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Smith HS, Leo M, Goddard K, Muessig K, Angelo F, Knight S, Outram S, Kelly NR, Rini C. Measuring health-related quality of life in children with suspected genetic conditions: validation of the PedsQL proxy-report versions. Qual Life Res 2024; 33:1541-1553. [PMID: 38472717 PMCID: PMC11116065 DOI: 10.1007/s11136-024-03623-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/26/2024] [Indexed: 03/14/2024]
Abstract
PURPOSE Measuring health-related quality of life (HRQoL) of children with suspected genetic conditions is important for understanding the effect of interventions such as genomic sequencing (GS). The Pediatric Quality of Life Inventory (PedsQL) is a widely used generic measure of HRQoL in pediatric patients, but its psychometric properties have not yet been evaluated in children undergoing diagnostic GS. METHODS In this cross-sectional study, we surveyed caregivers at the time of their child's enrollment into GS research studies as part of the Clinical Sequencing Evidence Generating Research (CSER) consortium. To evaluate structural validity of the PedsQL 4.0 Generic Core Scales and PedsQL Infant Scales parent proxy-report versions, we performed a confirmatory factor analysis of the hypothesized factor structure. To evaluate convergent validity, we examined correlations between caregivers' reports of their child's health, assessed using the EQ VAS, and PedsQL scores by child age. We conducted linear regression analyses to examine whether age moderated the association between caregiver-reported child health and PedsQL scores. We assessed reliability using Cronbach's alpha. RESULTS We analyzed data for 766 patients across all PedsQL age group versions (1-12 months through 13-18 years). Model fit failed to meet criteria for good fit, even after modification. Neither age group (categorical) nor age (continuous) significantly moderated associations between PedsQL scores and caregiver-reported child health. Cronbach's alphas indicated satisfactory internal consistency for most PedsQL scales. CONCLUSION The PedsQL Generic Core Scales and Infant Scales may be appropriate to measure HRQoL in pediatric patients with suspected genetic conditions across a wide age range. While we found evidence of acceptable internal consistency and preliminary convergent validity in this sample, there were some potential problems with structural validity and reliability that require further attention.
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Affiliation(s)
- Hadley Stevens Smith
- Department of Population Medicine, Harvard Medical School, 401 Park Drive, Suite 401, Boston, MA, 02215, USA.
| | - Michael Leo
- Kaiser Permanente Center for Health Research, Portland, OR, USA
| | - Katrina Goddard
- Department of Translational and Applied Genomics (TAG), Kaiser Permanente Center for Health Research, Portland, OR, USA
| | - Kristin Muessig
- Department of Translational and Applied Genomics (TAG), Kaiser Permanente Center for Health Research, Portland, OR, USA
| | - Frank Angelo
- Institute for Sexual and Gender Minority Health and Wellbeing, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Sara Knight
- Department of Internal Medicine, Division of Epidemiology, University of Utah, Salt Lake City, UT, USA
| | - Simon Outram
- Program in Bioethics, University of California San Francisco, San Francisco, CA, USA
| | - Nicole R Kelly
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA
| | - Christine Rini
- Department of Medical Social Sciences, Northwestern University Feinberg School of Medicine, The Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, USA
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Watkins WS, Hernandez EJ, Miller TA, Blue NR, Zimmerman R, Griffiths ER, Frise E, Bernstein D, Boskovski MT, Brueckner M, Chung WK, Gaynor JW, Gelb BD, Goldmuntz E, Gruber PJ, Newburger JW, Roberts AE, Morton SU, Mayer JE, Seidman CE, Seidman JG, Shen Y, Wagner M, Yost HJ, Yandell M, Tristani-Firouzi M. Genome Sequencing is Critical for Forecasting Outcomes following Congenital Cardiac Surgery. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.03.24306784. [PMID: 38746151 PMCID: PMC11092705 DOI: 10.1101/2024.05.03.24306784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
While genome sequencing has transformed medicine by elucidating the genetic underpinnings of both rare and common complex disorders, its utility to predict clinical outcomes remains understudied. Here, we used artificial intelligence (AI) technologies to explore the predictive value of genome sequencing in forecasting clinical outcomes following surgery for congenital heart defects (CHD). We report results for a cohort of 2,253 CHD patients from the Pediatric Cardiac Genomics Consortium with a broad range of complex heart defects, pre- and post-operative clinical variables and exome sequencing. Damaging genotypes in chromatin-modifying and cilia-related genes were associated with an elevated risk of adverse post-operative outcomes, including mortality, cardiac arrest and prolonged mechanical ventilation. The impact of damaging genotypes was further amplified in the context of specific CHD phenotypes, surgical complexity and extra-cardiac anomalies. The absence of a damaging genotype in chromatin-modifying and cilia-related genes was also informative, reducing the risk for adverse postoperative outcomes. Thus, genome sequencing enriches the ability to forecast outcomes following congenital cardiac surgery.
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Cheng X, Chen J, Yang X, Chan H, Yang X, Jiao J, Wang A, Zhang G, Chen X, Li X, Wang M, Yang B, Yang H, Li Q. Comparison of different genetic testing modalities applied in paediatric patients with steroid-resistant nephrotic syndrome. Ital J Pediatr 2024; 50:85. [PMID: 38654395 DOI: 10.1186/s13052-024-01655-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 04/07/2024] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND Steroid-resistant nephrotic syndrome (SRNS) are monogenic in some cases, however, there are still no clear guidelines on genetic testing in the clinical practice of SRNS in children. METHODS Three hundred thirty-two children were diagnosed with SRNS, and all children underwent genetic testing, including gene panels and/or whole-exome/genome sequencing (WES/WGS), during treatment. We analysed the relationship between clinical manifestation and genotype, and compared different genetic testing methods' detection rates and prices. RESULTS In this study, 30.12% (100/332) of children diagnosed with SRNS had monogenic causes of the disease. With 33.7% (122/332) of children achieving complete remission, 88.5% (108/122) received steroids combined with tacrolimus (TAC). In detectability, WES increased by 8.69% (4/46) on gene panel testing, while WGS increased by 4.27% (5/117) on WES, and WES was approximately 1/7 of the price of WGS for every further 1% increase in pathogenicity. CONCLUSIONS We verified that steroids combined with TAC were the most effective option in paediatric SRNS. In detection efficiency, we found that WGS was the highest, followed by WES. The panel was the lowest, but the most cost-effective method when considering the economic-benefit ratio, and thus it should be recommended first in SRNS.
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Affiliation(s)
- Xueting Cheng
- Department of Nephrology, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Jiahuan Chen
- Department of Nephrology, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Xueying Yang
- Department of Nephrology, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Han Chan
- Department of Nephrology, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Xia Yang
- Department of Nephrology, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Jia Jiao
- Department of Nephrology, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Anshuo Wang
- Department of Nephrology, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Gaofu Zhang
- Department of Nephrology, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Xuelan Chen
- Department of Nephrology, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Xiaoqin Li
- Department of Nephrology, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Mo Wang
- Department of Nephrology, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Baohui Yang
- Department of Nephrology, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Haiping Yang
- Department of Nephrology, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, Chongqing, China.
| | - Qiu Li
- Department of Nephrology, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, Chongqing, China.
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Schildt A, Stevenson DA, Yu L, Anguiano B, Suarez CJ. Time to diagnosis in rapid exome/genome sequencing in the clinical inpatient setting. Am J Med Genet A 2024; 194:e63483. [PMID: 38017634 DOI: 10.1002/ajmg.a.63483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 11/15/2023] [Accepted: 11/16/2023] [Indexed: 11/30/2023]
Abstract
Exome and genome sequencing are clinically available, with many laboratories offering expedited testing (e.g., "rapid" and "ultra-rapid"). With the increase in uptake of expedited testing, there is a need for the development of inpatient protocols for best practices based on real-life data. A retrospective 2-year review (October 2019-November 2021) of the utilization of rapid exome and genome sequencing for inpatient cases at a tertiary care center using a utilization management tracking database with subsequent chart review was performed. Thirty-three expedited "rapid/priority" exome/genome tests were performed clinically. The average total turnaround time (TAT) was 17.88 days (5-43 days) with an average TAT of 13.97 days (3-41 days) for the performing laboratory. There were 5 positive diagnostic results (15.2%), 3 likely positive diagnostic results (9%), 2 noncontributory results (6%), and 26 nondiagnostic results (69.7%). Real-life data suggest that there is an approximately 3.91-day lag in getting samples to the performing laboratory. Although laboratories may advertise their expected TAT, a number of factors can potentially impact the actual time from test order placement to communication of the results for clinical use. Understanding the points of delay will enable the development of internal protocols and policies to improve time to diagnosis.
