Biology subjects

Bronner, M. P.

Publications and source records attributed to Bronner, M. P..

3 recordsLinked to original sources

bioRxiv2019

Somalier: rapid relatedness estimation for cancer and germline studies using efficient genome sketches

When interpreting sequencing data from multiple spatial or longitudinal biopsies, detecting sample mix-ups is essential yet more difficult than in studies of germline variation. In most genomic studies of tumors, genetic variation is frequently detected through pairwise comparisons of the tumor and a matched normal tissue from the sample donor, and in many cases, only somatic variants are reported. The disjoint genotype information that results hinders the use of existing tools that detect sample swaps solely based on genotypes of germline variants. To address this problem, we have developed somalier, which can operate directly on the alignments, so as not to require jointly-called germline variants. Instead, somalier extracts a small sketch of informative genetic variation for each sample. Sketches from hundreds of biopsies and normal tissues can then be compared in under a second. This speed also makes it useful for checking relatedness in large cohorts of germline samples. Somalier produces both text output and an interactive visual report that facilitates the detection and correction of sample swaps using multiple relatedness metrics. We introduce the tool and demonstrate its utility on a cohort of five glioma samples each with a normal, tumor, and cell-free DNA sample. Applying somalier to high-coverage sequence data from the 1000 Genomes Project also identifies several related samples. Somalier can be applied to diverse sequencing data types and genome builds, and is freely available for academic use at github.com/brentp/somalier.

bioinformatics↗

bioRxiv2019

Unexpectedly High Subclonal Mutational Diversity in Human Colorectal Cancer and Its Significance

Human colorectal cancers (CRC) contain both clonal and subclonal mutations. Clonal mutations are positively selected, present in most cells and drive malignant progression. Subclonal mutations are randomly dispersed throughout the genome; they provide a vast reservoir of mutant cells that can expand, repopulate the tumor and result in the rapid emergence of resistance, as well as being a major contributor to tumor heterogeneity. Here, we apply Duplex Sequencing (DS) methodology to quantify subclonal mutations in CRC tumor with unprecedented depth (104) and accuracy (<10-7). We measured mutation frequencies in genes encoding replicative DNA polymerases and in genes frequently mutated in CRC, and found an unexpectedly high effective mutation rate, 7.1 x 10-7. The curve of subclonal mutation accumulation as a function of sequencing depth, using DNA obtained from five different tumors, is in accord with a neutral model of tumor evolution. We present a new theoretical approach to model neutral evolution independent of the infinite sites assumption (which states that a particular mutation arises only in one tumor cell at any given time). Our analysis indicates that the infinite sites assumption is not applicable once the number of tumor cells exceeds the reciprocal of the mutation rate, a circumstance relevant to even the smallest clinically diagnosable tumor. Our methods allow accurate estimation of the total mutation burden in clinical cancers. Our results indicate that no DNA locus is wild type in every malignant cell within a tumor at the time of diagnosis (probability of all cells wild type = 10-308).\n\nSignificance StatementCancers evolve many mutations. Clonal mutations are selected early. Subsequent evolution occurs in a branching fashion, possibly without selection (\"neutral evolution\"). Rarer mutations occur later on smaller branches of the evolutionary tree. Using a DNA sequencing method, duplex sequencing, with unprecedented accuracy and sensitivity, we quantified very rare unique subclonal mutations in diagnostic specimens from five human colorectal cancers. Rarer subclones probe later evolutionary timepoints than previously possible. We confirm neutral evolution at later times and find many more subclonal mutations than expected. A novel theoretical method allowed us to extrapolate further forward in time to diagnosis. At diagnosis, every base in DNA is mutated in at least one cancer cell. In particular any therapy resistance mutation would be present.

cancer biology↗

bioRxiv2017

Context-dependent Requirements for FimH and Other Canonical Virulence Factors in Gut Colonization by Extraintestinal Pathogenic Escherichia coli

Extraintestinal pathogenic Escherichia coli (ExPEC) act as commensals within the mammalian gut, but can induce pathology upon dissemination to other host environments such as the urinary tract and bloodstream. It is thought that ExPEC genomes are shaped in large part by evolutionary forces encountered within the gut where the bacteria spend much of their time, provoking the question of how their extraintestinal virulence traits arose. The principle of coincidental evolution, in which a gene that evolved in one niche happens to be advantageous in another, has been used to argue that ExPEC virulence factors originated in response to selective pressures within the gut ecosystem. As a test of this hypothesis, the fitness of ExPEC mutants lacking canonical virulence factors was assessed within the intact murine gut in the absence of any antibiotic treatment. We found that most of the tested factors--including CNF1, Usp, colibactin, flagella, and the plasmid pUTI89--were dispensable for gut colonization. Deletion of genes encoding the adhesin PapG or the toxin HlyA caused transient defects, but did not affect longer-term persistence. In contrast, a mutant missing the type 1 pilus-associated adhesin FimH displayed reduced persistence within the gut. However, this phenotype was variable, being dependent on the presence of specific competing strains and partially attributable to aberrant flagellin expression by the fimH mutant. These data indicate that FimH and other key ExPEC-associated factors are not strictly required for gut colonization, suggesting that selective pressures within the gut do not drive the development of all extraintestinal virulence traits.

microbiology↗