Cancer Research

Cancer is a disease for which some of the body’s cells grow uncontrollably and can spread to other parts of the body. Over 90% of cancers have some type of genetic alteration. Simply put, cancer is a disease of the genome. Using state-of-the-art genomic technologies and an unprecedented level of collaboration with the leading research institutions in and around New York, the NYGC is on the cutting edge of investigation into the origins, diagnosis, and evolution of cancer.

Focus on Cancer Genomics

The Computational Biology department has a dedicated group focused on cancer genomics, and in particular on processing and analyzing tumor-normal whole-genome sequencing (WGS) data. To that aim, they established (and regularly update and upgrade) a robust pipeline composed of multiple algorithms to detect, filter, and annotate germline and somatic variants (single-nucleotide variants SNV, small insertion-and-deletion, indels, copy-number alterations, and structural variants). The group is working with many different experimental designs such as large cohorts, multi-tumor cases (typically one normal, one or more primary tumor sample, and many metastatic tumor samples), xenograph (PDX) experiments, organoids or cell models, etc.

A student points out a key result on a laptop screen to a colleague

Program Highlights

The New York Genome Center has launched the MacMillan Center for the Study of the Non-Coding Cancer Genome (CSNCG), a major new initiative in cancer research to study the role and function of the non-coding genome and epigenome in the evolution, progression, and treatment of cancer. The “non-coding” genome constitutes 98% of the human genome. While it does not directly contain genes, it is responsible for gene regulation, the turning on and off of genes, and is implicated in having a role in various disease states including cancer.
For more information on the MacMillan Center go to csncg.org.

Team SAMBAI (Societal, Ancestry, Molecular, and Biological Analyses of Inequalities) was awarded up to $25M in funding from Cancer Grand Challenges to address the issue of inequities in cancer prevention, screening, and treatment. SAMBAI, a global, interdisciplinary team, will build an unprecedented resource of comprehensive measurements of social, environmental, genetic, and biological factors used to help define the causes of disparate outcomes in the selected populations. The team will focus on prostate, breast, and pancreatic cancers in diverse cohorts of African descent from regions within Africa, the UK, and the US. To learn more about team SAMBAI, click here.

In a collaborative effort organized by the NYGC, leaders of the New York City cancer research community have joined together to advance cancer genomics and its practice in clinical care by leveraging the City’s famously large and diverse population. The vision of this project is to deepen our understanding of the influence of different genetic backgrounds on the incidence and behavior of cancers, thereby improving outcomes for many patients, especially those who currently lack access to the most recent advances in medical science. To learn more about P-1000, click here.

Clinical Testing for Cancer

The Clinical group has a distinct oncology activity, with a unique Whole-Genome and Transcriptome Sequencing test, approved in all 50 states. When physicians order this test, samples are sequenced in the Clinical lab, data are processed with CLIA-approved pipelines, and clinical reports are written and submitted.

New technologies and new protocols are being developed at the NYGC and often have relevance for cancer research. Past examples include CITE-Seq for multi-modal single-cell data, protocols for nucleic acid extraction from FFPE samples, etc. Current activities include spatial transcriptomics and single-cell WGS using the DLP+ platform.

A scientist fills multiple vials at once with a manual tool inside a fume hood

Genome Center Cancer Group

The Genome Center Cancer Group (GCCG), led by Harold Varmus, MD, NYGC and Weill Cornell Medicine, and Charles Sawyers, MD, Memorial Sloan Kettering Cancer Center, is composed of leading clinicians and cancer researchers from the NYGC’s member institutions, including 7 NCI-Designated Cancer Centers. The GCCG launched Polyethnic-1000, a project to study cancer in New York’s ethnically diverse, underserved patient populations. NYGC Core Faculty Members Marcin Imielinski, MD, PhD; Dan Landau, MD, PhD; and Neville Sanjana, PhD, are all also engaged in pioneering cancer research.

Latest News & Publications

BMC Cancer · December 2, 2024

Patterns of breast cancer locoregional relapse, metastasis, and subtypes in Ghana.

Davis Lab Cancer
Nature Biotechnology · November 21, 2024

Pooled CRISPR screens with joint single-nucleus chromatin accessibility and transcriptome profiling.

Sanjana Lab Cancer
Nature Genetics · November 20, 2024

Luminal breast epithelial cells of BRCA1 or BRCA2 mutation carriers and noncarriers harbor common breast cancer copy number alterations.

Cancer