Christopher T. Saunders

Learn More
MOTIVATION Whole genome and exome sequencing of matched tumor-normal sample pairs is becoming routine in cancer research. The consequent increased demand for somatic variant analysis of paired samples requires methods specialized to model this problem so as to sensitively call variants at any practical level of tumor impurity. RESULTS We describe Strelka,(More)
Methods for automated prediction of deleterious protein mutations have utilized both structural and evolutionary information but the relative contribution of these two factors remains unclear. To address this, we have used a variety of structural and evolutionary features to create simple deleterious mutation models that have been tested on both(More)
With the advent of next generation sequencing technologies, the cost of sequencing whole genomes is poised to go below $1000 per human individual in a few years. As more and more genomes are sequenced, analysis methods are undergoing rapid development, making it tempting to store sequencing data for long periods of time so that the data can be re-analyzed(More)
We use flexible backbone protein design to explore the sequence and structure neighborhoods of naturally occurring proteins. The method samples sequence and structure space in the vicinity of a known sequence and structure by alternately optimizing the sequence for a fixed protein backbone using rotamer based sequence search, and optimizing the backbone for(More)
UNLABELLED : We describe Manta, a method to discover structural variants and indels from next generation sequencing data. Manta is optimized for rapid germline and somatic analysis, calling structural variants, medium-sized indels and large insertions on standard compute hardware in less than a tenth of the time that comparable methods require to identify(More)
SUMMARY An ultrafast DNA sequence aligner (Isaac Genome Alignment Software) that takes advantage of high-memory hardware (>48 GB) and variant caller (Isaac Variant Caller) have been developed. We demonstrate that our combined pipeline (Isaac) is four to five times faster than BWA + GATK on equivalent hardware, with comparable accuracy as measured by trio(More)
Using human adipose stromal cells in monolayer culture as a model system for study of the regulation of aromatase activity, as well as polyclonal antibodies raised in this laboratory against aromatase cytochrome P-450 (cytochrome P-450AROM), it was found that the rate of synthesis of cytochrome P-450AROM was stimulated by dibutyryl cyclic AMP. This(More)
Summary: We describe Manta, a method to discover structural variants and indels from next generation sequencing data. Manta is optimized for rapid clinical analysis, calling structural variants, medium-sized indels and large insertions on standard compute hardware in less than a tenth of the time that comparable methods require to identify only subsets of(More)
We develop an approximate maximum likelihood method to estimate flanking nucleotide context-dependent mutation rates and amino acid exchange-dependent selection in orthologous protein-coding sequences and use it to analyze genome-wide coding sequence alignments from mammals and yeast. Allowing context-dependent mutation provides a better fit to coding(More)
  • 1