Search Results - "KOBOLDT, C"

Best practices for variant calling in clinical sequencing by Koboldt, Daniel C

“…Next-generation sequencing technologies have enabled a dramatic expansion of clinical genetic testing both for inherited conditions and diseases such as…”
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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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MuSiC: identifying mutational significance in cancer genomes by Dees, Nathan D, Zhang, Qunyuan, Kandoth, Cyriac, Wendl, Michael C, Schierding, William, Koboldt, Daniel C, Mooney, Thomas B, Callaway, Matthew B, Dooling, David, Mardis, Elaine R, Wilson, Richard K, Ding, Li

“…Massively parallel sequencing technology and the associated rapidly decreasing sequencing costs have enabled systemic analyses of somatic mutations in large…”
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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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Activating HER2 mutations in HER2 gene amplification negative breast cancer by Bose, Ron, Kavuri, Shyam M, Searleman, Adam C, Shen, Wei, Shen, Dong, Koboldt, Daniel C, Monsey, John, Goel, Nicholas, Aronson, Adam B, Li, Shunqiang, Ma, Cynthia X, Ding, Li, Mardis, Elaine R, Ellis, Matthew J

“…Data from 8 breast cancer genome-sequencing projects identified 25 patients with HER2 somatic mutations in cancers lacking HER2 gene amplification. To…”
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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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The Genotypic and Phenotypic Spectrum of BICD2 Variants in Spinal Muscular Atrophy by Koboldt, Daniel C., Waldrop, Megan A., Wilson, Richard K., Flanigan, Kevin M.

“…The bicaudal D cargo adaptor 2 (BICD2) gene encodes a conserved cargo adaptor protein required for dynein‐mediated transport. Inherited and de novo variants in…”
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Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication by Montague, Michael J., Li, Gang, Gandolfi, Barbara, Khan, Razib, Aken, Bronwen L., Searle, Steven M. J., Minx, Patrick, Hillier, LaDeana W., Koboldt, Daniel C., Davis, Brian W., Driscoll, Carlos A., Barr, Christina S., Blackistone, Kevin, Quilez, Javier, Lorente-Galdos, Belen, Marques-Bonet, Tomas, Alkan, Can, Thomas, Gregg W. C., Hahn, Matthew W., Menotti-Raymond, Marilyn, O'Brien, Stephen J., Wilson, Richard K., Lyons, Leslie A., Murphy, William J., Warren, Wesley C.

“…Significance We present highlights of the first complete domestic cat reference genome, to our knowledge. We provide evolutionary assessments of the feline…”
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Recurrent mutations in the U2AF1 splicing factor in myelodysplastic syndromes by Graubert, Timothy A, Shen, Dong, Ding, Li, Okeyo-Owuor, Theresa, Lunn, Cara L, Shao, Jin, Krysiak, Kilannin, Harris, Christopher C, Koboldt, Daniel C, Larson, David E, McLellan, Michael D, Dooling, David J, Abbott, Rachel M, Fulton, Robert S, Schmidt, Heather, Kalicki-Veizer, Joelle, O'Laughlin, Michelle, Grillot, Marcus, Baty, Jack, Heath, Sharon, Frater, John L, Nasim, Talat, Link, Daniel C, Tomasson, Michael H, Westervelt, Peter, DiPersio, John F, Mardis, Elaine R, Ley, Timothy J, Wilson, Richard K, Walter, Matthew J

“…Matthew Walter and colleagues report the whole-genome sequencing of a secondary acute myeloid leukemia sample and a matched normal tissue sample. Further…”
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Detection of brain somatic variation in epilepsy‐associated developmental lesions by Bedrosian, Tracy A., Miller, Katherine E., Grischow, Olivia E., Schieffer, Kathleen M., LaHaye, Stephanie, Yoon, Hyojung, Miller, Anthony R., Navarro, Jason, Westfall, Jesse, Leraas, Kristen, Choi, Samantha, Williamson, Rachel, Fitch, James, Kelly, Benjamin J., White, Peter, Lee, Kristy, McGrath, Sean, Cottrell, Catherine E., Magrini, Vincent, Leonard, Jeffrey, Pindrik, Jonathan, Shaikhouni, Ammar, Boué, Daniel R., Thomas, Diana L., Pierson, Christopher R., Wilson, Richard K., Ostendorf, Adam P., Mardis, Elaine R., Koboldt, Daniel C.

“…Objective Epilepsy‐associated developmental lesions, including malformations of cortical development and low‐grade developmental tumors, represent a major…”
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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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Analysis of next-generation genomic data in cancer: accomplishments and challenges by Ding, Li, Wendl, Michael C., Koboldt, Daniel C., Mardis, Elaine R.

“…The application of next-generation sequencing technology has produced a transformation in cancer genomics, generating large data sets that can be analyzed in…”
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Single-nuclei transcriptomics enable detection of somatic variants in patient brain tissue by Townsend, Sydney E., Westfall, Jesse J., Navarro, Jason B., Koboldt, Daniel C., Mardis, Elaine R., Miller, Katherine E., Bedrosian, Tracy A.

“…Somatic variants are a major cause of human disease, including neurological disorders like focal epilepsies, but can be challenging to study due to their…”
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Caenorhabditis briggsae recombinant inbred line genotypes reveal inter-strain incompatibility and the evolution of recombination by Ross, Joseph A, Koboldt, Daniel C, Staisch, Julia E, Chamberlin, Helen M, Gupta, Bhagwati P, Miller, Raymond D, Baird, Scott E, Haag, Eric S

“…The nematode Caenorhabditis briggsae is an emerging model organism that allows evolutionary comparisons with C. elegans and exploration of its own unique…”
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Exome sequencing of case-unaffected-parents trios reveals recessive and de novo genetic variants in sporadic ALS by Steinberg, Karyn Meltz, Yu, Bing, Koboldt, Daniel C., Mardis, Elaine R., Pamphlett, Roger

“…The contribution of genetic variants to sporadic amyotrophic lateral sclerosis (ALS) remains largely unknown. Either recessive or de novo variants could result…”
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Editorial: From Sequence to Functional Interpretation: Sifting Through the Variation of Genomic Data by Ciolfi, Andrea, Caputo, Viviana, Koboldt, Daniel C., Uva, Paolo

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Identification of Functional Variants for Cleft Lip with or without Cleft Palate in or near PAX7, FGFR2, and NOG by Targeted Sequencing of GWAS Loci by Leslie, Elizabeth J., Taub, Margaret A., Liu, Huan, Steinberg, Karyn Meltz, Koboldt, Daniel C., Zhang, Qunyuan, Carlson, Jenna C., Hetmanski, Jacqueline B., Wang, Hang, Larson, David E., Fulton, Robert S., Kousa, Youssef A., Fakhouri, Walid D., Naji, Ali, Ruczinski, Ingo, Begum, Ferdouse, Parker, Margaret M., Busch, Tamara, Standley, Jennifer, Rigdon, Jennifer, Hecht, Jacqueline T., Scott, Alan F., Wehby, George L., Christensen, Kaare, Czeizel, Andrew E., Deleyiannis, Frederic W.-B., Schutte, Brian C., Wilson, Richard K., Cornell, Robert A., Lidral, Andrew C., Weinstock, George M., Beaty, Terri H., Marazita, Mary L., Murray, Jeffrey C.

“…Although genome-wide association studies (GWASs) for nonsyndromic orofacial clefts have identified multiple strongly associated regions, the causal variants…”
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