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Genetic DiseaseBeginNGSNCT06306521

An Adaptive Clinical Trial of BeginNGS Newborn Screening for Hundreds of Genetic Diseases by Genome Sequencing

A study testing BeginNGS Test in people with Genetic Disease, run by Rady Pediatric Genomics & Systems Medicine Institute at 1 site in United States.

Recruiting

Looking for participants now. Contact the study team or a site below to ask about taking part.

Sites and contacts
Official record
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Trial summary

The goal of this clinical trial is to test a new method for newborn screening using whole genome sequencing, called BeginNGS. Parents will be approached to provide informed consent to enroll their newborns in prenatal, postnatal, and outpatient settings. Read more about this study

Who is it for?
Ages 1 day to 28 daysHealthy volunteers can take part
Conditions the study is for
Genetic Disease
What is being tested?
BeginNGS Test
Could I receive a placebo?
No, everyone receives an active treatment
How many people
10,000 participants
Where
1 siteUnited States
Study dates
29 Feb 2024to Feb 2029
Phase
Interventional
Are there results?
Not yet: the study is under way

Key requirements

Who can take part, as listed by the sponsor. Only the study team can confirm whether you are eligible, so take this list to your doctor.

  • Ages 1 day to 28 days
  • All sexes
  • Healthy volunteers accepted
  • Child

Who may be able to join

  • Neonates (<28 days old) at enrollment sites.
  • Parents must have identified a primary care provider (or group).

Who cannot join

  • 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.
  • Parents with a home address outside the US or jurisdiction of the enrollment sites.
  • Neonates or fetuses who are ill and in whom enrollment or sampling is anticipated to interfere with healthcare provision at delivery. For example, fetuses or neonates who are likely to require transfer to a higher level of care, such as to a Level IV NICU upon delivery.
  • Neonates who are under consideration for a rapid diagnostic genome sequence or other diagnostic genetic testing.
  • Neonates who are not expected to survive the neonatal period.

Trial locations and contacts

1 site in 1 country. Contact the study team or a site near you to ask about taking part.

United States1 site, 1 recruiting
  • Rady Children's Hospital San Diego

    San Diego, California, 92123

    Lauren Olsen, MSN, 858-576-1700 ext. 228456, lolsen1@rchsd.org

    Recruiting

Other trials in United States

About this study

The goal of this clinical trial is to test a new method for newborn screening using whole genome sequencing, called BeginNGS. Parents will be approached to provide informed consent to enroll their newborns in prenatal, postnatal, and outpatient settings. The main questions this study aims to answer are:

What is the utility of BeginNGS as compared to state newborn screening? What is the acceptability and feasibility of BeginNGS as compared to state newborn screening? What is the cost effectiveness of BeginNGS as compared to state newborn screening?

Enrolled newborns will have a blood sample taken and will receive the BeginNGS test. Newborns will have also had the state newborn screening test.

