DOI: 10.1038/ng1746. Automating sequence-based detection and genotyping of SNPs from diploid samples

Automating sequence-based detection and genotyping of SNPs from diploid samples

10.1038/ng1746

Crossref journal-article

Springer Science and Business Media LLC

Nature Genetics (297)

Bibliography

Stephens, M., Sloan, J. S., Robertson, P. D., Scheet, P., & Nickerson, D. A. (2006). Automating sequence-based detection and genotyping of SNPs from diploid samples. Nature Genetics, 38(3), 375â381.

Authors 5

Matthew Stephens (first)
James S Sloan (additional)
P D Robertson (additional)
Paul Scheet (additional)
Deborah A Nickerson (additional)

References 17 Referenced 124

Carlson, C.S., Newman, T.L. & Nickerson, D.A. SNPing in the human genome. Curr. Opin. Chem. Biol. 5, 78–85 (2001). (10.1016/S1367-5931(00)00171-X) / Curr. Opin. Chem. Biol. by CS Carlson (2001)
Nickerson, D.A., Tobe, V.O. & Taylor, S.L. PolyPhred: automating the detection and genotyping of single nucleotide substitutions using fluorescence-based resequencing. Nucleic Acids Res. 25, 2745–2751 (1997). (10.1093/nar/25.14.2745) / Nucleic Acids Res. by DA Nickerson (1997)
Cargill, M. et al. Characterization of single-nucleotide polymorphisms in coding regions of human genes. Nat. Genet. 22, 231–238 (1999). (10.1038/10290) / Nat. Genet. by M Cargill (1999)
Carlson, C.S. et al. Additional SNPs and linkage-disequilibrium analyses are necessary for whole-genome association studies in humans. Nat. Genet. 33, 518–521 (2003). (10.1038/ng1128) / Nat. Genet. by CS Carlson (2003)
Marth, G.T. et al. A general approach to single-nucleotide polymorphism discovery. Nat. Genet. 23, 452–456 (1999). (10.1038/70570) / Nat. Genet. by GT Marth (1999)
Ning, Z., Cox, A.J. & Mullikin, J.C. SSAHA: a fast search method for large DNA databases. Genome Res. 11, 1725–1729 (2001). (10.1101/gr.194201) / Genome Res. by Z Ning (2001)
Ewing, B. & Green, P. Base-calling of automated sequencer traces using Phred. II. Error probabilities. Genome Res. 8, 186–194 (1998). (10.1101/gr.8.3.186) / Genome Res. by B Ewing (1998)
Weckx, S. et al. novoSNP, a novel computational tool for sequence variation discovery. Genome Res. 15, 436–442 (2005). (10.1101/gr.2754005) / Genome Res. by S Weckx (2005)
Kwok, P.Y., Carlson, C., Yager, T.D., Ankener, W. & Nickerson, D.A. Comparative analysis of human DNA variations by fluorescence-based sequencing of PCR products. Genomics 23, 138–144 (1994). (10.1006/geno.1994.1469) / Genomics by PY Kwok (1994)
Parker, L.T. et al. AmpliTaq DNA polymerase, FS dye-terminator sequencing: analysis of peak height patterns. Biotechniques 21, 694–699 (1996). (10.2144/96214rr02) / Biotechniques by LT Parker (1996)
Ewing, B., Hillier, L., Wendl, M.C. & Green, P. Base-calling of automated sequencer traces using Phred. I. accuracy assessment. Genome Res. 8, 175–185 (1998). (10.1101/gr.8.3.175) / Genome Res. by B Ewing (1998)
Hinds, D.A. et al. Whole-genome patterns of common DNA variation in three human populations. Science 307, 1072–1079 (2005). (10.1126/science.1105436) / Science by DA Hinds (2005)
The International HapMap Consortium. A haplotype map of the human genome. Nature 437, 1299–1320 (2005). (10.1038/nature04226)
Bhangale, T.R., Rieder, M.J., Livingston, R.J. & Nickerson, D.A. Comprehensive identification and characterization of diallelic insertion-deletion polymorphisms in 330 human candidate genes. Hum. Mol. Genet. 14, 59–69 (2005). (10.1093/hmg/ddi006) / Hum. Mol. Genet. by TR Bhangale (2005)
Olden, K. & Wilson, S. Environmental health and genomics: visions and implications. Nat. Rev. Genet. 1, 149–153 (2000). (10.1038/35038586) / Nat. Rev. Genet. by K Olden (2000)
Dempster, A.P., Laird, N.M. & Rubin, D.B. Maximum likelihood from incomplete data via the EM algorithm. J. R. Stat. Soc. Ser. B 34, 1–38 (1977). (10.1111/j.2517-6161.1977.tb01600.x) / J. R. Stat. Soc. Ser. B by AP Dempster (1977)
Gordon, D., Abajian, C. & Green, P. Consed: a graphical tool for sequence finishing. Genome Res. 8, 195–202 (1998). (10.1101/gr.8.3.195) / Genome Res. by D Gordon (1998)

Dates

Type	When
Created	19 years, 6 months ago (Feb. 21, 2006, 9:45 a.m.)
Deposited	7 months, 2 weeks ago (Jan. 7, 2025, 3:44 p.m.)
Indexed	4 months, 2 weeks ago (April 10, 2025, 5:50 a.m.)
Issued	19 years, 6 months ago (Feb. 19, 2006)
Published	19 years, 6 months ago (Feb. 19, 2006)
Published Online	19 years, 6 months ago (Feb. 19, 2006)
Published Print	19 years, 5 months ago (March 1, 2006)

Funders 0

None

BibTeX

@article{Stephens_2006, title={Automating sequence-based detection and genotyping of SNPs from diploid samples}, volume={38}, ISSN={1546-1718}, url={http://dx.doi.org/10.1038/ng1746}, DOI={10.1038/ng1746}, number={3}, journal={Nature Genetics}, publisher={Springer Science and Business Media LLC}, author={Stephens, Matthew and Sloan, James S and Robertson, P D and Scheet, Paul and Nickerson, Deborah A}, year={2006}, month=feb, pages={375–381} }

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