Search Results - "LARSON, David E"

The Next-Generation Sequencing Revolution and Its Impact on Genomics by Koboldt, Daniel C., Steinberg, Karyn Meltz, Larson, David E., Wilson, Richard K., Mardis, Elaine R.

“…Genomics is a relatively new scientific discipline, having DNA sequencing as its core technology. As technology has improved the cost and scale of genome…”
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VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing by Koboldt, Daniel C, Zhang, Qunyuan, Larson, David E, Shen, Dong, McLellan, Michael D, Lin, Ling, Miller, Christopher A, Mardis, Elaine R, Ding, Li, Wilson, Richard K

“…Cancer is a disease driven by genetic variation and mutation. Exome sequencing can be utilized for discovering these variants and mutations across hundreds of…”
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CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer by Griffith, Malachi, Spies, Nicholas C, Krysiak, Kilannin, McMichael, Joshua F, Coffman, Adam C, Danos, Arpad M, Ainscough, Benjamin J, Ramirez, Cody A, Rieke, Damian T, Kujan, Lynzey, Barnell, Erica K, Wagner, Alex H, Skidmore, Zachary L, Wollam, Amber, Liu, Connor J, Jones, Martin R, Bilski, Rachel L, Lesurf, Robert, Feng, Yan-Yang, Shah, Nakul M, Bonakdar, Melika, Trani, Lee, Matlock, Matthew, Ramu, Avinash, Campbell, Katie M, Spies, Gregory C, Graubert, Aaron P, Gangavarapu, Karthik, Eldred, James M, Larson, David E, Walker, Jason R, Good, Benjamin M, Wu, Chunlei, Su, Andrew I, Dienstmann, Rodrigo, Margolin, Adam A, Tamborero, David, Lopez-Bigas, Nuria, Jones, Steven J M, Bose, Ron, Spencer, David H, Wartman, Lukas D, Wilson, Richard K, Mardis, Elaine R, Griffith, Obi L

“…CIViC is an expert-crowdsourced knowledgebase for Clinical Interpretation of Variants in Cancer describing the therapeutic, prognostic, diagnostic and…”
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VarScan: variant detection in massively parallel sequencing of individual and pooled samples by Koboldt, Daniel C., Chen, Ken, Wylie, Todd, Larson, David E., McLellan, Michael D., Mardis, Elaine R., Weinstock, George M., Wilson, Richard K., Ding, Li

“…Massively parallel sequencing technologies hold incredible promise for the study of DNA sequence variation, particularly the identification of variants…”
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SomaticSniper: identification of somatic point mutations in whole genome sequencing data by Larson, David E., Harris, Christopher C., Chen, Ken, Koboldt, Daniel C., Abbott, Travis E., Dooling, David J., Ley, Timothy J., Mardis, Elaine R., Wilson, Richard K., Ding, Li

“…Motivation: The sequencing of tumors and their matched normals is frequently used to study the genetic composition of cancer. Despite this fact, there remains…”
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Functional equivalence of genome sequencing analysis pipelines enables harmonized variant calling across human genetics projects by Regier, Allison A., Farjoun, Yossi, Larson, David E., Krasheninina, Olga, Kang, Hyun Min, Howrigan, Daniel P., Chen, Bo-Juen, Kher, Manisha, Banks, Eric, Ames, Darren C., English, Adam C., Li, Heng, Xing, Jinchuan, Zhang, Yeting, Matise, Tara, Abecasis, Goncalo R., Salerno, Will, Zody, Michael C., Neale, Benjamin M., Hall, Ira M.

“…Hundreds of thousands of human whole genome sequencing (WGS) datasets will be generated over the next few years. These data are more valuable in aggregate:…”
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Clonal Architecture of Secondary Acute Myeloid Leukemia by Walter, Matthew J, Shen, Dong, Ding, Li, Shao, Jin, Koboldt, Daniel C, Chen, Ken, Larson, David E, McLellan, Michael D, Dooling, David, Abbott, Rachel, Fulton, Robert, Magrini, Vincent, Schmidt, Heather, Kalicki-Veizer, Joelle, O'Laughlin, Michelle, Fan, Xian, Grillot, Marcus, Witowski, Sarah, Heath, Sharon, Frater, John L, Eades, William, Tomasson, Michael, Westervelt, Peter, DiPersio, John F, Link, Daniel C, Mardis, Elaine R, Ley, Timothy J, Wilson, Richard K, Graubert, Timothy A

