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Exome and genome sequencing for pediatric patients with congenital anomalies or intellectual disability: an evidence-based clinical guideline of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2021; 23:2029-2037. [PMID: 34211152 DOI: 10.1038/s41436-021-01242-6] [Citation(s) in RCA: 232] [Impact Index Per Article: 77.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 05/26/2021] [Accepted: 05/26/2021] [Indexed: 01/22/2023] Open
Abstract
PURPOSE To develop an evidence-based clinical practice guideline for the use of exome and genome sequencing (ES/GS) in the care of pediatric patients with one or more congenital anomalies (CA) with onset prior to age 1 year or developmental delay (DD) or intellectual disability (ID) with onset prior to age 18 years. METHODS The Pediatric Exome/Genome Sequencing Evidence-Based Guideline Work Group (n = 10) used the Grading of Recommendations Assessment, Development and Evaluation (GRADE) evidence to decision (EtD) framework based on the recent American College of Medical Genetics and Genomics (ACMG) systematic review, and an Ontario Health Technology Assessment to develop and present evidence summaries and health-care recommendations. The document underwent extensive internal and external peer review, and public comment, before approval by the ACMG Board of Directors. RESULTS The literature supports the clinical utility and desirable effects of ES/GS on active and long-term clinical management of patients with CA/DD/ID, and on family-focused and reproductive outcomes with relatively few harms. Compared with standard genetic testing, ES/GS has a higher diagnostic yield and may be more cost-effective when ordered early in the diagnostic evaluation. CONCLUSION We strongly recommend that ES/GS be considered as a first- or second-tier test for patients with CA/DD/ID.
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102
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Dimmock D, Caylor S, Waldman B, Benson W, Ashburner C, Carmichael JL, Carroll J, Cham E, Chowdhury S, Cleary J, D’Harlingue A, Doshi A, Ellsworth K, Galarreta CI, Hobbs C, Houtchens K, Hunt J, Joe P, Joseph M, Kaplan RH, Kingsmore SF, Knight J, Kochhar A, Kronick RG, Limon J, Martin M, Rauen KA, Schwarz A, Shankar SP, Spicer R, Rojas MA, Vargas-Shiraishi O, Wigby K, Zadeh N, Farnaes L. Project Baby Bear: Rapid precision care incorporating rWGS in 5 California children's hospitals demonstrates improved clinical outcomes and reduced costs of care. Am J Hum Genet 2021; 108:1231-1238. [PMID: 34089648 PMCID: PMC8322922 DOI: 10.1016/j.ajhg.2021.05.008] [Citation(s) in RCA: 134] [Impact Index Per Article: 44.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 05/14/2021] [Indexed: 12/31/2022] Open
Abstract
Genetic disorders are a leading contributor to mortality in neonatal and pediatric intensive care units (ICUs). Rapid whole-genome sequencing (rWGS)-based rapid precision medicine (RPM) is an intervention that has demonstrated improved clinical outcomes and reduced costs of care. However, the feasibility of broad clinical deployment has not been established. The objective of this study was to implement RPM based on rWGS and evaluate the clinical and economic impact of this implementation as a first line diagnostic test in the California Medicaid (Medi-Cal) program. Project Baby Bear was a payor funded, prospective, real-world quality improvement project in the regional ICUs of five tertiary care children's hospitals. Participation was limited to acutely ill Medi-Cal beneficiaries who were admitted November 2018 to May 2020, were <1 year old and within one week of hospitalization, or had just developed an abnormal response to therapy. The whole cohort received RPM. There were two prespecified primary outcomes-changes in medical care reported by physicians and changes in the cost of care. The majority of infants were from underserved populations. Of 184 infants enrolled, 74 (40%) received a diagnosis by rWGS that explained their admission in a median time of 3 days. In 58 (32%) affected individuals, rWGS led to changes in medical care. Testing and precision medicine cost $1.7 million and led to $2.2-2.9 million cost savings. rWGS-based RPM had clinical utility and reduced net health care expenditures for infants in regional ICUs. rWGS should be considered early in ICU admission when the underlying etiology is unclear.
