Genomic Sequencing for Childhood Risk and Newborn Illness
NCT ID: NCT02422511
Last Updated: 2024-04-03
Study Results
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View full resultsBasic Information
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COMPLETED
NA
1205 participants
INTERVENTIONAL
2015-05-31
2021-08-05
Brief Summary
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The investigators will enroll 240 healthy infants and their parents from the Brigham and Women's Hospital (BWH) Well Newborn Nursery and 240 sick infants and their parents at Boston Children's Hospital (BCH) or the BWH Neonatal Intensive Care Unit (NICU). A small blood sample will be collected from each infant and genome sequencing may be performed. Six weeks later, results are returned and explained. Over 12 months the investigators are studying the experiences of parents and pediatricians of infants who receive sequencing to help understand how best to use genomics in pediatric care.
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Detailed Description
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The investigators will enroll 240 healthy infants and their parents from the Brigham and Women's Hospital (BWH) Well Newborn Nursery and 240 sick infants and their parents at Boston Children's Hospital (BCH) or the BWH Neonatal Intensive Care Unit (NICU).
A small blood sample will be obtained from each enrolled infant. Samples will be collected from all infants enrolled, regardless of the arm to which they are assigned, in order to follow the same protocol for all subjects prior to randomization.
Infants within each cohort will be randomized (1:1) to either standard-of-care (family history and standard newborn screening report) or to standard-of-care plus genomic sequencing.
A study physician and genetic counselor will disclose the infant's randomization assignment and study results during an in-person consultation with each family. The study physician and genetic counselor will provide the consultation to families utilizing all available medical information. In the sequencing arm of the study, this will include the medical history, physical exam, family history, standard newborn screening (NBS) report and sequencing report(s). In the non-sequencing arm of the study, this will include the medical history, physical exam, family history and standard NBS report.
Parents will be surveyed at four points over the 12 months after enrollment: baseline, immediately post-disclosure (approximately 6 weeks after enrollment), 3 months post-disclosure, and at 10 months post-disclosure.
Conditions
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Study Design
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RANDOMIZED
PARALLEL
OTHER
SINGLE
Study Groups
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Well Baby Family History Only
Parents of newborns in well-baby units receive an Annotated Family History Report only. Active Comparator: Standard of Care Only: Family History report only
Family history report
Participants from all arms of the study will have a family history taken by a study genetic counselor. Information collected through the family history will be summarized in a family history report that will be reviewed with all participants.
Well Baby Family History + Exome Sequencing
Parents of newborns in well-baby units receive a Genome Report and an Annotated Family History Report. Main Study Experimental: Genome Report and Family History report
Genomic sequencing
Both sick and healthy infants randomized to receive genomic sequencing will receive a 'Genomic Newborn Sequencing Report' (GNSR) which will include pathogenic or likely pathogenic variants identified in genes associated with childhood-onset disease.
Family history report
Participants from all arms of the study will have a family history taken by a study genetic counselor. Information collected through the family history will be summarized in a family history report that will be reviewed with all participants.
ICU Baby Family History Only
Parents of newborns in intensive care units receive an Annotated Family History Report only. Active Comparator: Standard of Care Only: Family History report only
Family history report
Participants from all arms of the study will have a family history taken by a study genetic counselor. Information collected through the family history will be summarized in a family history report that will be reviewed with all participants.
ICU Baby Family History + Exome Sequencing
Parents of newborns in intensive care units receive a Genome Report and an Annotated Family History Report. Main Study Experimental: Genome Report and Family History report
Genomic sequencing
Both sick and healthy infants randomized to receive genomic sequencing will receive a 'Genomic Newborn Sequencing Report' (GNSR) which will include pathogenic or likely pathogenic variants identified in genes associated with childhood-onset disease.
Family history report
Participants from all arms of the study will have a family history taken by a study genetic counselor. Information collected through the family history will be summarized in a family history report that will be reviewed with all participants.
Interventions
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Genomic sequencing
Both sick and healthy infants randomized to receive genomic sequencing will receive a 'Genomic Newborn Sequencing Report' (GNSR) which will include pathogenic or likely pathogenic variants identified in genes associated with childhood-onset disease.
