The Structure of Haplotype Blocks in the Human Genome

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Huy Nguyen Last modified: Fri Jun 7 14:35:08 EDT 2002

Introduction

As part of The SNP Consortium Allele Frequency Project, we characterized haplotype patterns across 51 autosomal regions that collectively span ~0.4% of the human genome, and compared the results across samples from Africa, Europe and Asia. Regions were selected to be evenly spaced throughout the genome, and subjected only to the availability of contiguous genomic sequence and an average density (in a core region of 150kb) of one candidate SNP discovered by The SNP Consortium every 2kb. Genotyping was performed by primer extension of multiplex products and detection by MALDI-TOF mass spectroscopy (Sequenom). Overall, we designed assays to 4,532 SNPs of which 3,738 (82%) were successfully genotyped. Details of the methods and findings of this project are described in Gabriel et al. (published online at ScienceXpress May 24, 2002). This website provides summary of the SNP coverage of each of the 51 regions, and access to the raw genotype data in linkage file format for all genotype data utilized in this study.

Genotype Data

Region Summary: using Golden Path HG8

	CHROM | REGION |  SNPS | POPS | START_POS     | END_POS       | SIZE(Kb)
----- | ------ | ----- | ---- | ------------- | ------------- | --------
    1 | 1a     |    55 |    4 |     2,920,112 |     3,076,857 |   156.75
    1 | 1b     |    16 |    4 |     3,626,300 |     3,678,525 |    52.23
    1 | 2b     |    15 |    4 |     4,495,628 |     4,520,067 |    24.44
    1 | 2a     |    81 |    4 |     4,543,840 |     4,803,009 |   259.17
    1 | 3a     |   119 |    4 |    74,754,000 |    75,073,226 |   319.23
    1 | 4a     |   104 |    4 |    77,419,928 |    77,850,612 |   430.68
    1 | 7a     |    65 |    4 |   226,528,186 |   226,708,716 |   180.53
    1 | 7b     |    16 |    4 |   267,659,212 |   267,713,505 |    54.29
    2 | 8a     |    73 |    4 |    13,001,455 |    13,164,396 |   162.94
    2 | 9a     |    69 |    4 |    19,128,488 |    19,277,935 |   149.45
    2 | 10a    |    66 |    4 |    86,248,197 |    86,475,064 |   226.87
    2 | 11a    |    49 |    4 |   158,261,352 |   158,355,714 |    94.36
    2 | 12b    |    19 |    4 |   158,701,947 |   158,729,707 |    27.76
    2 | 13a    |    57 |    4 |   160,080,221 |   160,250,495 |   170.27
    2 | 14a    |    76 |    4 |   232,488,104 |   232,658,354 |   170.25
    2 | 15a    |    51 |    4 |   233,331,030 |   233,511,284 |   180.25
    3 | 16a    |    14 |    4 |    68,962,231 |    69,001,754 |    39.52
    3 | 16b    |    54 |    4 |    69,051,642 |    69,157,633 |   105.99
    3 | 17a    |    78 |    4 |   132,138,962 |   132,343,483 |   204.52
    3 | 18a    |    85 |    4 |   201,062,441 |   201,348,748 |   286.31
    4 | 19a    |    84 |    4 |    50,185,234 |    50,480,063 |   294.83
    4 | 20a    |    81 |    4 |   126,461,792 |   126,690,397 |   228.61
    4 | 21a    |    41 |    4 |   207,161,616 |   207,306,064 |   144.45
    4 | 21b    |    11 |    4 |   207,257,278 |   207,283,582 |    26.30
    5 | 22a    |    68 |    4 |    63,284,503 |    63,459,414 |   174.91
    5 | 23a    |    89 |    4 |   135,471,341 |   135,646,636 |   175.30
    6 | 24a    |   121 |    4 |    21,507,393 |    21,951,398 |   444.01
    6 | 25a    |    18 |    4 |    88,278,088 |    88,312,980 |    34.89
    6 | 25b    |    22 |    4 |    88,340,641 |    88,395,014 |    54.37
    6 | 26a    |    67 |    4 |   185,214,680 |   185,384,850 |   170.17
    7 | 27a    |    81 |    4 |    50,097,394 |    50,419,517 |   322.12
    7 | 28a    |    99 |    4 |   127,720,132 |   128,122,659 |   402.53
    8 | 29a    |   104 |    4 |    37,170,126 |    37,417,430 |   247.30
    8 | 30a    |    77 |    4 |   106,163,223 |   106,340,850 |   177.63
    9 | 31a    |    28 |    4 |    29,109,122 |    29,291,103 |   181.98
    9 | 31b    |    51 |    4 |    29,555,787 |    29,658,244 |   102.46
    9 | 32a    |   110 |    4 |   113,465,768 |   113,930,995 |   465.23
   10 | 33a    |    68 |    4 |    27,036,716 |    27,229,783 |   193.07
   10 | 33b    |    11 |    4 |    27,346,240 |    27,385,275 |    39.04
   10 | 34a    |    89 |    4 |   108,148,096 |   108,544,565 |   396.47
   11 | 35a    |    68 |    4 |    26,986,814 |    27,154,841 |   168.03
   11 | 36a    |    58 |    4 |   104,086,142 |   104,283,102 |   196.96
   12 | 37a    |    58 |    4 |    32,949,376 |    33,116,507 |   167.13
   12 | 38a    |    84 |    4 |   131,383,027 |   131,717,127 |   334.10
   13 | 39a    |    77 |    4 |    33,420,195 |    33,593,592 |   173.40
   13 | 39b    |    10 |    4 |    33,458,579 |    33,509,225 |    50.65
   13 | 40a    |    97 |    4 |   105,682,085 |   106,005,068 |   322.98
   14 | 41a    |   141 |    4 |    81,112,246 |    81,552,062 |   439.82
   15 | 42a    |   116 |    4 |    35,320,182 |    35,730,101 |   409.92
   15 | 43a    |    56 |    4 |   103,020,578 |   103,196,887 |   176.31
   16 | 44a    |    42 |    4 |    65,828,511 |    65,916,227 |    87.72
   16 | 44b    |    53 |    4 |    65,920,138 |    66,044,818 |   124.68
   17 | 45a    |    73 |    4 |    36,100,799 |    36,278,785 |   177.99
   18 | 46a    |    85 |    4 |    24,252,610 |    24,552,651 |   300.04
   19 | 47a    |    59 |    4 |     7,304,781 |     7,480,473 |   175.69
   20 | 48a    |    71 |    4 |    12,459,462 |    12,637,757 |   178.30
   21 | 49a    |    41 |    4 |    10,000,599 |    10,171,621 |   171.02
   22 | 50a    |    75 |    4 |    24,115,889 |    24,366,984 |   251.10
   22 | 51a    |    58 |    4 |    32,043,178 |    32,297,897 |   254.72
   22 | 52a    |    56 |    4 |    40,077,996 |    40,315,218 |   237.22
   22 | 53a    |    59 |    4 |    46,118,155 |    46,296,646 |   178.49
   22 | 54a    |    66 |    4 |    46,131,355 |    46,386,830 |   255.48
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The Team