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Affiliation(s)
- David Dimmock
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92130, USA,Corresponding author
| | - Sara Caylor
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92130, USA
| | - Bryce Waldman
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92130, USA
| | - Wendy Benson
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92130, USA
| | | | | | - Jeanne Carroll
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92130, USA,University of California, San Diego, San Diego, CA 92093, USA
| | - Elaine Cham
- University of California, San Francisco, Benioff Children’s Hospital Oakland, Oakland, CA 94609, USA
| | - Shimul Chowdhury
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92130, USA
| | - John Cleary
- Children’s Hospital of Orange County, Orange, CA 92868, USA
| | - Arthur D’Harlingue
- University of California, San Francisco, Benioff Children’s Hospital Oakland, Oakland, CA 94609, USA
| | - A. Doshi
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92130, USA,University of California, San Diego, San Diego, CA 92093, USA
| | | | | | - Charlotte Hobbs
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92130, USA
| | - Kathleen Houtchens
- University of California, San Francisco, Benioff Children’s Hospital Oakland, Oakland, CA 94609, USA
| | - Juliette Hunt
- Children’s Hospital of Orange County, Orange, CA 92868, USA
| | - Priscilla Joe
- University of California, San Francisco, Benioff Children’s Hospital Oakland, Oakland, CA 94609, USA
| | | | | | | | - Jason Knight
- Children’s Hospital of Orange County, Orange, CA 92868, USA
| | | | - Richard G. Kronick
- Torrey Pines Health Group, Inc., San Diego, CA 92037, USA,Department of Family Medicine and Public Health, University of California, San Diego, San Diego, CA 92093, USA
| | - Jolie Limon
- Valley Children’s Hospital, Madera, CA 93636, USA
| | - Madelena Martin
- University of California, Davis and Davis Children’s Hospital, Sacramento, CA 95817, USA
| | - Katherine A. Rauen
- University of California, Davis and Davis Children’s Hospital, Sacramento, CA 95817, USA
| | - Adam Schwarz
- Children’s Hospital of Orange County, Orange, CA 92868, USA
| | - Suma P. Shankar
- University of California, Davis and Davis Children’s Hospital, Sacramento, CA 95817, USA
| | | | | | | | - Kristen Wigby
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92130, USA,University of California, San Diego, San Diego, CA 92093, USA
| | - Neda Zadeh
- Children’s Hospital of Orange County, Orange, CA 92868, USA
| | - Lauge Farnaes
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92130, USA
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103
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Franklin AD, Chaudhari BP, Koboldt DC, Machut KZ. Polymerase Gamma Mitochondrial DNA Depletion Syndrome Initially Presenting as Disproportionate Respiratory Distress in a Moderately Premature Neonate: A Case Report. Front Genet 2021; 12:664278. [PMID: 34194468 PMCID: PMC8238196 DOI: 10.3389/fgene.2021.664278] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 05/04/2021] [Indexed: 11/13/2022] Open
Abstract
A 32-week premature infant presented with respiratory failure, later progressing to pulmonary hypertension (PH), liver failure, lactic acidosis, and encephalopathy. Using exome sequencing, this patient was diagnosed with a rare Polymerase Gamma (POLG)-related mitochondrial DNA (mtDNA) depletion syndrome. This case demonstrates that expanding the differential to uncommon diagnoses is important for complex infants, even in premature neonates whose condition may be explained partially by their gestational age (GA). It also shows that patients with complex neonatal diseases with significant family history may benefit from exome sequencing for diagnosis.