Family history report
Participants from all arms of the study will have a family history taken by a study genetic counselor. Information collected through the family history will be summarized in a family history report that will be reviewed with all participants.
Eligibility Criteria
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Inclusion Criteria
2. At least one biological parent is physically available to have genetic counseling, donate DNA, and provide consent for testing the infant. If the second biological parent is known but not physically present, the second biological parent must be available to have genetic counseling by phone, return a signed consent form by mail, and donate DNA via a mailed saliva kit. If there is a "rearing parent" (an individual who is not biologically related to the infant, but who is dedicated to raising the child), that individual must also provide consent but will not be asked to submit a saliva sample.
3. Mother (either rearing or biological) carried the pregnancy
1. Infants admitted to BCH or the BWH NICU
2. At least one biological parent is physically available to have genetic counseling, donate DNA, and provide consent for testing the infant. If the second biological parent is known but not physically present, the second biological parent must be available to have genetic counseling by phone, return a signed consent form by mail, and donate DNA via a mailed saliva kit. If there is a "rearing parent" (an individual who is not biologically related to the infant, but who is dedicated to raising the child), that individual must also provide consent but will not be asked to submit a saliva sample.
3. Mother (either biological or rearing) carried the pregnancy
Exclusion Criteria
2. Parents are unwilling to have genomic reports placed in the medical record or sent to their primary care pediatrician
3. Mother or father younger than 18 years of age
4. Mother or father with impaired decisional capacity
5. Age of infant is older than 30 days
6. One of a multiple gestation
7. Any infant in which clinical considerations preclude drawing 1.0 ml of blood
8. Missing consent of either biological parent (if known) or rearing parent (if applicable)
Sick Newborns and Parents at Boston Children's Hospital (BCH) or the BWH NICU:
1. Parents are non-English speaking
2. Parents are unwilling to have genomic reports placed in the medical record or sent to their primary care pediatrician
3. Mother or father younger than 18 years of age
4. Mother or father with impaired decisional capacity
5. Age of infant is older than 30 days
6. One of a multiple gestation
7. Any infant in which clinical considerations preclude drawing 1.0 ml of blood
8. Hospital admission expected to be less than 72 hours
9. Missing consent of either biological parent (if known) or rearing parent (if applicable)
10. Previously performed exome/genome sequencing on patient
ALL
No
Sponsors
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Boston Children's Hospital
OTHER
Baylor College of Medicine
OTHER
Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)
NIH
National Human Genome Research Institute (NHGRI)
NIH
Massachusetts General Hospital
OTHER
Brigham and Women's Hospital
OTHER
Responsible Party
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Robert C. Green, MD, MPH
Professor of Medicine, Division of Genetics, Department of Medicine
Principal Investigators
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Robert C. Green, MD, MPH
Role: PRINCIPAL_INVESTIGATOR
Brigham and Women's Hospital
Alan Beggs, PhD
Role: PRINCIPAL_INVESTIGATOR
Boston Children's Hospital
Locations
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Boston Children's Hospital
Boston, Massachusetts, United States
Brigham and Women's Hospital
Boston, Massachusetts, United States
Countries
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References
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Waisbren SE, Back DK, Liu C, Kalia SS, Ringer SA, Holm IA, Green RC. Parents are interested in newborn genomic testing during the early postpartum period. Genet Med. 2015 Jun;17(6):501-4. doi: 10.1038/gim.2014.139. Epub 2014 Dec 4.
Green RC, Rehm HL, Kohane IS. Clinical genome sequencing. In: Ginsburg GS, Willard HF, eds. Genomic and Personalized Medicine. Vol 1. 2nd ed. San Diego: Academic Press; 2013: 102-122.
Dewey FE, Grove ME, Pan C, Goldstein BA, Bernstein JA, Chaib H, Merker JD, Goldfeder RL, Enns GM, David SP, Pakdaman N, Ormond KE, Caleshu C, Kingham K, Klein TE, Whirl-Carrillo M, Sakamoto K, Wheeler MT, Butte AJ, Ford JM, Boxer L, Ioannidis JP, Yeung AC, Altman RB, Assimes TL, Snyder M, Ashley EA, Quertermous T. Clinical interpretation and implications of whole-genome sequencing. JAMA. 2014 Mar 12;311(10):1035-45. doi: 10.1001/jama.2014.1717.