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Affiliation(s)
- Alison Schildt
- Department of Pediatrics, Division of Medical Genetics, Stanford University, Palo Alto, California, USA
| | - David A Stevenson
- Department of Pediatrics, Division of Medical Genetics, Stanford University, Palo Alto, California, USA
| | - Linbo Yu
- Genetic Testing Optimization Service, Stanford Hospitals and Clinics, Palo Alto, California, USA
| | - Beatriz Anguiano
- Genetic Testing Optimization Service, Stanford Hospitals and Clinics, Palo Alto, California, USA
| | - Carlos J Suarez
- Department of Pathology, Stanford University, Palo Alto, California, USA
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Gold J, Kripke CM, Drivas TG. Universal Exome Sequencing in Critically Ill Adults: A Diagnostic Yield of 25% and Race-Based Disparities in Access to Genetic Testing. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.03.11.24304088. [PMID: 38559092 PMCID: PMC10980115 DOI: 10.1101/2024.03.11.24304088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Numerous studies have underscored the diagnostic and therapeutic potential of exome or genome sequencing in critically ill pediatric populations. However, an equivalent investigation in critically ill adults remains conspicuously absent. We retrospectively analyzed whole exome sequencing (WES) data available through the PennMedicine Biobank (PMBB) from all 365 young adult patients, aged 18-40 years, with intensive care unit (ICU) admissions at the University of Pennsylvania Health System who met inclusion criteria for our study. For each participant, two Medical Genetics and Internal Medicine-trained clinicians reviewed WES reports and patient charts for variant classification, result interpretation, and identification of genetic diagnoses related to their critical illness. Of the 365 individuals in our study, 90 (24.7%) were found to have clearly diagnostic results on WES; an additional 40 (11.0%) had a suspicious variant of uncertain significance (VUS) identified; and an additional 16 (4.4%) had a medically actionable incidental finding. The diagnostic rate of exome sequencing did not decrease with increasing patient age. Affected genes were primarily involved in cardiac function (18.8%), vascular health (16.7%), cancer (16.7%), and pulmonary disease (11.5%). Only half of all diagnostic findings were known and documented in the patient chart at the time of ICU admission. Significant disparities emerged in subgroup analysis by EHR-reported race, with genetic diagnoses known/documented for 63.5% of White patients at the time of ICU admission but only for 28.6% of Black or Hispanic patients. There was a trend towards patients with undocumented genetic diagnoses having a 66% increased mortality rate, making these race-based disparities in genetic diagnosis even more concerning. Altogether, universal exome sequencing in ICU-admitted adult patients was found to yield a new definitive diagnosis in 11.2% of patients. Of these diagnoses, 76.6% conferred specific care-altering medical management recommendations. Our study suggests that the diagnostic utility of exome sequencing in critically ill young adults is similar to that observed in neonatal and pediatric populations and is age-independent. The high diagnostic rate and striking race-based disparities we find in genetic diagnoses argue for broad and universal approaches to genetic testing for critically ill adults. The widespread implementation of comprehensive genetic sequencing in the adult population promises to enhance medical care for all individuals and holds the potential to rectify disparities in genetic testing referrals, ultimately promoting more equitable healthcare delivery.
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Affiliation(s)
- Jessica Gold
- Division of Clinical Genetics, Department of Pediatrics, Northwell Health, Great Neck, NY 11021, USA
| | - Colleen M. Kripke
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19194, USA
| | | | | | - Theodore G. Drivas
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19194, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19194, USA
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6
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Pucel J, Briere LC, Reuter C, Gochyyev P, LeBlanc K. Exome and genome sequencing in a heterogeneous population of patients with rare disease: Identifying predictors of a diagnosis. Genet Med 2024; 26:101115. [PMID: 38436216 DOI: 10.1016/j.gim.2024.101115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 02/24/2024] [Accepted: 02/27/2024] [Indexed: 03/05/2024] Open
Abstract
PURPOSE Exome (ES) and genome sequencing (GS) are increasingly being utilized for individuals with rare and undiagnosed diseases; however, guidelines on their use remain limited. This study aimed to identify factors associated with diagnosis by ES and/or GS in a heterogeneous population of patients with rare and undiagnosed diseases. METHODS In this case control study, we reviewed data from 400 diagnosed and 400 undiagnosed randomly selected participants in the Undiagnosed Diseases Network, all of whom had undergone ES and/or GS. We analyzed factors associated with receiving a diagnosis by ES and/or GS. RESULTS Factors associated with a decreased odds of being diagnosed included adult symptom onset, singleton sequencing, and having undergone ES and/or GS before acceptance to the Undiagnosed Diseases Network (48%, 51%, and 32% lower odds, respectively). Factors that increased the odds of being diagnosed by ES and/or GS included having primarily neurological symptoms and having undergone prior chromosomal microarray testing (44% and 59% higher odds, respectively). CONCLUSION We identified several factors that were associated with receiving a diagnosis by ES and/or GS. This will ideally inform the utilization of ES and/or GS and help manage expectations of individuals and families undergoing these tests.
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Affiliation(s)
- Jenna Pucel
- MGH Institute of Health Professions, Boston, MA.
| | - Lauren C Briere
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
| | - Chloe Reuter
- Stanford Center for Undiagnosed Diseases, Cardiovascular Medicine, Stanford University, Palo Alto, CA
| | | | - Kimberly LeBlanc
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA
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7
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Seither K, Thompson W, Suhrie K. A Practical Guide to Whole Genome Sequencing in the NICU. Neoreviews 2024; 25:e139-e150. [PMID: 38425198 DOI: 10.1542/neo.25-3-e139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
The neonatal period is a peak time for the presentation of genetic disorders that can be diagnosed using whole genome sequencing (WGS). While any one genetic disorder is individually rare, they collectively contribute to significant morbidity, mortality, and health-care costs. As the cost of WGS continues to decline and becomes increasingly available, the ordering of rapid WGS for NICU patients with signs or symptoms of an underlying genetic condition is now feasible. However, many neonatal clinicians are not comfortable with the testing, and unfortunately, there is a dearth of geneticists to facilitate testing for every patient that needs it. Here, we will review the science behind WGS, diagnostic capabilities, limitations of testing, time to consider testing, test initiation, interpretation of results, developing a plan of care that incorporates genomic information, and returning WGS results to families.
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Affiliation(s)
- Katelyn Seither
- Division of Neonatal and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, and the Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH
| | - Whitney Thompson
- Division of Neonatal Medicine, and the Department of Clinical Genomics, Mayo Clinic, Rochester, MN
| | - Kristen Suhrie
- Division of Neonatology, Department of Pediatrics, and Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN
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Kingsmore SF, Nofsinger R, Ellsworth K. Rapid genomic sequencing for genetic disease diagnosis and therapy in intensive care units: a review. NPJ Genom Med 2024; 9:17. [PMID: 38413639 PMCID: PMC10899612 DOI: 10.1038/s41525-024-00404-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 02/15/2024] [Indexed: 02/29/2024] Open
Abstract
Single locus (Mendelian) diseases are a leading cause of childhood hospitalization, intensive care unit (ICU) admission, mortality, and healthcare cost. Rapid genome sequencing (RGS), ultra-rapid genome sequencing (URGS), and rapid exome sequencing (RES) are diagnostic tests for genetic diseases for ICU patients. In 44 studies of children in ICUs with diseases of unknown etiology, 37% received a genetic diagnosis, 26% had consequent changes in management, and net healthcare costs were reduced by $14,265 per child tested by URGS, RGS, or RES. URGS outperformed RGS and RES with faster time to diagnosis, and higher rate of diagnosis and clinical utility. Diagnostic and clinical outcomes will improve as methods evolve, costs decrease, and testing is implemented within precision medicine delivery systems attuned to ICU needs. URGS, RGS, and RES are currently performed in <5% of the ~200,000 children likely to benefit annually due to lack of payor coverage, inadequate reimbursement, hospital policies, hospitalist unfamiliarity, under-recognition of possible genetic diseases, and current formatting as tests rather than as a rapid precision medicine delivery system. The gap between actual and optimal outcomes in children in ICUs is currently increasing since expanded use of URGS, RGS, and RES lags growth in those likely to benefit through new therapies. There is sufficient evidence to conclude that URGS, RGS, or RES should be considered in all children with diseases of uncertain etiology at ICU admission. Minimally, diagnostic URGS, RGS, or RES should be ordered early during admissions of critically ill infants and children with suspected genetic diseases.
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Affiliation(s)
- Stephen F Kingsmore
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA.
| | - Russell Nofsinger
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA
| | - Kasia Ellsworth
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA
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9
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Wigby KM, Brockman D, Costain G, Hale C, Taylor SL, Belmont J, Bick D, Dimmock D, Fernbach S, Greally J, Jobanputra V, Kulkarni S, Spiteri E, Taft RJ. Evidence review and considerations for use of first line genome sequencing to diagnose rare genetic disorders. NPJ Genom Med 2024; 9:15. [PMID: 38409289 PMCID: PMC10897481 DOI: 10.1038/s41525-024-00396-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Accepted: 01/26/2024] [Indexed: 02/28/2024] Open
Abstract
Early use of genome sequencing (GS) in the diagnostic odyssey can reduce suffering and improve care, but questions remain about which patient populations are most amenable to GS as a first-line diagnostic test. To address this, the Medical Genome Initiative conducted a literature review to identify appropriate clinical indications for GS. Studies published from January 2011 to August 2022 that reported on the diagnostic yield (DY) or clinical utility of GS were included. An exploratory meta-analysis using a random effects model evaluated DY based on cohort size and diagnosed cases per cohort. Seventy-one studies met inclusion criteria, comprising over 13,000 patients who received GS in one of the following settings: hospitalized pediatric patients, pediatric outpatients, adult outpatients, or mixed. GS was the first-line test in 38% (27/71). The unweighted mean DY of first-line GS was 45% (12-73%), 33% (6-86%) in cohorts with prior genetic testing, and 33% (9-60%) in exome-negative cohorts. Clinical utility was reported in 81% of first-line GS studies in hospitalized pediatric patients. Changes in management varied by cohort and underlying molecular diagnosis (24-100%). To develop evidence-informed points to consider, the quality of all 71 studies was assessed using modified American College of Radiology (ACR) criteria, with five core points to consider developed, including recommendations for use of GS in the N/PICU, in lieu of sequential testing and when disorders with substantial allelic heterogeneity are suspected. Future large and controlled studies in the pediatric and adult populations may support further refinement of these recommendations.
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Affiliation(s)
- Kristen M Wigby
- University of California, Davis, CA, USA.