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Affiliation(s)
- Andrew D Franklin
- Division of Neonatology, NorthShore University HealthSystem, Evanston, IL, United States
| | - Bimal P Chaudhari
- Division of Genetic and Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, United States.,Division of Neonatology, Nationwide Children's Hospital, Columbus, OH, United States.,The Steve and Cindy Rasmussen Institute for Genomic Medicine at Nationwide Children's Hospital, Columbus, OH, United States.,Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, United States
| | - Daniel C Koboldt
- The Steve and Cindy Rasmussen Institute for Genomic Medicine at Nationwide Children's Hospital, Columbus, OH, United States
| | - Kerri Z Machut
- Division of Neonatology, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, United States.,Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
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104
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Owen MJ, Niemi AK, Dimmock DP, Speziale M, Nespeca M, Chau KK, Van Der Kraan L, Wright MS, Hansen C, Veeraraghavan N, Ding Y, Lenberg J, Chowdhury S, Hobbs CA, Batalov S, Zhu Z, Nahas SA, Gilmer S, Knight G, Lefebvre S, Reynders J, Defay T, Weir J, Thomson VS, Fraser L, Lajoie BR, McPhail TK, Mehtalia SS, Kunard CM, Hall KP, Kingsmore SF. Rapid Sequencing-Based Diagnosis of Thiamine Metabolism Dysfunction Syndrome. N Engl J Med 2021; 384:2159-2161. [PMID: 34077649 PMCID: PMC9844116 DOI: 10.1056/nejmc2100365] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Mallory J Owen
- Rady Children's Institute for Genomic Medicine, San Diego, CA
| | | | - David P Dimmock
- Rady Children's Institute for Genomic Medicine, San Diego, CA
| | | | | | - Kevin K Chau
- Rady Children's Institute for Genomic Medicine, San Diego, CA
| | | | | | | | | | - Yan Ding
- Rady Children's Institute for Genomic Medicine, San Diego, CA
| | - Jerica Lenberg
- Rady Children's Institute for Genomic Medicine, San Diego, CA
| | | | | | - Sergey Batalov
- Rady Children's Institute for Genomic Medicine, San Diego, CA
| | - Zhanyang Zhu
- Rady Children's Institute for Genomic Medicine, San Diego, CA
| | - Shareef A Nahas
- Rady Children's Institute for Genomic Medicine, San Diego, CA
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105
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罗 芳, 李 昊. [Application of the artificial intelligence-rapid whole-genome sequencing diagnostic system in the neonatal/pediatric intensive care unit]. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2021; 23:433-437. [PMID: 34020729 PMCID: PMC8140348 DOI: 10.7499/j.issn.1008-8830.2012143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Accepted: 03/10/2021] [Indexed: 06/12/2023]
Abstract
Pediatric patients in the neonatal intensive care unit (NICU) and the pediatric intensive care unit (PICU) have a high incidence rate of genetic diseases, and early rapid etiological diagnosis and targeted interventions can help to reduce mortality or improve prognosis. Whole-genome sequencing covers more comprehensive information including point mutation, copy number, and structural and rearrangement variations in the intron region and has become one of the powerful diagnostic tools for genetic diseases. Sequencing data require highly professional judgment and interpretation and are returned for clinical application after several weeks, which cannot meet the need for the diagnosis and treatment of genetic diseases in children. This article introduces the clinical application of rapid whole-genome sequencing in the NICU/PICU and briefly describes related techniques of artificial intelligence-rapid whole-genome sequencing diagnostic system, a rapid high-throughput automated platform for the diagnosis of genetic diseases. The diagnostic system introduces artificial intelligence into the processing of data after whole-genome sequencing and can solve the problems of long time and professional interpretation required for routine genome sequencing and provide a rapid diagnostic regimen for critically ill children suspected of genetic diseases within 24 hours, and therefore, it holds promise for clinical application.
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Affiliation(s)
- 芳 罗
- 浙江大学医学院附属第一医院儿科, 浙江杭州 310003Department of Pediatrics, First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
| | - 昊旻 李
- 浙江大学医学院附属儿童医院, 浙江杭州 310052
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106
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Preferences and values for rapid genomic testing in critically ill infants and children: a discrete choice experiment. Eur J Hum Genet 2021; 29:1645-1653. [PMID: 33811253 DOI: 10.1038/s41431-021-00874-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 03/09/2021] [Accepted: 03/16/2021] [Indexed: 12/23/2022] Open
Abstract
Healthcare systems are increasingly considering widespread implementation of rapid genomic testing of critically ill children, but evidence on the value of the benefits generated is lacking. This information is key for an optimal implementation into healthcare systems. A discrete choice experiment survey was designed to elicit preferences and values for rapid genomic testing in critically ill children. The survey was administered to members of the Australian public and families with lived experience of rapid genomic testing. A Bayesian D-efficient explicit partial profiles design was used, and data were analysed using a panel error component mixed logit model. Preference heterogeneity was explored using a latent class model and fractional logistic regressions. The public (n = 522) and families with lived experiences (n = 25) demonstrated strong preferences for higher diagnostic yield and clinical utility, faster result turnaround times, and lower cost. Society on average would be willing to pay an additional AU$9510 (US$6657) for rapid (2 weeks results turnaround time) and AU$11,000 (US$7700) for ultra-rapid genomic testing (2 days turnaround time) relative to standard diagnostic care. Corresponding estimates among those with lived experiences were AU$10,225 (US$7158) and AU$11,500 (US$8050), respectively. Our work provides further evidence that rapid genomic testing for critically ill children with rare conditions generates substantial utility. The findings can be used to inform cost-benefit analyses as part of broader healthcare system implementation.
