Genomic Sequencing in Acutely Ill Neonates

This is a randomized, blinded, prospective study examining the comparative effectiveness -
both clinical and cost effectiveness - of rapid NGS (StatSeq), compared to standard of care,
including an expanded newborn screen, in acutely ill neonates and infants with potential
genetic diseases. Acutely ill neonates and infants who have an undiagnosed illness, and
their families, will be eligible to participate in the study. The investigators will enroll
approximately 1,000 neonates and infants at a single study site. The study population will
be recruited from Children's Mercy Hospital inpatient population, primarily the intensive
care nursery (ICN, also known as the NICU), with a smaller subpopulation presenting to other
hospital services, such as the pediatric intensive care unit (PICU). All affected study
participants will receive an expanded newborn screen (NBS). Newborn screening is biochemical
testing of a heel-prick blood spot that is federally mandated to be performed on all US live
births. 67 diseases are tested for by NBS in MO, most of which are genetic diseases. The
expanded NBS proposed herein is the clinically available StepOne Newborn Screen® from Perkin
Elmer, and will be performed in addition to standard State of MO screening on all enrolled
infants in both arms. Half of the affected study participants will be randomized to receive
StatSeq in addition to standard testing for their acute illness and expanded NBS.
Additionally, all willing clinical providers will be enrolled and their perceptions on
clinical outcomes will be measured.

All subjects will have blood drawn for nucleic acid (DNA and RNA) isolation and the expanded
NBS at the time of enrollment in the study. All blood sample volumes will adhere to the CMH
policy on maximum blood in pediatric patients. If the volume allowed for in this policy
exceeds 5ml, 5 ml will be the maximum collected at enrollment. Buccal smears, heel-prick
blood spots, additional blood, urine and tissue samples may be collected, if available as
sample retains from other studies, and stored in the Center for Pediatric Genomic Medicine
(CPGM) per their approved IRB protocol (IRB Study #11120514). The latter samples will not
involve invasive sampling. Nucleic acids will be isolated and prepared for NGS with standard
protocols at the CPGM (Center for Pediatric Genomic Medicine). Familial samples (for
example, mother, father, affected or unaffected siblings) will also be obtained, and nucleic
acids will also be sequenced per the Genome Center Biorepository protocol, as indicated, to
assist in diagnosis of the acute medical condition in the newborn. All sequencing data will
be stored in the Genome Center Biorepository (IRB Study #11120514).

A minimum of two expert Center data analysts will be responsible for analyzing the DNA
variants following NGS. One of the analysts will then compile a report to be presented to
the Molecular Pathology Laboratory Director or Assistant Director. In the case of positive
study findings that may be diagnostic, the Molecular Pathology Laboratory Director or
Assistant Director will perform confirmatory clinical diagnostic testing and, if confirmed,
a standard clinical diagnostic report will be placed in the patient's medical record. In the
case of acutely material (actionable) positive study findings, the results will be verbally
conveyed to the primary clinical team directly prior to confirmatory testing. A generic
research note will be placed in the patient's medical record that indicates that a verbal,
provisional report was issued (Appendix A). Verbal, provisional reporting of results before
confirmatory testing will only be performed in cases where the delay in reporting necessary
for confirmation was likely to result in significant harm to the patient. Confirmatory
testing will be performed promptly in all cases, including those in which in which a verbal
report has been given. A case conference format may be utilized for return of results if the
complexity of the diagnosis or potential treatment for that diagnosis warrants detailed
discussion. If no potentially pathogenic variants are identified, a verbal report will be
provided to the clinical care physician of record to communicate that there were no
causative findings, and a generic research note will be placed in the medical record that
states that nondiagnostic research grade NGS was performed (Appendix B). No negative
diagnostic written report of results will be placed in the patient's chart in this instance,
as there is no available clinical grade testing to confirm negative results for all genes
tested. Follow up with the patient's family will be guided by the clinical care team. All
study participants and their clinicians will be notified of randomization assignment at/by
day 10 after randomization. This information will help alleviate anxiety on the part of the
family, and also provides a mechanism for patient crossover into the rapid NGS arm if the
patient is clinically deteriorating, and at the clinical care team's request. Rarely, those
participants and clinicians will be notified sooner if they were randomized to the rapid NGS
group and a diagnosis is made in less than 10 days. Both molecular diagnoses made and time
to diagnosis will be recorded as primary outcomes.

All positive results from the Perkin Elmer StepOne expanded NBS (received by all enrolled
infants and NOT a study variable) will be returned to the Genome Center personnel. Based on
these results, confirmatory testing through Perkin Elmer will be performed if this condition
was not identified on the standard State NBS screen for each infant. These provisional
results will be verbally communicated with the primary clinician team and additional samples
requested, if necessary, for confirmation. Upon confirmation, the results will be entered in
the patient's medical record.

Each time a study participant is enrolled, the primary clinical providers will be asked to
fill out a survey prior to StatSeq testing and after return of results. We will also review
the patient's medical record and collect clinical variables including laboratory testing,
radiology results, medications and other treatments received to further analyze the effect
rapid NGS has on clinical care. We plan to follow up with families annually up to 5 years
post enrollment and record clinical outcomes related to this study.

This study will be integrated with two other study protocols, one being the CMH Genomic
Medicine Repository (IRB 11120514) and the other Genomes in newborns (#13120442) that
studies the ethical and legal implications of rapid NGS in this population. Data records
will be requested from both studies. The participants must agree to enroll in the Genome
Center Biorepository. The Genomes in newborns study will be optional.

Inclusion Criteria: One of the following criteria required.

- Clinical genetic testing or a genetic consult is ordered

- Subject has one major structural anomaly or three or more minor anomalies

- Abnormal laboratory testing suggestive of a genetic disease

- Abnormal response to standard therapy for a major underlying condition

Exclusion Criteria:

- Previously confirmed genetic diagnosis that explains the clinical condition

- Has features pathognomonic for a large chromosomal aberration (Trisomy 13, 18, 21 or
other)