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA.
| | | | | | | | | | - John Belmont
- Genetics & Genomics Services Inc, Houston, TX, USA
| | | | - David Dimmock
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | | | - John Greally
- Albert Einstein College of Medicine, Bronx, NY, USA
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10
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Thompson L, Larson A, Salz L, Veith R, Tsai JP, Jayakar A, Chapman R, Gupta A, Kingsmore SF, Dimmock D, Bedrick A, Galindo MK, Casas K, Mohamed M, Straight L, Khan MA, Salyakina D. Multi-center implementation of rapid whole genome sequencing provides additional evidence of its utility in the pediatric inpatient setting. Front Pediatr 2024; 12:1349519. [PMID: 38440187 PMCID: PMC10909823 DOI: 10.3389/fped.2024.1349519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 02/01/2024] [Indexed: 03/06/2024] Open
Abstract
Objective Multi-center implementation of rapid whole genome sequencing with assessment of the clinical utility of rapid whole genome sequencing (rWGS), including positive, negative and uncertain results, in admitted infants with a suspected genetic disease. Study design rWGS tests were ordered at eight hospitals between November 2017 and April 2020. Investigators completed a survey of demographic data, Human Phenotype Ontology (HPO) terms, test results and impacts of results on clinical care. Results A total of 188 patients, on general hospital floors and intensive care unit (ICU) settings, underwent rWGS testing. Racial and ethnic characteristics of the tested infants were broadly representative of births in the country at large. 35% of infants received a diagnostic result in a median of 6 days. The most common HPO terms for tested infants indicated an abnormality of the nervous system, followed by the cardiovascular system, the digestive system, the respiratory system and the head and neck. Providers indicated a major change in clinical management because of rWGS for 32% of infants tested overall and 70% of those with a diagnostic result. Also, 7% of infants with a negative rWGS result and 23% with a variant of unknown significance (VUS) had a major change in management due to testing. Conclusions Our study demonstrates that the implementation of rWGS is feasible across diverse institutions, and provides additional evidence to support the clinical utility of rWGS in a demographically representative sample of admitted infants and includes assessment of the clinical impact of uncertain rWGS results in addition to both positive and negative results.
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Affiliation(s)
- Lauren Thompson
- Division of Genetics and Metabolism, Nicklaus Children’s Hospital, Miami, FL, United States
| | - Austin Larson
- Department of Pediatrics, Children’s Hospital Colorado, Aurora, CO, United States
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, United States
| | - Lisa Salz
- RCIGM, Rady Children’s Hospital San Diego, San Diego, CA, United States
| | - Regan Veith
- Genomic Medicine, Children’s Minnesota, Minneapolis, MN, United States
| | - John-Paul Tsai
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, United States
| | - Anuj Jayakar
- Division of Genetics and Metabolism, Nicklaus Children’s Hospital, Miami, FL, United States
| | - Rachel Chapman
- Fetal & Neonatal Institute, Children’s Hospital Los Angeles, Los Angeles, CA, United States
- Department of Pediatrics, USC Keck School of Medicine, Los Angeles, CA, United States
| | - Apeksha Gupta
- Division of Genetics and Metabolism, Nicklaus Children’s Hospital, Miami, FL, United States
| | | | - David Dimmock
- RCIGM, Rady Children’s Hospital San Diego, San Diego, CA, United States
| | - Alan Bedrick
- Department of Pediatrics, Banner Diamond Children’s Medical Center, Tucson, AZ, United States
- Department of Pediatrics, University of Arizona College of Medicine, Tucson, AZ, United States
| | - Maureen Kelly Galindo
- Department of Pediatrics, Banner Diamond Children’s Medical Center, Tucson, AZ, United States
| | - Kari Casas
- Department of Pediatrics, Sanford Children’s Fargo, Fargo, SD, United States
| | - Mohamed Mohamed
- Department of Pediatrics, Sanford Children’s Fargo, Fargo, SD, United States
| | - Lisa Straight
- Department of Pediatrics, Sanford Children’s Sioux Falls, Sioux Falls, SD, United States
| | - M. Akram Khan
- Department of Pediatrics, Sanford Children’s Sioux Falls, Sioux Falls, SD, United States
| | - Daria Salyakina
- Division of Genetics and Metabolism, Nicklaus Children’s Hospital, Miami, FL, United States
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11
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D'Gama AM, Hills S, Douglas J, Young V, Genetti CA, Wojcik MH, Feldman HA, Yu TW, G Parker M, Agrawal PB. Implementation of rapid genomic sequencing in safety-net neonatal intensive care units: protocol for the VIrtual GenOme CenteR (VIGOR) proof-of-concept study. BMJ Open 2024; 14:e080529. [PMID: 38320840 PMCID: PMC10859977 DOI: 10.1136/bmjopen-2023-080529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 01/17/2024] [Indexed: 02/15/2024] Open
Abstract
INTRODUCTION Rapid genomic sequencing (rGS) in critically ill infants with suspected genetic disorders has high diagnostic and clinical utility. However, rGS has primarily been available at large referral centres with the resources and expertise to offer state-of-the-art genomic care. Critically ill infants from racial and ethnic minority and/or low-income populations disproportionately receive care in safety-net and/or community settings lacking access to state-of-the-art genomic care, contributing to unacceptable health equity gaps. VIrtual GenOme CenteR is a 'proof-of-concept' implementation science study of an innovative delivery model for genomic care in safety-net neonatal intensive care units (NICUs). METHODS AND ANALYSIS We developed a virtual genome centre at a referral centre to remotely support safety-net NICU sites predominantly serving racial and ethnic minority and/or low-income populations and have limited to no access to rGS. Neonatal providers at each site receive basic education about genomic medicine from the study team and identify eligible infants. The study team enrols eligible infants (goal n of 250) and their parents and follows families for 12 months. Enrolled infants receive rGS, the study team creates clinical interpretive reports to guide neonatal providers on interpreting results, and neonatal providers return results to families. Data is collected via (1) medical record abstraction, (2) surveys, interviews and focus groups with neonatal providers and (3) surveys and interviews with families. We aim to examine comprehensive implementation outcomes based on the Proctor Implementation Framework using a mixed methods approach. ETHICS AND DISSEMINATION This study is approved by the institutional review board of Boston Children's Hospital (IRB-P00040496) and participating sites. Participating families are required to provide electronic written informed consent and neonatal provider consent is implied through the completion of surveys. The results will be disseminated via peer-reviewed publications and data will be made accessible per National Institutes of Health (NIH) policies. TRIAL REGISTRATION NUMBER NCT05205356/clinicaltrials.gov.
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Affiliation(s)
- Alissa M D'Gama
- Division of Newborn Medicine, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts, USA
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Sonia Hills
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Jessica Douglas
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Vanessa Young
- Division of Newborn Medicine, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Casie A Genetti
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Monica H Wojcik
- Division of Newborn Medicine, Department of Pediatrics, Harvard Medical School, Boston Children's Hospital, Boston, Massachusetts, USA
- Division of Genetics and Genomics, Department of Pediatrics, Harvard Medical School, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Henry A Feldman
- Division of Newborn Medicine, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Timothy W Yu
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts, USA
| | | | - Pankaj B Agrawal
- Division of Neonatology, Department of Pediatrics, University of Miami Miller School of Medicine, Miami, Florida, USA
- Jackson Health System, Holtz Children's Hospital, Miami, Florida, USA
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12
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Marom D, Mory A, Reytan-Miron S, Amir Y, Kurolap A, Cohen JG, Morhi Y, Smolkin T, Cohen L, Zangen S, Shalata A, Riskin A, Peleg A, Lavie-Nevo K, Mandel D, Chervinsky E, Fisch CF, Fleisher Sheffer V, Falik-Zaccai TC, Rips J, Shlomai NO, Friedman SE, Shporen CH, Ben-Yehoshua SJ, Simmonds A, Yaacobi RG, Bauer-Rusek S, Omari H, Weiss K, Hochwald O, Koifman A, Globus O, Batzir NA, Yaron N, Segel R, Morag I, Reish O, Eliyahu A, Leibovitch L, Schwartz ME, Abramsky R, Hochberg A, Oron A, Banne E, Portnov I, Samra NN, Singer A, Baris Feldman H. National Rapid Genome Sequencing in Neonatal Intensive Care. JAMA Netw Open 2024; 7:e240146. [PMID: 38386321 PMCID: PMC10884880 DOI: 10.1001/jamanetworkopen.2024.0146] [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: 02/23/2024] Open
Abstract
Importance National implementation of rapid trio genome sequencing (rtGS) in a clinical acute setting is essential to ensure advanced and equitable care for ill neonates. Objective To evaluate the feasibility, diagnostic efficacy, and clinical utility of rtGS in neonatal intensive care units (NICUs) throughout Israel. Design, Setting, and Participants This prospective, public health care-based, multicenter cohort study was conducted from October 2021 to December 2022 with the Community Genetics Department of the Israeli Ministry of Health and all Israeli medical genetics institutes (n = 18) and NICUs (n = 25). Critically ill neonates suspected of having a genetic etiology were offered rtGS. All sequencing, analysis, and interpretation of data were performed in a central genomics center at Tel-Aviv Sourasky Medical Center. Rapid results were expected within 10 days. A secondary analysis report, issued within 60 days, focused mainly on cases with negative rapid results and actionable secondary findings. Pathogenic, likely pathogenic, and highly suspected variants of unknown significance (VUS) were reported. Main Outcomes and Measures Diagnostic rate, including highly suspected disease-causing VUS, and turnaround time for rapid results. Clinical utility was assessed via questionnaires circulated to treating neonatologists. Results A total of 130 neonates across Israel (70 [54%] male; 60 [46%] female) met inclusion criteria and were recruited. Mean (SD) age at enrollment was 12 (13) days. Mean (SD) turnaround time for rapid report was 7 (3) days. Diagnostic efficacy was 50% (65 of 130) for disease-causing variants, 11% (14 of 130) for VUS suspected to be causative, and 1 novel gene candidate (1%). Disease-causing variants included 12 chromosomal and 52 monogenic disorders as well as 1 neonate with uniparental disomy. Overall, the response rate for clinical utility questionnaires was 82% (107 of 130). Among respondents, genomic testing led to a change in medical management for 24 neonates (22%). Results led to immediate precision medicine for 6 of 65 diagnosed infants (9%), an additional 2 (3%) received palliative care, and 2 (3%) were transferred to nursing homes. Conclusions and Relevance In this national cohort study, rtGS in critically ill neonates was feasible and diagnostically beneficial in a public health care setting. This study is a prerequisite for implementation of rtGS for ill neonates into routine care and may aid in design of similar studies in other public health care systems.