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107
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Abstract
PURPOSE OF REVIEW Perinatal disorders include stillbirth, congenital structural anomalies, and critical illnesses in neonates. The cause of these is often unknown despite a thorough clinical workup. Genetic diseases cause a significant portion of perinatal disorders. The purpose of this review is to describe recent advances in genetic testing of perinatal disorders of unknown cause and to provide a potential diagnostic strategy. RECENT FINDINGS Exome and genome sequencing (ES and GS) have demonstrated that significant portions of perinatal disorders are caused by genetic disease. However, estimates of the exact proportion have varied widely across fetal and neonatal cohorts and most of the genetic diagnoses found in recent studies have been unique to individual cases. Having a specific genetic diagnosis provides significant clinical utility, including improved prognostication of the outcome, tailored therapy, directed testing for associated syndromic manifestations, referral to appropriate subspecialists, family planning, and redirection of care. SUMMARY Perinatal disorders of unknown cause, with nonspecific presentations, are often caused by genetic diseases best diagnosed by ES or GS. Prompt diagnosis facilitates improved clinical care. Improvements in noninvasive sampling, variant interpretation, and population-level research will further enhance the clinical utility of genetic testing. VIDEO ABSTRACT http://links.lww.com/MOP/A61.
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Affiliation(s)
- Thomas Hays
- Division of Neonatology, Department of Pediatrics, Columbia University Irving Medical Center, New York, New York, USA
| | - Ronald J. Wapner
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, New York, USA
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, New York, USA
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108
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Genetic Testing for Neonatal Respiratory Disease. CHILDREN-BASEL 2021; 8:children8030216. [PMID: 33799761 PMCID: PMC8001923 DOI: 10.3390/children8030216] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 02/27/2021] [Accepted: 03/08/2021] [Indexed: 11/16/2022]
Abstract
Genetic mechanisms are now recognized as rare causes of neonatal lung disease. Genes potentially responsible for neonatal lung disease include those encoding proteins important in surfactant function and metabolism, transcription factors important in lung development, proteins involved in ciliary assembly and function, and various other structural and immune regulation genes. The phenotypes of infants with genetic causes of neonatal lung disease may have some features that are difficult to distinguish clinically from more common, reversible causes of lung disease, and from each other. Multigene panels are now available that can allow for a specific diagnosis, providing important information for treatment and prognosis. This review discusses genes in which abnormalities are known to cause neonatal lung disease and their associated phenotypes, and advantages and limitations of genetic testing.
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109
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Dorn KM, Burns KD, Trout MAR, Ward DI, Wagner KJ, Meyer LR, Baack ML, Rodel RL. Diamond-Blackfan Anemia: A Case Report and Review of the Literature. Neonatology 2021; 118:500-504. [PMID: 34004602 DOI: 10.1159/000516030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 03/19/2021] [Indexed: 11/19/2022]
Abstract
We report a case of a male neonate delivered urgently via cesarean at thirty-five 5/7 weeks gestation for non-reassuring fetal monitoring who was found to have severe anemia at birth that could not be explained by acute blood loss. He was born to a 24-year-old mother, whose pregnancy was complicated by abnormal ultrasound findings, including a radial ray defect and fetal growth restriction. Trio rapid whole-exome sequencing (rWES) confirmed Diamond-Blackfan anemia in both the neonate and mother. This case highlights the importance of fetal surveillance and the clinical utility of rWES in the neonatal intensive care setting.
