New York Genome Center (NYGC) Center for Genomics of Neurodegenerative Diseases (CGND)

Recent discoveries have indicated that genes may contribute to a much larger percentage of ALS cases than previously thought. Finding these genes and understanding how they work will allow development of new therapeutic approaches.

The Center for Genomics of Neurodegenerative Disease (CGND) at the New York Genome Center (NYGC) is dedicated to the study of neurodegenerative diseases such as ALS and Alzheimer’s disease. CGND’s vision is to establish a framework for applying state-of-the-art genetics, genomics and bioinformatics to the study of neurodegenerative disease mechanisms by building partnerships with clinicians, basic scientists, geneticists and computational biologists.

The CGND has formed an international ALS Consortium to apply integrated genomics to advance the clinical diagnosis and care of ALS. Through a multidisciplinary collaborative effort that spans multiple ALS centers and bridges ALS clinicians and scientists, researchers are using whole genome sequencing to discover and study mutations and mechanisms underlying ALS.

The ALS Association Commitment

The CGND’s research program in ALS was established with the help of generous support from The Tow Foundation and The ALS Association that was announced in October 2014. The Association, in partnership with the Greater New York Chapter of The Association, committed $2.5 million to fund this research, directly from money raised through the ALS Ice Bucket Challenge. This matched a gift of $2.5 million from The Tow Foundation.

Goals

The CGND’s goals are to use whole genome sequencing to identify mutations that cause neurodegenerative disease. To gain insights into the relationship between mutations, gene expression and disease mechanisms, whole genome sequencing data will ultimately be integrated with other genomic-scale data such as RNA-Seq (i.e. RNA sequencing), RNA-protein interactions and DNA methylation patterns (i.e. a type of post-translational modification).

The CGND is helping to create a uniform system of collecting clinical annotation to better enable the integration of genomic data with clinical profiles. This information will be freely available to the research community in a data warehouse for whole genome sequencing and RNA-Seq analyses.

How the NYGC advances the search for a treatment for ALS

• Target Groups: Familial ALS, Sporadic ALS, C9orf72 carriers
• Data being collected now:
• Blood samples to make DNA
• Autopsy tissue to make RNA
• Some induced pluripotent stem cells (iPSCs)
• Clinical data (longitudinal clinical data targeted for ~1300 of a total of 1800 participants)
• Pre-competitive Data Sharing with all Consortium Members, samples consented for broad sharing for all medical research
• Current Studies:
• ALS gene discovery efforts: (1) understanding unexplained familial ALS and (2) increasing power through increased numbers of sporadic patients for co-analysis with existing datasets
• Genotype (i.e. genetic code)-phenotype (i.e. observable clinical characteristics) correlations
• Integrating whole genome sequencing (i.e. reading the full sequence of DNA for each participant) with tissue-specific transcriptomics (i.e. study of messenger RNA (mRNA)) for understanding the impact of regulatory variation and cell type-specific contributions
• C9orf72 promoter methylation

Key Players

• Hemali Phatnani, Ph.D., Director of the Center for Genomics of Neurodegenerative Disease, NYGC
• Tom Maniatis, Ph.D., Columbia University, Advisor
• Cheryl Moore, NYGC, Advisor
• David Goldstein, Ph.D, Columbia University, Advisor
• Robert Darnell, M.D., Ph.D., Founding Director, NYGC

The consortium is composed of research teams from Columbia University Medical Center, University of Pennsylvania, Massachusetts General Hospital, Hershey Medical Center at Pennsylvania State University, University of Maryland, Johns Hopkins University, Henry Ford Health System, University of California at San Francisco, Massachusetts Institute of Technology, Academic Medical Center, University of Amsterdam.

The NYGC CGND maintains partnerships with the Answer ALS Consortium, Genomic Translation for ALS Clinical Care (GTAC) Consortium and Target ALS (for the Post Mortem Core, iPS Core, biospecimen collection).

Website

http://www.nygenome.org/lab-groups-overview/center-genomics-neurodegenerative-disease-phatnani-lab/