Estimating Haplotypes

Question

[soosus]

Hypothetical question just to illustrate what I'm trying to do:

A small gene "FOOBAR" on human chromosome 1 has been genotyped last year for three SNPs (in a LD block) for a total 1000 unrelated Finnish samples. The following are the summarized genotypes. Sample_1's genotypes for these three SNPs are "AG", "AC" and "CT", respectively. What are the estimated haplotypes for Sample_1 and the haplotype's probabilities?

SNP1     SNP2        SNP3      TotalSample
AA       CC          TT        160
GG       AA          CC        358
GG       AA          CT          2
AG       AC          CT        480

[Aaronquinlan]

Homework problem?

Answer 1

[dstram52]

Only 3 haps are needed to explain these data

GAC (freq 59.9 percent) ACT (freq 40 percent) GAT (freq 0.1 percent)

The first 160 are homozygous for ACT, the next 358 are homozygous for GAC, The next two are (GAC,GAT), and the last 480 are (ACT,GAC)

The first 160+358 subjects are "obvious" homozygous, and the last 480 are easily explained as having one copy each of the haplotypes that the first 160 and the next 358 share. The remaining two require the introduction of a new haplotype (GAT).

Answer 2

[Tky]

Sample_1 carries two haplotypes ACT/GAC, and SNPs in each haplotype are in strong LD with each other.