Cancer Genetics and Genomics
The 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.
The 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.
Birds of a feather do flock together
November 17, 2020
Researchers found a genetic mechanism for how brand new species acquire distinct traits.
Women’s Partnership luncheon raises $150,000 for research
September 29, 2020
The nineteenth annual Women’s Partnership for Science luncheon was held with social distancing to support CSHL women researchers.
Fuerth wins BBRF Young Investigator Grant in neuro research
September 25, 2020
Daniel Fuerth, a postdoctoral fellow in Assistant Professor Je Lee’s lab,will study the transfer of genetic material between neurons in the brain.
New genetic research to understand racial disparity in cancers
September 8, 2020
Cold Spring Harbor Laboratory will study the genetic contributions of ethnicity to colon, endometrial, and pancreas cancers in African Americans.
Why we’re a lot better at fighting cancer than we realized
August 12, 2020
Using data mining techniques, doctors have discovered dozens of anti-tumor drugs hiding in plain sight.
ENCODE3: Interpreting the human and mouse genomes
July 29, 2020
Researchers report on 900,000 regulatory elements in our genomes that could influence our health.
Smoking increases SARS-CoV-2 receptors in the lung
May 18, 2020
An increase in lung ACE2 may explain why smokers are particularly vulnerable to COVID-19.
Tuveson and Wigler elected AACR Academy Fellows
May 12, 2020
CSHL Cancer Center Director David Tuveson and Professor Michael Wigler were chosen as 2020 Fellows of the AACR Academy.
Dog adaptations are like brain adaptations
May 6, 2020
To understand autism, CSHL Professor Michael Wigler thinks about how biological systems adapt over generations.
The status of autism research—in verse
April 29, 2020
CSHL Professor Michael Wigler drafted a poem explaining what we know and what we need to learn about autism.
Predicting the evolution of genetic mutations
April 14, 2020
CSHL quantitative biologists have designed a computational approach for predicting the evolution of a rapidly mutating virus or cancer.
A science career path: David McCandlish
April 10, 2020
Assistant Professor David McCandlish is a quantitative biologist who walks the line between advanced mathematics and the life sciences at CSHL.
Carol Greider: Nobel Prize-winning rogue biologist
March 31, 2020
CSHL alumna Carol Greider won the Nobel Prize and is a champion for diversity. But her dyslexia almost derailed her career before it began.
New faculty Jeff Boyd studies breast cancer genomics
March 26, 2020
Professor Jeff Boyd joins the CSHL faculty, studying the growth and spread of breast cancer.
Extra chromosomes in cancers can be good or bad
February 24, 2020
Extra chromosomes are typical in cancerous tumor cells, but not all extra copies promote cancer growth.
The non-human living inside of you
January 9, 2020
A large part of human DNA doesn’t aid the normal workings of the body. This “junk DNA” contains ancient viruses that may spur diseases like ALS.
Ann Lin named in Forbes 30 Under 30 list for 2020
December 16, 2019
Ann Lin, a former intern in CSHL Fellow Jason Sheltzer’s lab, has been named a top entrepreneur on the Forbes 30 Under 30 list.
Bridge to education
December 15, 2019
CSHL’s DNA Learning Center builds new bridges between unique science education and diverse groups.
CSHL investigators rank among world’s most highly cited
December 11, 2019
Seven researchers affiliated with CSHL are among the scientists producing the top 1 percent of the most highly-cited research in the world.
Making sense of the genome…at last
December 6, 2019
Quantitative biologists like Cold Spring Harbor Laboratory’s Adam Siepel are finally making sense of the flood of data contained in the human genome.
The Lab partners with award-winning magazine
December 6, 2019
Nautilus, an award-winning science magazine, has partnered with CSHL to bring the story of the lab’s scientists and research to a brand-new audience.
Research profile: Adam Siepel
November 12, 2019
Adam Siepel, Chair of the Simons Center for Quantitative Biology, uses advanced computational methods to solve complex biological questions.
A home like no other, Cold Spring Harbor Laboratory
November 7, 2019
Hear why our campus, our community, and our collaborative nature makes us a place that so many scientists call "home."
Scientists take action to prevent sexual harassment and bias
November 7, 2019
Scientists gathered at Banbury Center last year to discuss ways to prevent gender bias and sexual harassment in science.
Nobel laureate William Kaelin draws a crowd
October 29, 2019
Nobel laureate and cancer researcher William Kaelin holds a seminar on his award-winning research at CSHL.
