Combinatorial Problems Arising in SNP and Haplotype Analysis
نویسندگان
چکیده
It is widely anticipated that the study of variation in the human genome will provide a means of predicting risk of a variety of complex diseases. This paper presents a number of algorithmic and combinatorial problems that arise when studying a very common form of genomic variation, single nucleotide polymorphisms (SNPs). We review recent results and present challenging open problems.
منابع مشابه
A Markov chain model for haplotype assembly from SNP fragments.
Single nucleotide polymorphism (SNP) is the most frequent form of human genetic variations and of importance for medical diagnosis and tracking disease genes. A haplotype is a sequence of SNPs from a single copy of a chromosome, and haplotype assembly from SNP fragments is based on DNA fragments with SNPs and the methodology of shotgun sequence assembly. In contrast to conventional combinatoria...
متن کاملSingle Nucleotide Polymorphism (SNP) in the Adiponectin Gene and Cardiovascular Disease
Dear Editor, The recent article by Mohammadzadeh et al.[1] on the latest issue of this Journal showed that the T allele +276G/T SNP of ADIPOQ gene is more associated with the increasing risk of coronary artery disease (CAD) in subjects with type 2 diabetes. Adipocytes were described in myocardial tissue of CAD patients and their role recently discussed[2,3]. Susceptibility to CAD by polymorp...
متن کاملFast Hare: A Fast Heuristic for Single Individual SNP Haplotype Reconstruction
We study the single individual SNP haplotype reconstruction problem. We introduce a simple heuristic and prove experimentally that is very fast and accurate. In particular, when compared with a dynamic programming of [8] it is much faster and also more accurate. We expect Fast Hare to be very useful in practical applications. We also introduce a combinatorial problem related to the SNP haplotyp...
متن کاملO-28: Endometriosis Is Influenced by The Promoter Haplotype-Based Expression of Macrophage Migration Inhibitory Factor (MIF)
Background: Macrophage migration inhibitory factor (MIF) is a key pro-inflammatory cytokine that is secreted by accumulated active macrophages in ectopic tissue of endometriosis. MIF is involved in pathophysiological events of endometriosis, such as angiogenesis and cell proliferation. MIF that stimulates the synthesis of PGE2, leads to over-expression of local estradiol synthesis in endometrio...
متن کاملComputational Haplotype Analysis: An overview of computational methods in genetic variation study
One of the major interests of current genomics research is disease-gene association, that is, identifying which DNA variation or a set of DNA variations is highly associated with a specific disease. In particular, single nucleotide polymorphisms (SNPs), which are the most common form of DNA variation on the human genome, and a set of SNPs on one chromosome, referred to as a haplotype, are at th...
متن کامل