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CSHL Cancer Center - Cancer Genetics

The Cancer Genetics Program is focused on revealing the structure and landscape of cancer genomes. Such information provides insight into how cancer develops, progresses, and responds to therapy. The Program includes a diverse collection of faculty who are developing new technology that is changing how researchers across the globe study cancer. The Program currently has three main focus areas: experimental technology, bioinformatics, and cancer progression.

Program Co-leaders
W. Richard McCombie, Ph.D.           Alea Mills, Ph.D.

Gurinder Atwal - Associate Professor

Applies insights from the physical and computational sciences to the study of population genetics and cancer. Recent work on the evolution of genetic variants identified a role of p53 tumor suppressor in female fertility. The lab also analyzes comparative genomics and physical organization of cancer related genes and their role in mediating tumorigenesis across numerous tissue types.
Kenneth Chang - Research Assistant Professor/Manager, Functional Genomics

Currently the Director of the Functional Genomics Shared Resource at CSHL. His studies focus on shRNA, microRNA, RNA interference, and siRNA. The lab has studied cancer proliferation gene discovery through functional genomics.
Christopher Hammell - Associate Professor

Studies the gene regulatory processes that give rise to robust phenotypes associated with normal development, and examines the alterations in these pathways that give rise to diseases such as cancer. The Hammell lab uses a variety of model systems to investigate this, including c elegans and patient-derived cancer cell lines.
Alexander Krasnitz - Associate Professor

Develops and applies statistical methods for analyzing and understanding the relationship between the genomics of individual cancer types and how cancer evolves and develops. He has developed a novel, comprehensive methodology to discover recurrent genomic aberrations in cancer genomes and has used it to analyze multiple genome data sets in breast, liver, ovarian, and prostate cancer.
Je Lee - Assistant Professor

Studies how cells interact with their microenvironment to regulate gene expression during development. Currently focusing on the role of non-coding RNA in chromatin remodeling and tumor progression using mouse and organoid models of human cancer. In situ sequencing, cell lineage tracing, and single-cell profiling are used, with a long-term goal, to develop better tumor classification tools and anti-cancer therapeutics.
Dan Levy - Assistant Professor

Develops algorithms to identify mutations associated with various cancer types from large, complex data sets. His work focuses on using targeted sequence data to identify copy number variants and multiscale genomic rearrangements, including most recently analysis of data obtained from single cells.
Scott Lyons - Research Assistant Professor/Manager, Animal Imaging

Applies non-invasive imaging methods and develops new imaging reagents to facilitate the use of genetically engineered mouse models of cancer in pre-clinical and basic cancer research. As Director of Animal Imaging, he provides collaborative research support to investigators at both CSHL and neighboring institutions and will an important role in the pre-clinical research facility at CSHL. 
W. Richard
W. Richard McCombie - Professor

Develops methods and strategies that use the new generation of sequencing instruments to determine variation in the genomes, transcriptomes and epigenomes of animals and plants. The McCombie lab is currently applying this technology to understand genetic variation in and different types of cancer. The lab is looking for genes that contribute to cancer progression using whole genome sequencing, or a method called exome sequencing, that looks at mutations in the regions of the genome that code for proteins.
Alea Mills - Professor

Uses chromosome engineering to identify tumor suppressive networks perturbed in cancer. Recently identified CHD5 as a tumor suppressor frequently deleted in a variety of human cancers, and is currently defining how CHD5 controls chromatin dynamics, stem cell fate, and tumorigenesis.
Jason Sheltzer - CSHL Fellow

Studies how aneuploidy - the presence of an abnormal number of chromosomes in a cell - impacts tumor initiation and tumor progression. A goal of this work is to exploit differences between aneuploid (cancer) cells and normal cells, with the hopes of developing therapies that can specifically eliminate cancer cells.
Adam Siepel - Professor

Uses mathematical analysis and computer science to study evolution of species, cells, and individual genes. Employs these methods to understand transcriptional regulation. His work has direct applications in studying tumorigenesis and evolution.
Michael Wigler - Professor

Studies human cancer and the contribution of new mutation to genetic disorders. The cancer effort (with Alex Krasnitz, and Lloyd Trotman) focuses on breast and prostate cancers. It involves collaborative clinical studies to discover mutational patterns predicting treatment response and outcome and the development of diagnostics to detect cancer cells in bodily fluids such as blood and urine. The major tools are single-cell DNA and RNA analysis.


