Home > SNP Bibliography

  • SNP Bibliography

References citing AcycloPrime Download PDF
Ahsan, H., Chen, Y., Wang, Q., Slavkovich, V., Graziano, J.H. and Santella, R.M. "DNA repair gene XPD and susceptibility to arsenic-induced hyperkeratosis", Toxicology Letters (2003) 143:123-131.
Bai, Y-J, Zhao, J-R, LV, G-T, Zhang, W-H, Wang, Y. and Yan, X-J. "Rapid and high throughput detection of HBV YMDD mutants with fluorescence polarization", World J. Gastroenterol (2003) 9:2344-2347.
Duan, S., Taillon-Miller, P., Miller, R. and Kwok, P-Y. "EXO-free SNP genotyping assay based on fluorescence polarization detection", abstract 1545, Am. J. Hum. Genet. (2003) 73:434
Freeman, B.D., Buchman, T.G., McGrath, S., Tabrizi, A.R. and Zehnbauer, B.A. "Single nucleotide polymorphisms implicated in sepsis", J. Mol. Diagn. (2002) 4:209-215.
Gill, G.P., Brown, G.R. and Neale, D.B. "A sequence mutation in the cinnamyl alcohol dehydrogenase gene associated with altered lignification in loblolly pine", Plant Biotechnology Journal (2003) 1:253-258.
Grant, S.F.A., Steinlicht, S., Nentwich, U., Kern, R., Burwinkel, B. and Tolle, R. "SNP genotyping on a genome-wide amplified DOP-PCR template", Nucleic Acids Res. (2002) 30:e125.
Greene, R.A., DiMeo, J.J., Malone, M.E., Swartwout, S., Liu, J. and Buzby, P.R. "AcycloPrime, a novel method for SNP analysis using fluorescence polarization", Proc. SPIE (2002) 4626:332-339.
Helms, C., Cao, L., Krueger, J.G. Wijsman, E.M., Chamian, F., Gordon, D., Heffernan, M., Daw, J.A.W., Robarge, J., Ott, J., Kwok, P-Y., Menter, A. and Bowcock, A.M. "A putative RUNX1 binding site variant between SLC9A3R1 and NAT9 is associated with susceptibility to psoriasis. Nature Genetics (2003) 35:349-356.
Hsu, T.M. and Kwok, P-Y. "Homogeneous primer extension assay with fluorescence polarization detection", Methods in Molecular Biology (2003) 212:177-187.
Newell, J.W., Seo, N-S., Enns, G.M., McCraken, M., Mantovani, J.F. and Freeze, H.H. "Congenital disorder of glycosylation Ic in patients of Indian origin", Molecular Genetics and Metabolism (2003) 79:221-228.
Nurmi, E.L., Amin, T., Olson, L.M., Jacobs, M.M., McCauley, J.L., Lam, A.Y., Organ, E.L., Folstein, S.E., Haines, J.L. and Sutcliffe, J.S. "Dense linkage disequilibrium mapping in the 15q11-q13 maternal expression domain yields evidence for association in autism", Molecular Psychiatry (2003) 8:624-634.
Schwab, S.G., Knapp, M., Mondabon, S., Hallmayer, J., Borrmann-Hassenbach, M., Albus, M., Lerer, B, Rietschel, M., Trixler, M., Maier, W., Wildenauer, D.B. "Support for association of schizophrenia with genetic variation in the 6p22.3 gene, dysbindin, in sib-pair families with linkage and in an additional sample of triad families", Amer. J. Human Genet. (2003) 72:185-190.
Speckman, R.A., Daw, J.A.W., Helms, C., Duan, S., Cao, L., Taillon-Miller, P., Kwok, P-Y., Menter, A., and Bowcock, A.M. "Novel immunoglobulin superfamily gene cluster mapping to a region of human chromosome 17q25 harboring a locus for psoriasis susceptibility", Human Genetics. (2002) 112:31-41.

Swan, K.A., Curtis, D.E., McKusick, K.B., Voinov, A.V., Mapa, F.A. and Cancilla, M.R. "High-throughput gene mapping in Caenorhabditis elegans", Genome Res. (2002) 12:1100-1105.

The first peer-reviewed publication on AcycloPrime.
Williams, N.M., Preece, A., Spurlock, G., Norton, N., Williams, H.J., McCreadie, R.G., Buckland, P., Sharkey, V., Chowdari, K.V., Zammit, S., Nimgaonkar, V., Kirov, G., Owen, M.J. and O'Donovan, M.C. "Support for RGS4 as a susceptibility gene for schizophrenia". Biol. Psychiatry (2003) 55:192-195.
Williams, N.M., Preece, A., Spurlock, G., Norton, N. Williams, H.J., Zammit, S., O'Donovan, M.C. and Owen, M.J. "Support for genetic variation in neuregulin 1 and susceptibility to schizophrenia". (2002) Molecular Psychiatry 8:485-487.
Xiao, M. and Kwok, P-Y. "DNA analysis by fluorescence quenching detection", Genome Res. (2003) 13:932-939.
Xiao, M., Latif, S.M. and Kwok, P-Y. "Kinetic FP-TDI assay for SNP allele frequency determination. BioTechniques (2003) 34:190-197.
The two preceding papers describe a method to perform allele frequency Measurements on pooled DNA samples with AcycloPrime.
References Citing TDI-FP Download PDF

Akula, N., Chen, Y.S., Hennessy, K., Schulze, T.G., Singh, G. and McMahon, F.J. "Utility and accuracy of template-directed dye-terminator incorporation with fluorescence polarization detection for genotyping single nucleotide polymorphisms", BioTechniques (2002) 32:1072-1078.

