Miller KE, Kelly B, Fitch J, Ross N, Avenarius MR, Varga E, Koboldt DC, et al. Genome sequencing identifies somatic BRAF duplication c.1794_1796dupTAC;p.Thr599dup in pediatric patient with low-grade ganglioglioma. Cold Spring Harb Mol Case Stud. 2018 Feb 6. PMID: 29434027

Koboldt DC, Mihalic Mosher T, Kelly BJ, Sites E, Bartholomew D, Hickey SE, McBride K, Wilson RK, White P. A de novo nonsense mutation in ASXL3 shared by siblings with Bainbridge-Ropers syndrome. Cold Spring Harb Mol Case Stud. 2018 Jan 5. PMID: 29305346

Beecham GW, Bis JC, Martin ER, Choi SH, DeStefano AL, van Duijn CM, Fornage M, Gabriel SB, Koboldt DC, et al. The Alzheimer’s Disease Sequencing Project: Study design and sample selection. Neurol Genet. 2017 Oct 13;3(5):e194. PMID: 29184913

Mashl RJ, Scott AD, Huang KL, Wyczalkowski MA, Yoon CJ, Niu B, DeNardo E, Yellapantula VD, Handsaker RE, Chen K, Koboldt DC, Ye K, Fenyö D, Raphael BJ, Wendl MC, Ding L. GenomeVIP: a cloud platform for genomic variant discovery and interpretation. Genome Res. 2017 Aug;27(8):1450-1459. doi: 10.1101/gr.211656.116. Epub 2017 May 18. PMID: 28522612

Sullivan LS, Bowne SJ, Koboldt DC, et al. A Novel Dominant Mutation in SAG, the Arrestin-1 Gene, Is a Common Cause of Retinitis Pigmentosa in Hispanic Families in the Southwestern United States. Invest Ophthalmol Vis Sci. 2017 May 1;58(5):2774-2784. PMID: 28549094

Xiao Y, Taub MA, Ruczinski I, et al. Evidence for SNP-SNP interaction identified through targeted sequencing of cleft case-parent trios. Genet Epidemiol. 2016 Dec 26. doi: 10.1002/gepi.22023. PMID: 28019042

Bowne SJ, Sullivan LS, Wheaton DK, Locke KG, Jones KD, Koboldt DC, et al. North Carolina macular dystrophy (MCDR1) caused by a novel tandem duplication of the PRDM13 gene. Mol Vis. 2016 Oct 17;22:1239-1247. PMID: 27777503

Koboldt DC, Kanchi KL, Gui B, et al. Rare Variation in TET2 Is Associated with Clinically Relevant Prostate Carcinoma in African-Americans. Cancer Epidemiol Biomarkers Prev. 2016 Aug 2. pii: cebp.0373.2016. PMID: 27486019

Troester MA, Hoadley KA, D’Arcy M, Cherniack AD, Stewart C, Koboldt DC, et al. DNA defects, epigenetics, and gene expression in cancer-adjacent breast: a study from The Cancer Genome Atlas. NPJ Breast Cancer. 2016 May 4;2:16007. PMID: 28721375

Pfefferle AD, Agrawal YN, Koboldt DC, et al. Genomic profiling of murine mammary tumors identifies potential personalized drug targets for p53-deficient mammary cancers. Dis Model Mech. 2016 Jul 1;9(7):749-57. doi: 10.1242/dmm.025239. PMID: 27149990

Lu C, Xie M, Wendl MC, Wang J, et al. Patterns and functional implications of rare germline variants across 12 cancer types. Nat Commun. 2015 Dec 22;6:10086. doi: 10.1038/ncomms10086. PMID: 26689913

Jane Churpek, Khateriaa Pyrtel, Krishna Kanchi, et al. Genomic analysis of germ line and somatic variants in familial myelodysplasia/acute myeloid leukemia. Blood. 2015 Nov 26;126(22):2484-90. PMID: 26492932

The 1000 Genomes Project Consortium. A global reference for human genetic variation. Nature. Nature. 2015 Oct 1;526(7571):68-74. doi: 10.1038/nature15393. PMID: 26432245

Leslie EJ, Koboldt DC, Kang CJ, Ma L, Hecht JT, Wehby GL, Christensen K, Czeizel AE, Deleyiannis FW, Fulton RS, Wilson RK, Beaty TH, Schutte BC, Murray JC, Marazita ML. IRF6 mutation screening in nonsyndromic orofacial clefting: analysis of 1521 families. Clin Genet. 2015 Sep 8. doi: 10.1111/cge.12675. PMID: 26346622

