Cyriac Kandoth PhD
Contact Information
Cyriac Kandoth, PhD
David Geffen School of Medicine
Department of Pathology and Laboratory Medicine
University of California at Los Angeles (UCLA)
Academic Title
Assistant Professor
Bio
Dr. Kandoth is a software engineer who studies the pathogenesis of genetic diseases like cancer. His interests center around improving the daily workflow of pathologists and clinicians with automation and user-interfaces. He led analyses on The Cancer Genome Atlas (TCGA) uterine cancer sequencing effort, and managed somatic mutation curation and analyses for the TCGA Pan-Cancer project, which led to the discovery of novel biomarkers and improved cancer subtyping in Kandoth et al., a highly cited article in Nature, 2013. Dr Kandoth was later recruited by NIH/NCI to co-chair the TCGA uveal melanoma working group, which led to senior authorship in Robertson et al., published in Cancer Cell, 2017. He played a central role in promoting reproducibility and reusability of bioinformatics methods during 4 years at Washington University in St Louis and 6 years in Memorial Sloan Kettering Cancer Center in New York, and continues to do so at UCLA.
Publications
1. Validation of an NSP-based (negative selection pattern) gene family identification strategy (2008) RL Frank, C Kandoth, F Ercal. BMC bioinformatics 9 (9), S2 Role: Data Curation, Methodology, Validation, Writing
2. Protein Secondary Structure Prediction Using Parallelized Rule Induction from Coverings (2010) L Lee, C Kandoth, JL Leopold, RL Frank. International Journal of Medicine and Medical Sciences 1 (2), 99-105 Role: Methodology, Software
3. A framework for automated enrichment of functionally significant inverted repeats in whole genomes (2010) C Kandoth, F Ercal, RL Frank. BMC bioinformatics 11 (S6), S20 Role: First author, Conceptualization, Data Curation, Software, Validation, Writing
4. DNMT3A Mutations in Acute Myeloid Leukemia (2010) TJ Ley, L Ding, MJ Walter, MD McLellan, T Lamprecht, DE Larson, C Kandoth, ..., ER Mardis, RK Wilson. New England Journal of Medicine 363 (25), 2424-2433 Role: Methodology, Visualization
5. Integrated genomic analyses of ovarian carcinoma (2011) Cancer Genome Atlas Research Network. Nature 474 (7353), 609 Role: Methodology, Data Curation, Validation
6. PathScan: a tool for discerning mutational significance in groups of putative cancer genes (2011) MC Wendl, JW Wallis, L Lin, C Kandoth, ER Mardis, RK Wilson, L Ding. Bioinformatics 27 (12), 1595-1602 Role: Methodology, Validation
7. Recurrent DNMT3A mutations in patients with myelodysplastic syndromes (2011) MJ Walter, L Ding, D Shen, J Shao, M Grillot, M McLellan, R Fulton, H Schmidt, JM Kalicki-Veizer, M O'Laughlin, C Kandoth, ..., TJ Ley. Leukemia 25 (7), 1153-1158 Role: Methodology, Visualization
8. BreakFusion: targeted assembly-based identification of gene fusions in whole transcriptome paired-end sequencing data (2012) K Chen, JW Wallis, C Kandoth, JM Kalicki-Veizer, KL Mungall, ..., L Ding. Bioinformatics 28 (14), 1923-1924 Role: Data curation
9. MuSiC: identifying mutational significance in cancer genomes (2012) ND Dees, Q Zhang, C Kandoth, MC Wendl, W Schierding, DC Koboldt, ..., L Ding. Genome research 22 (8), 1589-1598 Role: Conceptualization, Methodology, Software, Validation, Visualization
10. RNA-seq reveals a robust transcriptomic response during anoxia in the Western painted turtle (2013) DE Warren, CA Hill, C Kandoth, LT Buck. The FASEB Journal 27 (1), 937.21-937.21 Role: Methodology, Software
11. Integrated genomic characterization of endometrial carcinoma (2013) Cancer Genome Atlas Research Network, Nature 497 (7447), 67-73 Role: Co-first author, Methodology, Data curation, Writing
12. Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia (2013) Cancer Genome Atlas Research Network, New England Journal of Medicine 368 (22), 2059-2074 Role: Methodology, Data curation
13. Clonal diversity of recurrently mutated genes in myelodysplastic syndromes (2013) MJ Walter, D Shen, J Shao, L Ding, BS White, C Kandoth, CA Miller, B Niu, ..., TA Graubert. Leukemia 27 (6), 1275-1282 Role: Methodology, Data curation
