1. Consider that a sample of unrelated probands have been genotyped at three SNP
ID: 97005 • Letter: 1
Question
1. Consider that a sample of unrelated probands have been genotyped at three SNPs with alleles G and C, C and T, and A and G respectively. The overall size of the sample is of no concern, but six different genotype combinations as shown below have been observed. Reconstruct the haplotypes using Clark’s algorithm.
(3 points)
Person
1
2
3
4
5
6
Gene 1
GG
GG
GG
GG
GC
GC
Gene 2
CC
CT
CT
TT
CC
CT
Gene 3
AA
AA
AG
GG
AG
GG
Person
1
2
3
4
5
6
Gene 1
GG
GG
GG
GG
GC
GC
Gene 2
CC
CT
CT
TT
CC
CT
Gene 3
AA
AA
AG
GG
AG
GG
Explanation / Answer
The oldest Algorithm for reconstructing genotype combinations is Clark's algorithm.
This follows three steps to resolve reconstruction those are
i.Identification of haplotypes
ii.Resolving of haplotypes
iii.Rearranging
1.) identification is to identify all unambiguous haplotypes (all homozygotes and single-site heterozygotes) and considering them as ‘‘resolved’’.
2) Determining whether each of the resolved haplotypes could be one of the alleles in the remaining yet-to-be-phased genotypes, and
3) each time a new haplotype is identified as one of the resolved ones, this new haplotype is assumed to be known, and the remaining haplotype is added to the resolved haplotype set.
The rationale for this algorithm is that homozygous haplotypes are probably common, and that a phase-ambiguous genotype is likely to contain
For the given genotype combination the reconstructing of haplotypes is likely to be as follows using clark's algorithm.
Disadvantage with clark's algorithm:
1. The algorithm does not start when there is no homozygotes in the genotypes
2.This algorithm does not give unique solution becuase the phasing results depends on order of genotypes.
Person 1 2 3 4 5 6 Gene1 GG GC GG GC GG GG Gene2 CC CT TT CT CC CT Gene3 AA AG GG AG GG AARelated Questions
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