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Biased estimates of clonal evolution and subclonal heterogeneity can arise from PCR duplicates in deep sequencing experi... PDF available through Get Fulltext Research

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...

The nature, pattern and function of human sequence variation.

Eichler, Ee Kelly A. Frazer

Published in Genome Biology

Genetic determinants of phenotypic diversity in humans PDF available through Get Fulltext Research

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.

Detection of low prevalence somatic mutations in solid tumors with ultra-deep targeted sequencing PDF available through Get Fulltext Research

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...

Genetic ancestry of participants in the National Children’s Study PDF available through Get Fulltext Research

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, ...

Whole genome sequencing of Ethiopian highlanders reveals conserved hypoxia tolerance genes PDF available through Get Fulltext Research

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...

Multi-species sequence comparison: the next frontier in genome annotation.

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...

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