This diploma thesis describes work on a chip resequencing project of 20 ecotypes belonging to the plant model species Arabidopsis thaliana, and these ecotypes are accessions from natural populations. Chip resequencing primarily aims at identifying single nucleotide polymorphisms (SNPs), the most abundant class of naturally occurring sequence variation. For resequencing, DNA microarrays are empl...

In this paper we analyze the effect of fixed delay in conjunction with queueing and resequencing delay on the optimal distribution of traffic on multiple disjoint paths. We study a system of two hosts or end nodes, connected b y a high speed network, communicating on two virtual channels which follow disjoint physical paths. The paths have a different number of hops and/or physical length which...

Analyses of genetic polymorphism data have the potential to be highly informative about the demographic history of Native American populations, but due to a combination of historical and political factors, there are essentially no autosomal sequence polymorphism data from any Native American group. However, there are many resequencing studies involving Latinos, whose genomes contain segments in...

Identification of rare variants by resequencing is important both for detecting novel variations and for screening individuals for known disease alleles. New technologies enable low-cost resequencing of target regions, although it is still prohibitive to test more than a few individuals. We propose a novel pooling design that enables the recovery of novel or known rare alleles and their carrier...

Familial hypercholesterolemia (FH) is an autosomal dominant disorder. Although genetic testing is an important tool for detecting FH-causing mutations in patients, diagnostic methods for young patients with severe hypercholesterolemia are understudied. This study compares the target exome sequencing (TES) technique with the DNA resequencing array technique on young patients with severe hypercho...

Resequencing genomic DNA from pools of individuals is an effective strategy to detect new variants in targeted regions and compare them between cases and controls. There are numerous ways to assign individuals to the pools on which they are to be sequenced. The naïve, disjoint pooling scheme (many individuals to one pool) in predominant use today offers insight into allele frequencies, but does...

Although genomewide association studies have successfully identified associations of many common single-nucleotide polymorphisms (SNPs) with common diseases, the SNPs implicated so far account for only a small proportion of the genetic variability of tested diseases. It has been suggested that common diseases may often be caused by rare alleles missed by genomewide association studies. To ident...

BACKGROUND Ultra high throughput sequencing (UHTS) technologies find an important application in targeted resequencing of candidate genes or of genomic intervals from genetic association studies. Despite the extraordinary power of these new methods, they are still rarely used in routine analysis of human genomic variants, in part because of the absence of specific standard procedures. The aim o...

In this paper, we are going to solve the DNA resequencing problem. We are given a set of subseuqences obtained by the next generation sequencing (NGS) technology and we are asked to assembly them into a DNA sequence with the aid of a reference sequence. In this paper, we propose a progressive strategy to solve the resequencing problem. Our algorithm allows us to map data to reference sequence e...