Gilissen C, Hoischen A, Brunner HG, Veltman JA. Unlocking Mendelian disease using exome sequencing. Genome Biol. 2011 Sep 14;12(9):228. doi: 10.1186/gb-2011-12-9-228.
Gonzaga-Jauregui C, Lupski JR, Gibbs RA. Human genome sequencing in health and disease. Annu Rev Med. 2012;63:35-61. doi: 10.1146/annurev-med-051010-162644.
The President's Council on Bioethics. The changing moral focus of newborn screening: An ethical analysis by the President's Council on Bioethics. 2008; http://bioethics.georgetown.edu/pcbe/reports/newborn_screening.
Saunders CJ, Miller NA, Soden SE, Dinwiddie DL, Noll A, Alnadi NA, Andraws N, Patterson ML, Krivohlavek LA, Fellis J, Humphray S, Saffrey P, Kingsbury Z, Weir JC, Betley J, Grocock RJ, Margulies EH, Farrow EG, Artman M, Safina NP, Petrikin JE, Hall KP, Kingsmore SF. Rapid whole-genome sequencing for genetic disease diagnosis in neonatal intensive care units. Sci Transl Med. 2012 Oct 3;4(154):154ra135. doi: 10.1126/scitranslmed.3004041.
Yang Y, Muzny DM, Reid JG, Bainbridge MN, Willis A, Ward PA, Braxton A, Beuten J, Xia F, Niu Z, Hardison M, Person R, Bekheirnia MR, Leduc MS, Kirby A, Pham P, Scull J, Wang M, Ding Y, Plon SE, Lupski JR, Beaudet AL, Gibbs RA, Eng CM. Clinical whole-exome sequencing for the diagnosis of mendelian disorders. N Engl J Med. 2013 Oct 17;369(16):1502-11. doi: 10.1056/NEJMoa1306555. Epub 2013 Oct 2.
Biesecker LG, Green RC. Diagnostic clinical genome and exome sequencing. N Engl J Med. 2014 Sep 18;371(12):1170. doi: 10.1056/NEJMc1408914. No abstract available.
Vassy JL, Lautenbach DM, McLaughlin HM, Kong SW, Christensen KD, Krier J, Kohane IS, Feuerman LZ, Blumenthal-Barby J, Roberts JS, Lehmann LS, Ho CY, Ubel PA, MacRae CA, Seidman CE, Murray MF, McGuire AL, Rehm HL, Green RC; MedSeq Project. The MedSeq Project: a randomized trial of integrating whole genome sequencing into clinical medicine. Trials. 2014 Mar 20;15:85. doi: 10.1186/1745-6215-15-85.
Holm IA, Savage SK, Green RC, Juengst E, McGuire A, Kornetsky S, Brewster SJ, Joffe S, Taylor P. Guidelines for return of research results from pediatric genomic studies: deliberations of the Boston Children's Hospital Gene Partnership Informed Cohort Oversight Board. Genet Med. 2014 Jul;16(7):547-52. doi: 10.1038/gim.2013.190. Epub 2014 Jan 9.
Comeau AM, Parad RB, Dorkin HL, Dovey M, Gerstle R, Haver K, Lapey A, O'Sullivan BP, Waltz DA, Zwerdling RG, Eaton RB. Population-based newborn screening for genetic disorders when multiple mutation DNA testing is incorporated: a cystic fibrosis newborn screening model demonstrating increased sensitivity but more carrier detections. Pediatrics. 2004 Jun;113(6):1573-81. doi: 10.1542/peds.113.6.1573.
Wilfond BS, Parad RB, Fost N. Balancing benefits and risks for cystic fibrosis newborn screening: implications for policy decisions. J Pediatr. 2005 Sep;147(3 Suppl):S109-13. doi: 10.1016/j.jpeds.2005.08.019.
