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Chine Science Bulletin 2004 Vol. 49 No. 10 1044
8]
and even the whole chromosome 21[4].The International
HapMap project aims to genotype SNPs and construct the
map at the density of one SNP in every 5 kb genomic re-
gion initially[9]. However, the fine haplotype structures
constructed with high density SNPs at the level of each
individual gene are still lacking, which is particularly
more of medical interests for the candidate gene approach
in the mapping of dia-contributing variants.
The centromere of chromosome 15 is a region of
particularly medical interests. It confers the genes respon-
sible for Oculocutaneous Albinism Type
8]. We,
therefore, quenced 7 genes and the gene-related regions
(coding, intron-exon boundary, 5-UTR, 5
genomic regions) in a 1.7 Mb interval in this region,
from 22862015 to 24575950 bp (genome.ucsc.edu/),
constructed the high-density SNP haplotypes and the hap-
lotype block structures in 5 genes in a collection of 100
Chine Han subjects.
1 Materials and methods
(
) Genes lected in the study. 7 genes, 3 func-
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tional and 4 hypothetical, were lected in this study. Their positions and quences were retrieved from the UCSC Genome Browr (genome.ucsc.edu/), En-mbl Genome Browr (www ./) and NCBI (bi.v/).
(
and 3
of NT_026446.72 (GABRB3) is also quenced. The primers ud and the regions quenced are listed in the Supplement (omitted here). PCR mixture contained 500 ng genomic DNA, 0.2 mmol/L each of the dNTPs, 2.3 mmol/L Tris-HCl (pH 8.8 at 25
followed by 35 cycles of 30 s of denaturation at 94. The PCR products were analyzed
with the ABI 3100 (Applied Biosystems, Foster City, California, USA) by the manufacturer’s standard proce-dure. The accuracy of the SNPs identified by quencing was checked in the family and was confirmed by their transmission in each of the generations.
(
) Linkage diquilibrium test and the construction
of the block-like structures. The combined 2-point Chi-square test with a threshold of 0.05 (P < 0.05 indi-cates two loci may be in LD)[12] and the Pairwi Linkage Diquilibrium Test with |D
15] were ud in the construction. 2 Results
(
UTR, and 5 (14.7%) in ex-ons. The SNPs identified in each gene ranged from 5 to 9, with the mean of 6.8 SNPs per gene. The average SNP/quenced regions differed from 0.4/kb to 1.2/kb with the mean of 0.6/kb. (The total quenced region is 57480 bp, which is 3.38% of the 1.7 Mb region). The al-lele frequencies differed from 0.01 to 0.99.
(
3 with the mean of 2. The average block size is 43.1 kb, which differed from 1.2 to 228 kb. The total coverage of the blocked structure in the quenced region is 90%. The block-like structures in each of the genes and the haplotypes contained in each block are illustrated in Figs. 1
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Table 1 Distribution of the novel SNPs and the results of the Pairwi Linkage Diquilibrium Test and the 2-point Chi-square analysis Gene Pair No. SNP locus Position in gene SNP type SNP freq. Chi-square P _Chi D
upstream C/T 0.60/0.40 1.691
0.193
−0.683
Chr15: 24404760 intron 2 A/G
0.91/0.09
NT_026446.72 (NM_000814) (GABRB3)
2
Chr15: 24566158
5
upstream A/G 0.41/0.59 0.632
0.427
0.466
Chr15: 24404760 intron 2 A/G
0.91/0.09
4
Chr15: 24566963
5
upstream C/T 0.44/0.56 0.822
0.365
0.479
Chr15: 24404760 intron 2 A/G
0.91/0.09
6
Chr15: 24574036
5
upstream
C/T
0.73/0.27
0.057 0.812 −0.360 Chr15: 24564937 5
upstream C/G
0.41/0.59
54.247 0.000 c) −0.773 d) Chr15: 24564937 5
upstream A/G
0.41/0.59
54.247 0.000 c) −0.773 d) Chr15: 24564937 5
upstream A/G
0.44/0.56
52.036 0.000 c) −0.806 d) Chr15: 24564937 5
upstream C/T
0.44/0.56
52.036 0.000 c) −0.806 d) Chr15: 24564937 5
upstream G/A
0.90/0.10
0.015 0.903 0.167 Chr15: 24564937 5
upstream C/T
0.73/0.27
0.622 0.430 −0.208 Chr15: 24566158 5
upstream A/G
0.41/0.59
95.909 0.000 c) 1.000 d) Chr15: 24566158 5
upstream A/G
0.44/0.56
76.799 0.000 c) 0.954d) Chr15: 24566158 5
upstream C/T
0.44/0.56
76.799 0.000 c) 0.954 d) Chr15: 24566158 5
upstream G/A
0.90/0.10
0.037 0.848 −0.051 Chr15: 24566158 5
upstream C/T
0.73/0.27
0.619 0.431 0.203 Chr15: 24566298 5
upstream A/G
0.44/0.56
76.799 0.000 c) 0.954 d) Chr15: 24566298 5
upstream C/T
0.44/0.56
76.799 0.000 c) 0.954 d) Chr15: 24566298 5
upstream G/A
0.90/0.10
0.037 0.848 −0.051 Chr15: 24566298 5
upstream C/T
0.73/0.27
0.619 0.431 0.203 Chr15: 24566963 5
upstream C/T
0.44/0.56
95.983 0.000 c) 1.000 d) Chr15: 24566963 5
upstream G/A
0.90/0.10
0.096 0.757 −0.008 Chr15: 24566963 5
upstream C/T
0.73/0.27
0.032
0.859 0.076 Chr15: 24567021
5
upstream
G/A 0.90/0.10
0.096
0.757
0.038
(To be continued on the next page )
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(Continued) Gene Pair No. SNP locus Position in gene SNP type SNP freq. Chi-square P_Chi D
upstream C/T 0.44/0.56
27
Chr15: 24574265 5
upstream G/A 0.90/0.10
28
Chr15: 24574265 5
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(Continued) Gene Pair No. SNP locus Position in gene SNP type SNP freq. Chi-square P_Chi D
