CGM Collaborations

We are collaborating with Dr. Susan Slaugenhaupt’s laboratory to understand the functional genomic implications of aberrant splicing of the gene IKAP in familial dysautonomia, a rare genetic disorder that affects the development and survival of certain nerve cells. The effects of the IKAP splicing defect can be ameliorated by the compound kinetin, and we are investigating the regulatory consequences of kinetin on IKAP expression.

Publications:

Gao et al., bioRxiv 2020

Morini et al., Am J Hum Genet 2019

We are collaborating with Drs. Jim Gusella (MGH, HMS, Broad), Marcy MacDonald (MGH, HMS, Broad) and their labs along with the CHDI Foundation to understand the pathogenic mechanism of Huntington’s disease.

Publications:

Murthy et al., PLoS Genet 2019

Jacobsen et al., Sci Rep 2017

Macakova et al., Neurodegener Dis 2016

Biagioli et al., Hum Mol Genet 2015

We are collaborating with Drs. Jim Gusella (MGH, HMS, Broad), Vijaya Ramesh (MGH, HMS) and their labs along with the Synodos Consortium to uncover the genetic architecture of neurofibromatosis type II (NF2), a rare genetic disorder causing benign nerve tumors, by performing genomic and transcriptomic analyses of tumor samples associated with NF2 from human and mouse.

Publications:
Synodos for NF2 Consortium, et al., PLoS One, 2018

MGH Collaborations

The Analytic and Translational Genetics Unit is a Unit within the Department of Medicine at MGH working in partnership with the Broad Institute of MIT and Harvard. Their overall mission is learning to interpret genome sequence data for both the discovery of the genetic underpinnings of human disease and for the development of paradigms by which individuals’ genome sequence can be effectively integrated into clinical decision making.

In a collaborative study with Dr. David Jaffe, Director of Computational Research and Development at the Broad Institute, and Drs. Cristopher Bragg, Nutan Sharma, Xandra Breakefield, and others in the Department of Neurology at MGH, we are performing whole-genome de novo assemblies of the Filipino genome in the Island of Panay to determine the genetic cause of a rare disorder, X-Linked Dystonia Parkinsonism, that is indigenous to this population. This work is largely sponsored by the Collaborative Center for XDP (CCXDP) at MGH.

Publications:
Aneichyk, Hendriks, Yadav, Shin, Gao, et al., Cell, 2018

Bragg et al., PNAS, 2017

The goal of DGAP is to gain insight into human congenital anomalies by mapping the breakpoints of balanced chromosomal abnormalities (BCAs) and subsequently identify the pathogenic mechanisms by which they cause human disease. The project includes four distinct parts. Dr. Talkowski directs Project 1: Annotation of the Morbid Human Genome. This is the genomics hub of the project in which we perform whole-genome sequencing of subjects with congenital anomalies and cytogenetically identified de novo BCAs. We are further seeking to understand BCAs in phenotypically normal individuals, as well as individuals with congenital anomalies and no identified cytogenetic abnormalities. Project 2: Model Organisms, is led by Dr. Eric Liao, a craniofacial surgeon at MGH who performs zebrafish modeling of craniofacial abnormalities, with Co-Investigator Dr. Cynthia Morton, who is focused on hearing abnormalities using mouse models. Project 3: Neurodevelopmental Loci, is led by Dr. James Gusella and focused on cellular modeling of genes influencing neurodevelopmental disorders, which represents approximately 75% of DGAP cases. Dr. Talkowski’s lab closely collaborates on the functional genomics studies of Project 3, which includes genome editing in iPS models. Finally, the Coordinating Core is led by Dr. Cynthia Morton and Ms. Tammy Kammin, Genetic Counselor, is the recruitment face of DGAP, which enrolls subjects and performs all clinical assessments. For more information, please see the DGAP website: http://www.bwhpathology.org/dgap/

The mission of the Psychiatric & Neurodevelopmental Genetics Unit (PNGU) at Massachusetts General Hospital is to identify and characterize the genetic basis of psychiatric, behavioral and neurodevelopmental disorders.

In collaboration with the Reproductive Endocrine Unit (REU) at MGH and the National Centers for Translational Research in Reproduction and Infertility (NCTRI), the Talkowski lab is analyzing data from patients who have Isolated GnRH Deficiency (IGD) with expansion to include reproductive genes and pathways that cause polycystic ovarian syndrome (PCOS), premature ovarian insufficiency (POI), and hypothalamic amenorrhea (HA) to investigate the genetic controls of human reproduction.

External Collaborations

The All of Us Research Program (AoURP), part of the NIH, is building one of the largest biomedical data resources of its kind. The All of UsResearch Hub will store health data from one million or more diverse participants in the All of Us Research Program. The Talkowski lab is working with the Broad Institute, Color Genomics, and the Partners Healthcare Laboratory for Molecular Medicine (LMM) to serve as the genome center for the AoURP. Dr. Talkowski’s group is leading efforts to develop structural variation detection pipelines from WGS across the All of Us program, including the development of a clinical structural variant pipeline that will evaluate the impact of structural variation across phenotypic traits in the biobank and permit the program to return clinically significant results to participants.

The Foundation for Prader-Willi Research (FPWR) is dedicated to supporting research to advance the understanding and treatment of Prader-Willi syndrome (PWS).

The goal of the Gabriella Miller Kids First Pediatric Research Program (Kids First) is to develop a large-scale data resource to help researchers uncover new insights into the biology of childhood cancer and structural birth defects, including the discovery of shared genetic pathways between these disorders

The International Common Disease Alliance (ICDA) aims to improve prevention, diagnosis, and treatment of common diseases by accelerating discovery from genetic maps to biological mechanisms to physiology and medicine, to benefit people around the world.

Levo Therapeutics has a singular focus – understanding the pathophysiology of Prader-Willi syndrome (PWS) to advance treatments that will make a difference in the lives of patients and their families. We are performing highly parallelized CRISPR engineering to identify therapeutic targets of PWS in iPSC-derived induced neurons and hypothalamic neurons.

We are collaborating with Dr. Natalie Shaw on the discovery of causal genetic variants in an incredibly rare birth defect known as Arrhinia. We are investigating this phenotype with both whole-exome and whole-genome sequencing.

Publications:
Shaw and Brand et al., 2017, Nat Genet

The Simon’s Foundation Autism Research Initiative (SFARI)’s mission is to improve the understanding, diagnosis and treatment of autism spectrum disorders by funding innovative research of the highest quality and relevance. SPARK (Simons Foundation Powering Autism Research for Knowledge) is an autism research initiative that aims to recruit, engage and retain a community of 50,000 individuals with autism and their family members living in the U.S. The Talkowski lab is working to develop computational models for copy number variant detection from exome sequencing on this cohort.