NYGC research teams will work to accelerate our knowledge of the genetic variation within cells and tissues of the human body
The National Institutes of Health (NIH) Common Fund has selected the New York Genome Center (NYGC) as a multi-grant recipient under the Somatic Mosaicism across Human Tissues (SMaHT) Network.
The awarded grants will fund two research projects led by Soren Germer, PhD, Vice President of Genome Technologies, Sam Aparicio, BM, BCh, PhD, FRCPath, FRSC, Senior Scientific Director of Cancer Genomics, Dan Landau, MD, PhD, NYGC Core Faculty Member and Associate Professor of Medicine in the division of Hematology and Medical Oncology at Weill Cornell Medicine, and Rahul Satija, PhD, NYGC Core Faculty Member and Associate Professor of Biology at New York University.
The SMaHT Network, funded by the NIH Common Fund with $140 million over five years, is a trans-NIH initiative aimed at the discovery and systematic cataloging of somatic mosaicism in humans. The SMaHT Network encompasses five interconnected initiatives; the research led by Drs. Germer and Aparicio, falls under the umbrella of the Somatic Variant Discovery Initiative Genome Characterization Centers (GCCs), with the research led by Drs. Landau and Satija falling under the Technology and Tools Development Initiative.
The human genome is composed of the DNA sequence we inherit from our parents at fertilization, but also includes changes (or variants) that occur over time in individual cells, referred to as somatic mosaicism. Somatic mosaicism has the potential to alter how cells function and may influence human development, disease, aging, and other physiological measures across a person’s lifespan, including their susceptibility to certain diseases and disorders. In collecting data from normal human tissues, the SMaHT Network will establish the foundational knowledge necessary to enable a better understanding of the role that somatic genetic variation plays in human biology, aging, and disease.
The SMaHT Network will sample tissues from human donors with diverse ancestries, across life stages, and from different tissue types throughout the body. The collected data from the GCCs will generate a tissue-specific catalog of human somatic variation that will be made available to the community through a bespoke SMaHT Variant Catalog Portal and Integrated Data Workbench.
New York Genome Center’s SMaHT Genome Characterization Center
The NYGC GCC, led by Dr. Soren Germer and co-PI Dr. Sam Aparacio, is funded by a two-year grant (Grant Number 1UM1DA058236). In collaboration with other GCCs and SMaHT Network Centers, the NYGC GCC will generate a high-quality somatic variant catalog leveraging three core sequencing assays: mRNA sequencing, long-read Oxford Nanopore whole genome sequencing (WGS), and ultra-deep duplex WGS, which was developed by the Landau Lab at the NYGC. In addition, for a select number of tissues the team will sequence the genomes from individual single cells, using DLP+, a method developed by the Aparicio Lab. These assays will provide an unprecedented and comprehensive view of somatic mutations across a variety of healthy tissues.
The team will utilize the newest high-throughput sequencing platform, the Ultima Genomics UG100, to perform deep, short-read WGS for variant discovery supplemented by long-read genome sequencing using the Oxford Nanopore Technologies platform. Long-read genome sequencing will further enhance the discovery of large variants, including mobile elements, copy number changes, and structural events. The team will also perform RNA sequencing to analyze the expression of those variants in cells and evaluate the functional effects of somatic mosaicism.
“We are very excited to participate in this important initiative and collaborate with other Network Centers to bring our sequencing and analysis expertise to the creation of a comprehensive catalog of somatic mutations in human tissues. The importance of somatic mutations is increasingly being recognized beyond the realm of cancer research. Creating a comprehensive catalog contributes to, and lays the groundwork for, explorations of the role of somatic mutations in disease and aging processes,” said Dr. Germer.
The “Single-Cell Multi-Omics” Approach
The research team led by Dr. Dan Landau and co-PI Dr. Rahul Satija has received a two-year grant (Grant Number 1UG 3NS132139) to develop innovative tools for the study of somatic mosaicism in detail using a “single-cell multi-omics” approach. These novel technologies are capable of measuring multiple molecular layers of information from the same individual cell (e.g., DNA, RNA, protein etc.). Taking this approach, researchers can examine the co-dependence of these different layers and how they influence one another.
“Our overarching goal is to be able to make detailed comparisons between normal and mutant cells to comprehensively identify the underpinnings of fitness advantage in clonal outgrowths,” said Dr. Landau.
This project falls under the component of the SMaHT Network dedicated to creating new DNA sequencing and analysis technologies that directly address challenges in detecting rare genetic variants that occur in regions of repetitive DNA sequences and in small populations of cells.
All NIH Common Fund grant recipients will work closely under the highly-collaborative SMaHT Network.
About the New York Genome Center
The New York Genome Center (NYGC) is an independent, nonprofit academic research institution that serves as a multi-institutional hub for collaborative genomic research. Leveraging our strengths in technology development, computational biology, and whole genome sequencing, our mission is to advance genomic science and its application to novel biomedical discoveries. NYGC’s areas of focus include the development of computational and experimental genomic methods and disease-focused research to advance the understanding of the genetic basis of cancer, neurodegenerative disease, and neuropsychiatric disease. We are committed to prioritizing diversity, equity, and inclusion, which is fundamental to promoting greater collaboration, innovation, and discovery. nygenome.org
About the NIH Common Fund
The NIH Common Fund encourages collaboration and supports a series of exceptionally high-impact, NIH-wide programs. Common Fund programs are managed by the Office of Strategic Coordination in the Division of Program Coordination, Planning, and Strategic Initiatives in the NIH Office of the Director in partnership with the NIH Institutes, Centers, and Offices. More information is available at the Common Fund website: commonfund.nih.gov.
About the National Institutes of Health (NIH)
NIH, the nation’s medical research agency, includes 27 Institutes and Centers and is a component of the U.S. Department of Health and Human Services. NIH is the primary federal agency conducting and supporting basic, clinical, and translational medical research, and is investigating the causes, treatments, and cures for both common and rare diseases. For more information about NIH and its programs, visit nih.gov.
