Li Ding, PhD

David English Smith Distinguished Professor
Internal Medicine
Oncology
Genetics

Computational and Systems Biology Program
Molecular Genetics and Genomics Program
Cancer Biology Program
Developmental, Regenerative and Stem Cell Biology Program

  • 314-286-1848

  • (314) 286-1848

  • 314-286-1810

  • 3301 McKinley Bldg.

  • lding@wustl.edu

  • http://dinglab.wustl.edu/#ding-lab

  • Cancer Proteogenomics and Cancer Models

Research Abstract:

Li Ding, PhD, is the David English Smith Distinguished Professor of Medicine at Washington University. Dr. Ding's current research focuses on integrating cancer proteogenomics (including single cell omics), patient derived-cancer models, functional genomics, and drug treatment studies to advance cancer biology and precision medicine. Her research team has developed a collection of widely-used computational tools, including VarScan, SomaticSniper, SciClone, BreakDancer, BreakFusion, MSIsensor, Pindel-C, GenomeVIP, HotSpot3D, and MuSiC. Dr. Ding plays significant roles in The Cancer Genome Atlas (TCGA), the International Cancer Genome Consortium (ICGC), and the Clinical Proteomic Tumor Analysis Consortium (CPTAC), PDX (patient-derived xenografts) Development and Trial Centers Research Network (PDXNet), and Human Tumor Atlas Network (HTAN). She co-chairs the TCGA PanCanAtlas Oncogenic Process Group, the ICGC Mutation Calling Group, the CPTAC GBM Analysis Working Group, and the HTAN Data Analysis Working Group. Dr. Ding also serves on the Steering Committees of the Genomic Data Commons (GDC), CPTAC, TCGA, PDXnet, and HTAN. Dr. Ding has successfully led many large-scale, multi-institute studies on the genomics of lung adenocarcinomas, pancreatic cancer, clear cell renal carcinoma, AML, Multiple Myeloma, and breast cancer. Building on this foundation, her team has produced a series of seminal publications in the fields of cancer proteogenomics research and cancer biology.

Dr. Ding`s lab currently is focusing on understanding the interaction between tumor and tumor microenvironment using new imaging and omics technologies as well as on discovering new cancer treatments using PDX and organoid models.

Selected Publications:

Cui Zhou D*, Jayasinghe RG*, Chen S, Herndon JM, Iglesia MD, Navale P, Wendl MC, Caravan W, Sato K, Storrs E, Mo CK, Liu J, Southard-Smith AN, Wu Y, Naser Al Deen N, Baer JM, Fulton RS, Wyczalkowski MA, Liu R, Fronick CC, Fulton LA, Shinkle A, Thammavong L, Zhu H, Sun H, Wang LB, Li Y, Zuo C, McMichael JF, Davies SR, Appelbaum EL, Robbins KJ, Chasnoff SE, Yang X, Reeb AN, Oh C, Serasanambati M, Lal P, Varghese R, Mashl JR, Ponce J, Terekhanova NV, Yao L, Wang F, Chen L, Schnaubelt M, Lu RJ, Schwarz JK, Puram SV, Kim AH, Song SK, Shoghi KI, Lau KS, Ju T, Chen K, Chatterjee D, Hawkins WG, Zhang H, Achilefu S, Chheda MG, Oh ST, Gillanders WE, Chen F, DeNardo DG^, Fields RC^, Ding L^. Spatially Restricted Drivers and Transitional Cell Populations Cooperate With the Microenvironment in Untreated and Chemo-Resistant Pancreatic Cancer. Nature genetics, 2022 Aug 22

Chen F, Wendl MC, Wyczalkowski MA, Bailey MH, Li Y, Ding L^. Moving pan-cancer studies from basic research toward the clinic. Nature Cancer, 2021 Sep 16