Read the detailed description

Each year 98% of US newborns receive screening (NBS) of dried blood spots (DBS) for at least 35 Recommended Uniform Screening Panel (RUSP) genetic disorders for diagnosis and treatment at/before onset of symptoms. About 6,600 true positive infants are identified per year. NBS is well-accepted and has proven clinical utility. Between 2010 and 2022, however, while many new therapeutic interventions for childhood genetic diseases showed clinical utility and/or were approved by the Food and Drug Administration (FDA), only 6 disorders were added to the RUSP. As a result, ~700 childhood genetic diseases have effective treatments but are not yet screened by NBS, and affected children experience delayed diagnosis and treatment, and poor outcomes. To solve this problem the investigators are developing BeginNGS - NBS by genome sequencing (GS) of DBS for, ultimately, ~700 severe, childhood genetic diseases with effective therapeutic interventions. BeginNGS is adaptive: genetic disorders are added (or removed) as evidence emerges that early treatment improves (or does not improve) outcomes. BeginNGS version 1 (v1, 388 genetic disorders) had good sensitivity (88.8%) and false positive rate (0.27%) in a retrospective study of 458,000 subjects. An exploratory prospective clinical trial comparing BeginNGS v2 (with 409 disorders) and rapid diagnostic genome sequencing (RDGS) identified reportable findings in 24 (34%) of 71 acutely ill newborns who were not suspected of having a genetic disease. Only 2 of those disorders were detected by standard NBS. The investigators propose a single group, multicenter, adaptive clinical trial to compare utility, acceptability, feasibility, and cost effectiveness of BeginNGS (experimental intervention) with standard NBS (control) in a minimum of 10,000 neonates (aged <28 days, maximum of 100,000). The primary objective of the trial is to generate evidence to support broad implementation of BeginNGS. An adaptive design was chosen rather than a traditional, fixed design to allow accumulating results to make the trial more efficient, informative, and ethical by addition or removal of BeginNGS disorders and genetic variants, population enrichment (for minority racial, ethnic, and ancestral groups), and sample size re-estimation. Adaptive design will also facilitate meta-analysis with other clinical trials of NBS-by-GS, providing greater power to test utility in ultra-rare genetic diseases. NBS-by-GS has the potential to transform the way childhood genetic diseases are diagnosed and treatments started. Preliminary data suggest that national adoption of BeginNGS in all births has the potential to improve outcomes of >50,000 US children per year.

Conditions
Genetic Disease
Being tested
BeginNGS Test
Keywords
newborn screening
Medical subject headings
Genetic Diseases, Inborn

What participants receive

What participants receive. In a randomised study each person is assigned to one group by chance.

  • BeginNGS TestGenetic

    Genomic sequencing that screens for over 400 genetic diseases.

Study groups in NCT06306521
Study groupRoleWhat they receive
EnrolleesExperimentalEnrolled infants will receive the BeginNGS test in addition to the state newborn screen.
Receives: Genetic: BeginNGS Test

What is being measured

The primary outcome is the main question the study is designed to answer.

  1. Comparison of the clinical utility of BeginNGS and standard of care (state NBS), defined by the proportion of enrollees likely to benefit (likely to have an improved outcome) from an indicated therapeutic intervention

    The proportion of enrollees likely to benefit (likely to have an improved outcome) from an indicated therapeutic intervention (as per an electronic clinical management system, Genome-to-Treatment, GTRx)

    Measured: 5 years

Secondary outcomes (29)
  1. Utility secondary outcome 1

    The proportion of BeginNGS and state NBS of DBS that are positive (Positive rate)

    Measured: 5 years

  2. Utility secondary outcome 2

    The proportion of BeginNGS and state NBS of DBS positive results that are confirmed (true positive rate and positive predictive value)

    Measured: 5 years

  3. Utility secondary outcome 3

    The proportion of BeginNGS and state NBS of DBS that are true positive and diagnosed during infancy.

    Measured: 5 years

  4. Utility secondary outcome 4

    The proportion of BeginNGS and state NBS of DBS that are true positive and diagnosed at study end.

    Measured: 5 years

  5. Utility secondary outcome 5

    The proportion of BeginNGS and state NBS of DBS that are positive and in whom an indicated therapeutic intervention was commenced by study end.

    Measured: 5 years

  6. Utility secondary outcome 6

    The proportion of BeginNGS and state NBS of DBS that are positive and in whom a disease outcome changed due to a therapeutic intervention by study end.

    Measured: 5 years

  7. Utility secondary outcome 7

    Subgroup analysis of clinical utility (as defined by the primary outcome measure) by race (black, white, Asian), ethnicity (Hispanic, non-Hispanic), genetic ancestry, and disorder group

    Measured: 5 years

  8. Utility secondary outcome 8

    Subgroup analysis of positive rate (secondary utility outcome measure 1) by race, ethnicity, genetic ancestry, and disorder group.