Li Tai Fang, Pegah Tootoonchi Afshar, Aparna Chhibber, et al. An ensemble approach to accurately detect somatic mutations using SomaticSeq. Genome Biology. 2015 Sep 17;16(1):197. doi: 10.1186/s13059-015-0758-2. PMID: 26381235

Malachi Griffith, Obi L. Griffith, Scott M. Smith, et al. Genome Modeling System: A Knowledge Management Platform for Genomics. PLoS Comput Biol. 2015 Jul 9;11(7):e1004274. PMID: 26158448

Meltz Steinberg K, Nicholas TJ, Koboldt DC, Yu B, Mardis E, Pamphlett R. Whole genome analyses reveal no pathogenetic single nucleotide or structural differences between monozygotic twins discordant for amyotrophic lateral sclerosis. Amyotroph Lateral Scler Frontotemporal Degener. 2015 May 11:1-8. PMID: 25960086

Steinberg KM, Yu B, Koboldt DC, Mardis ER, Pamphlett R. Exome sequencing of case-unaffected-parents trios reveals recessive and de novo genetic variants in sporadic ALS. Sci Rep. 2015 Mar 16;5:9124. PMID: 25773295

Elizabeth J. Leslie, Margaret A. Taub, Huan Liu, Karyn Meltz Steinberg, Daniel C. Koboldt, et al. 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. Am J Hum Genet. 2015 Mar 5;96(3):397-411. PMID: 25704602

Montague MJ, Li G, Gandolfi B, Khan R, Aken BL, Searle SM, Minx P, Hillier LW, Koboldt DC, et al. (2014). Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication. Proceedings of the National Academy of Sciences USA. PMID: 25385592

Zhang Q, Wang L, Koboldt D, Boreki IB, & Province MA (2014). Adjusting family relatedness in data-driven burden test of rare variants. Genetic epidemiology PMID: 25169066

Sullivan LS, Koboldt DC, Bowne SJ, Lang S, Blanton SH, Cadena EL, Avery CE, Lewis RA, Webb-Jones K, Wheaton DK, Birch DG, Coussa RG, Ren H, Lopez I, Chakarova CF, Koenekoop R, Garcia CA, Fulton RS, Wilson RK, Weinstock GM, & Daiger SP (2014). A dominant mutation in hexokinase 1 (HK1) causes retinitis pigmentosa. Investigative ophthalmology & visual science PMID: 25190649

Colonna V, Ayub Q, Chen Y, Pagani L, Luisi P, Pybus M, Garrison E, Xue Y, Tyler-Smith C, 1000 Genomes Project Consortium, et al. (2014). Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences. Genome biology, 15 (6) PMID: 24980144

Koboldt DC, Larson DE, Sullivan LS, Bowne SJ, Steinberg KM, et al. Exome-based mapping and variant prioritization for inherited Mendelian disorders. Am J Hum Genet. 2014 Mar 6;94(3):373-84. doi:10.1016/j.ajhg.2014.01.016

KL Kanchi, KJ Johnson, C Lu, MD McLellan, MD Leiserson, MC Wendl, Q Zhang, DC Koboldt, et al. Integrated analysis of germline and somatic variants in ovarian cancer. 2014. Nature Comm. 5:3156. doi:10.1038/ncomms4156

Service SK, Teslovich TM, Fuchsberger C, Ramensky V, Yajnik P, Koboldt DC, Larson DE, Zhang Q, et al. (2013). Re-sequencing expands our understanding of the phenotypic impact of variants at GWAS loci. PLoS Genetics, 2014 Jan 30;10(1):e1004147. PMID: 24497850.

Zhan X, Larson DE, Wang C, Koboldt DC, Sergeev YV, Fulton RS, Fulton LL, Fronick CC, Branham KE, et al. (2013). Identification of a rare coding variant in complement 3 associated with age-related macular degeneration. Nature Genetics, 45 (11), 1375-9 PMID: 24036949

Jacoby MA, De Jesus Pizarro RE, Shao J, Koboldt DC, Fulton RS, Zhou G, Wilson RK, Walter MJ. The DNA double-strand break response is abnormal in myeloblasts from patients with therapy-related acute myeloid leukemia. Leukemia. 2013 Dec 5. PMID: 24304937.