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Affiliation(s)
- Daphna Marom
- The Genetics Institute and Genomics Center, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Adi Mory
- The Genetics Institute and Genomics Center, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Sivan Reytan-Miron
- The Genetics Institute and Genomics Center, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Yam Amir
- The Genetics Institute and Genomics Center, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Alina Kurolap
- The Genetics Institute and Genomics Center, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Julia Grinshpun Cohen
- Community Genetics Department, Public Health Services, Ministry of Health, Ramat Gan, Israel
| | - Yocheved Morhi
- Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Tatiana Smolkin
- Department of Neonatalogy, Baruch Padeh Medical Center, Tzafon Medical Center, Tiberias, Israel
- Azrieli Faculty of Medicine, Bar Ilan University, Ramat Gan, Israel
| | - Lior Cohen
- Genetics Unit, Barzilai University Medical Center, Ashkelon, Israel
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Be'er-Sheva, Israel
| | - Shmuel Zangen
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Be'er-Sheva, Israel
- Department of Neonatalogy, Barzilai University Medical Center, Ashkelon, Israel
| | - Adel Shalata
- Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
- Genetics Institute, Bnai Zion Medical Center, Haifa, Israel
| | - Arieh Riskin
- Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
- Department of Neonatalogy, Bnai Zion Medical Center, Haifa, Israel
| | - Amir Peleg
- Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
- Genetics Institute, Carmel Medical Center, Haifa, Israel
| | - Karen Lavie-Nevo
- Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
- Department of Neonatalogy, Carmel Medical Center, Haifa, Israel
| | - Dror Mandel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Department of Neonatalogy, Dana-Dwek Children's Hospital, Tel Aviv Medical Center, Tel Aviv, Israel
| | - Elana Chervinsky
- Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
- The Genetics Institute and Center of Rare Diseases, Emek Medical Center, Afula, Israel
| | - Clari Felszer Fisch
- Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
- Department of Neonatalogy, Emek Medical Center, Afula, Israel
| | - Vered Fleisher Sheffer
- Azrieli Faculty of Medicine, Bar Ilan University, Ramat Gan, Israel
- Department of Neonatalogy, Galilee Medical Center, Naharia, Israel
| | - Tzipora C Falik-Zaccai
- Azrieli Faculty of Medicine, Bar Ilan University, Ramat Gan, Israel
- Genetics Institute, Galilee Medical Center, Naharia, Israel
| | - Jonathan Rips
- Department of Genetics, Hadassah Medical Organization, Jerusalem, Israel
- Faculty of Medicine, The Hebrew University of Jerusalem, Ein Kerem, Jerusalem, Israel
| | - Noa Ofek Shlomai
- Faculty of Medicine, The Hebrew University of Jerusalem, Ein Kerem, Jerusalem, Israel
- Department of Neonatalogy, Hadassah Medical Organization, Jerusalem, Israel
| | - Smadar Eventov Friedman
- Faculty of Medicine, The Hebrew University of Jerusalem, Ein Kerem, Jerusalem, Israel
- Department of Neonatalogy, Hadassah Medical Organization, Jerusalem, Israel
| | - Calanit Hershkovich Shporen
- Faculty of Medicine, The Hebrew University of Jerusalem, Ein Kerem, Jerusalem, Israel
- Department of Neonatalogy, Kaplan Medical Center, Rehovot, Israel
| | - Sagie Josefsberg Ben-Yehoshua
- Faculty of Medicine, The Hebrew University of Jerusalem, Ein Kerem, Jerusalem, Israel
- Genetics Institute, Kaplan Medical Center, Rehovot, Israel
| | - Aryeh Simmonds
- Department of Neonatalogy, Laniado Hospital, Netanya, Israel
- Adelson School of Medicine, Ariel University, Ariel, Israel
| | - Racheli Goldfarb Yaacobi
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Genetics Institute, Meir Medical Center, Kefar-Sava, Israel
| | - Sofia Bauer-Rusek
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Department of Neonatalogy, Meir Medical Center, Kefar-Sava, Israel
| | - Hussam Omari
- Azrieli Faculty of Medicine, Bar Ilan University, Ramat Gan, Israel
- Department of Neonatalogy, Saint Vincent Hospital (French Hospital), Nazareth, Israel
| | - Karin Weiss
- Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
- Genetics Institute, Rambam Medical Center, Haifa, Israel
| | - Ori Hochwald
- Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
- Department of Neonatalogy, Rambam Medical Center, Haifa, Israel
| | - Arie Koifman
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Be'er-Sheva, Israel
- Genetics Institute, Samson Assuta University Medical Center, Ashdod, Israel
| | - Omer Globus
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Be'er-Sheva, Israel
- Department of Neonatalogy, Samson Assuta University Medical Center, Ashdod, Israel
| | - Nurit Assia Batzir
- Pediatric Genetics Unit, Schneider Children's Medical Center of Israel, Petach Tikva, Israel
| | - Naveh Yaron
- Faculty of Medicine, The Hebrew University of Jerusalem, Ein Kerem, Jerusalem, Israel
- Department of Neonatalogy, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Reeval Segel
- Faculty of Medicine, The Hebrew University of Jerusalem, Ein Kerem, Jerusalem, Israel
- Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Iris Morag
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Department of Neonatalogy, Shamir Medical Center, Zerifin, Israel
| | - Orit Reish
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Genetics Institute, Shamir Medical Center, Zerifin, Israel
| | - Aviva Eliyahu
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel-Hashomer, Israel
| | - Leah Leibovitch
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Neonatology Department, Sheba Medical Center, Tel-Hashomer, Israel
| | - Marina Eskin Schwartz
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Be'er-Sheva, Israel
- Genetics Institute, Soroka University Medical Center, Be'er Sheva, Israel
| | - Ramy Abramsky
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Be'er-Sheva, Israel
- Department of Neonatalogy, Soroka University Medical Center, Be'er Sheva, Israel
| | - Amit Hochberg
- Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
- Department of Neonatalogy, The Hillel Yaffe Medical Center, Hadera, Israel
| | - Anat Oron
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Department of Neonatalogy, Wolfson Medical Center, Holon, Israel
| | - Ehud Banne
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Genetics Institute, Wolfson Medical Center, Hadera, Israel
| | - Igor Portnov
- Azrieli Faculty of Medicine, Bar Ilan University, Ramat Gan, Israel
- Department of Neonatalogy, Ziv Medical Center Sefat, Tsfat, Israel
| | - Nadra Nasser Samra
- Azrieli Faculty of Medicine, Bar Ilan University, Ramat Gan, Israel
- Genetics Institute, Ziv Medical Center, Safed, Israel
| | - Amihood Singer
- Community Genetics Department, Public Health Services, Ministry of Health, Ramat Gan, Israel
| | - Hagit Baris Feldman
- The Genetics Institute and Genomics Center, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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Aekka A, Weisman AG, Papadakis J, Yerkes E, Baker J, Keswani M, Weinstein J, Finlayson C. Clinical utility of early rapid genome sequencing in the evaluation of patients with differences of sex development. Am J Med Genet A 2024; 194:351-357. [PMID: 37789729 DOI: 10.1002/ajmg.a.63377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/08/2023] [Accepted: 08/09/2023] [Indexed: 10/05/2023]
Abstract
Establishing an early and accurate genetic diagnosis among patients with differences of sex development (DSD) is crucial in guiding the complex medical and psychosocial care they require. Genetic testing routinely utilized in clinical practice for this population is predicated upon physical exam findings and biochemical and endocrine profiling. This approach, however, is inefficient and unstandardized. Many patients with DSD, particularly those with 46,XY DSD, never receive a molecular genetic diagnosis. Rapid genome sequencing (rGS) is gaining momentum as a first-tier diagnostic instrument in the evaluation of patients with DSD given its ability to provide greater diagnostic yield and timely results. We present the case of a patient with nonbinary genitalia and systemic findings for whom rGS identified a novel variant of the WT1 gene and resulted in a molecular diagnosis within two weeks of life. This timeframe of diagnosis for syndromic DSD is largely unprecedented at our institution. Rapid GS expedited mobilization of a multidisciplinary medical team; enabled early understanding of clinical trajectory; informed planning of medical and surgical interventions; and guided individualized psychosocial support provided to the family. This case highlights the potential of early rGS in transforming the evaluation and care of patients with DSD.
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Affiliation(s)
- Apoorva Aekka
- Division of Endocrinology, Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Allison Goetsch Weisman
- Division of Genetics, Genomics, and Metabolism, Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Jaclyn Papadakis
- Department of Psychiatry and Behavioral Health, Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Elizabeth Yerkes
- Division of Urology, Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Joshua Baker
- Division of Genetics, Genomics, and Metabolism, Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Mahima Keswani
- Division of Nephrology, Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Joanna Weinstein
- Division of Hematology, Oncology, Neuro-Oncology and Stem Cell Transplantation, Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Courtney Finlayson
- Division of Endocrinology, Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
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Romo L, Findlay SD, Burge CB. Regulatory features aid interpretation of 3'UTR variants. Am J Hum Genet 2024; 111:350-363. [PMID: 38237594 PMCID: PMC10870128 DOI: 10.1016/j.ajhg.2023.12.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 12/13/2023] [Accepted: 12/14/2023] [Indexed: 01/30/2024] Open
Abstract
Our ability to determine the clinical impact of variants in 3' untranslated regions (UTRs) of genes remains poor. We provide a thorough analysis of 3' UTR variants from several datasets. Variants in putative regulatory elements, including RNA-binding protein motifs, eCLIP peaks, and microRNA sites, are up to 16 times more likely than variants not in these elements to have gene expression and phenotype associations. Variants in regulatory motifs result in allele-specific protein binding in cell lines and allele-specific gene expression differences in population studies. In addition, variants in shared regions of alternatively polyadenylated isoforms and those proximal to polyA sites are more likely to affect gene expression and phenotype. Finally, pathogenic 3' UTR variants in ClinVar are up to 20 times more likely than benign variants to fall in a regulatory site. We incorporated these findings into RegVar, a software tool that interprets regulatory elements and annotations for any 3' UTR variant and predicts whether the variant is likely to affect gene expression or phenotype. This tool will help prioritize variants for experimental studies and identify pathogenic variants in individuals.