    Measured: 5 years

  9. Utility secondary outcome 9

    Subgroup analysis of true positive rate (secondary utility outcome measure 2) by race, ethnicity, genetic ancestry, and disorder group.

    Measured: 5 years

  10. Utility secondary outcome 10

    Subgroup analysis of the proportion of BeginNGS and state NBS of DBS that are true positive and diagnosed during infancy in infancy by race, ethnicity, genetic ancestry, and disorder group.

    Measured: 5 years

  11. Acceptability outcome 1

    Proportion of parents approached who agree to enroll their newborn (Figure 1c①). This is a "key outcome" (as defined by CONSORT PRO31).

    Measured: 5 years

  12. Acceptability outcome 2

    Physician and parental questionnaires (Figure 1c⑤) regarding perceptions of benefits and harms of BeginNGS by parents and primary care pediatricians.

    Measured: 5 years

  13. Acceptability outcome 3

    Subgroup analysis of enrollment rate (proportion of parents approached who agree to enroll their newborn; Figure 1c①) by race, ethnicity, genetic ancestry, and enrollment method.

    Measured: 5 years

  14. Acceptability outcome 4

    Subgroup analysis of parental questionnaires (regarding perceptions of benefits and harms of BeginNGS) by race, ethnicity, and genetic ancestry.

    Measured: 5 years

  15. Feasibility (ability of the study to be undertaken as designed) outcome 1

    Time to return of a result for BeginNGS and state NBS.

    Measured: 5 years

  16. Feasibility (ability of the study to be undertaken as designed) outcome 2

    Time to return of a confirmed true positive result of BeginNGS and state NBS.

    Measured: 5 years

  17. Feasibility (ability of the study to be undertaken as designed) outcome 3

    Proportion of enrollees with positive results who undergo confirmatory testing by BeginNGS and state NBS.

    Measured: 5 years

  18. Feasibility (ability of the study to be undertaken as designed) outcome 4

    Time to diagnosis (time until a clinical feature of the disorder is identified) for BeginNGS and state NBS.

    Measured: 5 years

  19. Feasibility (ability of the study to be undertaken as designed) outcome 5

    Proportion of enrollees lost to follow up at one year of age.

    Measured: 5 years

  20. Cost effectiveness outcome 1

    Average cost effectiveness ratio (ACER, average cost to prevent one infant death or adverse event).

    Measured: 5 years

  21. Cost effectiveness outcome 2

    Incremental cost effectiveness ratio (ICER, average change in cost associated with prevention of one infant death or adverse event).

    Measured: 5 years

  22. Cost effectiveness outcome 3

    Subgroup analysis of Average Cost Effectiveness Ratio (ACER, average cost to prevent one infant death or adverse event) by disorder group (for example metabolic disorders, immunodeficiency disorders, seizure disorders, endocrine disorders, vitamin and cofactor deficiency disorders, hematologic disorders, muscle disorders).

    Measured: 5 years

  23. Cost effectiveness outcome 4

    Subgroup analysis of Incremental cost effectiveness ratio (ICER, average change in cost associated with prevention of one infant death or adverse event) by disorder group (for example metabolic disorders, immunodeficiency disorders, seizure disorders, endocrine disorders, vitamin and cofactor deficiency disorders, hematologic disorders, muscle disorders).

    Measured: 5 years

  24. Accuracy outcome 1

    True positive rate (true positive/true positive+false negative, recall, sensitivity) of BeginNGS by comparison with state NBS of DBS (all enrollees).

    Measured: 5 years

  25. Accuracy outcome 2

    True positive rate of BeginNGS by comparison with other genetic tests (in infants who subsequently receive diagnostic testing for a suspected genetic disease).

    Measured: 5 years

  26. Utility secondary outcome 11

    Number needed to screen to prevent one infant death or adverse event.