“…Whole-genome sequencing of samples from seven subjects with secondary acute myeloid leukemia identified somatic mutations. These data, together with genotype…”
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Using VarScan 2 for Germline Variant Calling and Somatic Mutation Detection by Koboldt, Daniel C, Larson, David E, Wilson, Richard K

“…The identification of small sequence variants remains a challenging but critical step in the analysis of next-generation sequencing data. Our variant calling…”
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BreakDancer: an algorithm for high-resolution mapping of genomic structural variation by Chen, Ken, Wallis, John W, McLellan, Michael D, Larson, David E, Kalicki, Joelle M, Pohl, Craig S, McGrath, Sean D, Wendl, Michael C, Zhang, Qunyuan, Locke, Devin P, Shi, Xiaoqi, Fulton, Robert S, Ley, Timothy J, Wilson, Richard K, Ding, Li, Mardis, Elaine R

“…This software package provides genome-wide detection of structural variants (insertions, deletions, inversions and inter- and intrachromosomal translocations)…”
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The prognostic effects of somatic mutations in ER-positive breast cancer by Griffith, Obi L., Spies, Nicholas C., Anurag, Meenakshi, Griffith, Malachi, Luo, Jingqin, Tu, Dongsheng, Yeo, Belinda, Kunisaki, Jason, Miller, Christopher A, Krysiak, Kilannin, Hundal, Jasreet, Ainscough, Benjamin J, Skidmore, Zachary L., Campbell, Katie, Kumar, Runjun, Fronick, Catrina, Cook, Lisa, Snider, Jacqueline E., Davies, Sherri, Kavuri, Shyam M., Chang, Eric C., Magrini, Vincent, Larson, David E., Fulton, Robert S, Liu, Shuzhen, Leung, Samuel, Voduc, David, Bose, Ron, Dowsett, Mitch, Wilson, Richard K., Nielsen, Torsten O., Mardis, Elaine R, Ellis, Matthew J.

“…Here we report targeted sequencing of 83 genes using DNA from primary breast cancer samples from 625 postmenopausal (UBC-TAM series) and 328 premenopausal…”
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Integrated analysis of germline and somatic variants in ovarian cancer by Kanchi, Krishna L., Johnson, Kimberly J., Lu, Charles, McLellan, Michael D., Leiserson, Mark D. M., Wendl, Michael C., Zhang, Qunyuan, Koboldt, Daniel C., Xie, Mingchao, Kandoth, Cyriac, McMichael, Joshua F., Wyczalkowski, Matthew A., Larson, David E., Schmidt, Heather K., Miller, Christopher A., Fulton, Robert S., Spellman, Paul T., Mardis, Elaine R., Druley, Todd E., Graubert, Timothy A., Goodfellow, Paul J., Raphael, Benjamin J., Wilson, Richard K., Ding, Li

“…We report the first large-scale exome-wide analysis of the combined germline–somatic landscape in ovarian cancer. Here we analyse germline and somatic…”
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Background Mutations in Parental Cells Account for Most of the Genetic Heterogeneity of Induced Pluripotent Stem Cells by Young, Margaret A., Larson, David E., Sun, Chiao-Wang, George, Daniel R., Ding, Li, Miller, Christopher A., Lin, Ling, Pawlik, Kevin M., Chen, Ken, Fan, Xian, Schmidt, Heather, Kalicki-Veizer, Joelle, Cook, Lisa L., Swift, Gary W., Demeter, Ryan T., Wendl, Michael C., Sands, Mark S., Mardis, Elaine R., Wilson, Richard K., Townes, Tim M., Ley, Timothy J.

“…To assess the genetic consequences of induced pluripotent stem cell (iPSC) reprogramming, we sequenced the genomes of ten murine iPSC clones derived from three…”
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Aromatase inhibition remodels the clonal architecture of estrogen-receptor-positive breast cancers by Miller, Christopher A., Gindin, Yevgeniy, Lu, Charles, Griffith, Obi L, Griffith, Malachi, Shen, Dong, Hoog, Jeremy, Li, Tiandao, Larson, David E., Watson, Mark, Davies, Sherri R, Hunt, Kelly, Suman, Vera J., Snider, Jacqueline, Walsh, Thomas, Colditz, Graham A., DeSchryver, Katherine, Wilson, Richard K., Mardis, Elaine R., Ellis, Matthew J.

“…Resistance to oestrogen-deprivation therapy is common in oestrogen-receptor-positive (ER+) breast cancer. To better understand the contributions of tumour…”
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Csk-Deficient Boundary Cells Are Eliminated from Normal Drosophila Epithelia by Exclusion, Migration, and Apoptosis by Vidal, Marcos, Larson, David E., Cagan, Ross L.