Seeking better treatment for ALS, Lou Gehrig’s disease
October 29, 2019
Researchers found that ‘jumping genes’ were de-silenced in post-mortem tissue samples of ALS patients.
Peter Koo wants to understand how machines learn biology
September 20, 2019
Dr. Peter Koo joins the CSHL faculty as an assistant professor. His focus is on exploring how artificial intelligence integrates with biology and genomics.
Cancer drugs don’t always work as intended, researchers warn
September 11, 2019
Ten experimental cancer drugs kill tumors in ways that are entirely different than how clinicians thought they did, revealing important insights.
Event: Public Lecture: Seeing With Sequencing
August 8, 2019
Come hear from three quantitative biologists as they discuss how they see with sequencing to solve mysteries ranging from the genetics of evolution.
Sheltzer wins Presidential Early Career Award
July 9, 2019
CSHL Fellow Jason Sheltzer is a recipient of the Presidential Early Career Award for Scientists and Engineers for his work in cancer research.
Lee awarded Chan Zuckerberg Initiative Human Cell Atlas grant
June 21, 2019
Assistant Professor Je H. Lee has been named a recipient of one of the Seed Networks for the Human Cell Atlas to study breast tissue.
An essay from the President: Biology for the planet
May 16, 2019
CSHL plant scientists are looking for solutions to the biggest questions in agriculture as environments are reshaped by climate change.
Seeing with sequencing—A public lecture with three CSHL experts
April 19, 2019
Quantitative biologists discuss how physics, modern computing power, and a new perspective on biology can make sense of our complex genomes.
David McCandlish named Sloan Research Fellow
February 19, 2019
Assistant Professor David McCandlish has been named a 2019 Sloan Research Fellow for his promising work in the field of quantitative biology.
CSHL Fellow Jason Sheltzer wins innovation award
January 25, 2019
CSHL Fellow Jason Sheltzer wins the Damon Runyon-Rachleff Innovation Award for his work on cancer.
The year of CRISPR
December 26, 2018
A look at the various labs across CSHL that utilize CRISPR in their research, and the groundbreaking discoveries they help uncover.
How does natural selection affect the genome?
December 18, 2018
Adam Siepel explains how natural selection can tell researchers how informative sifting through the complex human genome will be.
How much are we learning? Natural selection is science’s best critic
December 17, 2018
Researchers determine that natural selection and our evolutionary history may be the best guides for future research.
Taking uncertainty out of cancer prognosis
December 11, 2018
An analysis of 20,000 patients has revealed that copy number variations in specific gene sites can help predict how deadly a cancer will be.
Taking uncertainty out of cancer prognosis
December 11, 2018
CSHL Fellow Jason Sheltzer has analyzed nearly 20,000 cancer patient histories and genetic data to take the guesswork out of prognosis.
Molly Hammell wins CZI award for ALS study
December 5, 2018
Associate Professor Molly Hammell wins award for proposed study to find transposable elements that are implicated in ALS.
Base Pairs Episode 17: Genomes, justice, and the journey here
September 15, 2018
A look at how gene-mapping works, what scientists can tell by looking at your genome, and what it means for your privacy.
Genomes, justice, and the journey here
September 15, 2018
CSHL Professor W. Richard McCombie discusses genomic privacy and sequencing technology in this episode of Base Pairs.
Massive genome havoc in breast cancer is revealed
July 12, 2018
Researchers have made a highly detailed map of 20,000 structural variations in a cancer cell’s genome
Alexander Dobin dives into genomic data
June 8, 2018
Alexander Dobin joins the faculty as its newest assistant professor, working on the computational side of genomics research
A science writer’s quest to understand heredity
May 30, 2018
LabDish spoke with science writer Carl Zimmer about what he learned about heredity as he zig-zagged through CSHL while writing his new book.
Portrait of a Neuroscience Powerhouse
April 27, 2018
A relatively small neuroscience group at CSHL is having an outsized impact on a dynamic and highly competitive field
Base Pairs Episode 14.5: Medicine and mad scientists
April 16, 2018
A follow-up discussion with CSHL Fellow Jason Sheltzer from Base Pairs episode 14, “The cancer answer that wasn’t.”
The cancer answer that wasn’t
March 15, 2018
We look at the "reproducibility crisis" in science, with a cancer researcher discovering something he didn't expect while experimenting with MELK
Base Pairs Episode 14: The cancer answer that wasn’t
March 15, 2018
We look at the "reproducibility crisis" in science, with a cancer researcher discovering something he didn't expect while experimenting with MELK.