Wang LB*, Karpova A*, Gritsenko MA*, Kyle JE*, Cao S*, Li Y*, Rykunov Dˉ, Colaprico Aˉ, Rothstein JHˉ, Hong Rˉ, Stathias Vˉ, Cornwell Mˉ, Petralia Fˉ, Wu Y, Reva B, Krug K, Pugliese P, Kawaler E, Olsen LK, Liang WW, Song X, Dou Y, Wendl MC, Caravan W, Liu W, Zhou DC, Ji J, Tsai CF, Petyuk VA, Moon J, Ma W, Chu RK, Weitz KK, Moore RJ, Monroe ME, Zhao R, Yang X, Yoo S, Krek A, Demopoulos A, Zhu H, Wyczalkowski MA, McMichael JF, Henderson BL, Lindgren CM, Boekweg H, Lu S, Baral J, Yao L, Stratton KG, Bramer LM, Zink E, Couvillion SP, Bloodsworth KJ, Satpathy S, Sieh W, Boca SM, Schürer S, Chen F, Wiznerowicz M, Ketchum KA, Boja ES, Kinsinger CR, Robles AI, Hiltke T, Thiagarajan M, Nesvizhskii AI, Zhang B, Mani DR, Ceccarelli M, Chen XS, Cottingham SL, Li QK, Kim AH, Fenyö D, Ruggles KV, Rodriguez H, Mesri M, Payne SH, Resnick AC, Wang P, Smith RD, Iavarone A, Chheda MG, Barnholtz-Sloan JS, Rodland KD^, Liu T^, Ding L^, Clinical Proteomic Tumor Analysis Consortium. Proteogenomic and metabolomic characterization of human glioblastoma. Cancer Cell 39, 1–20 April 12, 2021

Huang K, Mashl RJ, Wu Y, Ritter DI, Wang J, Oh C, Paczkowska M, Reynolds S, Wyczalkowski MA, Oak N, Scott AD, Krassowski M, Cherniack AD, Houlahan KE, Jayasinghe R, Wang L, Zhou DC, Liu D, Cao S, Kim YW, Koire A, McMichael JF, Hucthagowder V, Kim T, Hahn A, Wang C, McLellan MD, Al-Mulla F, Johnson KJ, The Cancer Genome Atlas Research Network , Lichtarge O, Boutros PC, Raphael B, Lazar AJ, Zhang W, Wendl MC, Govindan R, Jain S, Wheeler D, Kulkarni S, Dipersio JF, Reimand J, Meric-Bernstam F, Chen K, Shmulevich I, Plon SE, Chen F, Ding L. Pathogenic Germline Variants in 10,389 Adult Cancers. Cell. 2018 Apr 5.173(2):355-370

Bailey MH*, Tokheim C*, Porta-Pardo E*, Sengupta S, Bertrand D, Weerasinghe A, Colaprico A, Wendl MC, Kim J, Reardon B, Ng PK, Jeong KJ, Cao S, Wang Z, Gao J, Gao Q, Wang W, Liu EM, Mularoni L, Rubio-Perez C, Nagarajan N, Cortés-Ciriano I, Zhou DC, Liang W, Hess JM, Yellapantula VD, Tamborero D, Gonzalez-Perez A, Suphavilai C, Ko JY, Khurana E, Park PJ, Van Allen EM, Liang H, The MC3 Working Group, The Cancer Genome Atlas Research Network, Lawrence MS, Godzik A, Lopez-Bigas A, Stuart J, Wheeler D, Getz G, Chen K, Lazar AJ, Mills GB, Karchin R, Ding L. Comprehensive Characterization of Cancer Driver Genes and Mutations. Cell. 2018 Apr 5.173(2):371-385

Niu B, Scott AD, Sengupta S, Bailey MH, Batra P, Ning J, Wyczalkowski MA, Liang WW, Zhang Q, McLellan MD, Sun SQ, Tripathi P, Lou C, Ye K, Mashl RJ, Wallis J, Wendl MC, Chen F, Ding L. Protein-structure-guided discovery of functional mutations across 19 cancer types. Nature Genetics. 2016 Jun. PMID: 27294619

Lu C, Xie M, Wendl MC, Wang J, McLellan MD, Leiserson MD, Huang KL, Wyczalkowski MA, Jayasinghe R, Banerjee T, Ning J, Tripathi P, Zhang Q, Niu B, Ye K, Schmidt HK, Fulton RS, McMichael JF, Batra P, Kandoth C, Bharadwaj M, Koboldt DC, Miller CA, Kanchi KL, Eldred JM, Larson DE, Welch JS, You M, Ozenberger BA, Govindan R, Walter MJ, Ellis MJ, Mardis ER, Graubert TA, DiPersio JF, Ley TJ, Wilson RK, Goodfellow PJ, Raphael BJ, Chen F, Johnson KJ, Parvin JD, Ding L. Patterns and functional implications of rare germline variants across 12 cancer types. Nat Commun 2015 Dec 22;6:10086

Ye K, Wang J, Jayasinghe R, Lameijer EW, McMichael JF, Ning J, McLellan MD, Xie M, Cao S, Yellapantula V, Huang KL, Scott A, Foltz S, Niu B, Johnson KJ, Moed M, Slagboom PE, Chen F, Wendl MC, Ding L. Systematic discovery of complex insertions and deletions in human cancers. Nat Med 2015 Dec 14; [Epub ahead of print]

