SNP-specific extraction of haplotype-resolved targeted genomic regions

Nucleic Acids Research

Volumn 36, Issue 15, 2008, Pages

  Dapprich, Johannes ^a   Ferriola, Deborah ^a   Magira, Eleni E ^b,c   Kunkel, Mark ^a   Monos, Dimitri ^b,c  

^a Generation Biotech   (United States)

^b UNIVERSITY OF PENNSYLVANIA   (United States)

^c CHILDREN S HOSPITAL OF PHILADELPHIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA; OLIGONUCLEOTIDE; DNA; HLA ANTIGEN CLASS 1; HLA B ANTIGEN; HLA C ANTIGEN; MHC CLASS I RELATED CHAIN A; MHC CLASS I-RELATED CHAIN A; MICROSATELLITE DNA;

ARTICLE; BINDING AFFINITY; BIOTINYLATION; COMPUTER ANALYSIS; DNA EXTRACTION; DNA FLANKING REGION; DNA HYBRIDIZATION; DNA SEQUENCE; GENE TARGETING; GENOME ANALYSIS; GENOTYPE; HAPLOTYPE; MAJOR HISTOCOMPATIBILITY COMPLEX; MICROARRAY ANALYSIS; MOLECULAR DYNAMICS; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; STRUCTURE ACTIVITY RELATION; ALLELE; GENETICS; GENOMICS; HUMAN; ISOLATION AND PURIFICATION; METHODOLOGY;

ALLELES; DNA; GENOMICS; HAPLOTYPES; HISTOCOMPATIBILITY ANTIGENS CLASS I; HLA-B ANTIGENS; HLA-C ANTIGENS; HUMANS; MAJOR HISTOCOMPATIBILITY COMPLEX; MICROSATELLITE REPEATS; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 50849090561     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkn345     Document Type: Article

References (34)

