Identification of coding single nucleotide polymorphisms and mutations by combination of genome tiling arrays and enrichment/depletion of mismatch cDNAs

Analytical Biochemistry

Volumn 356, Issue 1, 2006, Pages 117-124

  Liu, Meng Min ^a   Weissman, Sherman M ^a   Tang, Ling ^b  

^a YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b AUBURN UNIVERSITY   (United States)

Author keywords

Encyclopedia of DNA elements; Genome tiling arrays; Melanoma; Mutation single nucleotide polymorphisms; Thymine DNA glycosylase

Indexed keywords

DERMATOLOGY; DNA; GENES; NUCLEOTIDES; ONCOLOGY;

DNA GLYCOSYLASE; GENOME TILING ARRAYS; INTENSITY VALUES; MELANOMA; MISMATCH REPAIR; MUTATION DETECTION; NUCLEOTIDE POLYMORPHISMS; SINGLE NUCLEOTIDE POLYMORPHISMS;

POLYMERASE CHAIN REACTION;

COMPLEMENTARY DNA; DNA FRAGMENT; DNA GLYCOSYLTRANSFERASE; THYMINE;

ARTICLE; CHEMICAL LABELING; COST; DNA HYBRIDIZATION; DNA MICROARRAY; GENE LOSS; GENE MUTATION; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC VARIABILITY; GENOME; HETEROZYGOSITY; MELANOCYTE; MELANOMA CELL; MISMATCH REPAIR; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; SAMPLE; SINGLE NUCLEOTIDE POLYMORPHISM;

EID: 33747177565     PISSN: 00032697     EISSN: 10960309     Source Type: Journal    
DOI: 10.1016/j.ab.2006.05.013     Document Type: Article

References (40)