Cancer Genome Atlas Research Network (2013). Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia. The New England Journal of Medicine, 368 (22), 2059-74 PMID: 23634996

Bose R, Kavuri SM, Searleman AC, Shen W, Shen D, Koboldt DC, Monsey J, Goel N, Aronson AB, Li S, Ma CX, Ding L, Mardis ER, & Ellis MJ (2013). Activating HER2 mtations in HER2 gene amplification negative breast cancer. Cancer Discovery PMID: 23220880

The 1000 Genomes Project Consortium (2012). An integrated map of genetic variation from 1,092 human genomes. Nature 491, 56-65. DOI: 10.1038/nature11632

Cancer Genome Atlas Network (2012). Comprehensive molecular portraits of human breast tumours. Nature, 490 (7418), 61-70 PMID: 23000897

Ellis MJ, Ding L, Shen D, Luo J, Suman VJ, Wallis JW, Van Tine BA, Hoog J, Goiffon RJ, Goldstein TC, Ng S, Lin L, Crowder R, Snider J, Ballman K, Weber J, Chen K, Koboldt DC, et al (2012). Whole-genome analysis informs breast cancer response to aromatase inhibition. Nature, 486 (7403), 353-60 PMID: 22722193

Welch JS, Ley TJ, Link DC, Miller CA, Larson DE, Koboldt DC, et al (2012). The origin and evolution of mutations in acute myeloid leukemia. Cell, 150 (2), 264-78 PMID: 22817890

Cancer Genome Atlas Network (2012). Comprehensive molecular characterization of human colon and rectal cancer. Nature, 487 (7407), 330-7 PMID: 22810696

Dees ND, Zhang Q, Kandoth C, Wendl MC, Schierding W, Koboldt DC, Mooney TB, Callaway MB, Dooling D, Mardis ER, Wilson RK, & Ding L (2012). MuSiC: identifying mutational significance in cancer genomes. Genome Research, 22 (8), 1589-98 PMID: 22759861

Walter MJ, Shen D, Ding L, Shao J, Koboldt DC, Chen K, Larson DE, McLellan MD, Dooling D, Abbott R, Fulton R, Magrini V, Schmidt H, Kalicki-Veizer J, O’Laughlin M, Fan X, Grillot M, Witowski S, Heath S, Frater JL, Eades W, Tomasson M, Westervelt P, DiPersio JF, Link DC, Mardis ER, Ley TJ, Wilson RK, & Graubert TA (2012). Clonal architecture of secondary acute myeloid leukemia. The New England Journal of Medicine, 366 (12), 1090-8 PMID: 22417201

Matsushita H, Vesely MD, Koboldt DC, Rickert CG, Uppaluri R, Magrini VJ, Arthur CD, White JM, Chen YS, Shea LK, Hundal J, Wendl MC, Demeter R, Wylie T, Allison JP, Smyth MJ, Old LJ, Mardis ER, & Schreiber RD (2012). Cancer exome analysis reveals a T-cell-dependent mechanism of cancer immunoediting. Nature, 482 (7385), 400-4 PMID: 22318521

Koboldt DC, Zhang Q, Larson DE, Shen D, McLellan MD, Lin L, Miller CA, Mardis ER, Ding L, & Wilson RK (2012). VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Research PMID: 22300766

Graubert TA, Shen D, Ding L, Okeyo-Owuor T, Lunn CL, Shao J, Krysiak K, Harris CC, Koboldt DC, et al (2011). Recurrent mutations in the U2AF1 splicing factor in myelodysplastic syndromes. Nature Genetics, 44 (1), 53-7 PMID: 22158538

Larson DE, Harris CC, Chen K, Koboldt DC, Abbott TE, Dooling DJ, Ley TJ, Mardis ER, Wilson RK, & Ding L. (2011). SomaticSniper: Identification of Somatic Point Mutations in Whole Genome Sequencing Data. Bioinformatics, Online : doi: 10.1093/bioinformatics/btr665

Cancer Genome Atlas Research Network (2011). Integrated genomic analyses of ovarian carcinoma. Nature, 474 (7353), 609-15 PMID: 21720365

Marth GT, Yu F, Indap AR, Garimella K, et al & the 1000 Genomes Project (2011). The functional spectrum of low-frequency coding variation. Genome Biology, 12 (9) PMID: 21917140

Ross JA, Koboldt DC, Staisch JE, Chamberlin HM, Gupta BP, Miller RD, Baird SE, & Haag ES (2011). Caenorhabditis briggsae recombinant inbred line genotypes reveal inter-strain incompatibility and the evolution of recombination. PLoS Genetics, 7 (7) PMID: 21779179

Bowne SJ, Humphries MM, Sullivan LS, Kenna PF, Tam LC, Kiang AS, Campbell M, Weinstock GM, Koboldt DC, Ding L, Fulton RS, Sodergren EJ, et al (2011). A dominant mutation in RPE65 identified by whole-exome sequencing causes retinitis pigmentosa with choroidal involvement. European Journal of Human Genetics 19 (10) PMID: 21938004

