relevance. Chem Res Toxicol (1998) 1.22

Establishment of a highly metastatic human ovarian cancer cell line (HO-8910PM) and its characterization. J Exp Clin Cancer Res (1999) 1.21

Solid-state NMR triple-resonance backbone assignments in a protein. J Biomol NMR (1999) 1.21

The birth and death of human single-nucleotide polymorphisms: new experimental evidence and implications for human history and medicine. Hum Mol Genet (2001) 1.21

Comparative genomic sequence analysis of the human and mouse cystic fibrosis transmembrane conductance regulator genes. Proc Natl Acad Sci U S A (2000) 1.19

Endogenous reverse transcription assays reveal high-level resistance to the triphosphate of (-)2'-dideoxy-3'-thiacytidine by mutated M184V human immunodeficiency virus type 1. J Virol (1996) 1.18

Peak height pattern in dichloro-rhodamine and energy transfer dye terminator sequencing. Biotechniques (1998) 1.17

The K65R mutation confers increased DNA polymerase processivity to HIV-1 reverse transcriptase. J Biol Chem (1996) 1.16

Regions of low single-nucleotide polymorphism incidence in human and orangutan xq: deserts and recent coalescences. Genomics (2001) 1.13

The homozygous complete hydatidiform mole: a unique resource for genome studies. Genomics (1997) 1.13

Effectiveness of 3TC in HIV clinical trials may be due in part to the M184V substitution in 3TC-resistant HIV-1 reverse transcriptase. AIDS (1996) 1.13

In vitro selection and molecular characterization of human immunodeficiency virus type 1 with reduced sensitivity to 9-[2-(phosphonomethoxy)ethyl]adenine (PMEA). Antiviral Res (1996) 1.12

Comparison of various blood compartments and reporting units for the detection and quantification of Epstein-Barr virus in peripheral blood. J Clin Microbiol (2007) 1.12

Selecting breast cancer patients for chemotherapy: the opening of the UK OPTIMA trial. Clin Oncol (R Coll Radiol) (2012) 1.10

Effects of 3'-deoxynucleoside 5'-triphosphate concentrations on chain termination by nucleoside analogs during human immunodeficiency virus type 1 reverse transcription of minus-strand strong-stop DNA. J Virol (1996) 1.09

Single nucleotide polymorphism libraries: why and how are we building them? Mol Med Today (1999) 1.09

Coamplification of prostate stem cell antigen (PSCA) and MYC in locally advanced prostate cancer. Genes Chromosomes Cancer (2000) 1.08

Comparison of cord blood and peripheral blood mononuclear cells as targets for viral isolation and drug sensitivity studies involving human immunodeficiency virus type 1. J Clin Microbiol (1994) 1.08

The construction and analysis of M13 libraries prepared from YAC DNA. Nucleic Acids Res (1995) 1.07

Genotyping single-nucleotide polymorphisms by the invader assay with dual-color fluorescence polarization detection. Clin Chem (2001) 1.07

Genomic DNA sequencing methods. Methods Cell Biol (1995) 1.06

Clinical correlates and molecular basis of HIV drug resistance. J Acquir Immune Defic Syndr (1993) 1.06

'That's the problem with living in a small town': privacy and sexual health issues for young rural people. Aust J Rural Health (1997) 1.06

Nip1p associates with 40 S ribosomes and the Prt1p subunit of eukaryotic initiation factor 3 and is required for efficient translation initiation. J Biol Chem (1998) 1.05

Body image satisfaction, dieting beliefs, and weight loss behaviors in adolescent girls and boys. J Youth Adolesc (1991) 1.04