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Cancer Genetics and Genomics

cancer geneticsThe Cancer Genetics and Genomics (CGG) Program seeks to better understand the cancer genome and leverage novel insights into cancer genomics to improve outcomes for cancer patients. The three main research themes of the CGG Program include: (1) invention of cancer genome and transcriptome profiling technology; (2) development of computational tools and resources for interpreting cancer genomes and transcriptomes; and (3) implementation of high-throughput genetic-screening technologies to comprehensively map cancer dependencies.

Program Co-leaders

Tobias Janowitz, M.D., Ph.D.

Adam Siepel, Ph.D.

cancer geneticsThe Cancer Genetics and Genomics Program seeks to advance our understanding of the cancer genome through genetic, technological, and computational innovations. In fitting with the mission of the Laboratory(麻豆传媒社区) Cancer Center as an NCI-designated Basic Laboratory Cancer Center, the Program focuses on fundamental research to better understand the genetic alterations that drive cancer development and progression. The research themes in the CGG Program are built on the premise that a deeper characterization of the cancer genome will improve the survival and quality of life for patients with cancer, and Program members are translating insights made about the cancer genome into novel diagnostic and prognostic biomarkers. In addition, the Program maintains a focus on the development of new genomic technologies and computational tools, which are being used to analyze the cancer genome, aid in cancer diagnosis, and discover novel cancer dependencies.

Over the last five years, several Program investigators have developed technologies for profiling cancer genomes and transcriptomes. These include diverse methods for in situ sequencing of RNA in tumors, methods to find structural variants, and single-cell analysis methods. Members are also developing computational tools for genome and transcriptome analysis, which reflects the interdisciplinary approach of members with expertise in both traditional bench research and computational biology. In addition, Program members are using high-throughput genetic-screening approaches for therapeutic target discovery and validation. This theme makes use of multiplexed screening technologies, pioneered by Program members, for high-throughput assessment of gene functions. To support these efforts, Program members are developing computational algorithms for interpreting the complex datasets generated through these studies. Several Cancer Center Shared Resources are pivotal for the discovery research in this Program, including the Flow Cytometry, Microscopy, and Sequencing Technologies & Analysis Shared Resources.

Building publication list.
Semir Beyaz

Semir Beyaz

Are you really what you eat? Our goal is to uncover the precise mechanisms that link nutrition to organismal health and disease states at the cellular and molecular level. A particular focus in our lab is to understand how dietary perturbations affect the immune system and contribute to the risk of diseases that are associated with immune dysfunction such as cancer.

Jeff Boyd

Jeff Boyd

My research interests are in the molecular genetics, genetics, and genomics of gynecologic and breast cancers. Currently I am focused on the early natural histories of ovarian carcinoma and metastatic breast cancer, the genomics of ovarian cancer stem/progenitor cells, and the hypothesis that most breast cancers result from polygenic susceptibility.

Nyasha Chambwe

Nyasha Chambwe

My research focuses on identifying the genetic and molecular features of cancers that differ across racial and ethnic groups, and the extent to which these differences reveal or explain race and ethnicity-based cancer health disparities.

Kenneth Chang

Kenneth Chang

RNA interference (RNAi) and CRISPR are widely used to functionally investigate mammalian genomes. It is our goal to develop and optimize these gene perturbation platforms to improve their effectiveness in understanding the biology of diseases.

Camila dos Santos

Camila dos Santos

Among the changes that occur during pregnancy, those affecting the breasts have been found to subsequently modify breast cancer risk. My laboratory investigates how the signals present during pregnancy permanently alter the way gene expression is controlled and how these changes affect normal and malignant mammary development.

Douglas Fearon

Douglas Fearon

I鈥檓 studying how to harness the power of the immune system to fight cancer. Our underlying premise is that the microenvironment within a tumor suppresses the immune system. We have found a way to eliminate this suppression in the mouse model of pancreatic cancer, which has led to development of a drug for human pancreatic cancer that will enter phase 1 clinical trials in 2015.