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Affiliation(s)
- Lindsay Romo
- Harvard Medical Genetics Training Program, Boston Children's Hospital, Boston, MA 02115, USA.
| | - Scott D Findlay
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Christopher B Burge
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
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15
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Marouane A, Neveling K, Deden AC, van den Heuvel S, Zafeiropoulou D, Castelein S, van de Veerdonk F, Koolen DA, Simons A, Rodenburg R, Westra D, Mensenkamp AR, de Leeuw N, Ligtenberg M, Matthijsse R, Pfundt R, Kamsteeg EJ, Brunner HG, Gilissen C, Feenstra I, de Boode WP, Yntema HG, van Zelst-Stams WAG, Nelen M, Vissers LELM. Lessons learned from rapid exome sequencing for 575 critically ill patients across the broad spectrum of rare disease. Front Genet 2024; 14:1304520. [PMID: 38259611 PMCID: PMC10800954 DOI: 10.3389/fgene.2023.1304520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 12/18/2023] [Indexed: 01/24/2024] Open
Abstract
Introduction: Rapid exome sequencing (rES) has become the first-choice genetic test for critically ill patients, mostly neonates, young infants, or fetuses in prenatal care, in time-sensitive situations and when it is expected that the genetic test result may guide clinical decision making. The implementation of rES has revolutionized medicine by enabling timely identification of genetic causes for various rare diseases. The utilization of rES has increasingly been recognized as an essential diagnostic tool for the identification of complex and undiagnosed genetic disorders. Methods: We conducted a retrospective evaluation of our experiences with rES performed on 575 critically ill patients from various age groups (prenatal to adulthood), over a four-year period (2016-2019). These patients presented with a wide spectrum of rare diseases, including but not limited to neurological disorders, severe combined immune deficiency, and cancer. Results: During the study period, there was a significant increase in rES referrals, with a rise from a total of two referrals in Q1-2016 to 10 referrals per week in Q4-2019. The median turnaround time (TAT) decreased from 17 to 11 days in the period 2016-2019, with an overall median TAT of 11 days (IQR 8-15 days). The overall diagnostic yield for this cohort was 30.4%, and did not significantly differ between the different age groups (e.g. adults 22.2% vs children 31.0%; p-value 0.35). However, variability in yield was observed between clinical entities: craniofacial anomalies yielded 58.3%, while for three clinical entities (severe combined immune deficiency, aneurysm, and hypogonadotropic hypogonadism) no diagnoses were obtained. Discussion: Importantly, whereas clinical significance is often only attributed to a conclusive diagnosis, we also observed impact on clinical decision-making for individuals in whom no genetic diagnosis was established. Hence, our experience shows that rES has an important role for patients of all ages and across the broad spectrum of rare diseases to impact clinical outcomes.
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Affiliation(s)
- Abderrahim Marouane
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
- Department of Neonatology, Radboud University Medical Center, Radboud Institute for Health Sciences, Amalia Children’s Hospital, Nijmegen, Netherlands
| | - Kornelia Neveling
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
- Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, Netherlands
| | - A. Chantal Deden
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Simone van den Heuvel
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Dimitra Zafeiropoulou
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Steven Castelein
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Frank van de Veerdonk
- Department of Internal Medicine, Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, Netherlands
| | - David A. Koolen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Annet Simons
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Richard Rodenburg
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Dineke Westra
- Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, Netherlands
| | - Arjen R. Mensenkamp
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Nicole de Leeuw
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Marjolijn Ligtenberg
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Rene Matthijsse
- Department of Neonatology, Radboud University Medical Center, Radboud Institute for Health Sciences, Amalia Children’s Hospital, Nijmegen, Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Erik Jan Kamsteeg
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Han G. Brunner
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Ilse Feenstra
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Willem P. de Boode
- Department of Neonatology, Radboud University Medical Center, Radboud Institute for Health Sciences, Amalia Children’s Hospital, Nijmegen, Netherlands
| | - Helger G. Yntema
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | | | - Marcel Nelen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Lisenka E. L. M. Vissers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
- Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, Netherlands
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Wambach JA, Wegner DJ, Kitzmiller J, White FV, Heins HB, Yang P, Paul AJ, Granadillo JL, Eghtesady P, Kuklinski C, Turner T, Fairman K, Stone K, Wilson T, Breman A, Smith J, Schroeder MC, Neidich JA, Whitsett JA, Cole FS. Homozygous, Intragenic Tandem Duplication of SFTPB Causes Neonatal Respiratory Failure. Am J Respir Cell Mol Biol 2024; 70:78-80. [PMID: 38156804 PMCID: PMC10768837 DOI: 10.1165/rcmb.2023-0156le] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024] Open
Affiliation(s)
| | | | | | | | | | - Ping Yang
- Washington University School of MedicineSt. Louis, Missouri
| | | | | | | | | | - Tiffany Turner
- Indiana University School of MedicineIndianapolis, Indiana
| | - Korre Fairman
- Indiana University School of MedicineIndianapolis, Indiana
| | - Kristyne Stone
- Indiana University School of MedicineIndianapolis, Indiana
| | | | - Amy Breman
- Indiana University School of MedicineIndianapolis, Indiana
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D'Gama AM, Agrawal PB. Genomic medicine in neonatal care: progress and challenges. Eur J Hum Genet 2023; 31:1357-1363. [PMID: 37789085 PMCID: PMC10689757 DOI: 10.1038/s41431-023-01464-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 09/01/2023] [Accepted: 09/13/2023] [Indexed: 10/05/2023] Open
Abstract
During the neonatal period, many genetic disorders present and contribute to neonatal morbidity and mortality. Genomic medicine-the use of genomic information in clinical care- has the potential to significantly reduce morbidity and mortality in the neonatal period and improve outcomes for this population. Diagnostic genomic testing for symptomatic newborns, especially rapid testing, has been shown to be feasible and have diagnostic and clinical utility, particularly in the short-term. Ongoing studies are assessing the feasibility and utility, including personal utility, of implementation in diverse populations. Genomic screening for asymptomatic newborns has also been studied, and the acceptability and feasibility of such an approach remains an active area of investigation. Emerging precision therapies, with examples even at the "n-of-1" level, highlight the promise of precision diagnostics to lead to early intervention and improve outcomes. To sustainably implement genomic medicine in neonatal care in an ethical, effective, and equitable manner, we need to ensure access to genetics and genomics knowledge, access to genomic tests, which is currently limited by payors, feasible processes for ordering these tests, and access to follow up in the clinical and research realms. Future studies will provide further insight into enablers and barriers to optimize implementation strategies.
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Affiliation(s)
- Alissa M D'Gama
- Division of Newborn Medicine, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
- Epilepsy Genetics Program, Department of Neurology, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Pankaj B Agrawal
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA.
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA.
- Division of Neonatology, Department of Pediatrics, University of Miami Miller School of Medicine, Holtz Children's Hospital, Jackson Health System, Miami, FL, USA.
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Abou Tayoun AN, Alsheikh-Ali A. A rapid whole-genome sequencing service for infants with rare diseases in the United Arab Emirates. Nat Med 2023; 29:2979-2980. [PMID: 37872224 DOI: 10.1038/s41591-023-02596-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Affiliation(s)
- Ahmad N Abou Tayoun
- Genomics Center of Excellence, Al Jalila Children's Specialty Hospital, Dubai, United Arab Emirates.
- Center for Genomic Discovery, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates.
- Dubai Academic Health Corporation, Dubai, United Arab Emirates.
| | - Alawi Alsheikh-Ali
- Dubai Academic Health Corporation, Dubai, United Arab Emirates
- Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
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19
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Shin S, Lee J, Kim YG, Ha C, Park JH, Kim JW, Lee J, Jang JH. Genetic Diagnosis of Children With Neurodevelopmental Disorders Using Whole Genome Sequencing. Pediatr Neurol 2023; 149:44-52. [PMID: 37776660 DOI: 10.1016/j.pediatrneurol.2023.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 06/05/2023] [Accepted: 09/05/2023] [Indexed: 10/02/2023]
Abstract
BACKGROUND Neurodevelopmental disorders (NDDs) have diverse phenotypes. Their genetic diagnoses are often challenged by difficulties of targeting causative genes due to heterogeneous genetic etiologies. The objective of this study was to perform genetic diagnosis of children with NDDs using whole genome sequencing. METHODS This study included 78 pediatric patients with NDDs and their 152 family members for whole genome sequencing (WGS). All cases except one were families with at least two members. Seventy-five patients had previously undergone other genetic tests besides WGS. Detected variants were classified according to the guidelines of the American College of Medical Genetics and Genomics. RESULTS Among 78 probands, 26 patients were genetically diagnosed with NDDs through WGS, showing a diagnostic rate of 33.3%. Of them, 22 cases had de novo variants (DNVs) identified through trio analysis. Of these DNVs, half were novel variants. Three structural variants, including a multiexon deletion, a contiguous gene deletion involving 13 Mb, and a retrotransposon insertion, were revealed by WGS. All cases except one had defects in different genes, consistent with the phenotypically diverse nature of NDDs. In addition, three patients were inconclusive, two of them had one likely pathogenic variant in a gene associated with autosomal recessive disease and the other one had no clinical phenotypes associated with the detected DNV. CONCLUSIONS Our experience demonstrates the advantage of WGS in the diagnosis of NDDs, including detection of copy number variations and also the advantage of trio sequencing for interpretation of DNVs.
