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For: Lippa N, Bier L, Revah-Politi A, May H, Kushary S, Vena N, Giordano JL, Rasouly HM, Cocchi E, Sands TT, Wapner RJ, Anyane-Yeboa K, Gharavi AG, Goldstein DB. Diagnostic sequencing to support genetically stratified medicine in a tertiary care setting. Genet Med 2022;24:862-869. [PMID: 35078725 DOI: 10.1016/j.gim.2021.12.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 12/14/2021] [Accepted: 12/16/2021] [Indexed: 11/27/2022] Open

For:	Lippa N, Bier L, Revah-Politi A, May H, Kushary S, Vena N, Giordano JL, Rasouly HM, Cocchi E, Sands TT, Wapner RJ, Anyane-Yeboa K, Gharavi AG, Goldstein DB. Diagnostic sequencing to support genetically stratified medicine in a tertiary care setting. Genet Med 2022;24:862-869. [PMID: 35078725 DOI: 10.1016/j.gim.2021.12.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 12/14/2021] [Accepted: 12/16/2021] [Indexed: 11/27/2022] Open

Number

Cited by Other Article(s)

French CE, Andrews NC, Beggs AH, Boone PM, Brownstein CA, Chopra M, Chou J, Chung WK, D'Gama AM, Doan RN, Ebrahimi-Fakhari D, Goldstein RD, Irons M, Jacobsen C, Kenna M, Lee T, Madden JA, Majmundar AJ, Mann N, Morton SU, Poduri A, Randolph AG, Roberts AE, Roberts S, Sampson MG, Shao DD, Shao W, Sharma A, Shearer E, Shimamura A, Snapper SB, Srivastava S, Thiagarajah JR, Whitman MC, Wojcik MH, Rockowitz S, Sliz P. Hospital-wide access to genomic data advanced pediatric rare disease research and clinical outcomes. NPJ Genom Med 2024;9:60. [PMID: 39622807 PMCID: PMC11612168 DOI: 10.1038/s41525-024-00441-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 10/14/2024] [Indexed: 12/06/2024] Open

Affiliation(s)

