Gavin Ha, 1, 2 Andrew Roth, 1, 2 Jaswinder Khattra, 1 Julie Ho, 3 Damian Yap, 1 Leah M.
Prentice, 3 Nataliya Melnyk, 3 Andrew McPherson, 1, 2 Ali Bashashati, 1 Emma Laks, 1 …

The evolution of cancer genomes within a single tumor creates mixed cell populations with
divergent somatic mutational landscapes. Inference of tumor subpopulations has been …

1. First, germline heterozygous SNP positions L={ti} T i= 1 are identified from the normal
genome using a genotyping tool, such as SAMtools mpileup (Li et al., 2009). The analysis …

This dissertation reports on the development of the mathematical and statistical framework
that was necessary for the analysis of data from a novel single-cell assay designed to …

Biological tools such as genetic lineage tracing, three-dimensional confocal microscopy and
next-generation DNA sequencing are providing new ways to quantify the distribution of …

Copy number variation (CNV) is a major type of chromosomal structural variation that play
important roles in many diseases including cancers. Due to genome instability, a large …

Until very recently, the standard model of DNA included two genes for each trait. This dated
model has given way to a model that includes copies of some genes well in excess of the …

Background The reconstruction of clonal haplotypes and their evolutionary history in
evolving populations is a common problem in both microbial evolutionary biology and …

Advances in single cell copy number sequencing technologies have enabled the generation
of data on hundreds to thousands of cells in parallel. Despite the rapid development in these …

Motivation New low-coverage single-cell DNA sequencing technologies enable the
measurement of copy number profiles from thousands of individual cells within tumors. From …