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Affiliation(s)
- Sunghwan Shin
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea; Department of Laboratory Medicine, Inje University Ilsan Paik Hospital, Goyang, Korea
| | - Jiwon Lee
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Young-Gon Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Changhee Ha
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jong-Ho Park
- Clinical Genomics Center, Samsung Medical Center, Seoul, Korea
| | - Jong-Won Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jeehun Lee
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Ja-Hyun Jang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.
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20
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Guzman H, Yazdani S, Harmon JL, Chapman KA, Vitola B, Pyle L, McKnight H, Sigal W, Lord K, De Leon DD, Merchant N, Ganetzky R. Case report: Two unexpected cases of DGUOK-related mitochondrial DNA depletion syndrome presenting with hyperinsulinemic hypoglycemia. Front Endocrinol (Lausanne) 2023; 14:1268135. [PMID: 38027095 PMCID: PMC10646319 DOI: 10.3389/fendo.2023.1268135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 10/02/2023] [Indexed: 12/01/2023] Open
Abstract
Timely diagnosis of persistent neonatal hypoglycemia is critical to prevent neurological sequelae, but diagnosis is complicated by the heterogenicity of the causes. We discuss two cases at separate institutions in which clinical management was fundamentally altered by the results of molecular genetic testing. In both patients, critical samples demonstrated hypoketotic hypoglycemia and a partial glycemic response to glucagon stimulation, thereby suggesting hyperinsulinism (HI). However, due to rapid genetic testing, both patients were found to have deoxyguanosine kinase (DGUOK)-related mitochondrial DNA depletion syndrome, an unexpected diagnosis. Patients with this disease typically present with either hepatocerebral disease in the neonatal period or isolated hepatic failure in infancy. The characteristic features involved in the hepatocerebral form of the disease include lactic acidosis, hypoglycemia, cholestasis, progressive liver failure, and increasing neurologic dysfunction. Those with isolated liver involvement experience hepatomegaly, cholestasis, and liver failure. Although liver transplantation is considered, research has demonstrated that for patients with DGUOK-related mitochondrial DNA depletion syndrome and neurologic symptoms, early demise occurs. Our report advocates for the prompt initiation of genetic testing in patients presenting with persistent neonatal hypoglycemia and for the incorporation of mitochondrial DNA depletion syndromes in the differential diagnosis of HI.
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Affiliation(s)
- Herodes Guzman
- Division of Endocrinology and Diabetes, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
- Division of Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Sahr Yazdani
- Division of General Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Jennifer L. Harmon
- Rare Disease Institute, Children’s National Hospital, Washington, DC, United States
| | - Kimberly A. Chapman
- Rare Disease Institute, Children’s National Hospital, Washington, DC, United States
| | - Bernadette Vitola
- Division of Gastroenterology, Hepatology and Nutrition, Children’s National Hospital, Washington, DC, United States
- Transplant Institute, MedStar Georgetown University Hospital, Washington, DC, United States
| | - Louise Pyle
- Rare Disease Institute, Children’s National Hospital, Washington, DC, United States
| | - Heather McKnight
- Division of Endocrinology and Diabetes, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Winnie Sigal
- Division of Endocrinology and Diabetes, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
| | - Katherine Lord
- Division of Endocrinology and Diabetes, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
| | - Diva D. De Leon
- Division of Endocrinology and Diabetes, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
| | - Nadia Merchant
- Rare Disease Institute, Children’s National Hospital, Washington, DC, United States
- Division of Endocrinology and Diabetes, Children’s National Hospital, Washington, DC, United States
| | - Rebecca Ganetzky
- Division of Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
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21
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Crouch EE, Damas C, Bartrug WC, Shamiyeh A, Scelfo M, Dreyfus M, Gano D, Segal S, Franck LS. Parents' Views on Autopsy, Organ Donation, and Research Donation After Neonatal Death. JAMA Netw Open 2023; 6:e2341533. [PMID: 37930699 PMCID: PMC10628732 DOI: 10.1001/jamanetworkopen.2023.41533] [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] [Received: 05/08/2023] [Accepted: 09/24/2023] [Indexed: 11/07/2023] Open
Abstract
Importance Parents who experience neonatal loss have the option to participate in autopsy, organ donation, and research donation. However, clinicians are uncomfortable discussing autopsy and may not be aware of research and organ donation opportunities. Objective To capture the perspectives of parents who had experienced neonatal loss about autopsy, organ donation, and research donation. Design, Setting, and Participants This qualitative study used virtual focus groups with parents who attended a local bereavement support group in the US. Participants were recruited from Helping After Neonatal Death, a support group with a local chapter. Participants self-selected from an email request if they met the following criteria: aged 18 years or older, English speaking, at least 6 months elapsed since neonatal death, and access to a video conference device with internet. Focus groups took place between April and September 2021. The recorded sessions were analyzed using a grounded theory-informed approach by the research team that included parents with experience of neonatal loss. Data were analyzed from December 2021 through December 2022. Results A total of 14 mothers engaged in the focus group; 9 (75%) were aged 30 to 39 years, and 8 (66%) were White. The mothers were overall well educated. The first main theme grew from the lived experience of neonatal loss, specifically the importance of offering all parents the option to donate, rather than prejudging who would or would not be interested. Parents of neonates who die have few opportunities to parent that child and make loving decisions for them. Participants emphasized that the conversation about autopsy, organ donation, and research donation, albeit difficult, can offer a meaningful parenting experience. A second main theme that emerged related to how organ or tissue donation could provide additional meaning to a child's life. These choices contributed to building a legacy to honor their child's memory, which also helped with grief and coping with their loss. A third theme included recommendations to clinicians and health systems for improving communication, including written information for parents and communication training for health care professionals. Conclusions and Relevance In this qualitative study, parents who experienced neonatal loss endorsed the importance of offering parents the choice of autopsy, organ donation, or research donation with skillful and empathetic communication. They provided practical recommendations to improve communication and empower families.
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Affiliation(s)
- Elizabeth E. Crouch
- Department of Pediatrics, University of California San Francisco
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco
| | - Carlos Damas
- Department of Pediatrics, University of California San Francisco
| | | | - Anne Shamiyeh
- Helping After Neonatal Death of the Bay Area, Redwood City, California
| | - Meghan Scelfo
- Department of Pediatrics, University of California San Francisco
| | | | - Dawn Gano
- Division of Pediatric Neurology, Department of Neurology, Benioff Children’s Hospital, University of California San Francisco
| | - Summer Segal
- Department of Pediatrics, Stad Center for Pain Palliative and Integrative Medicine, University of California San Francisco
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22
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Wang X, Sun Y, Guan XW, Wang YY, Hong DY, Zhang ZL, Li YH, Yang PY, Jiang T, Xu ZF. Newborn genetic screening is highly effective for high-risk infants: A single-centre study in China. J Glob Health 2023; 13:04128. [PMID: 37824171 PMCID: PMC10569371 DOI: 10.7189/jogh.13.04128] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023] Open
Abstract
Background Newborn genetic screening (NBGS) is promising for early detection of genetic diseases in newborns. However, little is known about its clinical effectiveness in special groups like high-risk infants. To address this gap, we aimed to investigate the impact of NBGS on high-risk infants. Methods We screened 10 334 healthy newborns from the general maternity unit and 886 high-risk infants from the neonatal ward using both traditional newborn screening (tNBS) and NBGS, and collected clinical data from electronic medical records. Results We found that high-risk infants had a higher proportion of eutocia (P < 0.01) and prematurity (P < 0.01). For high-risk infants vs healthy newborns screened by tNBS, the primary screening positive rate was 3.84% vs 1.31%, the false positive rate (FPR) was 3.62% vs 1.18% (P < 0.001), and the positive predictive value (PPV) was 5.88% vs 8.27%. For NBGS vs tNBS in high-risk infants, the primary screening positive rate was 0.54% vs 3.68%, the FPR was 0.22% vs 3.47%, and the PPV was 60.00% vs 5.88%. Conclusions We found that combined newborn screening can effectively reduce the FPR caused by the high-risk symptoms and improve the PPV in high-risk infants, sufficient for more accurately showing the true status of the disease.