Relationship between incorrect chromosome number and cancer is reassessed after surprising experiments | January 12, 2017
Pre-malignant aneuploid cells grew more slowly and formed smaller tumors than comparable cells with normal chromosome number


A theoretical physicist’s approach to breast cancer | October 21, 2016
Ideas borrowed from physics could help scientists improve treatments for breast cancer.  Associate Professor Mickey Atwal explains in this guest blog post.
CSHL scientists Bo Li and Je Lee win HFSP Research Grant awards | April 12, 2016
Two scientists, both leaders of research labs at Cold Spring Harbor Laboratory (CSHL), are among 25 teams that have won Human Frontier Science Program(HFSP) Research Program Grants for 2016. 


Introducing the mighty Panoramix – defender of genomes! | October 15, 2015
Organisms from bacteria to humans must defend themselves against parasitic genetic elements called transposons, and the stakes are high. These pieces of DNA, which disrupt genes by jumping around in the genome, can cause so much destruction that cells have dedicated surveillance mechanisms to keep them...
CSHL Fellow wins 2015 NIH Early Independence Award for cancer research | October 6, 2015
Cold Spring Harbor Laboratory (CSHL) today congratulates CSHL Fellow Jason Sheltzer, Ph.D. on receiving the 2015 Early Independence Award from the National Institutes of Health (NIH) High Risk, High Reward Research Program. With a Ph.D. in Biology from MIT, Sheltzer joined CSHL in August 2015 to pursue cancer research.
Scientists sequence genome of worm that can regrow body parts, seek stem cell insights | September 21, 2015
Tourists spending a recuperative holiday on the Italian coast may be envious of the regenerative abilities of locally found flatworm Macrostomum lignano. Named for its discovery near the Italian beach town of Lignano Sabbiadoro, this tiny worm can regenerate almost its whole body following an injury, and researchers have...
Mathematical ‘Gingko trees’ reveal mutations in single cells that characterize diseases | September 7, 2015
Seemingly similar cells often have significantly different genomes. This is often true of cancer cells, for example, which may differ one from another even within a small tumor sample, as genetic mutations within the cells spread in staccato-like bursts. Detailed knowledge of these mutations, called copy number variations, in individual...
12th annual LI2DAY Walk raises over $400,000 | September 1, 2015
Cold Spring Harbor Laboratory (CSHL) is among 17 Long Island-based organizations to receive funding from the 2015 Long Island 2 Day Walk to Fight Breast Cancer. This year’s walk raised over $400,000 for outreach services, educational programs and research to benefit women and their families affected by breast and....
The biggest beast in the Big Data forest? One field’s astonishing growth is, well, ‘genomical’! | July 7, 2015
Who’s about to become the biggest beast in the Big Data forest? A group of math and computing experts have arrived at what they say is a clear answer. It’s not YouTube or Twitter, social media sites that gobble up awesome quantities of bandwidth and generate hard-to-grasp numbers of electronic bytes every day. And it’s...
Scientists show the mammary gland ‘remembers’ prior pregnancy, spurring milk production | May 7, 2015
Anecdotal reports of nursing mothers have long suggested that giving milk is a lot easier in second and subsequent pregnancies, compared with a first pregnancy.
Tumor cells that mimic blood vessels could help breast cancer spread to other sites | April 8, 2015
Imitation may be the sincerest form of flattery, but it can also have deadly consequences, at least when it comes to tumor cells...
Cold Spring Harbor Laboratory engages Hairpin Technologies Inc. to license its short hairpin RNA (shRNA) technology | March 31, 2015
Cold Spring Harbor Laboratory (CSHL) has engaged Hairpin Technologies Inc. to expand the commercial distribution and research use of short hairpin RNA (shRNA) technology. Hairpin Technologies will serve as CSHL’s exclusive agent for negotiating and executing new license agreements with potential licensees...
CSHL quantitative biologist Michael Schatz awarded 2015 Sloan Foundation Research Fellowship | March 3, 2015
Associate Professor Michael Schatz of Cold Spring Harbor Laboratory (CSHL) will receive a 2015 Alfred P. Sloan Foundation Research Fellowship. This prestigious research award has been issued since 1955. Schatz is one of 126 outstanding early-career scientists from the U.S. and Canada recognized by the Foundation this year...
Harnessing data from Nature’s great evolutionary experiment | January 19, 2015
There are 3 billion letters in the human genome, and scientists have endlessly debated how many of them serve a functional purpose. There are those letters that encode genes, our hereditary information, and those that provide instructions about how cells can use the genes. But those sequences are written with a comparative...

