Familial searching in DNA databases

We start our introduction to DNA matching with the direct match case: we find DNA at a crime scene and find a direct match with a member of our database. To measure the strength of our case against the match, we use likelihoodratios. We differentiate between two different situations: the probable cause case, where we already suspect our match and...

Evaluation of DNA scaffolding techniques using PacBio long reads

The goal of this study was to dive into the novel techniques associated with the use of the available Third Generation DNA Sequencing (TGS) platform, PacBio. This 3-year old technology sounded promising right from the beginning but its groundbreaking attributes, like length and error content, required unconventional handling to yield worthwhile...

Low-Cost Smith-Waterman Acceleration

Due to advancing technology, genetic sequencing has become cheaper over the years. This has caused the demand for computational power to grow even faster than Moore's law. To remedy this problem, we analyzed low-cost hardware solutions to parallelize the computational part of the genetic sequencing. We proposed a novel method for calculating the...

DNA translocation: The effect of excluded volume interaction

Het sturen van DNA door een klein gaatje in een kunstmatig membraan biedt mogelijkheden voor het aflezen van een DNA streng. Tijdens dit proces beweegt de streng zich in een vloeistof, waardoor allerlei fysische effecten een rol gaan spelen. De krachten die op de streng werken zorgen ervoor dat de DNA streng zich van de ene kant van het membraan...

Detection of Fetal Copy Number Aberrations by Shallow Sequencing of Maternal Blood Samples

Motivation: Numerous genetic disorders can be detected in prenatal diagnosis using Chorionic Villus Sampling. As this brings a 1:100 chance for miscarriage, this method is only applied when the fetus is suspected to have an increased chance at having an aberration. It is known that a small percentage of DNA in maternal plasma is of fetal origin...

Translocatie van homogene polymeren door een nanoporie

Translocatie van een ketting met verschillende kraaltjes door een zeer kleine porie kan gebruikt worden als een eerste stap voor het modelleren van het transport van DNA door een membraan. Dit translocatieproces biedt een groot aantal kansen in chemische en biologische processen, zoals het snel kunnen afezen van DNA. Het translocatieproces wordt...

Evidential value of a Y-STR profile match: The Neighbor-Matching Method

Y-haplotype profiling presents special advantages for forensic casework, paternity and population studies. Y-chromosome DNA is male-specific and can sometimes be detected in stains where autosomal DNA cannot. When a suspect in a criminal case has the same Y-haplotype as found in a crime stain, what is the evidential value of the match? In such...

Translocation of Heterogeneous Polymers through a Nanopore

Translocating a chain of different beads through a very small pore can be used as a first step of modelling a DNA chain that passes through a nanopore. This translocation process offers a variety of possibilities in chemical and biological processes, for instance rapid DNA sequencing. In this thesis the chain is modelled as a polymer with...

FPGA Hardware acceleration of co-occurring aberrations in aCGH data

Unbalanced transaction can lead to addition and deletions in genes, which can be an indication of tumor cells. This is measured with array Comparative Genomic Hybridization. To find co-occurring aberrations in DNA, an algorithm was designed. However the execution takes days to find these DNA aberrations. This thesis proposes a partial FPGA based...

Multimodal Interface for DNA Alignment of Sequences

Major research efforts in Bioinformatics include sequence alignment, gene finding, genome assembly, protein structure alignment, protein structure prediction, prediction of gene expression and protein-protein interactions, and the modeling of evolution. To perform these specific tasks different tools are used. Using these tools separately is a...