Nicholas Navin, Ph.D.
Department of Genetics, Division of Basic Science
About Dr. Navin
Dr. Navin is an associate professor at the M.D. Anderson Cancer Center, with a joint appointment in the Department of Genetics and the Department of Bioinformatics. He is also the co-director of the Sequencing and Microarray Core Facility at MD Anderson. I conducted my graduate training and postdoctoral training at the Cold Spring Harbor laboratory under the mentorship of Dr. Michael Wigler. During this time, he invented the first single cell DNA sequencing method (Single-Nucleus-Sequencing) for sequencing the genome of a mammalian cell (Navin et al. 2011, Nature.). This work played a pivotal role in establishing the field of single cell genomics. The Navin laboratory continues to be at the forefront of the single cell cancer genomics field, where they have discovered a punctuated model of copy number evolution in triple-negative breast cancer (Gao et al. 2016, Nature Genetics) and elucidated the role mutator phentoypes and subclonal mutations in breast cancer evolution (Wang et al. 2014, Nature). Dr. Navin’s group continues to pioneer the developing novel technologies for performing single cell DNA and RNA sequencing, in addition to innovative computational and statistical methods for analyzing the resulting large-scale datasets. These methods are being applied to study cancer evolution in the context of invasion, metastasis and therapy resistance. His laboratory works closely with leading oncologists and pathologist at MD Anderson to translate these technologies into the clinic, where they are poised to make a major impact on reducing the morbidity in human patients. Dr. Navin has been the recipient of many prestigious awards in recognition of his work, including the Damon-Runyon Innovator Award, AAAS Wachtel Award, ACS Research Scholar Award, Wilson Stone Award and the Randall Innovator Award.
View a complete list of Dr. Navin's publications . Visit Dr. Navin's Lab Website.
Present Title & Affiliation
Primary Appointment
Associate Professor, Department of Genetics, Division of Basic Science Research, The University of Texas MD Anderson Cancer Center, Houston, TX
Co-Director, Sequencing Core Facility, The University of Texas MD Anderson Cancer Center, Houston, TX
Dual/Joint/Adjunct Appointment
Associate Professor, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX
Associate Professor, Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX
Research Interests
Single-cell sequencing Genome Evolution in cancer Intratumor Heterogeneity Cancer Genomics Computational Biology and Bioinformatics
My goal is to understand genome evolution in human cancers. As tumors evolve from a single cell, they acquire complex somatic mutations and diverge to form distinct lineages and subpopulations. This intratumor heterogeneity confounds basic research and clinical diagnosis, because tools do not exist to resolve it. To address this problem, we developed a single-cell sequencing method to profile genomic copy number in individual tumor cells ( Nature 472:90-4, 2011). I used this method to profile hundreds of single cells in two breast cancer patients to delineate clonal diversity and infer patterns of genome evolution. The data revealed multiple clonal subpopulations that shared a common evolutionary lineage. In contrast to the gradual models of tumor progression, the data suggest that these breast tumors grew by punctuated clonal expansions, in which hundreds of genomic rearrangements were acquired in short bursts of evolution. We have also recently developed a powerful new method to perform whole-genome sequencing on single tumor cells. This will enable us to study the evolution of many different classes of somatic mutations (point mutations, indels and structural variants) at base-pair resolution in single cells. In addition to single cell sequencing, my laboratory also uses many genomic and cytological methods to study how cancer genomes evolve. We are also actively developing new computational methods to quantify tumor heterogeneity and understand if these measures correlate with clinical parameters such as survival and resistance to chemotherapy. One method developed is called Ploidy-Seq to deep-sequence intratumor subpopulations and infer mutational chronology and ancestral tumor genomes.
View a complete list of Dr. Navin's publications . Visit Dr. Navin's Lab Website.
