An STS-Based map of the human genome

Science

Volumn 270, Issue 5244, 1995, Pages 1945-1954

  Hudson, Thomas J ^a   Stein, Lincoln D ^a,b   Gerety, Sebastian S ^a   Ma, Junli ^a   Castle, Andrew B ^a   Silva, James ^a   Slonim, Donna K ^a   Baptista, Rafael ^a   Kruglyak, Leonid ^a   Xu, Shu Hua ^a   Hu, Xintong ^a   Colbert, Angela M E ^a   Rosenberg, Carl ^a   Reeve Daly, Mary Pat ^a   Rozen, Steve ^a   Hui, Lester ^a   Wu, Xiaoyun ^a   Vestergaard, Christina ^a   Wilson, Kimberly M ^a   Bae, Jane S ^a   Maitra, Shanak ^a   Ganiatsas, Soula ^a   Evans, Cheryl A ^a   DeAngelis, Margaret M ^a   Ingalls, Kimberly A ^a   Nahf, Robert W ^a   Horton Jr , Lloyd T ^a   Anderson, Michele Oskin ^a   Collymore, Alville J ^a   Ye, Wenjuan ^a   Kouyoumjian, Vardouhie ^a   Zemsteva, Irena S ^a   Tam, James ^a   Devine, Richard ^a   Courtney, Dorothy F ^a   Renaud, Michelle Turner ^a   Nguyen, Huy ^a   O'Connor, Tara J ^a   Fizames, Cécile ^c   Fauré, Sabine ^c   Gyapay, Gabor ^c   Dib, Colette ^c   Morissette, Jean ^c,d   Orlin, James B ^e   Birren, Bruce W ^a   Goodman, Nathan ^a   Weissenbach, Jean ^c   Hawkins, Trevor L ^a   Foote, Simon ^a   Page, David C ^a,f   Lander, Eric S ^a,f   more..

^a WHITEHEAD INSTITUTE FOR BIOMEDICAL RESEARCH   (United States)

^b BRIGHAM AND WOMEN S HOSPITAL   (United States)

^c GÉNÉTHON   (France)

^d UNIVERSITÉ LAVAL   (Canada)

^e MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^f MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; GENE LIBRARY; GENE LOCUS; GENE MAPPING; GENE SEQUENCE; HUMAN; HYBRID; PRIORITY JOURNAL; RADIATION; YEAST ARTIFICIAL CHROMOSOME;

EID: 0029416826     PISSN: 00368075     EISSN: None     Source Type: Journal    
DOI: 10.1126/science.270.5244.1945     Document Type: Article

References (63)