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Affiliation(s)
- Kaitlyn M Dorn
- Department of Obstetrics and Gynecology, University of South Dakota Sanford School of Medicine, Sioux Falls, South Dakota, USA
| | - Kaitlyn D Burns
- Department of Obstetrics and Gynecology, University of South Dakota Sanford School of Medicine, Sioux Falls, South Dakota, USA.,Sanford Children's Specialty Clinic, Sanford USD Medical Center, Sioux Falls, South Dakota, USA.,Department of Genetics, Augustana University, Sioux Falls, South Dakota, USA
| | - Maija A R Trout
- Department of Obstetrics and Gynecology, University of South Dakota Sanford School of Medicine, Sioux Falls, South Dakota, USA.,Department of Genetics, Augustana University, Sioux Falls, South Dakota, USA.,Department of Obstetrics and Gynecology, Sanford USD Medical Center, Sioux Falls, South Dakota, USA
| | - D Isum Ward
- Sanford Children's Specialty Clinic, Sanford USD Medical Center, Sioux Falls, South Dakota, USA.,Department of Pediatrics, University of South Dakota Sanford School of Medicine, Sioux Falls, South Dakota, USA
| | - KayeLyn J Wagner
- Sanford Children's Specialty Clinic, Sanford USD Medical Center, Sioux Falls, South Dakota, USA.,Department of Pediatrics, University of South Dakota Sanford School of Medicine, Sioux Falls, South Dakota, USA
| | - Lauritz R Meyer
- Sanford Children's Specialty Clinic, Sanford USD Medical Center, Sioux Falls, South Dakota, USA.,Department of Pediatrics, University of South Dakota Sanford School of Medicine, Sioux Falls, South Dakota, USA
| | - Michelle L Baack
- Sanford Children's Specialty Clinic, Sanford USD Medical Center, Sioux Falls, South Dakota, USA.,Department of Pediatrics, University of South Dakota Sanford School of Medicine, Sioux Falls, South Dakota, USA.,Environmental Exposures on Health and Disease Group, Sanford Research, Sioux Falls, South Dakota, USA
| | - Rachel L Rodel
- Department of Obstetrics and Gynecology, University of South Dakota Sanford School of Medicine, Sioux Falls, South Dakota, USA.,Department of Obstetrics and Gynecology, Sanford USD Medical Center, Sioux Falls, South Dakota, USA
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110
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Cakici JA, Dimmock DP, Caylor SA, Gaughran M, Clarke C, Triplett C, Clark MM, Kingsmore SF, Bloss CS. A Prospective Study of Parental Perceptions of Rapid Whole-Genome and -Exome Sequencing among Seriously Ill Infants. Am J Hum Genet 2020; 107:953-962. [PMID: 33157008 DOI: 10.1016/j.ajhg.2020.10.004] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 10/12/2020] [Indexed: 01/05/2023] Open
Abstract
Rapid diagnostic genomic sequencing recently became feasible for infants in intensive care units (ICUs). However, research regarding parents' perceived utility, adequacy of consent, and potential harms and benefits is lacking. Herein we report results of parental surveys of these domains from the second Newborn Sequencing in Genomic Medicine and Public Health (NSIGHT2) study, a randomized, controlled trial of rapid diagnostic genomic sequencing of infants in regional ICUs. More than 90% of parents reported feeling adequately informed to consent to diagnostic genomic sequencing. Despite only 23% (27) of 117 infants receiving genomic diagnoses, 97% (156) of 161 parents reported that testing was at least somewhat useful and 50.3% (88/161) reported no decisional regret (median 0, mean 10, range 0-100). Five of 117 families (4.3%) reported harm. Upon follow-up, one (1%) confirmed harm to child and parent related to negative results/no diagnosis, two (2%) reported stress or confusion, and two (2%) denied harm. In 81% (89) of 111 infants, families and clinicians agreed that genomic results were useful. Of the families for whom clinicians perceived harm from genomic testing, no parents reported harm. Positive tests/genomic diagnosis were more frequently perceived to be useful by parents, to benefit their infant, and to help manage potential symptoms (p < .05). In summary, the large majority of parents felt that first-tier, rapid, diagnostic genomic sequencing was beneficial for infants lacking etiologic diagnoses in ICUs. Most parents in this study perceived being adequately informed to consent, understood their child's results, and denied regret or harm from undergoing sequencing.
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