Wartman LD, Larson DE, Xiang Z, Ding L, Chen K, Lin L, Cahan P, Klco JM, Welch JS, Li C, Payton JE, Uy GL, Varghese N, Ries RE, Hoock M, Koboldt DC, et al. (2011). Sequencing a mouse acute promyelocytic leukemia genome reveals genetic events relevant for disease progression. J Clin Invest. 121(4):1445-55. PMID: 21436584

Link DC, Schuettpelz LG, Shen D, Wang J, Walter MJ, Kulkarni S, Payton JE, Ivanovich J, Goodfellow PJ, Le Beau M, Koboldt DC, Dooling DJ, Fulton RS, et al (2011). Identification of a novel TP53 cancer susceptibility mutation through whole-genome sequencing of a patient with therapy-related AML. JAMA : the Journal of the American Medical Association, 305 (15), 1568-76 PMID: 21505135

Ley T, Ding L, Walter M, McLellan M, Lamprecht T, Larson D, Kandoth C, Payton J, Baty J, Welch J, Harris C, Lichti C, Townsend R, Fulton R, Dooling D, Koboldt D, et al. (2010). DNMT3A Mutations in Acute Myeloid Leukemia
The New England Journal of Medicine DOI: 10.1056/NEJMoa1005143

Sudmant PH, Kitzman JO, Antonacci F, Alkan C, Malig M, Tsalenko A, Sampas N, Bruhn L, Shendure J, 1000 Genomes Project, & Eichler EE (2010). Diversity of human copy number variation and multicopy genes. Science (New York, N.Y.), 330 (6004), 641-6 PMID: 21030649

The 1000 Genomes Project Consortium (2010). A map of human genome variation from population-scale sequencing. Nature, 467 (7319), 1061-1073 DOI: 10.1038/nature09534

Bowne SJ, Sullivan LS, Koboldt DC, Ding L, Fulton R, Abbott RM, Sodergren EJ, Birch DG, Wheaton DH, Heckenlively JR, Liu Q, Pierce EA, Weinstock GM, & Daiger SP (2010). Identification of Disease-Causing Mutations in Autosomal Dominant Retinitis Pigmentosa (adRP) Using Next-Generation DNA Sequencing. Investigative Ophthalmology & Visual Science PMID: 20861475

Fehniger, T., Wylie, T., Germino, E., Leong, J., Magrini, V., Koul, S., Keppel, C., Schneider, S., Koboldt, D., Sullivan, R., Heinz, M., Crosby, S., Nagarajan, R., Ramsingh, G., Link, D., Ley, T., & Mardis, E. (2010). Next-generation sequencing identifies the natural killer cell microRNA transcriptome Genome Research DOI: 10.1101/gr.107995.110

Ramsingh G, Koboldt DC, Trissal M, Chiappinelli KB, Wylie T, Koul S, Chang LW, Nagarajan R, Fehniger TA, Goodfellow P, Magrini V, Wilson RK, Ding L, Ley TJ, Mardis ER, & Link DC (2010). Complete characterization of the microRNAome in a patient with acute myeloid leukemia. Blood PMID: 20876853

Ding L, Ellis MJ, Li S, Larson DE, Chen K, Wallis JW, Harris CC, McLellan MD, Fulton RS, Fulton LL, Abbott RM, Hoog J, Dooling DJ, Koboldt DC, et al. (2010). Genome remodelling in a basal-like breast cancer metastasis and xenograft. Nature, 464 (7291), 999-1005 PMID: 20393555

Koboldt DC, Staisch J, Thillainathan B, Haines K, Baird SE, Chamberlin HM, Haag ES, Miller RD, & Gupta BP (2010). A toolkit for rapid gene mapping in the nematode Caenorhabditis briggsae. BMC Genomics, 11 (1) PMID: 20385026

Voora D, Koboldt DC, King CR, Lenzini PA, Eby CS, Porche-Sorbet R, Deych E, Crankshaw M, Milligan PE, McLeod HL, Patel SR, Cavallari LH, Ridker PM, Grice GR, Miller RD, & Gage BF (2010). A polymorphism in the VKORC1 regulator calumenin predicts higher warfarin dose requirements in African Americans. Clinical Pharmacology and Therapeutics, 87 (4), 445-51 PMID: 20200517

Zhang Q, Ding L, Larson DE, Koboldt DC, McLellan MD, Chen K, Shi X, Kraja A, et al (2009). CMDS: a population-based method for identifying recurrent DNA copy number aberrations in cancer from high-resolution data. Bioinformatics (Oxford, England) PMID: 20031968

