Search

Whole-genome sequencing (WGS) holds great potential as a diagnostic test. However, the majority of patients currently undergoing WGS lack a molecular diagnosis, largely due to the vast number of undiscovered disease genes and our inability to assess the pathogenicity of most genomic variants. The CAGI SickKids challenges attempted to address this knowledge gap by assessing state-of-the-art methods for clinical phenotype prediction from genomes. CAGI4 and CAGI5 participants were provided with WGS data and clinical descriptions of 25 and 24 undiagnosed patients from the SickKids Genome Clinic Project, respectively. Predictors were asked to identify primary and secondary causal variants. In addition, for CAGI5, groups had to match each genome to one of three disorder categories (neurologic, ophthalmologic, and connective), and separately to each patient. The performance of matching genomes to categories was no better than random but two groups performed significantly better than chance in matching genomes to patients. Two of the ten variants proposed by two groups in CAGI4 were deemed to be diagnostic, and several proposed pathogenic variants in CAGI5 are good candidates for phenotype expansion. We discuss implications for improving in silico assessment of genomic variants and identifying new disease genes.

Plasmids are extrachromosomal elements that can disseminate between strains or even between different bacterial species. Plasmids can also acquire novel genetic traits by acquisition of transposons or cointegration with other plasmids thereby providing host bacterial strains novel adaptive traits. These inherent characteristics make plasmids optimal vectors for disseminating antimicrobial resistance (AMR). Plasmid-mediated AMR dissemination often follows a Russian-Doll model in which nested genomic elements intervene in resistance propagation by vertical and horizontal transmission. However, current epidemiological studies on AMR dissemination often solely focus on clonal outbreaks. Traditional typing methods such as MLST, but also current whole genome sequence (WGS)-based epidemiological studies fail to resolve the dynamics of plasmids and thus challenge the monitoring of plasmid-mediated AMR. A main reason for this focus on clonal dissemination is the challenge of reconstructing plasmid sequences from short-read WGS as explained in chapter 2. The scope of this thesis was to develop a new set of tools in order to overcome this limitation and accurately detect and trace plasmid sequences, from short-read WGS data, in the nosocomial pathogen Enterococcus faecium.This was especially relevant to investigate the dissemination of antimicrobial resistance (AMR), in particular vancomycin resistance, as well as other disseminated genes.

Expansions of short tandem repeats are responsible for over 40 monogenic disorders, and undoubtedly many more pathogenic repeat expansions (REs) remain to be discovered. Existing methods for detecting REs in short-read sequencing data require predefined repeat catalogs. However recent discoveries have emphasized the need for detection methods that do not require candidate repeats to be specified in advance. To address this need, we introduce ExpansionHunter Denovo, an efficient catalog-free method for genome-wide detection of REs. Analysis of real and simulated data shows that our method can identify large expansions of 41 out of 44 pathogenic repeats, including nine recently reported non-reference REs not discoverable via existing methods.ExpansionHunter Denovo is freely available at https://github.com/Illumina/ExpansionHunterDenovo