“…The construction and maintenance of normal epithelia relies on local signals that guide cells into their proper niches and remove unwanted cells. Failure to…”
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Exome-Based Mapping and Variant Prioritization for Inherited Mendelian Disorders by Koboldt, Daniel C., Larson, David E., Sullivan, Lori S., Bowne, Sara J., Steinberg, Karyn M., Churchill, Jennifer D., Buhr, Aimee C., Nutter, Nathan, Pierce, Eric A., Blanton, Susan H., Weinstock, George M., Wilson, Richard K., Daiger, Stephen P.

“…Exome sequencing in families affected by rare genetic disorders has the potential to rapidly identify new disease genes (genes in which mutations cause…”
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Truncating Prolactin Receptor Mutations Promote Tumor Growth in Murine Estrogen Receptor-Alpha Mammary Carcinomas by Griffith, Obi L., Chan, Szeman Ruby, Griffith, Malachi, Krysiak, Kilannin, Skidmore, Zachary L., Hundal, Jasreet, Allen, Julie A., Arthur, Cora D., Runci, Daniele, Bugatti, Mattia, Miceli, Alexander P., Schmidt, Heather, Trani, Lee, Kanchi, Krishna-Latha, Miller, Christopher A., Larson, David E., Fulton, Robert S., Vermi, William, Wilson, Richard K., Schreiber, Robert D., Mardis, Elaine R.

“…Estrogen receptor alpha-positive (ERα+) luminal tumors are the most frequent subtype of breast cancer. Stat1−/− mice develop mammary tumors that closely…”
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The clonal evolution of metastatic colorectal cancer by Dang, Ha X, Krasnick, Bradley A, White, Brian S, Grossman, Julie G, Strand, Matthew S, Zhang, Jin, Cabanski, Christopher R, Miller, Christopher A, Fulton, Robert S, Goedegebuure, S Peter, Fronick, Catrina C, Griffith, Malachi, Larson, David E, Goetz, Brian D, Walker, Jason R, Hawkins, William G, Strasberg, Steven M, Linehan, David C, Lim, Kian H, Lockhart, A Craig, Mardis, Elaine R, Wilson, Richard K, Ley, Timothy J, Maher, Christopher A, Fields, Ryan C

“…Tumor heterogeneity and evolution drive treatment resistance in metastatic colorectal cancer (mCRC). Patient-derived xenografts (PDXs) can model mCRC biology;…”
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Author Correction: The prognostic effects of somatic mutations in ER-positive breast cancer by Griffith, Obi L., Spies, Nicholas C., Anurag, Meenakshi, Griffith, Malachi, Luo, Jingqin, Tu, Dongsheng, Yeo, Belinda, Kunisaki, Jason, Miller, Christopher A, Krysiak, Kilannin, Hundal, Jasreet, Ainscough, Benjamin J, Skidmore, Zachary L., Campbell, Katie, Kumar, Runjun, Fronick, Catrina, Cook, Lisa, Snider, Jacqueline E., Davies, Sherri, Kavuri, Shyam M., Chang, Eric C., Magrini, Vincent, Larson, David E., Fulton, Robert S, Liu, Shuzhen, Leung, Samuel, Voduc, David, Bose, Ron, Dowsett, Mitch, Wilson, Richard K., Nielsen, Torsten O., Mardis, Elaine R, Ellis, Matthew J.

“…The original version of this Article contained errors in the depiction of confidence intervals in the NF1 BCSS data illustrated in Figure 3b. These have now…”
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CMDS: a population-based method for identifying recurrent DNA copy number aberrations in cancer from high-resolution data by Zhang, Qunyuan, Ding, Li, Larson, David E., Koboldt, Daniel C., McLellan, Michael D., Chen, Ken, Shi, Xiaoqi, Kraja, Aldi, Mardis, Elaine R., Wilson, Richard K., Borecki, Ingrid B., Province, Michael A.

“…Motivation: DNA copy number aberration (CNA) is a hallmark of genomic abnormality in tumor cells. Recurrent CNA (RCNA) occurs in multiple cancer samples across…”
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Computer simulation of cellular patterning within the Drosophila pupal eye by Larson, David E, Johnson, Ruth I, Swat, Maciej, Cordero, Julia B, Glazier, James A, Cagan, Ross L

“…We present a computer simulation and associated experimental validation of assembly of glial-like support cells into the interweaving hexagonal lattice that…”
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