Bhattacharjee A, Sokolsky T, Wyman SK, Reese MG, Puffenberger E, Strauss K, Morton H, Parad RB, Naylor EW. Development of DNA confirmatory and high-risk diagnostic testing for newborns using targeted next-generation DNA sequencing. Genet Med. 2015 May;17(5):337-47. doi: 10.1038/gim.2014.117. Epub 2014 Sep 25.
Connolly M, Holm I, Beggs A, Agrawal P. Bringing current research technology to the clinic: The Manton Center for Orphan Disease Research Gene Discovery Core (Platform Abstract/Program 45). Paper presented at: 12th International Congress of Human Genetics/61st Annual Meeting of The American Society of Human Genetics; October 12, 2011, 2011; Montreal, Canada.
McGuire AL, Caulfield T, Cho MK. Research ethics and the challenge of whole-genome sequencing. Nat Rev Genet. 2008 Feb;9(2):152-6. doi: 10.1038/nrg2302.
Waisbren SE, Levy HL. Expanded screening of newborns for genetic disorders. JAMA. 2004 Feb 18;291(7):820-1; author reply 821. doi: 10.1001/jama.291.7.820-c. No abstract available.
Berg JS, Agrawal PB, Bailey DB Jr, Beggs AH, Brenner SE, Brower AM, Cakici JA, Ceyhan-Birsoy O, Chan K, Chen F, Currier RJ, Dukhovny D, Green RC, Harris-Wai J, Holm IA, Iglesias B, Joseph G, Kingsmore SF, Koenig BA, Kwok PY, Lantos J, Leeder SJ, Lewis MA, McGuire AL, Milko LV, Mooney SD, Parad RB, Pereira S, Petrikin J, Powell BC, Powell CM, Puck JM, Rehm HL, Risch N, Roche M, Shieh JT, Veeraraghavan N, Watson MS, Willig L, Yu TW, Urv T, Wise AL. Newborn Sequencing in Genomic Medicine and Public Health. Pediatrics. 2017 Feb;139(2):e20162252. doi: 10.1542/peds.2016-2252. Epub 2017 Jan 17.
Ceyhan-Birsoy O, Machini K, Lebo MS, Yu TW, Agrawal PB, Parad RB, Holm IA, McGuire A, Green RC, Beggs AH, Rehm HL. A curated gene list for reporting results of newborn genomic sequencing. Genet Med. 2017 Jul;19(7):809-818. doi: 10.1038/gim.2016.193. Epub 2017 Jan 12.
Murry JB, Machini K, Ceyhan-Birsoy O, Kritzer A, Krier JB, Lebo MS, Fayer S, Genetti CA, VanNoy GE, Yu TW, Agrawal PB, Parad RB, Holm IA, McGuire AL, Green RC, Beggs AH, Rehm HL; BabySeq Project Team. Reconciling newborn screening and a novel splice variant in BTD associated with partial biotinidase deficiency: a BabySeq Project case report. Cold Spring Harb Mol Case Stud. 2018 Aug 1;4(4):a002873. doi: 10.1101/mcs.a002873. Print 2018 Aug.
Holm IA, Agrawal PB, Ceyhan-Birsoy O, Christensen KD, Fayer S, Frankel LA, Genetti CA, Krier JB, LaMay RC, Levy HL, McGuire AL, Parad RB, Park PJ, Pereira S, Rehm HL, Schwartz TS, Waisbren SE, Yu TW; BabySeq Project Team; Green RC, Beggs AH. The BabySeq project: implementing genomic sequencing in newborns. BMC Pediatr. 2018 Jul 9;18(1):225. doi: 10.1186/s12887-018-1200-1.
Genetti CA, Schwartz TS, Robinson JO, VanNoy GE, Petersen D, Pereira S, Fayer S, Peoples HA, Agrawal PB, Betting WN, Holm IA, McGuire AL, Waisbren SE, Yu TW, Green RC, Beggs AH, Parad RB; BabySeq Project Team. Parental interest in genomic sequencing of newborns: enrollment experience from the BabySeq Project. Genet Med. 2019 Mar;21(3):622-630. doi: 10.1038/s41436-018-0105-6. Epub 2018 Sep 13.
