Research Projects

Autism

Study Title

Comprehensive Autism and Neurodevelopmental Disorders (CANDo)

Principal Investigator Kristen Wigby (RCIGM, PI)
Funding Source Rady Children’s Foundation and RCIGM
Award Period 2018-2022
Description CANDo is evaluating the clinical utility of WGS at time of first evaluation for Autism Spectrum Disorders (ASD) both in prediction of outcomes and clinical utility for precision management.

Cardiomyopathy

Study Title

Oligogenic Models of Cardiomyopathy

Principal Investigators Matthew Bainbridge (RCIGM, PI)
Neil C. Chi (UCSD, Co-PI)
Funding Source National Heart, Lung and Blood Institute of NIH
ID #5R01HL145175-02
Award Period 2019 - 2023
Description Cardiomyopathy is a devastating set of heart diseases that affect millions in the United States, with about 200,000 new cases diagnosed annually.
This study seeks to understand how multiple genes work together to increase the risk of developing genetic cardiomyopathy. Gaining a better understanding of the genetic mechanisms that influence the severity and propensity toward cardiomyopathy will help clinicians provide better treatment and guidance to patients

Clinical Trials

Study
Title

Genomic Medicine for III Neonates and Infants (GEMINI) Clinical Trial

Principal Investigator Jonathan M. Davis, (Tufts, PI) Jill Maron, (Tufts, Co-PI) Stephen Kingsmore (RCIGM, Site PI) Kristen Wigby (RCIGM, Co-I)
Funding Source National Center for Advancing Translational Sciences of NIH
5U01TR002271-03
Award Period 2019 - 2024
Description This multicenter, prospective clinical trial will examine the diagnostic yield and clinical utility of NewbornDx and rWGS testing in high-risk infants with signs/symptoms consistent with a possible genetic disorder. The target is enrollment is 400 infants across 6 sites. Infants undergo both NewbornDx and rWGS testing in parallel. The study aim is to assess the clinical utility of genomic sequencing and to examine the economic impact and health outcomes of NewbornDx and rWGS in infants compared with standard of care diagnostic testing. A web-based clinical reference database to provide references, clinical management guidelines, opportunities for clinical trial participation, and support groups for each condition will be developed with separate interfaces for the parent/guardian(s) and medical provider. The clinical reference database will be qualitatively assessed by a survey of medical providers.
The goals of this $8M study are to:
  • Compare the efficacy and clinical utility of a multi-gene panel and rWGS® in infants in five NICUs
  • Examine the economic impact of clinical multiplexed sequencing in high-risk neonates compared with current standard of care testing
  • Develop and evaluate the use of an electronic mechanism for accelerated return of results
Participating sites:
  • Rady Children’s Institute for Genomic Medicine
  • University of North Carolina, School of Medicine
  • Floating Hospital for Children at Tufts Medical Center
  • Cincinnati Children’s
  • University of Pittsburgh Medical Center, Children’s Hospital of Pittsburgh
Study Title

Discovery, Biology and Risk of Inherited Variants in Glioma

Principal Investigators Melissa Bondy (Stanford University, PI)
Matthew Bainbridge (RCIGM, Co-PI)
Benjamin Deneen (Baylor College of Medicine, Co-PI)
Funding Source RO1/NIH-Baylor/Stanford
ID # 5R01CA217105-04
Award Period 2018-2023
Description Glioma is a rare, devastating disease with median survival of 14 months. It occurs in approximately 1 per 10,000 individuals and 5% of glioma cases are thought to be familial. This project seeks to identify new genes that cause an inherited form of glioma.

In this study we have whole genome sequenced 203 individuals from 189 families with a history of familial glioma. We identified both coding and non-coding variants across 90 genes with diverse function, only 3 of which were previously associated with glioma.

We found significant enrichment for rare, loss of function variants in 7 known cancer predisposition genes (p=0.0071), which have not previously been implicated in familial glioma. We also found coding variants in genes involved in cell cycle regulation and DNA damage response.

We continue to recruit and sequence individuals with glioma in the hopes of increasing our understanding of this terrible disease.

Gastroenterology

Study Title

Integration of pharmacogenomics and pharmacometabolomics with pharmacokinetics for biomarker discovery in pediatric inflammatory bowel disease

Principal Investigator Amy Hemperly (UCSD / RCIGM, PI)
Funding Source American Gastroenterological Association
Award Period 2019 - 2022
Description The goal of this research is to integrate the key components of precision medicine including pharmacokinetics, pharmacogenomics, and pharmacometabolomics (Dorrestein lab) to study drug response in pediatric Inflammatory Bowel Disease.

