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| Study Title | Comprehensive Autism and Neurodevelopmental Disorders (CANDo) |
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| 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. |
| Study Title | Oligogenic Models of Cardiomyopathy |
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| 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 |
| Study Title | Discovery, Biology and Risk of Inherited Variants in Glioma |
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| 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. For more information and to participate in the study: www.gliogene.org |
| Publication | Dong-Joo Choi et al., The genomic landscape of familial glioma. Sci. Adv. 9, eade2675 (2023). DOI: 10.1126/sciadv.ade2675 |
| Study Title | Genomic Medicine for III Neonates and Infants (GEMINI) Clinical Trial |
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| 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:
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| Study Title | Integration of pharmacogenomics and pharmacometabolomics with pharmacokinetics for biomarker discovery in pediatric inflammatory bowel disease |
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| 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. |
| Study Title | Genome-to-Treatment (GTRx) |
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| 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 a virtual, automated system 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. Request access to GTRx |
| Publication | Owen, M.J., Lefebvre, S., Hansen, C. et al. An automated 13.5 hour system for scalable diagnosis and acute management guidance for genetic diseases. Nat Commun 13, 4057 (2022). https://doi.org/10.1038/s41467-022-31446-6 |
| Study Title | Genomic and environmental determinants of infant deaths in San Diego County 2015-2022 |
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| 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. |
| Publication | Owen MJ, et al., Reclassification of the Etiology of Infant Mortality With Whole-Genome Sequencing. JAMA Netw Open. 2023 Feb 1;6(2):e2254069. doi: 10.1001/jamanetworkopen.2022.54069. PMID: 36757698; PMCID: PMC9912130. |
| Study Title | Molecular Tumor Profiling Platform for Oncology Patients |
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| Principal Investigators |
Megan Paul, M.D. Lukas Chavez, PhD. |
| 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:
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| Study Title | Developmental Mechanisms of Human Meningomyelocele |
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| 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. |
| Study Title | Tipping Point 10k |
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| 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:
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