Ceyhan-Birsoy O, Murry JB, Machini K, Lebo MS, Yu TW, Fayer S, Genetti CA, Schwartz TS, Agrawal PB, Parad RB, Holm IA, McGuire AL, Green RC, Rehm HL, Beggs AH; BabySeq Project Team. Interpretation of Genomic Sequencing Results in Healthy and Ill Newborns: Results from the BabySeq Project. Am J Hum Genet. 2019 Jan 3;104(1):76-93. doi: 10.1016/j.ajhg.2018.11.016.
Pereira S, Robinson JO, Gutierrez AM, Petersen DK, Hsu RL, Lee CH, Schwartz TS, Holm IA, Beggs AH, Green RC, McGuire AL; BabySeq Project Group. Perceived Benefits, Risks, and Utility of Newborn Genomic Sequencing in the BabySeq Project. Pediatrics. 2019 Jan;143(Suppl 1):S6-S13. doi: 10.1542/peds.2018-1099C.
Holm IA, McGuire A, Pereira S, Rehm H, Green RC, Beggs AH; BabySeq Project Team. Returning a Genomic Result for an Adult-Onset Condition to the Parents of a Newborn: Insights From the BabySeq Project. Pediatrics. 2019 Jan;143(Suppl 1):S37-S43. doi: 10.1542/peds.2018-1099H.
VanNoy GE, Genetti CA, McGuire AL, Green RC, Beggs AH, Holm IA; BabySeq Project Group. Challenging the Current Recommendations for Carrier Testing in Children. Pediatrics. 2019 Jan;143(Suppl 1):S27-S32. doi: 10.1542/peds.2018-1099F.
Lu CY, Hendricks-Sturrup RM, Mazor KM, McGuire AL, Green RC, Rehm HL. The case for implementing sustainable routine, population-level genomic reanalysis. Genet Med. 2020 Apr;22(4):815-816. doi: 10.1038/s41436-019-0719-3. Epub 2019 Dec 12. No abstract available.
Mackay ZP, Dukhovny D, Phillips KA, Beggs AH, Green RC, Parad RB, Christensen KD; BabySeq Project Team. Quantifying Downstream Healthcare Utilization in Studies of Genomic Testing. Value Health. 2020 May;23(5):559-565. doi: 10.1016/j.jval.2020.01.017. Epub 2020 Mar 20.
Armstrong B, Christensen KD, Genetti CA, Parad RB, Robinson JO, Blout Zawatsky CL, Zettler B, Beggs AH, Holm IA, Green RC, McGuire AL, Smith HS, Pereira S; BabySeq Project Team. Parental Attitudes Toward Standard Newborn Screening and Newborn Genomic Sequencing: Findings From the BabySeq Study. Front Genet. 2022 Apr 27;13:867371. doi: 10.3389/fgene.2022.867371. eCollection 2022.
Pereira S, Smith HS, Frankel LA, Christensen KD, Islam R, Robinson JO, Genetti CA, Blout Zawatsky CL, Zettler B, Parad RB, Waisbren SE, Beggs AH, Green RC, Holm IA, McGuire AL; BabySeq Project Team. Psychosocial Effect of Newborn Genomic Sequencing on Families in the BabySeq Project: A Randomized Clinical Trial. JAMA Pediatr. 2021 Nov 1;175(11):1132-1141. doi: 10.1001/jamapediatrics.2021.2829.
Schwartz TS, Christensen KD, Uveges MK, Waisbren SE, McGuire AL, Pereira S, Robinson JO, Beggs AH, Green RC; BabySeq Project Team; Bachmann GA, Rabson AB, Holm IA. Effects of participation in a U.S. trial of newborn genomic sequencing on parents at risk for depression. J Genet Couns. 2022 Feb;31(1):218-229. doi: 10.1002/jgc4.1475. Epub 2021 Jul 26.
Knapp B, Decker C, Lantos JD. Neonatologists' Attitudes About Diagnostic Whole-Genome Sequencing in the NICU. Pediatrics. 2019 Jan;143(Suppl 1):S54-S57. doi: 10.1542/peds.2018-1099J.
Provided Documents
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Document Type: Study Protocol and Statistical Analysis Plan
Related Links
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Related Info
Other Identifiers
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The BabySeq Project
Identifier Type: -
Identifier Source: org_study_id
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