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Affiliation(s)
| | | | - Xian-Wei Guan
- Genetic Medicine Center, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu Province of China, China
| | - Yan-Yun Wang
- Genetic Medicine Center, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu Province of China, China
| | - Dong-Yang Hong
- Genetic Medicine Center, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu Province of China, China
| | - Zhi-Lei Zhang
- Genetic Medicine Center, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu Province of China, China
| | - Ya-Hong Li
- Genetic Medicine Center, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu Province of China, China
| | - Pei-Ying Yang
- Genetic Medicine Center, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu Province of China, China
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23
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Kurosawa R, Iida K, Ajiro M, Awaya T, Yamada M, Kosaki K, Hagiwara M. PDIVAS: Pathogenicity predictor for Deep-Intronic Variants causing Aberrant Splicing. BMC Genomics 2023; 24:601. [PMID: 37817060 PMCID: PMC10563346 DOI: 10.1186/s12864-023-09645-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 09/01/2023] [Indexed: 10/12/2023] Open
Abstract
BACKGROUND Deep-intronic variants that alter RNA splicing were ineffectively evaluated in the search for the cause of genetic diseases. Determination of such pathogenic variants from a vast number of deep-intronic variants (approximately 1,500,000 variants per individual) represents a technical challenge to researchers. Thus, we developed a Pathogenicity predictor for Deep-Intronic Variants causing Aberrant Splicing (PDIVAS) to easily detect pathogenic deep-intronic variants. RESULTS PDIVAS was trained on an ensemble machine-learning algorithm to classify pathogenic and benign variants in a curated dataset. The dataset consists of manually curated pathogenic splice-altering variants (SAVs) and commonly observed benign variants within deep introns. Splicing features and a splicing constraint metric were used to maximize the predictive sensitivity and specificity, respectively. PDIVAS showed an average precision of 0.92 and a maximum MCC of 0.88 in classifying these variants, which were the best of the previous predictors. When PDIVAS was applied to genome sequencing analysis on a threshold with 95% sensitivity for reported pathogenic SAVs, an average of 27 pathogenic candidates were extracted per individual. Furthermore, the causative variants in simulated patient genomes were more efficiently prioritized than the previous predictors. CONCLUSION Incorporating PDIVAS into variant interpretation pipelines will enable efficient detection of disease-causing deep-intronic SAVs and contribute to improving the diagnostic yield. PDIVAS is publicly available at https://github.com/shiro-kur/PDIVAS .
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Affiliation(s)
- Ryo Kurosawa
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan.
| | - Kei Iida
- Faculty of Science and Engineering, Kindai University, 3-4-1 Kowakae, Higashi-osaka, Osaka, 577-8502, Japan
- Medical Research Support Center, Graduate School of Medicine, Kyoto University, Yoshida- Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Masahiko Ajiro
- Division of Cancer RNA Research, National Cancer Center Research Institute, Tokyo, 104- 0045, Japan
- Department of Drug Discovery Medicine, Graduate School of Medicine, Kyoto University, Yoshida Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Tomonari Awaya
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
- Laboratory of Tumor Microenvironment and Immunity, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Mamiko Yamada
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, 160-8582, Japan
| | - Kenjiro Kosaki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, 160-8582, Japan
| | - Masatoshi Hagiwara
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan.
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Jo HS, Yang M, Ahn SY, Sung SI, Park WS, Jang JH, Chang YS. Optimal Protocols and Management of Clinical and Genomic Data Collection to Assist in the Early Diagnosis and Treatment of Multiple Congenital Anomalies. CHILDREN (BASEL, SWITZERLAND) 2023; 10:1673. [PMID: 37892336 PMCID: PMC10605914 DOI: 10.3390/children10101673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 10/01/2023] [Accepted: 10/07/2023] [Indexed: 10/29/2023]
Abstract
Standardized protocols have been designed and developed specifically for clinical information collection and obtaining trio genomic information from infants affected with congenital anomalies (CA) and their parents, as well as securing human biological resources. The protocols include clinical and genomic information collection on multiple CA that were difficult to diagnose using pre-existing screening methods. We obtained human-derived resources and genomic information from 138 cases, including 45 families of infants with CA and their parent trios. For the clinical information collection protocol, criteria for target patient selection and a consent system for collecting and utilizing research resources are crucial. Whole genome sequencing data were generated for all participants, and standardized protocols were developed for resource collection and manufacturing. We recorded the phenotype information according to the Human Phenotype Ontology term, and epidemiological information was collected through an environmental factor questionnaire. Updating and recording of clinical symptoms and genetic information that have been newly added or changed over time are significant. The protocols enabled long-term tracking by including the growth and development status that reflect the important characteristics of newborns. Using these clinical and genetic information collection protocols for CA, an essential platform for early genetic diagnosis and diagnostic research can be established, and new genetic diagnostic guidelines can be presented in the near future.
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Affiliation(s)
- Heui Seung Jo
- Department of Pediatrics, Kangwon National University Hospital, Kangwon National University School of Medicine, Kangwon 24289, Republic of Korea
| | - Misun Yang
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Republic of Korea
- Cell and Gene Therapy Institute, Samsung Medical Center, Seoul 06351, Republic of Korea
| | - So Yoon Ahn
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Republic of Korea
- Cell and Gene Therapy Institute, Samsung Medical Center, Seoul 06351, Republic of Korea
| | - Se In Sung
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Republic of Korea
- Cell and Gene Therapy Institute, Samsung Medical Center, Seoul 06351, Republic of Korea
| | - Won Soon Park
- Department of Pediatrics, CHA Gangnam Medical Center, CHA University, Seoul 06135, Republic of Korea
| | - Ja-Hyun Jang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Republic of Korea
| | - Yun Sil Chang
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Republic of Korea
- Cell and Gene Therapy Institute, Samsung Medical Center, Seoul 06351, Republic of Korea
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul 06351, Republic of Korea
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25
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Wojcik MH, Callahan KP, Antoniou A, Del Rosario MC, Brunelli L, ElHassan NO, Gogcu S, Murthy K, Rumpel JA, Wambach JA, Suhrie K, Fishler K, Chaudhari BP. Provision and availability of genomic medicine services in Level IV neonatal intensive care units. Genet Med 2023; 25:100926. [PMID: 37422715 PMCID: PMC10592224 DOI: 10.1016/j.gim.2023.100926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/30/2023] [Accepted: 07/02/2023] [Indexed: 07/10/2023] Open
Abstract
PURPOSE To describe variation in genomic medicine services across level IV neonatal intensive care units (NICUs) in the United States and Canada. METHODS We developed and distributed a novel survey to the 43 level IV NICUs belonging to the Children's Hospitals Neonatal Consortium, requesting a single response per site from a clinician with knowledge of the provision of genomic medicine services. RESULTS Overall response rate was 74% (32/43). Although chromosomal microarray and exome or genome sequencing (ES or GS) were universally available, access was restricted for 22% (7/32) and 81% (26/32) of centers, respectively. The most common restriction on ES or GS was requiring approval by a specialist (41%, 13/32). Rapid ES/GS was available in 69% of NICUs (22/32). Availability of same-day genetics consultative services was limited (41%, 13/32 sites), and pre- and post-test counseling practices varied widely. CONCLUSION We observed large inter-center variation in genomic medicine services across level IV NICUs: most notably, access to rapid, comprehensive genetic testing in time frames relevant to critical care decision making was limited at many level IV Children's Hospitals Neonatal Consortium NICUs despite a significant burden of genetic disease. Further efforts are needed to improve access to neonatal genomic medicine services.
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Affiliation(s)
- Monica H Wojcik
- Divisions of Newborn Medicine and Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, MA; Neonatal Genomics Program, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, MA.
| | - Katharine P Callahan
- Division of Neonatology, Children's Hospital of Philadelphia, Philadelphia, PA; Division of Medical Ethics and Health Policy, University of Pennsylvania, Philadelphia, PA
| | - Austin Antoniou
- Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH
| | - Maya C Del Rosario
- Neonatal Genomics Program, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, MA
| | - Luca Brunelli
- Division of Neonatology, University of Utah Health and Primary Children's Hospital, Salt Lake City, UT
| | - Nahed O ElHassan
- Division of Neonatology, Arkansas Children's Hospital, University of Arkansas for Medical Sciences, Little Rock, AR
| | - Semsa Gogcu
- Wake Forest School of Medicine, Department of Pediatrics, Winston-Salem, NC
| | - Karna Murthy
- Ann & Robert H Lurie Children's Hospital of Chicago and Northwestern University, Chicago, IL; Children's Hospitals Neonatal Consortium, Dover, DE
| | - Jennifer A Rumpel
- Division of Neonatology, Arkansas Children's Hospital, University of Arkansas for Medical Sciences, Little Rock, AR
| | - Jennifer A Wambach
- Washington University School of Medicine and St Louis Children's Hospital, St Louis, MO
| | - Kristen Suhrie
- Department of Pediatrics, Division of Neonatal-Perinatal Medicine, and Department of Medical and Molecular Genetics, Riley Hospital for Children and Indiana University School of Medicine, Indianapolis, IN
| | - Kristen Fishler
- Munroe-Meyer Institute for Genetics and Rehabilitation, University of Nebraska Medical Center, Omaha, NE
| | - Bimal P Chaudhari
- Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH; Divisions of Neonatology and Genetics and Genomic Medicine, Department of Pediatrics, Nationwide Children's Hospital and The Ohio State University College of Medicine, Columbus, OH
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26
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Tesi B, Boileau C, Boycott KM, Canaud G, Caulfield M, Choukair D, Hill S, Spielmann M, Wedell A, Wirta V, Nordgren A, Lindstrand A. Precision medicine in rare diseases: What is next? J Intern Med 2023; 294:397-412. [PMID: 37211972 DOI: 10.1111/joim.13655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Molecular diagnostics is a cornerstone of modern precision medicine, broadly understood as tailoring an individual's treatment, follow-up, and care based on molecular data. In rare diseases (RDs), molecular diagnoses reveal valuable information about the cause of symptoms, disease progression, familial risk, and in certain cases, unlock access to targeted therapies. Due to decreasing DNA sequencing costs, genome sequencing (GS) is emerging as the primary method for precision diagnostics in RDs. Several ongoing European initiatives for precision medicine have chosen GS as their method of choice. Recent research supports the role for GS as first-line genetic investigation in individuals with suspected RD, due to its improved diagnostic yield compared to other methods. Moreover, GS can detect a broad range of genetic aberrations including those in noncoding regions, producing comprehensive data that can be periodically reanalyzed for years to come when further evidence emerges. Indeed, targeted drug development and repurposing of medicines can be accelerated as more individuals with RDs receive a molecular diagnosis. Multidisciplinary teams in which clinical specialists collaborate with geneticists, genomics education of professionals and the public, and dialogue with patient advocacy groups are essential elements for the integration of precision medicine into clinical practice worldwide. It is also paramount that large research projects share genetic data and leverage novel technologies to fully diagnose individuals with RDs. In conclusion, GS increases diagnostic yields and is a crucial step toward precision medicine for RDs. Its clinical implementation will enable better patient management, unlock targeted therapies, and guide the development of innovative treatments.