1. M. Olson et al., Proc. Natl. Acad. Sci. U.S.A. 83, 7826 (1986); A. Coulson et al., ibid., p. 7821; Y. Kohara et al., Cell 50, 495 (1987).
2. M. Olson et al., Proc. Natl. Acad. Sci. U.S.A. 83, 7826 (1986); A. Coulson et al., ibid., p. 7821; Y. Kohara et al., Cell 50, 495 (1987).
3. M. Olson et al., Proc. Natl. Acad. Sci. U.S.A. 83, 7826 (1986); A. Coulson et al., ibid., p. 7821; Y. Kohara et al., Cell 50, 495 (1987).
4. M. Olson, L. Hood, C. Cantor, D. Botstein, Science 245, 1434 (1989).
5. S. Foote, D. Vollrath, A. Hilton, D. C. Page, ibid. 258, 60 (1992).
6. I. Chumakov et al., Nature 359, 380 (1992).
7. F. Collins and D. Galas, Science 262, 43 (1993).
8. L. Selleri et al., Genomics 14, 536 (1992); M. Haldi et al., ibid. 24, 478 (1994).
9. L. Selleri et al., Genomics 14, 536 (1992); M. Haldi et al., ibid. 24, 478 (1994).
10. I. Chumakov et al., Nature 377, S175 (1995).
11. H. Shizuya et al., Proc. Natl. Acad. Sci. U.S.A. 89, 8794 (1992); P. A. Ioannous et al., Nature Genet. 6, 84 (1994).
12. H. Shizuya et al., Proc. Natl. Acad. Sci. U.S.A. 89, 8794 (1992); P. A. Ioannous et al., Nature Genet. 6, 84 (1994).
13. R. M. Gemmill et al., Nature 377, S299 (1995); N. A. Doggett et al., ibid., p. S335; J. E. Collins et al., ibid., p. S367.
14. R. M. Gemmill et al., Nature 377, S299 (1995); N. A. Doggett et al., ibid., p. S335; J. E. Collins et al., ibid., p. S367.
15. R. M. Gemmill et al., Nature 377, S299 (1995); N. A. Doggett et al., ibid., p. S335; J. E. Collins et al., ibid., p. S367.
16. K. Krauter et al., ibid., p. S321.
17. E. D. Green et al., Hum. Mol. Genet. 3, 489 (1994); J. Quackenbush et al., Genomics 29, 512 (1995); T. Alitalo et al., ibid. 25, 691 (1995).
18. E. D. Green et al., Hum. Mol. Genet. 3, 489 (1994); J. Quackenbush et al., Genomics 29, 512 (1995); T. Alitalo et al., ibid. 25, 691 (1995).
19. E. D. Green et al., Hum. Mol. Genet. 3, 489 (1994); J. Quackenbush et al., Genomics 29, 512 (1995); T. Alitalo et al., ibid. 25, 691 (1995).
20. E. D. Green and M. V. Olson, Science 250, 94 (1990).
21. D. R. Cox, M. Burmeister, E. Roydon Price, S. Kim, R. M. Myers, ibid., p. 245; M. A. Walter et al., Nature Genet. 7, 22 (1994).
22. D. R. Cox, M. Burmeister, E. Roydon Price, S. Kim, R. M. Myers, ibid., p. 245; M. A. Walter et al., Nature Genet. 7, 22 (1994).
23. D. Botstein et al., Am. J. Hum. Genet. 32, 314 (1980); J. L. Weber and P. E. May, ibid. 44, 388 (1989).
24. D. Botstein et al., Am. J. Hum. Genet. 32, 314 (1980); J. L. Weber and P. E. May, ibid. 44, 388 (1989).
25. J. Murray et al., Science 265, 2049 (1994).
26. J. Ott, Analysis of Human Genetic Linkage (Johns Hopkins Press, Baltimore, MD, 1991).
27. R. Arratia et al., Genomics 11, 806 (1991).
28. Loci were used only if they produced a single clear band visible by ethidium bromide staining, except for genetic markers, which were used even when they produced more than one band on an agarose gel (in view of their value in providing top-down orientation). Assays meeting this criterion are more likely, although not certain, to represent single unique loci in the genome.
29. m (temperature at which 50% of double-stranded DNA is denatured) for primers set at 58°C.
30. M. Boguski and G. Schuler, Nature Genet. 10, 369 (1995).
31. Nonredundant ESTs were part of the UniEST set prepared by M. Boguski and G. Schuler at the National Center for Biotechnology Information, derived from the dbEST database. These ESTs were taken from the Washington University-Merck EST project and the GenExpress project; R. Houlgatte et al., Genome Res. 5, 272 (1995).
32. R. Berry et al., Nature Genet. 10, 415 (1995); M. D. Adams et al., Nature 377, S3 (1995).
33. R. Berry et al., Nature Genet. 10, 415 (1995); M. D. Adams et al., Nature 377, S3 (1995).
34. To select primers from ESTs, we modified the STS pipeline (79) to select shorter PCR products of 100 to 150 bp near the end of the 3′-UTRs {but 20 bp away from the polyadenylate [poly(A)J tract} in a region of high sequence quality.
35. J. Weissenbach et al., Nature 359, 794 (1992); G. Gyapay et al., Nature Genet. 7, 247 (1994); C. Dib et al. Nature, in press.
36. J. Weissenbach et al., Nature 359, 794 (1992); G. Gyapay et al., Nature Genet. 7, 247 (1994); C. Dib et al. Nature, in press.
37. J. Weissenbach et al., Nature 359, 794 (1992); G. Gyapay et al., Nature Genet. 7, 247 (1994); C. Dib et al. Nature, in press.
38. C. J. Bell et al., Hum. Mol. Genet. 4, 59 (1995).
39. STSs were kindly shared by D. Cox and R. Myers, Stanford University, Stanford, CA, and J. Gastier, Harvard University, Cambridge, MA.
40. Some incomplete addresses could be resolved by a simple band-matching test with complete addresses by using CEPH fingerprint data, as described (25). Others could be resolved by virtue of comparison with complete addresses for nearby STSs.
41. m of 58°C. Computer images of each hybridization were obtained with a CCD camera. VIEW software (C. Rosenberg; Whitehead Institute) was used to locate and determine the intensity of positive dots. A small proportion of STSs were screened by standard agarose gel stained with ethidium bromide.
42. It is not possible to draw conclusions about library coverage from the overall number of STSs with no definite addresses, because many of these represented weak PCR assays that sometimes worked on human control DNAs but failed on YAC pools.
43. The probability that a unique sequence would occur more than 15 times in a random library with 8.4-fold coverage is about 1%. Some of these STSs may thus be unique loci, but they were excluded to guard against repeats.