    Measured: 5 years

  27. Feasibility outcome 6

    Incidence of variants and haplotypes associated with individual genetic diseases in newborns.

    Measured: 5 years

  28. Feasibility outcome 7

    Categorical determination of genetic pattern of inheritance (for example dominant, recessive) of individual genetic diseases in newborns (where this has not been unequivocally established).

    Measured: 5 years

  29. Utility secondary outcome 12

    Subgroup categorical analysis of efficacy of individual therapeutic interventions in infants.

    Measured: 5 years

Timeline

From the start of the study to its completion; the mark is today. Estimated dates are the sponsor’s plan.

  1. First posted12 Mar 2024
  2. Study start29 Feb 2024
  3. Primary completionFeb 2029 (estimated)
  4. Study completionFeb 2029 (estimated)

Resources

More details

For doctors and researchers: how the study is designed, who runs it, and its registry IDs.

Study design
Study type
Interventional
Phase
Phase N/A
Primary purpose
Screening
Allocation
Not applicable
Intervention model
Single group
Masking
None (open label)
Enrolment
10,000 participants (estimated)
IDs, dates and publications
ClinicalTrials.gov ID
NCT06306521
Sponsor's protocol ID
20235517
Acronym
BeginNGS
Status last verified
Mar 2024
First submitted
22 Feb 2024
Last updated
12 Mar 2024
Results posted
No
Data monitoring committee
No
FDA-regulated drug
No
FDA-regulated device
No

Publications

  • Reimers R, Bailey M, Brown C, Chan K, Defay T, Finkel T, Kahn S, Protopsaltis L, Stoddard L, Talati AJ, Wigby K, Akil ASA, Wright M, Kingsmore SF; BeginNGS Consortium. Clinical utility and cost-effectiveness of BeginNGS newborn screening by genome sequencing and standard newborn screening for severe childhood genetic diseases: an adaptive, international and comparative clinical trial. BMJ Open. 2025 Nov 13;15(11):e098609. doi: 10.1136/bmjopen-2024-098609.

    PubMed 41238356

Questions about this trial

What is this clinical trial studying?

A study testing BeginNGS Test in people with Genetic Disease, run by Rady Pediatric Genomics & Systems Medicine Institute at 1 site in United States.

The full registered description is in the About this study section and the official record.

Who may be eligible to take part?

The sponsor lists 2 inclusion and 7 exclusion criteria. Eligibility is decided by the study team after screening, so read the full criteria and contact a listed site.

Is this clinical trial currently recruiting?

The record says: looking for participants now, as of the sponsor's last update on 12 Mar 2024. Status can change between updates, so confirm with the study contact before making plans.

Where is the study taking place?

The record lists 1 site in United States. Whether a site is taking part right now should be confirmed with that site. See every site.

What are the possible benefits and risks?

They depend on the study and the treatment, and no study can promise a benefit. The study team explains the known risks during informed consent, before anyone joins; the record itself does not list them.

Are results available for this study?

This study is still under way. Results are not available in the source record yet.

How can a doctor refer a patient or contact the research team?

Contact Lauren Olsen, MSN (858-576-1700 ext. 228456, lolsen1@rchsd.org), or a site near the patient. AzTrials does not enrol participants or take referrals.

What does the primary outcome measure?

Comparison of the clinical utility of BeginNGS and standard of care (state NBS), defined by the proportion of enrollees likely to benefit (likely to have an improved outcome) from an indicated therapeutic intervention (time frame: 5 years). It is what the study was designed to measure, not a finding.

Where can I read the original study information?

On the ClinicalTrials.gov record for NCT06306521, which also lists 1 linked publication.

Does a listing mean the treatment is approved or proven to work?

No. A listing means the study is registered. It does not show that the treatment is safe, works, or is approved by a regulator.

How often is this information updated?

AzTrials copies changed records from ClinicalTrials.gov every night and reloads the whole registry every week. The sponsor last updated this record on 12 Mar 2024.

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