Clinical trial NCT02650622: Genetic and Metabolic Disease in Children
Official title: Genetic Regulators of Metabolism and Development in Children
Study type: OBSERVATIONAL
Overall status: RECRUITING
Conditions: Genetic Diseases
Metabolic Diseases
Keywords: Metabolism
Genetics
Metabolomics
Genomics
Lead sponsor: University of Texas Southwestern Medical Center
Sponsor class: OTHER
First posted: 2016-01-08
Enrollment: 1550
Sex: ALL
Minimum age (years): 1
Standard ages: CHILD
ADULT
OLDER_ADULT
Accepts healthy volunteers: no
Observational model: COHORT
Time perspective: PROSPECTIVE
Sampling method: NON_PROBABILITY_SAMPLE
Study population: Two populations will be enrolled in this study, control and diseased. Healthy newborns and older children will be recruited into the control population from Parkland Postpartum units and Children's Medical Center (CMC), respectively. The diseased population will be recruited from the clinics of the Pediatric Genetics and Metabolism Division in the Department of Pediatrics of CMC.

Brief summary: This is a prospective, non-randomized, non-blinded observational study. The overarching goal is to discover new disease-associated genes in children, while establishing a specific focus on disorders where molecular characterization is most likely to lead to novel therapies. This study will merge detailed phenotypic characterization of patients presenting to the Pediatric Genetics and Metabolism Division in the Department of Pediatrics/Children's Medical Center at Dallas and collaborating clinics with Next-Generation sequencing techniques to identify disease-producing mutations. The primary objective of the study is to identify novel pathogenic mutations in children with rare Mendelian disorders. A secondary objective of the study is to establish normative ranges of a large number of metabolites from healthy newborns and older children.

Detailed description: Discovery of genetic basis of impaired metabolism has greatly advanced treatment of patients with known metabolic diseases. However, many more genetic and metabolic disorders and their molecular causes remain to be discovered. The overall goal of this study is to discover new disease-associated genes in children, while establishing a specific focus on metabolic disorders where molecular characterization is most likely to lead to novel therapies. The primary objective is to identify novel pathogenic mutations in children with rare Mendelian disorders. The secondary objectives are: 1) Optimize methodology for metabolomic sample collection, processing and analysis; and 2) Establish normative ranges for a large number (potentially up to 1000) of metabolites in healthy newborns and older children.

Approximately one in three admissions to tertiary care pediatric hospitals results from conditions with a genetic basis. Although the majority of these conditions are rare, they collectively account for a disproportionate amount of illness and death in children. Discovery of the genetic basis of rare conditions often uncovers the pathophysiological basis of common diseases. This is particularly true for genetic diseases of impaired metabolism (inborn errors of metabolism, IEMs). There are many more genetic and metabolic disorders yet to be discovered. Of approximately 20,000 known human genes, less than one-fifth are currently associated with a disease phenotype. IEMs are a particular area of focus for us for two major reasons. First, of the several hundred known IEMs, many are already effectively treated with dietary modifications and/or medical therapy. This indicates to us that discovery of new IEM genes has great potential to produce clinically actionable insights into pathophysiology and therapeutic opportunities, ultimately leading to treatment of children that would otherwise be impossible to treat. Second, the PI of this study, Dr. Ralph DeBerardinis, is an expert in metabolomics, the practice of identifying and quantifying metabolites from biological systems. We will therefore implement research-based metabolomic profiling to the evaluation of patients with suspected IEMs or other genetic diseases. This detailed analysis will substantially increase the likelihood of identifying clinically relevant metabolic perturbations in children with growth failure, acidosis, hypoglycemia, hyperammonemia, and other abnormalities of putative genetic origin. It would also enable us to interpret mutations uncovered by clinical or research-based genomic sequencing. We believe that establishing a systematic procedure to evaluate both the metabolome and the genome in sick children will produce new insights into the genetic basis of pediatric disease, and ultimately new ways to treat these conditions.