Education & Training
Degree-Granting Education
| 2010 | Cold Spring Harbor Laboratory and Stony Brook University, Cold Spring Harbor, NY, USA, PHD, Molecular Genetics |
| 2003 | Skidmore College, Saratoga Springs, NY, USA, BS, Cell Biology |
Postgraduate Training
| 2010-2011 | Postdoctoral Fellow, Cancer Genetics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY |
Experience & Service
Academic Appointments
Assistant Professor, Department of Bioinformatics and Computational Biology, Division of Quantitative Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, 2011 - 2016
Assistant Professor, Department of Genetics, Division of Basic Science Research, The University of Texas MD Anderson Cancer Center, Houston, TX, 2011 - 2016
Assistant Professor, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, 2011 - 2016
Honors & Awards
| 2018 | Faculty Educator Award, University of Texas M.D. Anderson Cancer Center |
| 2018 | The Dallas/Fort Worth Living Legend Faculty Achievement Award in Basic Research, University of Texas M.D. Anderson Cancer Center |
| 2017 | Jack and Beverly Randall Prize for Excellence in Cancer Treatment, Randall Family Foundation |
| 2017 | Challenge Award, Prostate Cancer Foundation |
| 2017 | 40 under 40 Award, Stoney Brook University |
| 2016 | President's Scholar Award, University of Texas M.D. Anderson Cancer Center |
| 2016 | Sabin Fellowship, Andrew Sabin Family Foundation |
| 2016 | ACS Research Scholar, American Cancer Society (ACS) |
| 2016 | President's Recognition for Faculty Excellence, University of Texas M.D. Anderson Cancer Center |
| 2016 | Faculty Scholar Award, University of Texas M.D. Anderson Cancer Center |
| 2015 | AAAS Martin & Rose Wachtel Award, American Association for the Advancement of Science |
| 2014 | Faculty Educator Award, University of Texas M.D. Anderson Cancer Center |
| 2013 | T.C. Hsu Award, Young Investigator Award |
| 2013 | Wilson S. Stone Memorial Award |
| 2013 | Stone Award, Wilson Stone Foundation |
| 2013 | Damon-Runyon Innovator Award, Damon-Runyon Rachleff Foundation |
| 2010 | Young Investigator Award, Genome Technology Magazine |
| 2009 | T32 NCI Fellowship, National Cancer Institute |
| 2009 | Abraham's Award, Stony Brook University |
| 2008 | King and Miller Fellowship, Stony Brook University |
| 2006 | Scientific Poster Award, Molecular Genetics Symposium, Stony Brook, NY |
| 2005 | Lindsey-Goldberg Fellowship, Cold Spring Harbor Laboratory |
Selected Publications
Peer-Reviewed Articles
- Kim C & Gao R, Sei E, Brandt R, Hartman J, Hatshek T, Crosetto N, Foukakis T and Navin N.. Chemoresistance Evolution in Triple-Negative Breast Cancer Delineated by Single Cell Sequencing. Cell 173(4):879-893, 2018. PMID: 29681456.
- Casasent AK, Schalck A, Gao R, Sei E, Long A, Pangburn W, Casasent T, Meric-Bernstam F, Edgerton ME, Navin NE. Multiclonal Invasion in Breast Tumors Identified by Topographic Single Cell Sequencing. Cell 172(1-2):205-217, 2018. PMID: 29307488.
- Leung ML, Davis A, Gao R, Casasent A, Wang Y, Sei E, Vilar E, Maru D, Kopetz, Navin, N. Single-cell DNA sequencing reveals a late-dissemination model in metastatic colorectal cancer. Genome Res 27(8):1287-1299, 2017. PMID: 28546418.
- Gao R, Davis A, McDonald TO, Sei E, Shi X, Wang Y, Tsai PC, Casasent A, Waters J, Zhang H, Meric-Bernstam F, Michor F, Navin NE. Punctuated copy number evolution and clonal stasis in triple-negative breast cancer. Nat Genet 48(10):1119-30, 2016. e-Pub 2016. PMID: 27526321.
- Mann KM, Newberg JY, Black MA, Jones DJ, Amaya-Manzanares F, Guzman-Rojas L, Kodama T, Ward JM, Rust AG, van der Weyden L, Yew CC, Waters JL, Leung ML, Rogers K, Rogers SM, McNoe LA, Selvanesan L, Navin N, Jenkins NA, Copeland NG, Mann MB. Analyzing tumor heterogeneity and driver genes in single myeloid leukemia cells with SBCapSeq. Nature Biotech 34(9):962-72, 2016. PMID: 27479497.