Garvin, T. and Aboukhalil, R. and Kendall, J. and Baslan, T. and Atwal, G. S. and Hicks, J. and Wigler, M. and Schatz, M. C. (2015) Interactive analysis and assessment of single-cell copy-number variations. Nat Methods 12pp. 1058-1060.

Goodwin, S. and Gurtowski, J. and Ethe-Sayers, S. and Deshpande, P. and Schatz, M. C. and McCombie, W. R. (2015) Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome. Genome Res 25(11) pp. 1750-1756.

Pendleton, M. and Sebra, R. and Pang, A. W. and Ummat, A. and Franzen, O. and Rausch, T. and Stutz, A. M. and Stedman, W. and Anantharaman, T. and Hastie, A. and Dai, H. and Fritz, M. H. and Cao, H. and Cohain, A. and Deikus, G. and Durrett, R. E. and Blanchard, S. C. and Altman, R. and Chin, C. S. and Guo, Y. and Paxinos, E. E. and Korbel, J. O. and Darnell, R. B. and McCombie, W. R. and Kwok, P. Y. and Mason, C. E. and Schadt, E. E. and Bashir, A. (2015) Assembly and diploid architecture of an individual human genome via single-molecule technologies. Nat Methods 12(8) pp. 780-786.

Stephens, Z. D. and Lee, S. Y. and Faghri, F. and Campbell, R. H. and Zhai, C. and Efron, M. J. and Iyer, R. and Schatz, M. C. and Sinha, S. and Robinson, G. E. (2015) Big Data: Astronomical or Genomical?. PLoS Biol 13(7) pp. e1002195.

Wasik, K. A. and Tam, O. H. and Knott, S. R. and Falciatori, I. and Hammell, M. and Vagin, V. V. and Hannon, G. J. (2015) RNF17 blocks promiscuous activity of PIWI proteins in mouse testes. Genes Dev 29(13) pp. 1403-1415.

Wang, X. and Yu, X. and Zhu, W. and McCombie, W. R. and Antoniou, E. and Powers, R. S. and Davidson, N. O. and Li, E. and Williams, J. (2015) A trimming-and-retrieving alignment scheme for reduced representation bisulfite sequencing. Bioinformatics 31(12) pp. 2040-2042.

Dos Santos, C. O. and Dolzhenko, E. and Hodges, E. and Smith, A. D. and Hannon, G. J. (2015) An Epigenetic Memory of Pregnancy in the Mouse Mammary Gland. Cell Reports

Danko, C. G. and Hyland, S. L. and Core, L. J. and Martins, A. L. and Waters, C. T. and Lee, H. W. and Cheung, V. G. and Kraus, W. L. and Lis, J. T. and Siepel, A. (2015) Identification of active transcriptional regulatory elements from GRO-seq data. Nat Methods 12(5) pp. 433-8.

Lyons, S. K. (2015) Imaging Mouse Models of Cancer. Cancer J 21(3) pp. 152-164.

Baslan, T. and Kendall, J. and Ward, B. and Cox, H. and Leotta, A. and Rodgers, L. and Riggs, M. and D'Italia, S. and Sun, G. and Yong, M. and Miskimen, K. and Gilmore, H. and Saborowski, M. and Dimitrova, N. and Krasnitz, A. and Harris, L. and Wigler, M. and Hicks, J. (2015) Optimizing sparse sequencing of single cells for highly multiplex copy number profiling. Genome Research 25(5) pp. 714-724.

Teixeira, F. K. and Sanchez, C. G. and Hurd, T. R. and Seifert, J. R. and Czech, B. and Preall, J. B. and Hannon, G. J. and Lehmann, R. (2015) ATP synthase promotes germ cell differentiation independent of oxidative phosphorylation. Nature Cell Biology 17(5) pp. 689-696.

Wagenblast, E. and Soto, M. and Gutierrez-Angel, S. and Hartl, C. A. and Gable, A. L. and Maceli, A. R. and Erard, N. and Williams, A. M. and Kim, S. Y. and Dickopf, S. and Harrell, J. C. and Smith, A. D. and Perou, C. M. and Wilkinson, J. E. and Hannon, G. J. and Knott, S. R. (2015) A model of breast cancer heterogeneity reveals vascular mimicry as a driver of metastasis. Nature 520(7547) pp. 358-362.