In this study, subjects will be recruited as two populations: control and diseased. In the control population, plasma samples of healthy newborns will be acquired at the time of blood collection for state-mandated newborn screening from Parkland. We will also collect blood from healthy children from the clinics at Children's Medical Center (CMC), again piggybacking this research sample with venipuncture for clinically indicated blood collection. All plasma samples will be subjected to metabolomics to determine the healthy ranges for a large number of metabolites. This comprehensive profile of metabolites in children will be used as normative ranges to identify outlying metabolites in diseased subjects. Additionally, if suspected metabolic outliers are detected from this normal population, DNA samples extracted from the leftover packed cells or blood samples will be subjected to genomic sequencing to profile the associated gene mutations. The diseased population will be recruited from the clinics of the Pediatric Genetics and Metabolism Division in the Department of Pediatrics/CMC. Blood and DNA samples will be collected from patients for metabolomic analysis and next-generation sequencing respectively to define the metabolic abnormalities and associated gene mutations. Skin fibroblasts from patients will also be collected and used for biological validation of the metabolic effects of novel mutations, in particular by complementing diseased fibroblasts with wild-type alleles of genes mutated in the patient. If any rare Mendelian disorder is considered in a subject, blood from his/her family members will be acquired and subjected to metabolomic and genomic analyses to facilitate identification of the diseased-associated genes.

Eligibility criteria: Inclusion criteria of Cohort 1- Newborn:

* Subjects aged 1-2 days
* Subjects with gestational age 37-42 weeks
* Subjects with stable clinical status (admitted to normal newborn nursery)

Inclusion criteria of Cohort 2 - Older children:

• Subjects aged 0-18 years

Inclusion criteria of Cohort 3 - Diseased children:

Subjects (no age limit) with ANY phenotype as below:

* Confirmed metabolic or genetic diseases
* Suspected metabolic or genetic diseases
* Episodic metabolic decompensation (e.g. hypoglycemia, hyperammonemia, metabolic acidosis)
* Developmental regression
* Major congenital malformation
* Other unexplained symptoms of potential genetic origin

Exclusion criteria of Cohort 1 - Newborn:

* Subjects with gestational age \<37 weeks or \>42 weeks
* Subjects with overt signs of metabolic dysfunction, distress or genetic diseases including hypoglycemia, hyperglycemia, sepsis/shock, hypoxemia, or major congenital malformation
* Subjects with mothers whose pregnancies were complicated by gestational diabetes, gestational hyperglycemia, gestational hypertension, preeclampsia, or any other major disorders.

Exclusion criteria of Cohort 2 - Older children:

* Subjects with confirmed metabolic or genetic diseases
* Subjects with suspected metabolic or genetic diseases
* Subjects with episodic metabolic decompensation (e.g. hypoglycemia, hyperammonemia, metabolic acidosis)
* Subjects with developmental regression
* Subjects with major congenital malformation

Exclusion criteria of Cohort 3 - Diseased children No.

Primary outcomes:
measure: Perform metabolomic profiling and exome sequencing in children with presumed genetic and metabolic diseases
timeFrame: 3-4 years
Secondary outcomes:
measure: Perform metabolomic profiling in healthy children
timeFrame: 3-4 years
Other outcomes:
measure: Establish a specimen repository of healthy and diseased children
timeFrame: 3 years
Locations:
city: Dallas
country: United States
facility: Children's Medical Center at Dallas
state: Texas
Study officials:
affiliation: UT Southwestern Medical Center, Children's Medical Center at Dallas
name: Ralph J DeBerardinis, MD, PhD
role: PRINCIPAL_INVESTIGATOR
References:
citation: Scriver CR, Neal JL, Saginur R, Clow A. The frequency of genetic disease and congenital malformation among patients in a pediatric hospital. Can Med Assoc J. 1973 May 5;108(9):1111-5.
citation: Ng SB, Buckingham KJ, Lee C, Bigham AW, Tabor HK, Dent KM, Huff CD, Shannon PT, Jabs EW, Nickerson DA, Shendure J, Bamshad MJ. Exome sequencing identifies the cause of a mendelian disorder. Nat Genet. 2010 Jan;42(1):30-5. doi: 10.1038/ng.499. Epub 2009 Nov 13.