1. West,M., Ginsburg,G.S., Huang,A.T. and Nevins,J.R. (2006) Embracing the complexity of genomic data for personalized medicine. Genome Res., 16, 559-566.
2. Brookes,A.J. (1999) The essence of SNPs. Gene, 234, 177-186.
3. Paabo,S. (2003) The mosaic that is our genome. Nature, 421, 409-412.
4. Reich,D.E., Schaffner,S.F., Daly,M.J., McVean,G., Mullikin,J.C., Higgins,J.M, Richter,D.J., Lander,E.S. and Altshuler,D. (2002) Human genome sequence variation and the influence of gene history, mutation and recombination. Nat. Genet., 32, 135-142.
5. Margulies,M., Egholm,M., Altman,W.E., Attiya,S., Bader,J.S., Bemben,L.A, Berka,J., Braverman,M.S., Chen,Y. and Chen,Z. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature, 437 376-380.
6. Lin,P.I., Vance,J.M., Pericak-Vance,M.A. and Martin,E.R. (2007) No gene is an island: The flip-flop phenomenon. Am. J. Hum. Genet., 80 531-538.
7. Terwilliger,J.D. and Weiss,K.M. (2003) Confounding, ascertainment bias, and the blind quest for a genetic 'fountain of youth'. Ann. Med., 35, 532-544.
8. Kaplan,N. and Morris,R. (2001) Issues concerning association studies for fine mapping a susceptibility gene for a complex disease. Genet. Epidemiol., 20, 432-457.
9. Haines,J.L., Hauser,M.A., Schmidt,S., Scott,W.K., Olson,L.M., Gallins,P., Spencer,K.L., Kwan,S.Y., Noureddine,M., Gilbert,J.R. et al. (2005) Complement factor H variant increases the risk of age-related macular degeneration. Science, 308, 419-421.
10. Grant,S.F., Thorleifsson,G., Reynisdottir,I., Benediktsson,R., Manolescu,A., Sainz,J., Helgason,A., Stefansson,H., Emilsson,V., Helgadottir,A. et al. (2006) Variant of transcription factor 7-like 2 (TCF7L2) gene confers risk of type 2 diabetes. Nat. Genet. 38, 320-323.
11. Duerr,R.H., Taylor,K.D., Brant,S.R., Rioux,J.D., Silverberg,M.S., Daly,M.J., Steinhart,A.H., Abraham,C., Regueiro,M., Griffiths,A. et al. (2006) A genome-wide association study identifies IL23R as an inflammatory bowel disease gene. Science, 314, 1461-1463.
12. Hakonarson,H., Grant,S.F.A., Bradfield,J.P., Marchand,L., Kim,C.E., Glessner,J.T., Grabs,R., Casalunovo,T., Taback,S.P., Frackelton,E.C. et al. (2007) A genome-wide association study identifies KIAA0350 as a type 1 diabetes gene. Nature, 448, 591-594.
13. Rioux,J.D., Xavier,R.J., Taylor,K.D., Silverberg,M.S., Goyette,P., Huett,A., Green,T., Kuballa,P., Barmada,M.M., Datta,L.W. et al. (2007) Genome-wide association study identifies new susceptibility loci for Crohn disease and implicates autophagy in disease pathogenesis. Nat. Genet., 39, 596-604.
14. Wellcome Trust Case Control Consortium. (2007) Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature, 447, 661-678.
15. Pettersson,M., Bylund,M. and Alderborn,A. (2003) Molecular haplotype determination using allele-specific PCR and pyrosequencing technology. Genomics, 82, 390-396.
16. Tost,J., Brandt,O., Boussicault,F., Derbala,D., Caloustian,C., Lechner,D. and Gut,I.G. (2002) Molecular haplotyping at high throughput. Nucleic Acid Res., 30.
17. Raymond,C.K., Subramanian,S., Paddock,M., Qiu,R., Deodato,C., Palmieri,A., Chang,J., Radke,T., Haugen,E., Kas,A. et al. (2005) Targeted, haplotype-resolved resequencing of long segments of the human genome. Genomics, 86, 759-766.
18. Burgtorf,C., Kepper,P., Hoehe,M., Schmitt,C., Reinhardt,R., Lehrach,H. and Sauer,S. (2003) Clone-based systematic haplotyping (CSH): A procedure for physical haplotyping of whole genomes. Genome Res., 13, 2717-2724.
19. Yan,H., Papadopoulos,N., Marra,G., Perrera,C., Jiricny,J., Boland,C.R., Lynch,H.T., Chadwick,R.B., de la Chapelle,A., Berg,K. et al. (2000) Conversion of diploidy to haploidy. Nature, 403, 723-724.
20. Zhang,K., Zhu,J., Shendure,J., Porreca,G.J., Aach,J.D., Mitra,R.D. and Church,G.M. (2006) Long-range polony haplotyping of individual human chromosome molecules. Nat. Genet., 38, 382-387.
21. Xiao,M., Gordon,M.P., Phong,A., Ha,C., Chan,T.F., Cai,D., Selvin,P.R. and Kwok,P.Y. (2007) Determination of haplotypes from single DNA molecules: A method for single-molecule barcoding. Hum. Mutat., 28, 913-921.
22. Dapprich,J. and Cleary,M.A. (2001) Method for selectively isolating a nucleic acid. U.S. Patent application #20010031467: Australian Patent #785211.
23. Gabriel,A., Dapprich,J., Kunkel,M., Gresham,D., Pratt,S.C. and Dunham,M.J. (2006) Global mapping of transposon location. PLoS Genet. 2, e212.
24. Dapprich,J., Cleary,M.A., Gabel,H.W., Akkapeddi,A., Iglehart,B., Turino,C, Beaudet,L., Lian,J. and Murphy,N.B. (2006) A rapid, automatable method for molecular haplotyping. In Hansen,J.A. (ed.), Proceedings of the 13th International Histocompatibility Workshop and Congress, Vol. II, IHWG Press, Seattle, WA, pp. 271-274.
25. Dapprich,J., Magira,E., Samonte,M.A., Rosenman,K. and Monos,D. (2007) Identification of a novel HLA-DPB1 allele (DPB1*1902) by haplotype specific extraction and nucleotide sequencing. Tissue Antigens, 69, 282-224.
26. Miller,S.A., Dykes,D.D. and Polesky,H.F. (1988) A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic Acids Res., 16, 1215.
27. Zou,Y., Han,M., Wang,Z. and Stastny,P. (2006) MICA allele-level typing by sequence-based typing with computerized assignment of polymorphic sites and short tandem repeats within the transmembrane region. Hum. Immunol., 67, 145-151.
28. Holmberg,A., Blomstergren,A., Nord,O., Lukacs,M., Lundeberg,J. and Uhlen,M. (2005) The biotin-streptavidin interaction can be reversibly broken using water at elevated temperatures. Electrophoresis, 26, 501-510.
29. Mrazek,F., Fae,I., Ambruzova,Z., Raida,L., Indrak,K., Petrek,M. and Fischer,G.F. (2005) A novel HLA-B*420502 allele identified by PCR-SSO/SSP routine typing and confirmed by Sequencing-based typing. Tissue Antigens, 65, 275-277.
30. Nagy,M., Entz,P., Otremba,P., Schoenemann,C., Murphy,N. and Dapprich,J. (2007) Haplotype-specific extraction: A universal method to resolve ambiguous genotypes and detect new alleles - demonstrated on HLA-B. Tissue Antigens, 69, 176-180.
31. Carver,T.E., Hochstrasser,R.A. and Millar,D.P. (1994) Proofreading DNA: recognition of aberrant DNA termini by the Klenow fragment of DNA polymerase I. Proc. Natl Acad. Sci. USA, 91, 10670-10674.
32. Matsuzaki,H., Dong,S., Loi,H., Di,X., Liu,G., Hubbell,E., Law,J., Berntsen,T., Chadha,M., Hui,H. et al. (2004) Genotyping over 100,000 SNPs on a pair of oligonucleotide arrays. Nat. Methods, 1, 109-111.
33. Affymetrix. (2005-2006) GeneChip Human Mapping 500K Array Set Data Sheet. Part No. 702087, Rev.4, 1-4
34. Anderson,E.C. and Novembre,J. (2003) Finding haplotype block boundaries by using the minimum-description-length principle. Am. J. Hum. Genet. 73, 336-354.