Courtney E French Children's Rare Disease Collaborative, Boston Children's Hospital, Boston, MA, USA
Nancy C Andrews Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA Department of Pediatrics, Harvard Medical School, Boston, MA, USA
Alan H Beggs Children's Rare Disease Collaborative, Boston Children's Hospital, Boston, MA, USA Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA Department of Pediatrics, Harvard Medical School, Boston, MA, USA The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA Broad Institute of MIT and Harvard, Cambridge, MA, USA
Philip M Boone Children's Rare Disease Collaborative, Boston Children's Hospital, Boston, MA, USA Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA Department of Pediatrics, Harvard Medical School, Boston, MA, USA
Catherine A Brownstein Children's Rare Disease Collaborative, Boston Children's Hospital, Boston, MA, USA Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA Department of Pediatrics, Harvard Medical School, Boston, MA, USA The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA
Maya Chopra Children's Rare Disease Collaborative, Boston Children's Hospital, Boston, MA, USA Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Boston, MA, USA
Janet Chou Children's Rare Disease Collaborative, Boston Children's Hospital, Boston, MA, USA Department of Pediatrics, Harvard Medical School, Boston, MA, USA Division of Immunology, Boston Children's Hospital, Boston, MA, USA
Wendy K Chung Children's Rare Disease Collaborative, Boston Children's Hospital, Boston, MA, USA Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA Department of Pediatrics, Harvard Medical School, Boston, MA, USA Broad Institute of MIT and Harvard, Cambridge, MA, USA
Alissa M D'Gama Children's Rare Disease Collaborative, Boston Children's Hospital, Boston, MA, USA Department of Pediatrics, Harvard Medical School, Boston, MA, USA Division of Newborn Medicine, Boston Children's Hospital, Boston, MA, USA Department of Neurology, Boston Children's Hospital, Boston, MA, USA
Ryan N Doan Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA Department of Pediatrics, Harvard Medical School, Boston, MA, USA
Darius Ebrahimi-Fakhari Children's Rare Disease Collaborative, Boston Children's Hospital, Boston, MA, USA Department of Neurology, Boston Children's Hospital, Boston, MA, USA F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA
Richard D Goldstein Children's Rare Disease Collaborative, Boston Children's Hospital, Boston, MA, USA Department of Pediatrics, Harvard Medical School, Boston, MA, USA Division of General Pediatrics, Boston Children's Hospital, Boston, MA, USA
Mira Irons Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA Department of Pediatrics, Harvard Medical School, Boston, MA, USA
Christina Jacobsen Children's Rare Disease Collaborative, Boston Children's Hospital, Boston, MA, USA Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA Department of Pediatrics, Harvard Medical School, Boston, MA, USA Division of Endocrinology, Boston Children's Hospital, Boston, MA, USA
Margaret Kenna Children's Rare Disease Collaborative, Boston Children's Hospital, Boston, MA, USA Department of Otolaryngology and Communication Enhancement, Boston Children's Hospital, Boston, MA, USA Department of Otolaryngology Head and Neck Surgery, Harvard Medical School, Boston, MA, USA
Ted Lee Children's Rare Disease Collaborative, Boston Children's Hospital, Boston, MA, USA Department of Urology, Boston Children's Hospital, Boston, MA, USA Department of Surgery, Harvard Medical School, Boston, MA, USA
Jill A Madden Children's Rare Disease Collaborative, Boston Children's Hospital, Boston, MA, USA Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA Department of Pediatrics, Harvard Medical School, Boston, MA, USA The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA
Amar J Majmundar Children's Rare Disease Collaborative, Boston Children's Hospital, Boston, MA, USA Department of Pediatrics, Harvard Medical School, Boston, MA, USA Division of Nephrology, Boston Children's Hospital, Boston, MA, USA
Nina Mann Children's Rare Disease Collaborative, Boston Children's Hospital, Boston, MA, USA Department of Pediatrics, Harvard Medical School, Boston, MA, USA Division of Nephrology, Boston Children's Hospital, Boston, MA, USA
Sarah U Morton Department of Pediatrics, Harvard Medical School, Boston, MA, USA The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA Broad Institute of MIT and Harvard, Cambridge, MA, USA Division of Newborn Medicine, Boston Children's Hospital, Boston, MA, USA
Annapurna Poduri Children's Rare Disease Collaborative, Boston Children's Hospital, Boston, MA, USA Department of Neurology, Boston Children's Hospital, Boston, MA, USA Department of Neurology, Harvard Medical School, Boston, MA, USA
Adrienne G Randolph Children's Rare Disease Collaborative, Boston Children's Hospital, Boston, MA, USA Department of Pediatrics, Harvard Medical School, Boston, MA, USA Department of Anesthesiology, Critical Care and Pain Medicine, Boston Children's Hospital, Boston, MA, USA Department of Anaesthesia, Harvard Medical School, Boston, MA, USA
Amy E Roberts Children's Rare Disease Collaborative, Boston Children's Hospital, Boston, MA, USA Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA Department of Pediatrics, Harvard Medical School, Boston, MA, USA Department of Cardiology, Boston Children's Hospital, Boston, MA, USA
Stephanie Roberts Children's Rare Disease Collaborative, Boston Children's Hospital, Boston, MA, USA Department of Pediatrics, Harvard Medical School, Boston, MA, USA Division of Endocrinology, Boston Children's Hospital, Boston, MA, USA
Matthew G Sampson Children's Rare Disease Collaborative, Boston Children's Hospital, Boston, MA, USA Department of Pediatrics, Harvard Medical School, Boston, MA, USA Broad Institute of MIT and Harvard, Cambridge, MA, USA Division of Nephrology, Boston Children's Hospital, Boston, MA, USA Division of Nephrology, Brigham and Women's Hospital, Boston, MA, USA
Diane D Shao Children's Rare Disease Collaborative, Boston Children's Hospital, Boston, MA, USA Department of Neurology, Boston Children's Hospital, Boston, MA, USA
Wanqing Shao Children's Rare Disease Collaborative, Boston Children's Hospital, Boston, MA, USA
Aditi Sharma Children's Rare Disease Collaborative, Boston Children's Hospital, Boston, MA, USA
Eliot Shearer Children's Rare Disease Collaborative, Boston Children's Hospital, Boston, MA, USA Department of Otolaryngology and Communication Enhancement, Boston Children's Hospital, Boston, MA, USA Department of Otolaryngology Head and Neck Surgery, Harvard Medical School, Boston, MA, USA
Akiko Shimamura Children's Rare Disease Collaborative, Boston Children's Hospital, Boston, MA, USA Department of Pediatrics, Harvard Medical School, Boston, MA, USA Department of Hematology and Oncology, Boston Children's Hospital, Boston, MA, USA Dana Farber Cancer Institute, Boston, MA, USA
Scott B Snapper Children's Rare Disease Collaborative, Boston Children's Hospital, Boston, MA, USA Department of Pediatrics, Harvard Medical School, Boston, MA, USA Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, USA
Siddharth Srivastava Children's Rare Disease Collaborative, Boston Children's Hospital, Boston, MA, USA Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Boston, MA, USA Department of Neurology, Boston Children's Hospital, Boston, MA, USA
Jay R Thiagarajah Children's Rare Disease Collaborative, Boston Children's Hospital, Boston, MA, USA Department of Pediatrics, Harvard Medical School, Boston, MA, USA Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, USA
Mary C Whitman Children's Rare Disease Collaborative, Boston Children's Hospital, Boston, MA, USA F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA Department of Ophthalmology, Boston Children's Hospital, Boston, MA, USA Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
Monica H Wojcik Children's Rare Disease Collaborative, Boston Children's Hospital, Boston, MA, USA Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA Department of Pediatrics, Harvard Medical School, Boston, MA, USA The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA Broad Institute of MIT and Harvard, Cambridge, MA, USA Division of Newborn Medicine, Boston Children's Hospital, Boston, MA, USA
Shira Rockowitz Children's Rare Disease Collaborative, Boston Children's Hospital, Boston, MA, USA Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA Department of Pediatrics, Harvard Medical School, Boston, MA, USA The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA
Piotr Sliz Children's Rare Disease Collaborative, Boston Children's Hospital, Boston, MA, USA. Department of Pediatrics, Harvard Medical School, Boston, MA, USA. The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA. Division of Molecular Medicine, Boston Children's Hospital, Boston, MA, USA. Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.

