Sheikhi_2014_statistical.pdf (1.04 MB)
Statistical methods for the detection of single nucleotide polymorphisms (SNPs) using new generation genome sequencers
A single nucleotide polymorphism, or SNP, is a site of
the genome where variation occurs within a population.
Almost all SNPs have only two alleles (variants).
Variations in the DNA sequences of humans can affect
how humans develop diseases and respond to pathogens,
chemicals, drugs, vaccines, and other agents. SNPs are
also thought to be key enablers in realizing the concept
of personalized medicine. The importance of SNPs also
comes from their ability to in
uence disease risk, drug efficacy and side-effects. Thus, there should be confidence
in the methods for the detection of SNPs that a SNP
found is not a sequencing error.
In this work, a statistical method based on a likelihood
ratio test has been considered to detect these SNPs. The
effciency of this test has been compared with a threshold
test using simulations. Results of the analysis of real
genome sequence data are also presented.
History
Degree
- Doctoral
First supervisor
Ramsey, GordonSecond supervisor
MacKenzie, GilbertNote
peer-reviewedOther Funding information
SFILanguage
EnglishAlso affiliated with
- BIO-SI - Bio-Statistics & Informatics Project
Department or School
- Mathematics & Statistics