Genome-to-Treatment

Study Title

Genome-to-Treatment (GTRx)

Principal Investigator Stephen Kingsmore (RCIGM, PI)
Funding Source Alexion Pharmaceuticals
Description There are hundreds of rare genetic diseases that have established treatments; however, these treatments are not always enacted promptly after a new genetic diagnosis, leading to loss of clinical utility. Genome-To-Treatment (GTRx™) is a first step in ending the therapeutic odyssey for rare genetic conditions.

GTRx™ is an online database for frontline clinicians in intensive care settings that provides immediate management plans for critically ill infants and children with a new diagnosis of an identified rare genetic disease.

Currently under development, GTRx™ will be integrated into RCIGM’s automated sequencing pipeline, providing clinicians with the tools they need to initiate time-sensitive treatments in the NICU and PICU.
Ultimately, GTRx™ will incorporate crowdsourced natural history information, clinical trial links, and treatment response resources for clinicians. GTRx™ is a first step in ending the therapeutic odyssey for rare genetic conditions.

Infant Mortality

Study Title

Genomic and environmental determinants of infant deaths in San Diego County 2015-2022

Principal Investigator Stephen Kingsmore (RCIGM, PI)
Christina Chambers (UCSD, Co-PI)
Funding Source NIH Eunice Kennedy Shriver National Institute of Child Health and Human Development
ID# 5R01HD101540-02
Award Period 2020 - 2025
Description Infant mortality is one of the leading indicators of a nation’s health. We seek to better understand which infant deaths are linked to genetic diseases. That information can then be used to focus resources to improve diagnosis and treatment for those conditions.
We are seeking to decode genomes associated with 1,000 infant deaths from dried blood spots to investigate the role genetic errors and environmental factors may play in infant mortality and how these findings may potentially be used to prevent infant deaths.

Neuro-oncology

Study Title

Molecular Tumor Profiling Platform for Oncology Patients

Principal Investigators Robert Wechsler-Reya (SBP co-I)
John Crawford (UCSD PI)
Funding Source Joseph Clayes III Charitable Trust
Description

The study aims to determine if genetic testing and a molecular tumor board (MTB) can guide the treatment of children with cancer. Specific short- and long-term goals include:

  1. Develop a platform for testing tumor, patient, and family genetics
  2. Have a Pediatric molecular tumor board (MTB) review the genetic results in a clinical context
  3. Provide insight into diagnosis and therapeutic options
  4. Establish a biorepository that will collect samples and information

Spina Bifida

Study Title

Developmental Mechanisms of Human Meningomyelocele

Principal Investigator Joseph Gleeson (RCIGM/UCSD, PI)
Funding Source Eunice Kennedy Shriver National Institute of Child Health & Human Development of NIH
ID# P01HD104436
Award Period 2020 - 2025
Description This study seeks to identify the molecular mechanisms responsible for neural tube defects or spina bifida, the most common of the structural defects of the central nervous system. Previous research has established by folic acid, or vitamin B9, can halve the risk of spina bifida when taken by women prior to conceiving a child. This research aims to understand how B9 reduces the risk of this disease. As part of this work, an international registry of spina bifida patients will be established with the cooperation of the Spina Bifida Association, Shriner’s Hospitals and spina bifida clinics around the world.

Tipping Point 10k

Study Title

Tipping Point 10k

Principal Investigator Stephen Kingsmore (RCIGM, PI)
Funding Source Rady Children's Hospital Foundation
Marriott Family Foundation
Award Period 2018 - 2024
Description

This initiative seeks to complete whole genome sequencing of 10,000 infants and children by 2024. Children from multiple locations will be enrolled to provide a representative sample. Data generated will help expand the knowledge base about the genetic origins of rare disease and establishing foundational knowledge for developing targeted treatments. Project goals include:

  • Preventing morbidity and mortality in hundreds of children nationwide annually
  • Achieving national reimbursement
  • Educating pediatricians with regard to the value of a genetic diagnosis
  • Training hundreds of pediatricians in ICU rapid precision medicine
  • Implementing rapid precision medicine in hundreds of pediatric ICUs
  • Defining indications for Rapid and Ultra Rapid Whole Genome Sequencing and best practices for rapid precision medicine based on results
  • Informing greater understanding of hundreds of ultra-rare diseases

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