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Rogerson D, Alkelai A, Giordano J, Pantrangi M, Hsiao MC, Nhan-Chang CL, Motelow JE, Aggarwal V, Goldstein D, Wapner R, Shawber CJ. Investigation into the genetics of fetal congenital lymphatic anomalies. Prenat Diagn 2023;43:703-716. [PMID: 36959127 PMCID: PMC10330091 DOI: 10.1002/pd.6345] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 02/10/2023] [Accepted: 03/12/2023] [Indexed: 03/25/2023]

Graifman JL, Lippa NC, Mulhern MS, Bergner AL, Sands TT. Clinical utility of exome sequencing in a pediatric epilepsy cohort. Epilepsia 2023;64:986-997. [PMID: 36740579 DOI: 10.1111/epi.17534] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 02/02/2023] [Accepted: 02/02/2023] [Indexed: 02/07/2023]

Abstract

OBJECTIVE

Exome sequencing (ES) has played an important role in the identification of causative variants for individuals with epilepsy and has proven to be a valuable diagnostic tool. Less is known about its clinical utility once a diagnosis is received. This study systematically reviewed the impact of ES results on clinical decision-making and patient care in a pediatric epilepsy cohort at a tertiary care medical center.

METHODS

Pediatric patients with unexplained epilepsy were referred by their neurologist, and informed consent was obtained through an institutional review board-approved research ES protocol. For patients who received a genetic diagnosis, a retrospective chart review was completed of the probands and their relatives' medical records prior to and after genetic diagnosis. The following outcomes were explored: provider management recommendations, changes in care actually implemented, and anticipatory guidance provided regarding the proband's condition.

RESULTS

Fifty-three probands met the inclusion criteria. Genetic diagnosis led to at least one provider recommendation in 41.5% families (22/53). Recommendations were observed in the following categories: medication, screening for non-neurological comorbidities/referrals to specialists, referrals to clinical research/trials, and cascade testing. Anticipatory guidance including information about molecular diagnosis, prognosis, and relevant foundations/advocacy groups was also observed.

SIGNIFICANCE

Results demonstrate the clinical utility of ES for individuals with epilepsy across multiple aspects of patient care, including anti-seizure medication (ASM) selection; screening for non-neurological comorbidities and referrals to appropriate medical specialists; referral to reproductive genetic counseling; and access to research, information, and support resources. To our knowledge, this is the first study to evaluate the clinical utility of ES for a pediatric epilepsy cohort with broad epilepsy phenotypes. This work supports the implementation of ES as part of clinical care in this population.