44. G. Gyapay et al., Hum. Mol. Genet., in press.
45. n, because the latter produced high background.
46. H. L. Drwinga et al., Genomics 16, 311 (1993); T. J. Hudson et al., ibid. 13, 622 (1992). In 300 cases, ambiguous or conflicting assignments were resolved by using the NIGMS Human/Rodent Somatic Cell Hybrid Panel #2, described in B. L. Dubois and S. Naylor et al., ibid. 16, 315 (1993).
47. H. L. Drwinga et al., Genomics 16, 311 (1993); T. J. Hudson et al., ibid. 13, 622 (1992). In 300 cases, ambiguous or conflicting assignments were resolved by using the NIGMS Human/Rodent Somatic Cell Hybrid Panel #2, described in B. L. Dubois and S. Naylor et al., ibid. 16, 315 (1993).
48. H. L. Drwinga et al., Genomics 16, 311 (1993); T. J. Hudson et al., ibid. 13, 622 (1992). In 300 cases, ambiguous or conflicting assignments were resolved by using the NIGMS Human/Rodent Somatic Cell Hybrid Panel #2, described in B. L. Dubois and S. Naylor et al., ibid. 16, 315 (1993).
49. In 151 cases, STSs were chromosomally assigned by virtue of having at least three single links to other markers on a chromosome and no links to any loci on any other chromosome.
50. About 200 such conflicts were resolved. Half were resolved by repeating the typing of the somatic cell hybrid panel. For the other half, an STS was demonstrated to amplify products from more than one chromosome. Such STSs were discarded.
51. RHMAPPER (L. Kruglyak, D. K. Slonim, L. D. Stein, E. S. Lander, unpublished data) uses a hidden Markov model to account for breaks in diploid DNA and for false positives and negatives, as in E. S. Lander and P. Green, Proc. Natl. Acad. Sci. U.S.A. 84, 2363 (1987); and E. S. Lander and S. Lincoln, Genomics 14, 604 (1992). Framework maps were initiated and extended by a greedy algorithm and then subjected to local permutation tests, thereby allowing for efficient exploration of a vast space of possible orders.
52. RHMAPPER (L. Kruglyak, D. K. Slonim, L. D. Stein, E. S. Lander, unpublished data) uses a hidden Markov model to account for breaks in diploid DNA and for false positives and negatives, as in E. S. Lander and P. Green, Proc. Natl. Acad. Sci. U.S.A. 84, 2363 (1987); and E. S. Lander and S. Lincoln, Genomics 14, 604 (1992). Framework maps were initiated and extended by a greedy algorithm and then subjected to local permutation tests, thereby allowing for efficient exploration of a vast space of possible orders.
53. In most cases, frameworks for the two chromosomal arms were constructed separately and then oriented and joined by using information from the genetic map. There is significant pairwise RH linkage (at lod > 5.0) between framework markers on opposite sides of the centromere on nine of the final framework maps, but not on the other 14.
54. M. R. James et al., Nature Genet. 8, 70 (1994).
55. +-, were thus determined directly from the data and were not optimized. The two weighting parameters for conflicts with the genetic and framework RH maps were chosen by optimization in test cases.
56. S. Saccone et al., Proc. Natl. Acad. Sci. U.S.A. 89, 4913 (1992).
57. Three markers mapped into large centromeric intervals on the correct chromosome; they had high lod scores but were about 30 cR away from the closest marker. All were confirmed by double-linkage with YACs. For three other markers, chromosomal assignment could not be obtained from polycrtromosomal hybrid panels because of rodent background.
58. For one of these four loci, there was a (presumably chimeric) single YAC link to a marker on the same chromosome but located 70 cR from the correct location.
59. Three of the loci belonged to doubly linked contigs that were anchored by virtue of a CHLC genetic marker.
60. If gene promoters on chromosome X have the same average expression level as on autosomes, then the fact that only one X chromosome is active (due to hemizygosity in males and X inactivation in females) would cause transcripts from X-linked genes to be half as abundant. Because half of the cDNAs came from nonnormalized libraries and half from normalized libraries, the occurrence of ESTs in the relatively small set examined will partly reflect abundance. This issue will recede when enough ESTs have been isolated to overcome issues related to message levels. Underrepresentation of chromosome X could also conceivably represent some other systematic bias of which we are not aware.
61. T. J. Hudson et al., data not shown.
62. J. S. Heslop-Harrison et al., Hum. Genet. 84, 27 (1989).
63. Wethank A. Kaufman, O. Merport, and J. Spencer for technical assistance; L. Bennett for computer system administration; G. Rogers and M. Foley for assistance with media preparation and glass washing; S. Gordon, A. Christopher, P. Mansfield, and others at Intelligent Automation Systems for assistance in design, construction, and maintenance of automation equipment; D. Cox, R. Myers, J. Sikela, M. Adams, J. Murray, and K. Buetow for sharing data including sequences and markers; M. Boguski and G. Schule for assistance in analysis of EST sequences; and D. Cohen and I. Chumakov for sharing the CEPH YAC library in 1992 and for public distribution of their STS-content, Alu-PCR, and fingerprint data. Supported by NIH award HG00098 to E.S.L: and by the Whitehead Institute for Biomedical Research. T.J.H. was a recipient of a Clinician Scientist Award from the Medical Research Council of Canada. L.K. is a recipient of a Special Emphasis Research Career Award (HG00017) from the National Center for Human Genome Research.