Zobrazeno 1 - 10
of 166
pro vyhledávání: '"Brent S. Pedersen"'
Autor:
Harriet Dashnow, Brent S. Pedersen, Laurel Hiatt, Joe Brown, Sarah J. Beecroft, Gianina Ravenscroft, Amy J. LaCroix, Phillipa Lamont, Richard H. Roxburgh, Miriam J. Rodrigues, Mark Davis, Heather C. Mefford, Nigel G. Laing, Aaron R. Quinlan
Publikováno v:
Genome Biology, Vol 23, Iss 1, Pp 1-20 (2022)
Abstract Expansions of short tandem repeats (STRs) cause many rare diseases. Expansion detection is challenging with short-read DNA sequencing data since supporting reads are often mapped incorrectly. Detection is particularly difficult for “novel
Externí odkaz:
https://doaj.org/article/b354d34ff2e44f32a24f0158d94420d9
Publikováno v:
BMC Bioinformatics, Vol 23, Iss 1, Pp 1-32 (2022)
Abstract Background Despite numerous molecular and computational advances, roughly half of patients with a rare disease remain undiagnosed after exome or genome sequencing. A particularly challenging barrier to diagnosis is identifying variants that
Externí odkaz:
https://doaj.org/article/16695b18f8474f139af9cbf5a7074e01
Autor:
Brent S. Pedersen, Joe M. Brown, Harriet Dashnow, Amelia D. Wallace, Matt Velinder, Martin Tristani-Firouzi, Joshua D. Schiffman, Tatiana Tvrdik, Rong Mao, D. Hunter Best, Pinar Bayrak-Toydemir, Aaron R. Quinlan
Publikováno v:
npj Genomic Medicine, Vol 6, Iss 1, Pp 1-8 (2021)
Abstract In studies of families with rare disease, it is common to screen for de novo mutations, as well as recessive or dominant variants that explain the phenotype. However, the filtering strategies and software used to prioritize high-confidence v
Externí odkaz:
https://doaj.org/article/709f6f141917434d9d3529666fde6ab7
Autor:
Jonathan R. Belyeu, Murad Chowdhury, Joseph Brown, Brent S. Pedersen, Michael J. Cormier, Aaron R. Quinlan, Ryan M. Layer
Publikováno v:
Genome Biology, Vol 22, Iss 1, Pp 1-13 (2021)
Abstract Visual validation is an important step to minimize false-positive predictions from structural variant (SV) detection. We present Samplot, a tool for creating images that display the read depth and sequence alignments necessary to adjudicate
Externí odkaz:
https://doaj.org/article/3469a82678f7486a86d417d184bb1a2f
Publikováno v:
PLoS Computational Biology, Vol 18, Iss 5, p e1009123 (2022)
Since its introduction in 2011 the variant call format (VCF) has been widely adopted for processing DNA and RNA variants in practically all population studies-as well as in somatic and germline mutation studies. The VCF format can represent single nu
Externí odkaz:
https://doaj.org/article/3ae05fe830ed411c84fe85dcbdd6247b
Autor:
Michael J. Cormier, Jonathan R. Belyeu, Brent S. Pedersen, Joseph Brown, Johannes Köster, Aaron R. Quinlan
Publikováno v:
Nature Communications, Vol 12, Iss 1, Pp 1-6 (2021)
Modern biological research is complicated by the difficulty of collecting, transforming, annotating, and integrating datasets. Here, the authors present Go Get Data, a fast, reproducible approach to installing standardized data recipes, with an appli
Externí odkaz:
https://doaj.org/article/229a1630d4cf43f5bf84c23578b10f64
Autor:
Brent S. Pedersen, Preetida J. Bhetariya, Joe Brown, Stephanie N. Kravitz, Gabor Marth, Randy L. Jensen, Mary P. Bronner, Hunter R. Underhill, Aaron R. Quinlan
Publikováno v:
Genome Medicine, Vol 12, Iss 1, Pp 1-9 (2020)
Abstract Background 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 variatio
Externí odkaz:
https://doaj.org/article/7318c11f0de746678b1a13cc3f314054
Autor:
Amelia D Wallace, Thomas A Sasani, Jordan Swanier, Brooke L Gates, Jeff Greenland, Brent S Pedersen, Katherine E Varley, Aaron R Quinlan
Publikováno v:
PLoS ONE, Vol 16, Iss 4, p e0241253 (2021)
A substantial fraction of the human genome is difficult to interrogate with short-read DNA sequencing technologies due to paralogy, complex haplotype structures, or tandem repeats. Long-read sequencing technologies, such as Oxford Nanopore's MinION,
Externí odkaz:
https://doaj.org/article/b40febd6e2ea4665b168e7184b3bf972
Autor:
Samuel W. Brady, Jasmine A. McQuerry, Yi Qiao, Stephen R. Piccolo, Gajendra Shrestha, David F. Jenkins, Ryan M. Layer, Brent S. Pedersen, Ryan H. Miller, Amanda Esch, Sara R. Selitsky, Joel S. Parker, Layla A. Anderson, Brian K. Dalley, Rachel E. Factor, Chakravarthy B. Reddy, Jonathan P. Boltax, Dean Y. Li, Philip J. Moos, Joe W. Gray, Laura M. Heiser, Saundra S. Buys, Adam L. Cohen, W. Evan Johnson, Aaron R. Quinlan, Gabor Marth, Theresa L. Werner, Andrea H. Bild
Publikováno v:
Nature Communications, Vol 8, Iss 1, Pp 1-15 (2017)
In metastatic breast cancer, subclonal evolution can drive drug resistance. Here, the authors genetically and transcriptionally follow the evolution of four breast cancers over time and treatment, and suggest a phenotype-targeted treatment strategy t
Externí odkaz:
https://doaj.org/article/f22c7e1eec644bd49c349e24a268484e
Autor:
Thomas A Sasani, Brent S Pedersen, Ziyue Gao, Lisa Baird, Molly Przeworski, Lynn B Jorde, Aaron R Quinlan
Publikováno v:
eLife, Vol 8 (2019)
The number of de novo mutations (DNMs) found in an offspring's genome increases with both paternal and maternal age. But does the rate of mutation accumulation in human gametes differ across families? Using sequencing data from 33 large, three-genera
Externí odkaz:
https://doaj.org/article/0e035b5e105c4e8098986e24d5b97694