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Motelow JE, Lippa NC, Hostyk J, Feldman E, Nelligan M, Ren Z, Alkelai A, Milner JD, Gharavi AG, Tang Y, Goldstein DB, Kernie SG. Risk Variants in the Exomes of Children With Critical Illness. JAMA Netw Open 2022;5:e2239122. [PMID: 36306130 PMCID: PMC9617179 DOI: 10.1001/jamanetworkopen.2022.39122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open

Abstract

IMPORTANCE

Diagnostic genetic testing can lead to changes in management in the pediatric intensive care unit. Genetic risk in children with critical illness but nondiagnostic exome sequencing (ES) has not been explored.

OBJECTIVE

To assess the association between loss-of-function (LOF) variants and pediatric critical illness.

DESIGN, SETTING, AND PARTICIPANTS

This genetic association study examined ES first screened for causative variants among 267 children at the Morgan Stanley Children's Hospital of NewYork-Presbyterian, of whom 22 were otherwise healthy with viral respiratory failure; 18 deceased children with bronchiolitis from the Office of the Chief Medical Examiner of New York City, of whom 14 were previously healthy; and 9990 controls from the Institute for Genomic Medicine at Columbia University Irving Medical Center. The ES data were generated between January 1, 2015, and December 31, 2020, and analyzed between January 1, 2017, and September 2, 2022.

EXPOSURE

Critical illness.

MAIN OUTCOMES AND MEASURES

Odds ratios and P values for genes and gene-sets enriched for rare LOF variants and the loss-of-function observed/expected upper bound fraction (LOEUF) score at which cases have a significant enrichment.

RESULTS

This study included 285 children with critical illness (median [range] age, 4.1 [0-18.9] years; 148 [52%] male) and 9990 controls. A total of 228 children (80%) did not receive a genetic diagnosis. After quality control (QC), 231 children harbored excess rare LOF variants in genes with a LOEUF score of 0.680 or less (intolerant genes) (P = 1.0 × 10-5). After QC, 176 children without a diagnosis harbored excess ultrarare LOF variants in intolerant genes but only in those without a known disease association (odds ratio, 1.8; 95% CI, 1.3-2.5). After QC, 25 children with viral respiratory failure harbored excess ultrarare LOF variants in intolerant genes but only in those without a known disease association (odds ratio, 2.8; 95% CI, 1.1-6.6). A total of 114 undiagnosed children were enriched for de novo LOF variants in genes without a known disease association (observed, 14; expected, 6.8; enrichment, 2.05).

CONCLUSIONS AND RELEVANCE

In this genetic association study, excess LOF variants were observed among critically ill children despite nondiagnostic ES. Variants lay in genes without a known disease association, suggesting future investigation may connect phenotypes to causative genes.

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Affiliation(s)

Joshua E. Motelow Institute for Genomic Medicine, Columbia University Medical Center, New York, New York Division of Critical Care and Hospital Medicine, Department of Pediatrics, Columbia University Irving Medical Center, NewYork-Presbyterian Morgan Stanley Children's Hospital, New York, New York
Natalie C. Lippa Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
Joseph Hostyk Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
Evin Feldman Division of Critical Care and Hospital Medicine, Department of Pediatrics, Columbia University Irving Medical Center, NewYork-Presbyterian Morgan Stanley Children's Hospital, New York, New York
Matthew Nelligan Division of Critical Care and Hospital Medicine, Department of Pediatrics, Columbia University Irving Medical Center, NewYork-Presbyterian Morgan Stanley Children's Hospital, New York, New York
Zhong Ren Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
Anna Alkelai Institute for Genomic Medicine, Columbia University Medical Center, New York, New York Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, New York
Joshua D. Milner
Ali G. Gharavi Institute for Genomic Medicine, Columbia University Medical Center, New York, New York Division of Nephrology, Department of Medicine, Columbia University Irving Medical Center, NewYork-Presbyterian, New York, New York
Yingying Tang Molecular Genetics Laboratory, New York City Office of Chief Medical Examiner, New York, New York
David B. Goldstein Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
Steven G. Kernie Division of Critical Care and Hospital Medicine, Department of Pediatrics, Columbia University Irving Medical Center, NewYork-Presbyterian Morgan Stanley Children's Hospital, New York, New York NewYork-Presbyterian Hospital, New York, New York

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