- Zafar H, Wang Y, Nakhlem L, Navin N, Chen K. Monovar: Single Nucleotide Variant Detection in Single Cells. Nature Methods, 2016. PMID: 27088313.
- Leung ML, Wang Y, Kim C, Gao R, Jiang J, Sei E, Navin NE. Highly multiplexed targeted DNA sequencing from single nuclei. Nat Protoc 11(2):214-35, 2016. e-Pub 2016. PMID: 26741407.
- Leung M, Wang Y, Waters J, Navin N. SNES: Single Nuclei Exome Sequencing. Genome Biol 25(16):55, 2015. PMID: 25853327.
- Molhatra A, Wang Y, Waters J, Hall I, Navin N. Ploidy-Seq: inferring mutational chronology by sequencing polyploid tumor subpopulations. Genomic Med 7(1):6, 2015. PMID: 25729435.
- Wang Y, Waters J, Unruh A, Roh W, Shi X, Chen K, Scheet P, Vattathil S, Liang H, Multani A, Zhang H, Zhao R, Michor F, Meric-Bernstam F, Navin NE.. Clonal evolution in breast cancer revealed by single nucleus genome sequencing. Nature 512(7513):155-60, 2014. PMID: 25079324.
- Baslan T, Kendall J, Troge J, Stepansky A, Wigler M, Navin N, Hicks J. Genome-wide Copy Number Analysis of Single Cells. Nature Protocols 7(6):1024-41, 2012. PMID: 22555242.
- Navin N, Kendall J, Troge J, Rodgers L, Cook K, Stepansky A, Levy D, Lee Y, Esposito D, Muthuswamy L, Hicks J, Wigler M. Tumor Evolution Inferred by Single Cell Sequencing. Nature 7(472):90-4, 2011. PMID: 21399628.
Invited Articles
- Wang Y, Navin N. Advances and Applications of Single-Cell Sequencing Technologies. Molecular Cell 58(4):598-609, 2015. PMID: 26000845.
Grant & Contract Support
| Title: | Single-Cell Sequencing of Breast Tumors to Investigate Genome Evolution |
| Funding Source: | NIH/NIMH |
| Role: | Principal Investigator |
| Title: | Investigating Clonal Evolution in Triple-Negative Breast Cancers with Single-Cell Sequencing |
| Funding Source: | Agilent University Relations Grant |
| Role: | Principal Investigator |
| Title: | Investigating Mutational Evolution and Intratumor Heterogeneity in TNBC |
| Funding Source: | American Cancer Society (ACS) |
| Role: | Principal Investigator |
| Title: | Investigating Chemotherapy Resistance Application in TNBC by Single-Cell Sequencing |
| Funding Source: | Sabin Fellows Award |
| Role: | Principal Investigator |
| Title: | Linking the Effect of Local Therapy to Molecularly Defined 'Androgen-Responsive' and 'Androgen-Indifferent' Prostate Cancer Subsets in Men with de novo Metastatic Disease |
| Funding Source: | Prostate Cancer Research Foundation |
| Role: | Co-Principal Investigator |
| Title: | Integrated Single Cell Genomics Core Facility |
| Funding Source: | Cancer Prevention & Research Institute of Texas (CPRIT) |
| Role: | Principal Investigator |
| Title: | Pan-omics single-cell data integration for joint cell-type identification |
| Funding Source: | Silicon Valley Community Foundation/Chan Zuckerberg Initiative |
| Role: | Co-Investigator |
| Title: | Statistical methods for genomic analysis of heterogeneous tumors |
| Funding Source: | NIH/NCI |
| Role: | Co-Principal Investigator |
| Title: | Characterizing cancer genome instability and translational impact using new sequencing technologies |
| Funding Source: | Cancer Prevention & Research Institute of Texas (CPRIT) |
| Role: | Collaborator |
| Title: | Cancer Center Support Grant, Sequencing and Microarray Facility (SMF) |
| Funding Source: | NIH/NCI |
| Role: | Co-Investigator |