Newborn Genomic Sequencing Pilot Study | NCT06276348

Studies
Newborn Genomic Sequencing Pilot Study

NCT06276348

Sponsor

Rady Pediatric Genomics & Systems Medicine Institute

Status

Completed

Last Update Posted

Nov 14, 2024Actual

Enrollment

120Actual

Phase

Not Applicable

Conditions

Genetic Disease

Interventions

Whole genome sequencing
BeginNGS test
WES

Countries

United States

Protocol Section

Identification Module Status Module Sponsor/Collaborators Module Oversight Module Description Module Conditions Module Design Module Arms/Interventions Module Outcomes Module Eligibility Module Contacts/Locations Module References Module IPD Sharing Statement Module

Results Section

Participant Flow Module Baseline Characteristics Module Outcome Measures Module Adverse Events Module More Info Module

Annotation Section

Annotation Module

Document Section

Large Document Module

Derived Section

Miscellaneous Info Module Condition Browse Module Intervention Browse Module

Protocol Section

Identification Module

NCT ID

Results Section

No data available

No data is available for this block.

Annotation Section

No data available

No data is available for this block.

Document Section

No data available

No data is available for this block.

Derived Section

Miscellaneous Info Module

Version Holder

Status Module

Record Verification Date

Nov 2024

Overall Recruitment Status or Expanded Access Status

Completed

Last Known Status

Not provided

Delayed Posting

Not provided

Why Stopped

Not provided

Expanded Access Info

Start Date

Mar 13, 2023Actual

Primary Completion Date

Feb 28, 2024Actual

Completion Date

Nov 12, 2024Actual

First Submitted Date

Feb 16, 2024

First Submission Date that Met QC Criteria

Feb 16, 2024

First Posted Date

Feb 26, 2024Actual

Results Waived

Not provided

Results First Submitted Date

Not provided

Results First Submitted that Met QC Criteria

Not provided

Results First Posted Date

Not provided

Certification/Extension (aka Delayed Results) First Submitted Date

Not provided

Certification/Extension First Submitted that Passed QC Review

Not provided

Certification/Extension First Posted Date

Not provided

Last Update Submitted Date

Nov 12, 2024

Last Update Posted Date

Nov 14, 2024Actual

Sponsor/Collaborators Module

Responsible Party, by Official Title

Stephen F. Kingsmore, President and CEO, Rady Pediatric Genomics & Systems Medicine InstitutePrincipal Investigator

Lead Sponsor

Rady Pediatric Genomics & Systems Medicine InstituteOTHER

Collaborators

Not provided

Oversight Module

Has Data Monitoring Committee (DMC)

Is FDA Regulated Drug

Is FDA Regulated Device

Is Unapproved Device

Not provided

Pediatric Postmarket Surveillance of a Device Product

Not provided

Product Exported from US

Not provided

FDAAA801 Violation

Not provided

Description Module

Brief Summary

The goal of this clinical trial is to test a new method for newborn screening using whole genome sequencing, called BeginNGS. Newborns who are not suspected of having genetic diseases and who are admitted to the NICU at Rady Children's Hospital, San Diego, will be enrolled. The main questions this study aims to answer are:

What is the diagnostic yield of diagnostic whole genome sequencing (DWGS) in this population?
What is the diagnostic sensitivity and specificity of BeginNGS and whole exome sequencing (WES) as compared to DWGS?
What are the potential issues related to implementing DWGS in this population?