14. Enabling transparent and collaborative computational analysis of 12 tumor types within The Cancer Genome Atlas (2013) L Omberg, K Ellrott, Y Yuan, C Kandoth, C Wong, MR Kellen, SH Friend, ..., AA Margolin. Nature genetics 45 (10), 1121-1126 Role: Methodology, Data curation, Writing
15. Mutational landscape and significance across 12 major cancer types (2013) C Kandoth, MD McLellan, F Vandin, K Ye, B Niu, C Lu, M Xie, Q Zhang, ..., L Ding. Nature 502 (7471), 333-339 Role: First author, Conceptualization, Methodology, Data curation, Validation, Writing
16. Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin (2014) KA Hoadley, C Yau, DM Wolf, AD Cherniack, D Tamborero, S Ng, MDM Leiserson, B Niu, MD McLellan, V Uzunangelov, J Zhang, C Kandoth, ..., JM Stuart. Cell 158 (4), 929-944 Role: Data curation
17. Transcriptomic responses of the heart and brain to anoxia in the Western Painted Turtle (2015) SW Keenan, CA Hill, C Kandoth, LT Buck, DE Warren. PLoS One 10 (7) Role: Methodology, Data curation
18. Molecular characterization of mucinous ovarian cancer (2016) B Schlappe, JJ Mueller, N Olvera, F Dao, C Kandoth, F Bogomolniy, YR Hussein, B Taylor, RA Soslow, DA Levine. Gynecologic Oncology 141, 99-100 Role: Methodology, Data curation
19. Identifying recurrent mutations in cancer reveals widespread lineage diversity and mutational specificity (2016) MT Chang, S Asthana, SP Gao, BH Lee, JS Chapman, C Kandoth, JJ Gao, ..., BS Taylor. Nature biotechnology 34 (2), 155 Role: Methodology, Data curation, Software
20. Integrated molecular characterization of uterine carcinosarcoma (2017) Cancer Genome Atlas Research Network, Cancer cell 31 (3), 411-423 Role: Methodology, Data curation
21. Extraordinary survivorship after colorectal liver metastasis resection to identify a distinct molecular profile associated with survival in an independent cohort of 965 patients (2017) JJ Smith, C Kandoth, JC McAuliffe, E Vakiani, T Frankel, I Wasserman, ..., M Berger, CL Sawyers. Journal of Clinical Oncology 35 (15_suppl), 3581-3581 Role: Conceptualization, Methodology, Validation, Visualization
22. Integrative analysis identifies four molecular and clinical subsets in uveal melanoma (2017) Cancer Genome Atlas Research Network. Cancer cell 32 (2), 204-220. e15 Role: Co-senior author, Conceptualization, Methodology, Visualization, Supervision
23. Copy Number Gains in HER2 and VEGF May Predict Poor Outcome in Early Gastric Cancer (2018) AE Russo, EM Da Silva, C Kandoth, JM Hernandez, E Van Beek, BS Taylor, YY Janjigian, LH Tang, D Solit, VE Strong. Annals of Surgical Oncology 25, S68-S68 Role: Conceptualization, Methodology, Validation, Visualization
24. Regional differences in gallbladder cancer pathogenesis: Insights from a comparison of tumor mutations (2018) RR Narayan, JM Creasy, C Kandoth, DA Goldman, M Gonen, PJ Allen, VP Balachandran, MI D'Angelica, RP DeMatteo, JA Drebin, TP Kingham, G Askan, DS Klimstra, O Basturk, JM Butte, I Endo, WR Jarnagin. HPB 20, S1 Role: Methodology, Validation, Visualization
25. Multi-Center Mutation Calling in Multiple Cancers: The MC3 Project (2018) K Ellrott, M Bailey, G Saksena, K Covington, C Kandoth, C Kandoth, MD McLellan, H Sofia, C Hutter, G Getz, D Wheeler, L Ding. Cancer Research 78 (13 Supplement), 926-926 Role: Methodology, Data curation, Validation
26. Genetic and epigenetic evolution as a contributor to WT1-mutant leukemogenesis (2018) E Pronier, RL Bowman, J Ahn, J Glass, C Kandoth, TR Merlinsky, JT Whitfield, BH Durham, A Gruet, H Somasundara, A Varshini, R Rampal, A Melnick, RP Koche, BS Taylor, RL Levine. blood 132 (12), 1265-1278 Role: Methodology, Visualization
27. GNAQ mutations in diffuse and solitary choroidal hemangiomas (2019) JH Francis, T Milman, H Grossniklaus, D Albert, R Folberg, G Levitin, S Coupland, F Catalanotti, D Rabady, C Kandoth, K Busam, D Abramson. Ophthalmology 126 (5), 759-763 Role: Data curation, Visualization