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Dr. Russell Thomson

Dr. Russell Thomson. A Haplotype. One individual. Marker 1. Marker 2. Marker 3. …AGCTA T ATTA…..GGCT G CTC…..AGCA G CGA… …AGCTA A ATTA…..GGCT C CTC…..AGCA G CGA…. T G G. A C G. Recombination Hotspots. Recombinations do NOT occur at random positions across the genome.

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Dr. Russell Thomson

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  1. Dr. Russell Thomson

  2. A Haplotype. One individual. Marker 1 Marker 2 Marker 3 …AGCTATATTA…..GGCTGCTC…..AGCAGCGA… …AGCTAAATTA…..GGCTCCTC…..AGCAGCGA… T G G A C G

  3. Recombination Hotspots. Recombinations do NOT occur at random positions across the genome. Instead they are more likely to occur at “recombination hotspots”. “Recombination hotspots” are positions where recombinations are more likely To occur. Reed & Tishkoff, Genetics (2006).

  4. Haplotype Blocks A haplotype block occurs between recombination hotspots. Within a haplotype block, there is LD between all the markers. Not all markers need to be genotyped within a haplotype block.

  5. Defining Haplotype Blocks • Many Proposed Rules. For example: Solid Spine of LD “the first and last markers in a block are in strong LD with all intermediate markers” LD can be defined using r2, D’ and/or LOD. VarFlow and Haploview can be used to define haplotype blocks

  6. A Haplotype. One individual. Marker 1 Marker 2 Marker 3 …AGCTATATTA…..GGCTGCTC…..AGCAGCGA… …AGCTAAATTA…..GGCTCCTC…..AGCAGCGA… T G G A C G You can associate disease risk to a haplotype, instead of an allele.

  7. A Haplotype. One individual. Marker 1 Marker 2 Marker 3 …AGCTATATTA…..GGCTGCTC…..AGCAGCGA… …AGCTAAATTA…..GGCTCCTC…..AGCAGCGA… T G G A C G Genotypic Data:

  8. Haplotype or Phase Inference T G G A C G

  9. Haplotype Inference using pedigrees C/C A/A G/C A/T father mother daughter This family structure is sometimes called a TRIO G/C A/T

  10. Haplotype Inference using pedigrees C/C A/A G/C A/T C A C A G/C A/T

  11. Haplotype Inference using pedigrees C/C A/A G/C A/T C A C A C A G/C A/T

  12. Haplotype Inference using pedigrees C/C A/A G/C A/T C A C A C A G T G/C A/T

  13. Haplotype Inference using pedigrees C/C A/A G/C A/T C A G T C A C A C A G T G/C A/T

  14. Programs to conduct Haplotype Inference using pedigrees • Haploview – using trios only. • Merlin, Allegro and other linkage analysis software – any type of pedigree.

  15. Haplotype Inference using population data. G/C A/A G/G A/A C/C T/T G/G A/T G/C A/T

  16. Haplotype Inference using population data. G/C A/A G/G A/A C/C T/T G/G A/T G/C A/T G A C A G A G A C T C T G A G T

  17. Haplotype Inference using population data. G/C A/A G/G A/A C/C T/T G/G A/T G/C A/T Probably G A C A G A G A C T C T G A G T G A C T

  18. Haplotype Inference using population data. • There are many algorithms to do this. • They assign haplotype probabilities, given genotypes. • Haploview implements one and VarFlow implements many Haplotype inference algorithms.

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