Stacey B. Gabriel 1, Stephen F. Schaffner 1, Huy Nguyen 1, Jamie M. Moore 1, Jessica Roy 1, Brendan Blumenstiel 1, John Higgins 1, Mathew DeFelice 1, Amy Lochner 1, Maura Faggart 1, Shau Neen Liu-Cordero 2, Charles Rotimi 3, Adebowale Adeyemo 4, Richard Cooper 5, Ryk Ward 6, Eric S. Lander 2, Mark J. Daly 1, David Altshuler 7*

1 Whitehead/MIT Center for Genome Research, Cambridge, MA 02139, USA.
2 Whitehead/MIT Center for Genome Research, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
3 National Human Genome Center, Howard University, Washington, DC 20059, USA.
4 Department of Pediatrics, College of Medicine, University of Ibadan, Ibadan, Nigeria.
5 Department of Preventive Medicine and Epidemiology, Loyola University Medical School, Maywood, IL 60143, USA.
6 Institute of Biological Anthropology, University of Oxford, Oxford, England OX2 6QS.
7 Whitehead/MIT Center for Genome Research, Cambridge, MA 02139, USA; Departments of Genetics and Medicine, Harvard Medical School; Department of Molecular Biology and Diabetes Unit, Massachusetts General Hospital, Boston, MA 02114, USA.

Funding

This project was done with funding by and as a part of the TSC allele frequency project.