Mardis ER, Ding L, Dooling DJ, Larson DE, McLellan MD, Chen K, Koboldt DC, et al (2009). Recurring mutations found by sequencing an acute myeloid leukemia genome. The New England Journal of Medicine, 361 (11), 1058-66 PMID: 19657110

Koboldt DC, Chen K, Wylie T, Larson DE, McLellan MD, Mardis ER, Weinstock GM, Wilson RK, & Ding L (2009). VarScan: variant detection in massively parallel sequencing of individual and pooled samples. Bioinformatics (Oxford, England), 25 (17), 2283-5 PMID: 19542151

Ley TJ, Mardis ER, Ding L, Fulton B, McLellan MD, Chen K, Dooling D, Dunford-Shore BH, McGrath S, Hickenbotham M, Cook L, Abbott R, Larson DE, Koboldt DC, et al (2008). DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome. Nature, 456 (7218), 66-72 PMID: 18987736

Ding L, Getz G, Wheeler DA, Mardis ER, McLellan MD, Cibulskis K, Sougnez C, et al (2008). Somatic mutations affect key pathways in lung adenocarcinoma. Nature, 455 (7216), 1069-75 PMID: 18948947

Cancer Genome Atlas Research Network (2008). Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature, 455 (7216), 1061-8 PMID: 18772890

International HapMap Consortium (2007). A second generation human haplotype map of over 3.1 million SNPs. Nature, 449 (7164), 851-61 PMID: 17943122

Sabeti PC, Varilly P, Fry B, et al (2007). Genome-wide detection and characterization of positive selection in human populations. Nature, 449 (7164), 913-8 PMID: 17943131

Hillier LW, Miller RD, Baird SE, Chinwalla A, Fulton LA, Koboldt DC, & Waterston RH (2007). Comparison of C. elegans and C. briggsae genome sequences reveals extensive conservation of chromosome organization and synteny. PLoS Biology, 5 (7) PMID: 17608563

Stanley SL Jr, Frey SE, Taillon-Miller P, Guo J, Miller RD, Koboldt DC, Elashoff M, Christensen R, Saccone NL, & Belshe RB (2007). The immunogenetics of smallpox vaccination. The Journal of Infectious Diseases, 196 (2), 212-9 PMID: 17570108

Koboldt DC, Miller RD, & Kwok PY (2006). Distribution of human SNPs and its effect on high-throughput genotyping. Human Mutation, 27 (3), 249-54 PMID: 16425292

The International HapMap Consortium (2005). A haplotype map of the human genome. Nature, 437 (7063), 1299-1320 PMID: 16255080

Miller RD, Phillips MS, et al (2005). High-density single-nucleotide polymorphism maps of the human genome. Genomics, 86 (2), 117-26 PMID: 15961272

Del-Aguila JL, Koboldt DC, Black K, Chasse R, Norton J, Wilson RK, Cruchaga C. Alzheimer’s disease: rare variants with large effect sizes. Curr Opin Genet Dev. 2015 Aug 22;33:49-55. doi: 10.1016/j.gde.2015.07.008. PMID: 26311074

Daiger SP, Bowne SJ, Sullivan LS, Blanton SH, Weinstock GM, Koboldt DC, Fulton RS, Larsen D, Humphries P, Humphries MM, Pierce EA, Chen R, & Li Y (2014). Application of next-generation sequencing to identify genes and mutations causing autosomal dominant retinitis pigmentosa (adRP). Advances in experimental medicine and biology, 801, 123-9 PMID: 24664689

Koboldt DC, Steinberg KM, Larson DE, Wilson RK, & Mardis ER (2013). The next-generation sequencing revolution and its impact on genomics. Cell, 155 (1), 27-38 PMID: 24074859

Koboldt DC, Larson DE, Chen K, Ding L, & Wilson RK (2012). Massively parallel sequencing approaches for characterization of structural variation. Methods in molecular biology (Clifton, N.J.), 838, 369-84 PMID: 22228022

Ding L, Wendl MC, Koboldt DC, & Mardis ER (2010). Analysis of next-generation genomic data in cancer: accomplishments and challenges. Human Molecular Genetics, 19 (R2):R188-96. PMID: 20843826

Koboldt DC, Ding L, Mardis ER & Wilson RK. (2010). Challenges of sequencing human genomes. Briefings in Bioinformatics DOI: 10.1093/bib/bbq016

Koboldt DC and Miller RD (2010). Identification of polymorphic markers for genetic mapping. Genomics: Essential Methods, Published online 22 Nov 2010. DOI: 10.1002/9780470711675.ch2