Sepideh Gholami

Sepideh Gholami

Dr. Sepideh Gholami M.D., M.A.S. is a board-certified surgeon scientist with dual fellowship training in Complex General Surgical Oncology and Hepatopancreatobiliary Surgery. Dr. Gholami serves as the Director of the Liver Multidisciplinary Clinic, Hepatic Artery Infusion Pump Program, and Translational Research in Surgical Oncology at Northwell Health. She has focused her efforts on building a multidisciplinary liver surgery program with liver-directed therapies/regional therapies, including a hepatic artery infusion pump program for patients with hepatobiliary and metastatic malignancies. Dr. Gholami鈥檚 mission is to diversify and improve the research and clinical trial portfolio at Northwell Health Cancer Institute. She also has a joint appointment as an Adjunct Associate Professor at 麻豆传媒社区.

Sara Goodwin

Sara Goodwin

I work on adapting and developing new methods/techniques for genome and transcriptome sequencing.

Tobias Janowitz

Tobias Janowitz

Cancer is a systemic disease. Using both laboratory and clinical research, my group investigates the connections between metabolism, endocrinology, and immunology to discover how the body鈥檚 response to a tumor can be used to improve treatment for patients with cancer.

Alexander Krasnitz

Alexander Krasnitz

Many types of cancer display bewildering intra-tumor heterogeneity on a cellular and molecular level, with aggressive malignant cell populations found alongside normal tissue and infiltrating immune cells. I am developing mathematical and statistical tools to disentangle tumor cell population structure, enabling an earlier and more accurate diagnosis of the disease and better-informed clinical decisions.

Dan Levy

Dan Levy

We have recently come to appreciate that many unrelated diseases, such as autism, congenital heart disease and cancer, are derived from rare and unique mutations, many of which are not inherited but instead occur spontaneously. I am generating algorithms to analyze massive datasets comprising thousands of affected families to identify disease-causing mutations.

W. Richard McCombie

W. Richard McCombie

Over the last two decades, revolutionary improvements in DNA sequencing technology have made it faster, more accurate, and much cheaper. We are now able to sequence up to 10 trillion DNA letters in just one month. I harness these technological advancements to assemble genomes for a variety of organisms and probe the genetic basis of neurological disorders, including autism and schizophrenia, better understand cancer progression and understand the complex structures of the genomes of higher plants.

Hannah Meyer

Hannah Meyer

A properly functioning immune system must be able to recognize diseased cells and foreign invaders among the multitude of healthy cells in the body. This ability is essential to both prevent autoimmune diseases and fight infections and cancer. We study how a specific type of immune cells, known as T cells, are educated to make this distinction during development.

Adam Siepel

Adam Siepel

I am a computer scientist who is fascinated by the challenge of making sense of vast quantities of genetic data. My research group focuses in particular on questions involving molecular evolution and transcriptional regulation, with applications to cancer and other diseases as well as to plant breeding and agriculture.

Jessica Tollkuhn

Jessica Tollkuhn

My lab studies how estrogen and testosterone regulate gene expression in the brain. The receptors for these steroid hormones directly bind DNA to turn genes on or off. We have found that sex differences in gene expression are a dynamic readout of hormone actions across the lifespan. We aim to understand how these hormone-regulated genes contribute to sex-variable biology, behavior, and disease risk.

Chris Vakoc

Chris Vakoc

Cancer cells achieve their pathogenicity by changing which genes are on and off. To maintain these changes in gene expression, cancer cells rely on proteins that interact with DNA or modify chromatin. My group investigates how such factors sustain the aberrant capabilities of cancer cells, thereby identifying new therapeutic targets.

Peter Westcott

Peter Westcott

The mutational processes that drive cancer also expose it to the immune system. Therapies that invigorate anticancer immunity can be astonishingly effective, but only in a subset of patients. We are developing powerful new strategies to study how the immune system and cancer coevolve, with the goal of expanding the curative potential of immunotherapy to more patients.

Michael Wigler

Michael Wigler

Devastating diseases like cancer and autism can be caused by spontaneous changes to our DNA—mutations first appearing in the child, or in our tissues as we age. We are developing methods to discover these changes in individuals, tumors, and even single cells, to promote early detection and treatments