Enrolled newborns will have a blood sample taken and will receive three tests:

DWGS
BeginNGS
WES

Detailed Description

Newborn screening (NBS) by testing dried blood spots (DBS) identifies newborns with a few diseases for which effective treatments are available to enable treatment at or before symptom onset. Because NBS improves outcomes in these diseases, it is performed on almost all US babies. The current Federal recommended NBS list is limited to 35 conditions and identifies ~6,600 affected children per year. In genetic diseases not screened by NBS, however, outcomes remain poor because of delays in diagnosis and treatment. The investigators recently developed a system for NBS for 434 severe, childhood genetic diseases for which effective treatments are available using whole genome sequencing (WGS), called BeginNGS. Retrospective studies showed BeginNGS to have a true negative rate (specificity) of 99.7% and true positive rate (sensitivity) of 88.8%. The investigators now propose to undertake a first prospective study in newborns admitted to the Neonatal Intensive Care Unit (NICU) at Rady Children's Hospital, San Diego (RCHSD) to compare the sensitivity and specificity of BeginNGS with that of standard, diagnostic rapid whole genome sequencing (DWGS) and whole exome sequencing (WES). This study is in preparation for larger, future clinical trials.

Design Module

Study Type

Interventional

Number of References to an Expanded Access Study

Not provided

Expanded Access Types

Not provided

Patient Registry

Not provided

Target Follow-Up Duration

Not provided

Phases

Not Applicable

Interventional Study Design

Allocation

Biospecimen

No data available

No data is available for this block.

Enrollment

120Actual

Arms/Interventions Module

Arm Groups

Label	Type	Description	Intervention Names
Enrollees	Experimental	Enrolled infants will receive 3 tests (DWGS, BeginNGS, and WES). DWGS will be performed in a standard manner. BeginNGS and WES will be performed in a batch after completion of enrollment. The diagnostic sensitivity and specificity of BeginNGS and WES will be compared to DWGS (a standard clinical test compliant with the Clinical Laboratory Improvement Amendments Act).	Genetic: Whole genome sequencing Genetic: BeginNGS test Genetic: WES

Interventions

Name	Type	Description	Arm Group Labels	Other Names
Whole genome sequencing	Genetic	Standard diagnostic whole genome sequencing will be performed.	Enrollees

Outcomes Module

Primary Outcomes

Measure	Description	Time Frame
Proportion of enrolled infants who are diagnosed with a genetic disease by DWGS.	Proportion	18 months

Secondary Outcomes

Measure	Description	Time Frame
Proportion of enrolled infants who are identified with a genetic disease by BeginNGS.	Proportion	18 months
Proportion of enrolled infants who are identified with a genetic disease by WES.	Proportion

Other Outcomes

Not provided

Eligibility Module

Eligibility Criteria

Inclusion Criteria:

Neonates less than or equal to 10 days old who are admitted to the RCHSD NICU.

Exclusion Criteria:

Neonates who have enrolled in another clinical study at Rady Children's Institute for Genomic Medicine or in whom DWGS has been ordered or is being considered.
Neonates whose mother is less than 18 years of age.
Neonates who are wards of the state.
Neonates whose parent/legal guardian is unable to provide consent.

Accepts Healthy Volunteers

Yes

Sex

All

Sex/Gender Based

Not provided

Sex/Gender Description

Not provided

Minimum Age

1 Day

Maximum Age

10 Days

Standard Ages

Child

Study Population

Not provided

Sampling Method

Not provided

Contacts/Locations Module

Central Contacts

Not provided

Overall Officials

Name	Affiliation	Role
Stephen Kingsmore, MD DSc	Rady Children's Institute for Genomic Medicine	Principal Investigator

Locations

Facility	Status	City	State	ZIP	Country	Contacts
Rady Children's Hospital San Diego		San Diego	California	92123	United States

Condition Browse Module

MeSH Terms

ID	Term
D030342	Genetic Diseases, Inborn

Ancestor Terms

ID	Term
D009358	Congenital, Hereditary, and Neonatal Diseases and Abnormalities

Browse Leaves

Not provided

Browse Branches

Not provided

Intervention Browse Module

MeSH Terms

ID	Term
D000073336	Whole Genome Sequencing

Ancestor Terms

ID	Term
D017422	Sequence Analysis, DNA
D017421	Sequence Analysis
D005821	Genetic Techniques
D008919	Investigative Techniques

Browse Leaves

Not provided

Browse Branches

Not provided