Science self-corrects: cancer gene does not pass reproducibility test
February 13, 2018
CSHL Fellow Jason Sheltzer and his research team use CRISPR to discover that MELK is not actually involved in cancer.
Autism genetics study calls attention to impaired motor skills, general cognitive impairment
February 7, 2018
New research on the genetic causes of autism calls attention to diminished motor skills and suggests the importance of broad cognitive impairment
Evolving sets of gene regulators explain some of our differences from other primates
January 29, 2018
What makes us different from our primate relatives? Gene regulation is one important evolutionary factor
Base Pairs Episode 13: A lesson in class
December 15, 2017
We share three stories about classification in life sciences and how genetic information is changing how we define important categories.
A lesson in class
December 15, 2017
In this episode of Base Pairs, we discuss how genetic information is changing how we define important categories.
New method to determine before surgery which prostate tumors pose a lethal threat
December 1, 2017
The news about prostate cancer can be confusing. It’s the third most common cancer type among Americans.
Next-gen cancer test
November 24, 2017
Knowing that cancers become lethal when they spread, investigators at Cold Spring Harbor Laboratory seek a way of detecting tumors much earlier
CRISPR helps scientists find cancer’s (true) weaknesses
August 23, 2017
Jennifer Doudna (co-discoverer of the CRISPR gene editing tool) and CSHL's Jason Sheltzer talk breast cancer research.
New statistical method finds shared ancestral gene variants involved in autism’s cause
June 21, 2017
Researchers find children with autism are genetically more like other autistic children than their unaffected siblings.
Reconstructing ancient human history from DNA
June 20, 2017
Free public lecture featuring Adam Siepel, Ph.D., CSHL Professor and Chair of the Simons Center for Quantitative Biology.
Base Pairs Episode 9.5: Redefining biologists, redefining genes
May 16, 2017
We talk with Molly Hammell about peering into deep space using a high-tech telescope, we also talk to Tom Gingeras about redefining the gene.
Redefining biologists, redefining genes
May 16, 2017
Drs. Molly Hammell and Thomas Gingeras talk about redefining what a biologist is and what genes are.
Base Pairs Episode 9: Dark matter of the genome, part 2
April 15, 2017
In this episode of Base Pairs, we question the mythos that is “junk DNA” and explore the mysterious non-coding portions of the genome.
Dark matter of the genome, part 2
April 15, 2017
This episode of Base Pairs deals with the myth of "junk DNA" and why scientists are interested in non-coding portions of the genome.
What is single-cell genome viewer?
March 31, 2017
Single-cell genome viewer is a graphical interface, integrating single-cell genomics and conventional pathology of tumors.
Research suggests a possible role for a storm of ‘jumping genes’ in ALS
March 27, 2017
New research demonstrates that some transposons are no longer effectively inhibited, resulting in a storm of jumping genes, leading to DNA damage.
What a real-life science test looks like
March 24, 2017
By revealing evidence that contradicts the rationale for a new cancer drug, a pair of student scientists learns firsthand that when you do science.
Dark matter of the genome, part 1
March 15, 2017
This episode of Base Pairs digs into "dark matter" a type of genetic information that could help scientists better understand diseases like
Base Pairs Bonus Episode: Molecules and a mission
January 27, 2017
In this bonus episode, we explain the molecules and the metaphor of our podcast name: Base Pairs.
Relationship between incorrect chromosome number and cancer is reassessed
January 13, 2017
CSHL and MIT colleagues report surprising results of experiments intended to explore the consequences of having too many or too few chromosomes.
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, CSHL researchers found.
The 2016 Cold Spring Harbor Laboratory Double Helix Medal Dinner
December 2, 2016
Dr. Bruce Stillman, President and CEO, Cold Spring Harbor Laboratory, discusses the history of the Lab and current research in biology and genomics.
A theoretical physicist’s approach to breast cancer
October 21, 2016
Associate Professor Mickey Atwal explains how exploring numbers and patterns could lead to a new cancer treatment strategy.
August 15, 2016
This episode on Base Pairs explores how genetic information to better understand human history.
Riding out of the shadows of ALS, toward better treatments
August 1, 2016
Graduate student Lisa Krug discusses her research and personal connection to ALS, and Ride for Life, a not-for-profit organization for ALS research.
ALS Ride for Life comes to Cold Spring Harbor Laboratory
May 23, 2016
CSHL gathered to welcome Chris Pendergast and his ALS Ride for Life team to campus on Monday, May 16.