A paper on utility and accuracy of primer extension.

Chen, X., Levine, L. and Kwok, P-Y. "Fluorescence polarization in homogeneous nucleic acid analysis", Genome Res. (1999) 9:492-498.

The initial publication on TDI-FP.

Hamilton, S.P., Slager, S.L., Heiman, G.A., Deng, Z., Haghighi, F., Klein, D.F., Hodge, S.E., Weissman, M.M., Fyer, A.J. and Knowles, J.A. "Evidence for a susceptibility locus for panic disorder near the catechol-O-methyltransferase gene on chromosome 22", Biol. Psychiatry (2002) 51:591-601.
Hamilton, S.P., Slager, S.L., Helleby, L., Heiman, G.A., Klein, D.F., Hodge, S.E., Weissman, M.M., Fyer, A.J. and Knowles, J.A. "No association of linkage between polymorphisms in the genes encoding cholecystokinin and the cholecystokinin B receptor and panic disorder", Molecular Psychiatry (2001) 6:59-65.

Hsu, T.M., Chen, X., Duan, S., Miller, R.D. and Kwok, P-Y. "Universal SNP genotyping assay with fluorescence polarization detection", BioTechniques (2001) 31:560-570.

Follow-up paper to Chen, et al. (1999).

Sawyer, M.B., Innocenti, F., Das, S., Cheng, C., Ramirez, J., Pantle-Fisher, F.H., Wright, C., Badner, J., Pei, D., Boyett, J.M., Cook, E. Jr. and Ratain, M.J. "A pharmacogenetic study of uridine diphosphate-glucuronosyltransferase 2B7 in patients receiving morphine", Clin. Pharmacol. Ther. (2003) 73:566-574.
Sun, H-X., Du, W-N., Zuo, J., Wu, G-D., Shi, G-B., Shen, Y., Qiang, B-Q., Yao, Z-J., Hang, J-M., Wang, H., Huang, W., Chen, Z. and Fang, F-D. "The association of two single nucleotide polymorphisms in PRKCZ and UTS2 respectively with type 2 diabetes in Han people of northern China", Acta Academiae Medicinae Siniae (2002) 24:223-227. (Chinese)
Sun, H-X, Du, W-N, Li, Y-F, Zuo, J., Wu, G-D, Shen, Y., Qiang, B-Q., Yao, Z-J, Hang, J-M, Luo, H-Y., Wang, H., Huang, W., Chen, Z. and Fang, F-D. "Linkage disequilibrium analysis of the single nucleotide polymorphisms in the PRKCZ gene", Acta Academiae Medicinae Siniae (2002) 24:474-480. (Chinese)
van den Oord, E.J.C.G., Jiang, Y., Riley, B.P., Kendler, K.S. and Chen, X. "FP-TDI SNP scoring by manual and statistical procedures: A study of error rates and types", BioTechniques (2003) 34:610-624.
Zhang, J., Yan, X., Sun, J., Chen, Z., Gao, Y., Bai, Y. and Liu, Z. "A high throughput assay for human papillomavirus genotypes with fluorescence polarization", Chin. Med. J. (2003) 116:1137-1140.
Review Articles Download PDF
Chen, X. "Fluorescence polarization for single nucleotide polymorphism genotyping", Combinatorial Chemistry & High Throughput Screening (2003) 6, 213-223.
Chen, X. and Sullivan, P.F. "Single nucleotide polymorphism genotyping: biochemistry, protocol, cost and throughput", The Pharmacogenomics Journal (2003) 3, 77-96.
Kwok, P-Y. "High-throughput genotyping assay approaches", Pharmacogenomics (2000) 1, 1-5.
Kwok, P-Y. "Methods for genotyping single nucleotide polymorphisms", Ann. Rev. Genomics Hum. Genet. (2001) 2, 235-258.
Kwok, P-Y. "SNP genotyping with fluorescence detection", Human Mutation (2002) 19:315-323 (in Korean).
Kwok, P-Y. and Chen, X. "Detection of single nucleotide polymorphisms", Curr. Issues Mol. Biol. (2003) 5, 43-60.
Syvanen, A-C. "Accessing genetic variation: Genotyping single nucleotide polymorphisms", Nature Reviews, Genetics (2001) 2:930-942.
Miscellaneous Related References Download PDF
DiGiusto, D. and King, G.C. "Single base extension (SBE) with proofreading polymerases and phosphorothioate primers: Improved fidelity in single-substrate assays", Nucleic Acids Res. (2003) 31:No. 3e7.
Gardner, A.F. and Jack, W.E. "Acyclic and dideoxy terminator preferences denote divergent sugar recognition by archaeon and Taq DNA polymerases", Nucleic Acids Res. (2002) 30:605-613.  

Miller, S.E., Taillon-Miller, P. and Kwok, P-Y. "Cost-effective staining of DNA with SYBR® Green in preparative agarose gel electrophoresis", BioTechniques (1999) 27:34-36.

Cost-effective purification of starting DNA.

Vieux, E.F., Kwok, P-Y. and Miller, R.D. "Primer Design for PCR and Sequencing in High-Throughput Analysis of SNPs". 32S:28-32 (2002).

This paper describes the construction of a database of computer-designed assays.