Assignment IV

Assignment IV

After haploview installation and dumped genotype data from hapmap project. SNP genotypes is on the part of chromosome X consists of 30 SNP .

This is some part of hapmap file that was loaded from hapmap project.

Haplotype block finding and SNP tagging were performed step-by-step down here.

1. Genotype file was loaded into haploview package

2. After OK. clicking, The SNP descriptive statistic was shown here by;

3. Linkage disequilibrium plot told about a number of haplotype blocks based upon 3 algorithms

Key menu told about classification, i.e blue means inconclusive such as high LD but also high recombination.

Gabrille method, based on LD codes derived from 95% CI of D’ coefficient, a haplotype block is created if 95% of pairwise SNP comparisons yield strong LD.

Picture zoom

Four gamete rule

Solid LD Spine method, Searches for a spine of strong LD running from one marker to another.A block defined this way suggests that the 1st and last SNPs in a block are in strong LD.

Customize block provided parameter adjustment for each algorithm.

SNP tagging

Gabrille method

There are 3 haplotype blocks.

Tagging SNP

Block 1; SNP position 8 and 9

Block 2; SNP position 13 and 15

Block 3; SNP posiotion 24

Four gamete rule

There are 6 haplotype blocks.

Tagging SNP

Block1; SNP postion 1 and 2

Block2; SNP position 3, 4 and 5

Block3; SNP position 6 and 7

Block4; SNP position 8 and 9

Block5; SNP position 13 and 15

Block6; SNP position 22, 23 and 24

Solid LD Spine method

There are 7 haplotype blocks.

Tagging SNP

Block1; SNP postion 1 and 2

Block2; SNP position 3, 4 and 5

Block3; SNP position 6 and 7

Block4; SNP position 8, 9 and 11

Block5; SNP position 12,13 and 15

Block6; SNP position 19, 20, 21, 22 and 23

Block7; SNP position 24 and 30

Created by Miss Patiya Pengon

4737611 SCFS/M Forensic Science

Science, Mahidol University

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