Smith, Erin N Jepsen, Kristen Khosroheidari, Mahdieh Rassenti, Laura Z D’Antonio, Matteo Ghia, Emanuela M Carson, Dennis A Jamieson, Catriona HM Kipps, Thomas J Frazer, Kelly A
...
Published in
Genome Biology
Accurate allele frequencies are important for measuring subclonal heterogeneity and clonal evolution. Deep-targeted sequencing data can contain PCR duplicates, inflating perceived read depth. Here we adapted the Illumina TruSeq Custom Amplicon kit to include single molecule tagging (SMT) and show that SMT-identified duplicates arise from PCR. We de...
Eichler, Ee Kelly A. Frazer
Published in
Genome Biology
Rahim, Nazli G Harismendy, Olivier Topol, Eric J Frazer, Kelly A
Published in
Genome Biology
New technologies for rapidly assaying DNA sequences have revealed that the degree and nature of human genetic variation is far more complex then previously realized. These same technologies have also resulted in the identification of common genetic variants associated with more than 30 human diseases and traits.
Harismendy, Olivier Schwab, Richard B Bao, Lei Olson, Jeff Rozenzhak, Sophie Kotsopoulos, Steve K Pond, Stephanie Crain, Brian Chee, Mark S Messer, Karen
...
Published in
Genome Biology
Ultra-deep targeted sequencing (UDT-Seq) can identify subclonal somatic mutations in tumor samples. Early assays' limited breadth and depth restrict their clinical utility. Here, we target 71 kb of mutational hotspots in 42 cancer genes. We present novel methods enhancing both laboratory workflow and mutation detection. We evaluate UDT-Seq true sen...
Smith, Erin N Jepsen, Kristen Arias, Angelo D Shepard, Peter J Chambers, Christina D Frazer, Kelly A
Published in
Genome Biology
BackgroundThe National Children’s Study (NCS) is a prospective epidemiological study in the USA tasked with identifying a nationally representative sample of 100,000 children, and following them from their gestation until they are 21 years of age. The objective of the study is to measure environmental and genetic influences on growth, development, ...
Udpa, Nitin Ronen, Roy Zhou, Dan Liang, Junbin Stobdan, Tsering Appenzeller, Otto Yin, Ye Du, Yuanping Guo, Lixia Cao, Rui
...
Published in
Genome Biology
BackgroundAlthough it has long been proposed that genetic factors contribute to adaptation to high altitude, such factors remain largely unverified. Recent advances in high-throughput sequencing have made it feasible to analyze genome-wide patterns of genetic variation in human populations. Since traditionally such studies surveyed only a small fra...
Dubchak, I Kelly A. Frazer
Published in
Genome Biology
Multi-species comparisons of DNA sequences are more powerful for discovering functional sequences than pairwise DNA sequence comparisons. Most current computational tools have been designed for pairwise comparisons, and efficient extension of these tools to multiple species will require knowledge of the ideal evolutionary distance to choose and the...