1. Kwok P.Y., Deng Q., Zakeri H., Taylor S.L., and Nickerson D.A. Increasing the information content of STS-based genome maps: identifying polymorphisms in mapped STSs. Genomics 31 (1996) 123-126
2. Wang D.G., Fan J.B., Siao C.J., Berno A., Young P., Sapolsky R., Ghandour G., Perkins N., et al. Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science 280 (1998) 1077-1082
3. Taillon-Miller P., Gu Z., Li Q., Hillier L., and Kwok P.Y. Overlapping genomic sequences: a treasure trove of single-nucleotide polymorphisms. Genome Res. 8 (1998) 748-754
4. Lander E.S. The new genomics: global views of biology. Science 274 (1996) 536-539
5. Risch N., and Merikangas K. The future of genetic studies of complex human diseases. Science 273 (1996) 1516-1517
6. Kruglyak L., and Nickerson D.A. Variation is the spice of life. Nat. Genet. 27 (2001) 234-236
7. Stephens J.C., Schneider J.A., Tanguay D.A., Choi J., Acharya T., Stanley S.E., Jiang R.H., and Messer C.J. Haplotype variation and linkage disequilibrium in 313 human genes. Science 293 (2001) 489-493
8. Reich D.E., Gabriel S.B., and Altshuler D. Quality and completeness of SNP databases. Nat. Genet. 33 (2003) 457-458
9. The International SNP Map Working Group, A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms, Nature 409 (2001) 928-933.
10. Collins F.S., Guyer M.S., and Charkravarti A. Variations on a theme: cataloging human DNA sequence variation. Science 278 (1997) 1580-1581
11. Kristensen V.N., Kelefiotis D., Kristensen T., and Borresen-Dale A.L. High-throughput methods for detection of genetic variation. Biotechniques 30 (2001) 318-322 324, 326 passim
12. Kirk B.W., Feinsod M., Favis R., Kliman R.M., and Barany F. Single nucleotide polymorphism seeking long term association with complex disease. Nucleic Acids Res. 30 (2002) 3295-3311
13. Sellick G.S., Longman C., Tolmie J., Newbury-Ecob R., Geenhalgh L., Hughes S., Whiteford M., and Garrett C. Genomewide linkage searches for Mendelian disease loci can be efficiently conducted using high-density SNP genotyping arrays. Nucleic Acids Res. 32 (2004) e164
14. Matsuzaki H., Dong S., Loi H., Di X., Liu G., Hubbell E., Law J., and Berntsen T. Genotyping over 100,000 SNPs on a pair of oligonucleotide arrays. Nat. Methods 1 (2004) 109-111
15. Patil N., Berno A.J., Hinds D.A., Barrett W.A., Doshi J.M., Hacker C.R., Kautzer C.R., and Lee D.H. Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome 21. Science 294 (2001) 1719-1723
16. Kwok P.Y. Genetic association by whole-genome analysis?. Science 294 (2001) 1669-1670
17. Warrington J.A., Shah N.A., Chen X., Janis M., Liu C., Kondapalli S., Reyes V., and Savage M.P. New developments in high-throughput resequencing and variation detection using high density microarrays. Hum. Mutat. 19 (2002) 402-409
18. Nelson S.F., McCusker J.H., Sander M.A., Kee Y., Modrich P., and Brown P.O. Genomic mismatch scanning: a new approach to genetic linkage mapping. Nat. Genet. 4 (1993) 11-18
19. McAllister L., Penland L., and Brown P.O. Enrichment for loci identical-by-descent between pairs of mouse or human genomes by genomic mismatch scanning. Genomics 47 (1998) 7-11
20. Cheung V.G., Gregg J.P., Gogolin-Ewens K.J., Bandong J., Stanley C.A., Baker L., Higgins M.J., and Nowak N.J. Linkage-disequilibrium mapping without genotyping. Nat. Genet. 18 (1998) 225-230
21. Smirnov D., Bruzel A., Morley M., and Cheung V.G. Direct IBD mapping: identical-by-descent mapping without genotyping. Genomics 83 (2004) 335-345
22. Bertone P., Stolc V., Royce T.E., Rozowsky J.S., Urban A.E., Zhu X., Rinn J.L., and Tongprasit W. Global identification of human transcribed sequences with genome tiling arrays. Science 306 (2004) 2242-2246
23. Mockler T.C., and Ecker J.R. Applications of DNA tiling arrays for whole-genome analysis. Genomics 85 (2005) 1-15
24. Lippman Z., Gendrel A.V., Colot V., and Martienssen R. Profiling DNA methylation patterns using genomic tiling microarrays. Nat. Methods 2 (2005) 219-224
25. Royce T.E., Rozowsky J.S., Bertone P., Samanta M., Stolc V., Weissman S., Snyder M., and Gerstein M. Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping. Trends Genet. 21 (2005) 466-475
26. Pan X., and Weissman S.M. An approach for global scanning of single nucleotide variations. Proc. Natl. Acad. Sci. USA 99 (2002) 9346-9351
27. Hoek K., Rimm D.L., Williams K.R., Zhao H., Ariyan S., Lin A., Kluger H.M., and Berger A.J. Expression profiling reveals novel pathways in the transformation of melanocytes to melanomas. Cancer Res. 64 (2004) 5270-5282
28. Kiss C., Nishikawa J., Dieckmann A., Takada K., Klein G., and Szekely L. Improved subtractive suppression hybridization combined with high density cDNA array screening identifies differentially expressed viral and cellular genes. J. Virol. Methods 107 (2003) 195-203
29. The ENCODE Project Consortium, The ENCODE (ENCyclopedia Of DNA Elements) Project, Science 306 (2004) 636-640.
30. Kapranov P., Cawley S.E., Drenkow J., Bekiranov S., Strausberg R.L., Fodor S.P., and Gingeras T.R. Large-scale transcriptional activity in chromosomes 21 and 22. Science 296 (2002) 916-919
31. Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., and Wu H.C. Empirical analysis of transcriptional activity in the Arabidopsis genome. Science 302 (2003) 842-846
32. Kampa D., Cheng J., Kapranov P., Yamanaka M., Brubaker S., Cawley S., Drenkow J., and Piccolboni A. Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22. Genome Res. 14 (2004) 331-342
33. Schadt E.E., Edwards S.W., GuhaThakurta D., Holder D., Ying L., Svetnik V., Leonardson A., and Hart K.W. A comprehensive transcript index of the human genome generated using microarrays and computational approaches. Genome Biol. 5 (2004) R73
34. Rinn J.L., Euskirchen G., Bertone P., Martone R., Luscombe N.M., Hartman S., Harrison P.M., and Nelson F.K. The transcriptional activity of human chromosome 22. Genes Dev. 17 (2003) 529-540
35. Waters T.R., Gallinari P., Jiricny J., and Swann P.F. Human thymine DNA glycosylase binds to apurinic sites in DNA but is displaced by human apurinic endonuclease 1. J. Biol. Chem. 274 (1999) 67-74
36. Chakrabarti S., Price B.D., Tetradis S., Fox E.A., Zhang Y., Maulik G., and Makrigiorgos G.M. Highly selective isolation of unknown mutations in diverse DNA fragments: toward new multiplex screening in cancer. Cancer Res. 60 (2000) 3732-3737
37. Yao M., and Kow Y.W. Further characterization of Escherichia coli endonuclease V. Mechanism of recognition for deoxyinosine, deoxyuridine, and base mismatches in DNA. J. Biol. Chem. 272 (1997) 30774-30779
38. Mashal R.D., Koontz J., and Sklar J. Detection of mutations by cleavage of DNA heteroduplexes with bacteriophage resolvases. Nat. Genet. 9 (1995) 177-183
39. Zhang J., and Maquat L.E. Evidence that translation reinitiation abrogates nonsense-mediated mRNA decay in mammalian cells. EMBO J. 16 (1997) 826-833
40. van der Velden P.A., Zuidervaart W., Hurks M.H., Pavey S., Ksander B.R., Krijgsman E., Frants R.R., and Tensen C.P. Expression profiling reveals that methylation of TIMP3 is involved in uveal melanoma development. Int. J. Cancer 106 (2003) 472-479