Genetic and Metabolic Disease in Children

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.

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.