SNP genotyping and molecular haplotyping of DNA pools

Cold Spring Harbor Symposia on Quantitative Biology

Volumn 68, Issue , 2003, Pages 65-67

  Kwok, P Y ^a   Xiao, M ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

CONFERENCE PAPER; DNA DETERMINATION; DNA SCREENING; DNA STRUCTURE; GENE IDENTIFICATION; GENE SEQUENCE; GENOME ANALYSIS; GENOTYPE; HAPLOTYPE; HUMAN; HUMAN GENOME; MOLECULAR BIOLOGY; MOLECULAR GENETICS; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; ARTICLE; GENETIC ASSOCIATION STUDY;

EID: 3242676870     PISSN: 00917451     EISSN: None     Source Type: Book Series    
DOI: 10.1101/sqb.2003.68.65     Document Type: Conference Paper

References (27)

1. Barratt B.J., Payne F., Rance H.E., Nutland S., Todd J.A., and Clayton D.G. 2002. Identification of the sources of error in allele frequency estimations from pooled DNA indicates an optimal experimental design. Ann. Hum. Genet. 66: 393.
2. Botstein D. and Risch N. 2003. Discovering genotypes underlying human phenotypes: Past successes for Mendelian disease, future approaches for complex disease. Nat. Genet. (suppl.) 33: 228.
3. Breen G., Harold D., Ralston S., Shaw D., and St Clair D. 2000. Determining SNP allele frequencies in DNA pools. Biotechniques 28: 464.
4. Collins F.S., Green E.D., Guttmacher A.E., Guyer M.S., and U.S. National Human Genome Research Institute. 2003. A vision for the future of genomics research. Nature 422: 835.
5. Eitan Y. and Kashi Y. 2002. Direct micro-haplotyping by multiple double PCR amplifications of specific alleles (MD-PASA). Nucleic Acids Res. 30: e62.
6. Excoffier L. and Slatkin M. 1995. Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population. Mol. Biol. Evol. 12: 921.
7. Germer S., Holland M.J., and Higuchi R. 2000. High-throughput SNP allele-frequency determination in pooled DNA samples by kinetic PCR. Genome Res. 10: 258.
8. Giordano M., Mellai M., Hoogendoorn B., and Momigliano-Richiardi P. 2001. Determination of SNP allele frequencies in pooled DNAs by primer extension genotyping and denaturing high-performance liquid chromatography. J. Biochem. Biophys. Methods 47: 101.
9. Ito T., Chiku S., Inoue E., Tomita M., Morisaki T., Morisaki H., and Kamatani N. 2003. Estimation of haplotype frequencies, linkage-disequilibrium measures, and combination of haplotype copies in each pool by use of pooled DNA data. Am. J. Hum. Genet. 72: 384.
10. Jarvius J., Nilsson M., and Landegren U. 2003. Oligonucleotide ligation assay. Methods Mol. Biol. 212: 215.
11. Long J.C., Williams R.C., and Urbanek M. 1995. An E-M algorithm and testing strategy for multiple-locus haplotypes. Am. J. Hum. Genet. 56: 799.
12. Lyamichev V., Mast A.L., Hall J.G., Prudent J.R., Kaiser M.W., Takova T., Kwiatkowski R.W., Sander T.J., de Arruda M., Arco D.A., Neri B.P., and Brow M.A. 1999. Polymorphism identification and quantitative detection of genomic DNA by invasive cleavage of oligonucleotide probes. Nat. Biotechnol. 17: 292.
13. McDonald O.G., Krynetski E.Y., and Evans W.E. 2002. Molecular haplotyping of genomic DNA for multiple single-nucleotide polymorphisms located kilobases apart using long-range polymerase chain reaction and intramolecular ligation. Pharmacogenetics 12: 93.
14. Mohlke K.L., Erdos M.R., Scott L.J., Fingerlin T.E., Jackson A.U., Silander K., Hollstein P., Boehnke M., and Collins F.S. 2002. High-throughput screening for evidence of association by using mass spectrometry genotyping on DNA pools. Proc. Natl. Acad. Sci. 99: 16928.
15. Nilsson M., Malmgren H., Samiotaki M., Kwiatkowski M., Chowdhary B.P., and Landegren U. 1994. Padlock probes: Circularizing oligonucleotides for localized DNA detection. Science 265: 2085.
16. Nystuen A., Benke P.J., Merren J., Stone E.M., and Sheffield V.C. 1996. A cerebellar ataxia locus identified by DNA pooling to search for linkage disequilibrium in an isolated population from the Cayman Islands. Hum. Mol. Genet. 5: 525.
17. Patil N., Berno A.J., Hinds D.A., Barrett W.A., Doshi J.M., Hacker C.R., Kautzer C.R., Lee D.H., Marjoribanks C., McDonough D.P., Nguyen B.T., Norris M.C., Sheehan J.B., Shen N., Stern D., Stokowski R.P., Thomas D.J., Trulson M.O., Vyas K.R., Frazer K.A., Fodor S.P., and Cox D.R. 2001. Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome 21. Science 294: 1719.
18. Sarkar G. and Sommer S.S. 1991. Haplotyping by double PCR amplification of specific alleles. Biotechniques 10: 436.
19. Scott D.A., Carmi R., Elbedour K., Yosefsberg S., Stone E.M., and Sheffield V.C. 1996. An autosomal recessive nonsyndromic-hearing-loss locus identified by DNA pooling using two inbred Bedouin kindreds. Am. J. Hum. Genet. 59: 385.
20. Sham P., Bader J.S., Craig I., O'Donovan M., and Owen M. 2002. DNA Pooling: A tool for large-scale association studies. Nat. Rev. Genet. 3: 862.
21. Shaw S.H., Carrasquillo M.M., Kashuk C., Puffenberger E.G., and Chakravarti A. 1998. Allele frequency distributions in pooled DNA samples: Applications to mapping complex disease genes. Genome Res. 8: 111.
22. Shifman S., Pisante-Shalom A., Yakir B., and Darvasi A. 2002. Quantitative technologies for allele frequency estimation of SNPs in DNA pools. Mol. Cell. Probes 16: 429.
23. Tost J., Brandt O., Boussicault F., Derbala D., Caloustian C., Lechner D., and Gut I.G. 2002. Molecular haplotyping at high throughput. Nucleic Acids Res. 30: e96.
24. Wang S., Kidd K.K., and Zhao H. 2003. On the use of DNA pooling to estimate haplotype frequencies. Genet. Epidemiol. 24: 74.
25. Wasson J., Skolnick G., Love-Gregory L., and Permutt M.A. 2002. Assessing allele frequencies of single nucleotide polymorphisms in DNA pools by pyrosequencing technology. Biotechniques 32: 1144.
26. Xiao M. and Kwok P.Y. 2003. DNA analysis by fluorescence quenching detection. Genome Res. 13: 932.
27. Yang Y., Zhang J., Hoh J., Matsuda F., Xu P., Lathrop M., and Ott J. 2003. Efficiency of single-nucleotide polymorphism haplotype estimation from pooled DNA. Proc. Natl. Acad. Sci. 100: 7225.