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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

Christopher Vakoc, 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 Cold Spring Harbor Laboratory (CSHL) 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.
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.

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.

Alexander Dobin

Alexander Dobin

Next generation sequencing technologies revolutionized many areas of genetics and molecular biology, enabling quantitative analyses of the entire genomes and paving the way for Personalized Medicine. We develop novel statistical methods and computational algorithms for multi-omics processing and integration, and leverage Big Genomic Data to elucidate various problems in precision health, such as genetic and epigenetic mechanisms of cancer development and progression, and clinical impact of functional variants.

Thomas Gingeras

Thomas Gingeras

Only a small portion of the RNAs encoded in any genome are used to make proteins. My lab investigates what these noncoding RNAs (ncRNAs) do within and outside of cells, where regulators of their expression are located in the genome. This is particularly important in cancer. Our laboratory works on endometrial cancer and its relationship to age and obesity.

Molly Gale Hammell

Molly Gale Hammell

To ensure that cells function normally, tens of thousands of genes must be turned on or off together. To do this, regulatory molecules—transcription factors and non-coding RNAs—simultaneously control hundreds of genes. My group studies how the resulting gene networks function and how they can be compromised in aging associated diseases, such as neurodegeneration and 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.

Je H. Lee

Je H. Lee

Cells are amazingly complex, with the ability to sense, and remember timing, location and history. I am exploring how cells store this information, and how their surroundings influence their communication with other cells. I am also developing various imaging and molecular sequencing methods for tracking genes, molecules, and cells to understand how cancer cells arise and evolve.

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.

David McCandlish

David McCandlish

Some mutations are harmful but others are benign. How can we predict the effects of mutations, both singly and in combination? Using data from experiments that simultaneously measure the effects of thousands of mutations, I develop computational tools to predict the functional impact of mutations and apply these tools to problems in protein design, molecular evolution, and cancer.

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.

Jason Sheltzer

Jason Sheltzer

Nearly all tumors exhibit a condition known as aneuploidy—their cells contain the wrong number of chromosomes. We’re working to understand how aneuploidy impacts cancer progression, in hopes of developing therapies that can specifically eliminate aneuploid cancers while leaving normal cells unharmed.

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.

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.

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