Rye, I. H. and Lundin, P. and Maner, S. and Fjelldal, R. and Naume, B. and Wigler, M. and Hicks, J. and Borresen-Dale, A. L. and Zetterberg, A. and Russnes, H. G. (2015) Quantitative multigene FISH on breast carcinomas identifies der(1;16)(q10;p10) as an early event in luminal A tumors. Genes, Chromosomes & Cancer 54(4) pp. 235-48.

Fuda, N. J. and Guertin, M. J. and Sharma, S. and Danko, C. G. and Martins, A. L. and Siepel, A. and Lis, J. T. (2015) GAGA Factor Maintains Nucleosome-Free Regions and Has a Role in RNA Polymerase II Recruitment to Promoters. Plos Genetics 11(3) pp. e1005108.

Marinov, Georgi K and Wang, Jie and Handler, Dominik and Wold, Barbara J and Weng, Zhiping and Hannon, Gregory J and Aravin, Alexei A and Zamore, Phillip D and Brennecke, Julius and Toth, Katalin Fejes (2015) Pitfalls of Mapping High-Throughput Sequencing Data to Repetitive Sequences: Piwi’s Genomic Targets Still Not Identified. Developmental Cell 32(6) pp. 765-771.

Lee, J. H. and Daugharthy, E. R. and Scheiman, J. and Kalhor, R. and Ferrante, T. C. and Terry, R. and Turczyk, B. M. and Yang, J. L. and Lee, H. S. and Aach, J. and Zhang, K. and Church, G. M. (2015) Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues. Nat Protoc 10(3) pp. 442-58.

Kirschner, K. and Samarajiwa, S. A. and Cairns, J. M. and Menon, S. and Perez-Mancera, P. A. and Tomimatsu, K. and Bermejo-Rodriguez, C. and Ito, Y. and Chandra, T. and Narita, M. and Lyons, S. K. and Lynch, A. G. and Kimura, H. and Ohbayashi, T. and Tavare, S. and Narita, M. (2015) Phenotype specific analyses reveal distinct regulatory mechanism for chronically activated p53. PLoS Genet 11(3) pp. e1005053.

Stein, P. and Rozhkov, N. V. and Li, F. and Cardenas, F. L. and Davydenk, O. and Vandivier, L. E. and Gregory, B. D. and Hannon, G. J. and Schultz, R. M. (2015) Essential Role for Endogenous siRNAs during Meiosis in Mouse Oocytes. PLoS Genetics 11(2) pp. e1005013.

Jayaprakash, A. D. and Benson, E. K. and Gone, S. and Liang, R. and Shim, J. and Lambertini, L. and Toloue, M. M. and Wigler, M. and Aaronson, S. A. and Sachidanandam, R. (2015) Stable heteroplasmy at the single-cell level is facilitated by intercellular exchange of mtDNA. Nucleic Acids Research 43(4) pp. 2177-2187.

Ruiz, C. and Li, J. and Luttgen, M. S. and Kolatkar, A. and Kendall, J. T. and Flores, E. and Topp, Z. and Samlowski, W. E. and McClay, E. and Bethel, K. and Ferrone, S. and Hicks, J. and Kuhn, P. (2015) Limited genomic heterogeneity of circulating melanoma cells in advanced stage patients. Physical biology 12(1) pp. 16008.

Church, D. M. and Schneider, V. A. and Steinberg, K. M. and Schatz, M. C. and Quinlan, A. R. and Chin, C. S. and Kitts, P. A. and Aken, B. and Marth, G. T. and Hoffman, M. M. and Herrero, J. and Mendoza, M. L. Z. and Durbin, R. and Flicek, P. (2015) Extending reference assembly models. Genome Biology 16pp. Article no. 13.

Patrick, P. S. and Rodrigues, T. B. and Kettunen, M. I. and Lyons, S. K. and Neves, A. A. and Brindle, K. M. (2015) Development of Timd2 as a reporter gene for MRI. Magn Reson Med

Narzisi, G. and Schatz, M. C. (2015) The challenge of small-scale repeats for indel discovery. Front Bioeng Biotechnol 3pp. 8.

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