Neanderthals mated with modern humans much earlier than previously thought
May 17, 2016
Using several methods of DNA analysis, a research team has found strong evidence of interbreeding between Neanderthals and modern humans.
Why is autism more common in boys?
April 29, 2016
Ivan Iossifov talks about some of the reasons why autism disproportionately effects boys on a genetic level.
CSHL scientists Bo Li and Je Lee win HFSP Research Grant awards
April 12, 2016
Associate Professor Bo Li and Assistant Professor Je Lee, are among 25 teams that have won Human Frontier Science Program Research Program Grants
Where does autism come from when it doesn’t run in the family?
April 7, 2016
Associate Professor Ivan Iossifov discusses how parents who are not autistic can pass autism onto their children through their genes.
Neanderthals mated with modern humans much earlier than previously thought, study finds
February 12, 2016
Using several different methods of DNA analysis, an international research team has found what they consider to be strong evidence of interbreeding.
Finding huge promise in a single cell with student Robert Aboukhalil
November 2, 2015
Robert Aboukhalil use his skills as a computational biologist to make single-cell genomic data easy for scientists and clinicians to access and use.
Breaking down breast cancer at CSHL
October 30, 2015
A look at how several researchers at CSHL contribute to the field of breast cancer research.
Ride For Life gives $300,000 for ALS research at Cold Spring Harbor Laboratory (CSHL)
October 20, 2015
ALS Ride For Life this month presented $300,000 to CSHL Assistant Professor Molly Hammell and Associate Professor Josh Dubnau
Introducing the mighty Panoramix–defender of genomes!
October 15, 2015
Scientists have identified a protein the Piwi system uses to guide a cell's gene-silencing machinery to the right spots in the genome.
CSHL Fellow wins 2015 NIH Early Independence Award for cancer research
October 6, 2015
CSHL Lab Fellow Jason Sheltzer won the 2015 Early Independence Award from the National Institutes of Health High Risk, High Reward Research Program
Genetic analysis supports prediction that spontaneous rare mutations cause half of autism
September 22, 2015
Scientists find evidence suggesting that devastating “ultra-rare” mutations play a causal role in roughly half of all autism spectrum disorders.
Scientists sequence genome of worm that can regrow body parts, seek stem cell insights
September 21, 2015
Worm’s genome could lead to better understanding of its regenerative prowess and advance stem cell biology.
Mathematical ‘Gingko trees’ reveal mutations in single cells that characterize diseases
September 4, 2015
Online app could help clinicians choose the best treatments by comparing genetic fingerprints of individual cells.
12th annual LI2DAY Walk raises over $400,000
September 1, 2015
The $19,000 donation received by CSHL will support breast cancer research in the laboratory of Professor Alea Mills.
The biggest beast in the Big Data forest? One field’s astonishing growth is, well, ‘genomical’!
July 6, 2015
Scientists work to figure out how to capture, store, process and interpret all that genome-encoded biological information.
Seeking out cancer: From early detection to treatment
June 26, 2015
'Seeking Out Cancer: From Early Detection to Treatment' by Michael Wigler.
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.
Tumor cells that mimic blood vessels could help breast cancer spread to other sites
April 8, 2015
“Vascular mimicry” observed in mice could be helping tumors evade anti-angiogenesis drugs
Cold Spring Harbor Laboratory engages Hairpin Technologies Inc. to license its short hairpin RNA (shRNA) technology
March 31, 2015
Cold Spring Harbor Laboratory engaged Hairpin Technologies Inc. to expand the commercial distribution and research use of short hairpin RNA.
CSHL quantitative biologist Michael Schatz awarded 2015 Sloan Foundation Research Fellowship
February 20, 2015
Associate Professor Michael Schatz receives a 2015 Alfred P. Sloan Foundation Research Fellowship
Harnessing data from nature’s great evolutionary experiment
January 21, 2015
Scientists develop a computational method to estimate the importance of each letter in the human genome
Variation in expression of thousands of genes is kept under tight constraint in mice and humans, in all cells and tissues
November 19, 2014
Researchers have identified some 6600 genes whose level of expression varies within a comparatively restricted range in humans and mice
New junior faculty join CSHL
November 12, 2014
Interviews with new junior faculty members Jessica Tollkuhn and Je Lee.
New senior faculty join CSHL
November 10, 2014
Interviews with new faculty Adam Siepel and Douglas Fearon.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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