Zhang J, Walsh MF, Wu G, Edmonson MN, Gruber TA, Easton J, Hedges D, Ma X, Zhou X, Yergeau DA, Wilkinson MR, Vadodaria B, Chen X, McGee RB, Hines-Dowell S, Nuccio R, Quinn E, Shurtleff SA, Rusch M, Patel A, Becksfort JB, Wang S, Weaver MS, Ding L, Mardis ER, Wilson RK, Gajjar A, Ellison DW, Pappo AS, Pui CH, Nichols KE, Downing JR. Germline mutations in predisposition genes in pediatric cancer. N Engl J Med 2015 Dec 10;373(24):2336-2346

Xie M, Lu C, Wang J, McLellan MD, Johnson KJ, Wendl MC, McMichael JF, Schmidt HK, Yellapantula V, Miller CA, Ozenberger BA, Welch JS, Link DC, Walter MJ, Mardis ER, Dipersio JF, Chen F, Wilson RK, Ley TJ, Ding L. Age-related mutations associated with clonal hematopoietic expansion and malignancies. Nature Medicine. 2014 Oct 19. PMID: 25326804.

Ding L, Wendl MC, McMichael JF, Raphael BJ. Expanding the computational toolbox for mining cancer genomes. Nat Rev Genet. 2014 July. PMID: 25001846.

Kanchi K, Johnson K, Lu C, McLellan MD, Leiserson MD, Wendl MC, Zhang Q6, Koboldt DC, Xie M, Kandoth C, McMichael JF, Wyczalkowski MA, Larson DE, Schmidt HK, Miller CA, Fulton RS, Spellman PT, Mardis ER, Druley TE, Graubert TA, Goodfellow PJ, Raphael BJ, Wilson RK, Ding L. Integrated analysis of germline and somatic variants in ovarian cancer. Nature Communications. 2014 Jan 22;5, Article number: 3156 doi:10.1038/ncomms4156 PMID: 24448499.

Kandoth C, McLellan MD, Vandin F, Ye K, Niu B, Lu C, Xie M, Zhang Q, McMichael JF, Wyczalkowski MA, Leiserson MD, Miller CA, Welch JS, Walter MJ, Wendl MC, Ley TJ, Wilson RK, Raphael BJ, Ding L. Mutational landscape and significance across 12 major cancer types. Nature. 2013 Oct 17;502(7471):333-9. doi: 10.1038/nature12634. PMID: 24132290.

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

Ding L, Ley TJ, Larson DE, Miller CA, Koboldt DC, Welch JS, Ritchey JK, Young MA, Lamprecht T, McLellan MD, et al. Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing. Nature. 2012 Jan 11;481(7382):506-10. PMID: 22237025.

Zhang J, Ding L, Holmfeldt L, Wu G, Heatley SL, Payne-Turner D, Easton J, Chen X, Wang J, Rusch M, et al. The genetic basis of early T-cell precursor acute lymphoblastic leukaemia. Nature. 2012 Jan 11;481(7380):157-63. PMID: 22237106.

Ley TJ, Ding L, Walter MJ, McLellan MD, Lamprecht T, Larson DE, Kandoth C, Payton JE, Baty J, Welch J, et al. N Engl J Med. 2010 Dec 16;363(25):2424-33. PMID: 21067377.

Ding L, Ellis MJ, Li S, Larson DE, Chen K, Wallis JW, Harris CC, McLellan MD, Fulton RS, Fulton LL, et al. Genome remodelling in a basal-like breast cancer metastasis and xenograft. Nature 2010 Apr 15:464(7291):999-1005. PMID: 20393555

Chen K, Wallis JW, McLellan MD, Larson DE, Kalicki JM, Pohl CS, McGrath SD, Wendl MC, Zhang Q, Locke DP, Shi X, Fulton RS, Ley TJ, Wilson RK, Ding L, Mardis ER. BreakDancer: An algorithm for high-resolution mapping of genomic structural variation. Nat Methods 2009 Sep:6(9):677-81. PMID: 19668202

Koboldt DC, Chen K, Wylie T, Larson DE, McLellan MD, Mardis ER, Weinstock GM, Wilson RK, Ding L. VarScan: Variant detection in massively parallel sequencing of individual and pooled samples. Bioinformatics 2009 Sep 1:25(17):2283-5. PMID: 19542151.

Last Updated: 12/8/2022 10:06:16 AM

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