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NullHap--a versatile application to estimate haplotype frequencies from unphased genotypes in the presence of alleles.

Nowak RM, Płoski R - BMC Bioinformatics (2008)

Bottom Line: Laboratory techniques used to determine haplotypes are often too expensive for large-scale studies and lack of phase information is commonly overcome using likelihood-based calculations.Whereas a number of programs are available for that purpose, none of them can handle loci with both multiple and alleles.Here we present a description of a modified Expectation - Maximization algorithm as well as its implementation (NullHap) which allow to effectively overcome these limitations.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Electronics and Information Technology, Institute of Electronic Systems, Warsaw University of Technology, Warsaw, Poland. r.m.nowak@elka.pw.edu.pl

ABSTRACT

Background: Laboratory techniques used to determine haplotypes are often too expensive for large-scale studies and lack of phase information is commonly overcome using likelihood-based calculations. Whereas a number of programs are available for that purpose, none of them can handle loci with both multiple and alleles.

Results: Here we present a description of a modified Expectation - Maximization algorithm as well as its implementation (NullHap) which allow to effectively overcome these limitations. As an example of application we used Nullhap to reanalyze published data on distribution of KIR genotypes in Polish psoriasis patients and controls showing that the KIR2DS4/1D locus may be a marker of KIR2DS1 haplotypes with different effects on disease susceptibility.

Conclusion: The developed application can estimate haplotype frequencies for every type of polymorphism and can effectively be used in genetic research as illustrated by a novel finding regarding the genetic susceptibility to psoriasis.

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Related in: MedlinePlus

Effect of HWE violation on accuracy of estimation. Effect of HWE violation on the accuracy of the algorithm. The figure shows the error in function of inbreeding coefficient f for two polymorphisms characterized in Table 2 (example 5 – red line, example 6 – blue line).
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Figure 2: Effect of HWE violation on accuracy of estimation. Effect of HWE violation on the accuracy of the algorithm. The figure shows the error in function of inbreeding coefficient f for two polymorphisms characterized in Table 2 (example 5 – red line, example 6 – blue line).

Mentions: As can be seen from Figure 2, there was a linear correlation of inbreeding coefficient f with the accuracy of estimation of haplotype frequencies.


NullHap--a versatile application to estimate haplotype frequencies from unphased genotypes in the presence of alleles.

Nowak RM, Płoski R - BMC Bioinformatics (2008)

Effect of HWE violation on accuracy of estimation. Effect of HWE violation on the accuracy of the algorithm. The figure shows the error in function of inbreeding coefficient f for two polymorphisms characterized in Table 2 (example 5 – red line, example 6 – blue line).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2526998&req=5

Figure 2: Effect of HWE violation on accuracy of estimation. Effect of HWE violation on the accuracy of the algorithm. The figure shows the error in function of inbreeding coefficient f for two polymorphisms characterized in Table 2 (example 5 – red line, example 6 – blue line).
Mentions: As can be seen from Figure 2, there was a linear correlation of inbreeding coefficient f with the accuracy of estimation of haplotype frequencies.

Bottom Line: Laboratory techniques used to determine haplotypes are often too expensive for large-scale studies and lack of phase information is commonly overcome using likelihood-based calculations.Whereas a number of programs are available for that purpose, none of them can handle loci with both multiple and alleles.Here we present a description of a modified Expectation - Maximization algorithm as well as its implementation (NullHap) which allow to effectively overcome these limitations.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Electronics and Information Technology, Institute of Electronic Systems, Warsaw University of Technology, Warsaw, Poland. r.m.nowak@elka.pw.edu.pl

ABSTRACT

Background: Laboratory techniques used to determine haplotypes are often too expensive for large-scale studies and lack of phase information is commonly overcome using likelihood-based calculations. Whereas a number of programs are available for that purpose, none of them can handle loci with both multiple and alleles.

Results: Here we present a description of a modified Expectation - Maximization algorithm as well as its implementation (NullHap) which allow to effectively overcome these limitations. As an example of application we used Nullhap to reanalyze published data on distribution of KIR genotypes in Polish psoriasis patients and controls showing that the KIR2DS4/1D locus may be a marker of KIR2DS1 haplotypes with different effects on disease susceptibility.

Conclusion: The developed application can estimate haplotype frequencies for every type of polymorphism and can effectively be used in genetic research as illustrated by a novel finding regarding the genetic susceptibility to psoriasis.

Show MeSH
Related in: MedlinePlus