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Affiliation(s)
- Bianca Tesi
- Department of Molecular Medicine and Surgery and Centre of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
- Center for Hematology and Regenerative Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Catherine Boileau
- Département de Génétique, APHP, Hôpital Bichat-Claude Bernard, Université Paris Cité, Paris, France
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Guillaume Canaud
- INSERM U1151, Unité de médecine translationnelle et thérapies ciblées, Hôpital Necker-Enfants Malades, Université Paris Cité, AP-HP, Paris, France
| | - Mark Caulfield
- William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Daniela Choukair
- Division of Pediatric Endocrinology and Diabetes, Center for Pediatrics and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany and Center for Rare Diseases, University Hospital Heidelberg, Heidelberg, Germany
| | - Sue Hill
- Chief Scientific Officer, NHS England, London, UK
| | - Malte Spielmann
- Institute of Human Genetics, University Hospitals Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Kiel, Germany
| | - Anna Wedell
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Valtteri Wirta
- Science for Life Laboratory, Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institutet of Technology, Stockholm, Sweden
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery and Centre of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
- Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery and Centre of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
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Lenahan AL, Squire AE, Miller DE. Panels, Exomes, Genomes, and More-Finding the Best Path Through the Diagnostic Odyssey. Pediatr Clin North Am 2023; 70:905-916. [PMID: 37704349 DOI: 10.1016/j.pcl.2023.06.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 09/15/2023]
Abstract
Selecting the ideal test to evaluate an individual with a suspected genetic disorder can be challenging. While several clinical testing options are available, no single test yet captures all potentially causative genetic variants. Thus, clinicians may order testing in a stepwise fashion, and what to order after non-diagnostic testing can be challenging to determine. Here, we provide an overview of commonly used clinical genetic tests, guidance on when they are best used, and what they may miss. We conclude with a discussion of how new technologies might be used to identify challenging variants and simplify clinical testing in the future.
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Affiliation(s)
- Arthur L Lenahan
- Division of Genetic Medicine, Department of Pediatrics, University of Washington and Seattle Children's Hospital, 4800 Sand Point Way, Seattle, WA 98105, USA
| | - Audrey E Squire
- Division of Genetic Medicine, Department of Pediatrics, University of Washington and Seattle Children's Hospital, 4800 Sand Point Way, Seattle, WA 98105, USA
| | - Danny E Miller
- Division of Genetic Medicine, Department of Pediatrics, University of Washington and Seattle Children's Hospital, 4800 Sand Point Way, Seattle, WA 98105, USA; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA.
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28
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McBride DJ, Fielding C, Newington T, Vatsiou A, Fischl H, Bajracharya M, Thomson VS, Fraser LJ, Fujita PA, Becq J, Kingsbury Z, Ross MT, Moat SJ, Morgan S. Whole-Genome Sequencing Can Identify Clinically Relevant Variants from a Single Sub-Punch of a Dried Blood Spot Specimen. Int J Neonatal Screen 2023; 9:52. [PMID: 37754778 PMCID: PMC10532340 DOI: 10.3390/ijns9030052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 09/01/2023] [Accepted: 09/06/2023] [Indexed: 09/28/2023] Open
Abstract
The collection of dried blood spots (DBS) facilitates newborn screening for a variety of rare, but very serious conditions in healthcare systems around the world. Sub-punches of varying sizes (1.5-6 mm) can be taken from DBS specimens to use as inputs for a range of biochemical assays. Advances in DNA sequencing workflows allow whole-genome sequencing (WGS) libraries to be generated directly from inputs such as peripheral blood, saliva, and DBS. We compared WGS metrics obtained from libraries generated directly from DBS to those generated from DNA extracted from peripheral blood, the standard input for this type of assay. We explored the flexibility of DBS as an input for WGS by altering the punch number and size as inputs to the assay. We showed that WGS libraries can be successfully generated from a variety of DBS inputs, including a single 3 mm or 6 mm diameter punch, with equivalent data quality observed across a number of key metrics of importance in the detection of gene variants. We observed no difference in the performance of DBS and peripheral-blood-extracted DNA in the detection of likely pathogenic gene variants in samples taken from individuals with cystic fibrosis or phenylketonuria. WGS can be performed directly from DBS and is a powerful method for the rapid discovery of clinically relevant, disease-causing gene variants.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Stuart J. Moat
- Wales Newborn Screening Laboratory, University Hospital of Wales, Cardiff CF14 4XW, UK
- School of Medicine, Cardiff University, Cardiff CF14 4XW, UK
| | - Sian Morgan
- All Wales Genetics Laboratory, University Hospital of Wales, Cardiff CF14 4XW, UK
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29
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Lenahan A, Mietzsch U, Wood TR, Callahan KP, Weiss EM, Miller DE, German K, Natarajan N, Puia-Dumitrescu M, Esposito V, Kolnik S, Law JB. Characteristics, Genetic Testing, and Diagnoses of Infants with Neonatal Encephalopathy Not Due to Hypoxic Ischemic Encephalopathy: A Cohort Study. J Pediatr 2023; 260:113533. [PMID: 37269901 DOI: 10.1016/j.jpeds.2023.113533] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 04/29/2023] [Accepted: 05/30/2023] [Indexed: 06/05/2023]
Abstract
OBJECTIVE To characterize the presentation and evaluation of infants with neonatal encephalopathy (NE) not due to hypoxic-ischemic encephalopathy (non-HIE NE) and to describe the genetic abnormalities identified. STUDY DESIGN Retrospective cohort study of 193 non-HIE NE neonates admitted to a level IV NICU from 2015 through 2019. For changes in testing over time, Cochrane-Armitage test for trend was used with a Bonferroni-corrected P-value, and comparison between groups was performed using Fisher exact test. RESULT The most common symptom of non-HIE NE was abnormal tone in 47% (90/193). Ten percent (19/193) died prior to discharge, and 48% of survivors (83/174) required medical equipment at discharge. Forty percent (77/193) underwent genetic testing as an inpatient. Of 52 chromosomal studies, 54 targeted tests, and 16 exome sequences, 10%, 41%, and 69% were diagnostic, respectively, with no difference in diagnostic rates between infants with and without an associated congenital anomaly and/or dysmorphic feature. Twenty-eight genetic diagnoses were identified. CONCLUSIONS Neonates with non-HIE NE have high rates of morbidity and mortality and may benefit from early genetic testing, even in the absence of other exam findings. This study broadens our knowledge of genetic conditions underlying non-HIE NE, which may enable families and care teams to anticipate the needs of the individual, allow early initiation of targeted therapies, and facilitate decisions surrounding goals of care.
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Affiliation(s)
- Arthur Lenahan
- Department of Pediatrics, University of Washington School of Medicine and Seattle Children's Hospital, Seattle, WA
| | - Ulrike Mietzsch
- Department of Pediatrics, University of Washington School of Medicine and Seattle Children's Hospital, Seattle, WA
| | - Thomas R Wood
- Department of Pediatrics, University of Washington School of Medicine and Seattle Children's Hospital, Seattle, WA
| | - Katharine Press Callahan
- Department of Pediatrics, Children's Hospital of Philadelphia, PA; Department of Medical Ethics and Health Policy, The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Elliott M Weiss
- Department of Pediatrics, University of Washington School of Medicine and Seattle Children's Hospital, Seattle, WA
| | - Danny E Miller
- Department of Pediatrics, University of Washington School of Medicine and Seattle Children's Hospital, Seattle, WA; Department of Laboratory Medicine and Pathology, University of Washington School of Medicine and Seattle Children's Hospital, Seattle, WA
| | - Kendell German
- Department of Pediatrics, University of Washington School of Medicine and Seattle Children's Hospital, Seattle, WA
| | - Niranjana Natarajan
- Department of Pediatrics, University of Washington School of Medicine and Seattle Children's Hospital, Seattle, WA; Division of Pediatric Neurology, Department of Neurology, University of Washington School of Medicine and Seattle Children's Hospital, Seattle, WA
| | - Mihai Puia-Dumitrescu
- Department of Pediatrics, University of Washington School of Medicine and Seattle Children's Hospital, Seattle, WA
| | - Valentine Esposito
- Department of Pediatrics, University of Washington School of Medicine and Seattle Children's Hospital, Seattle, WA
| | - Sarah Kolnik
- Department of Pediatrics, University of Washington School of Medicine and Seattle Children's Hospital, Seattle, WA
| | - Janessa B Law
- Department of Pediatrics, University of Washington School of Medicine and Seattle Children's Hospital, Seattle, WA.
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Fishler KP, Steber HS, Brunelli L, Shope RJ. Exploring collaboration models between geneticists and intensivists for implementing rapid genome sequencing in critical care settings. Am J Med Genet A 2023; 191:2290-2299. [PMID: 37318250 DOI: 10.1002/ajmg.a.63318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 04/13/2023] [Accepted: 05/13/2023] [Indexed: 06/16/2023]
Abstract
The availability of rapid genome sequencing (rGS) for children in a critical-care setting is increasing. This study explored the perspectives of geneticists and intensivists on optimal collaboration and division of roles when implementing rGS in neonatal and pediatric intensive care units (ICUs). We conducted an explanatory mixed methods study involving a survey embedded within an interview with 13 genetics and intensive care providers. Interviews were recorded, transcribed, and coded. Geneticists endorsed higher confidence in performing a physical exam and interpreting/communicating positive results. Intensivists endorsed highest confidence in determining whether genetic testing was appropriate, communicating negative results, and consenting. Major qualitative themes that emerged were: (1) concerns with both "genetics-led" and "intensivist-led" models with workflows and sustainability (2) shift the role of determining rGS eligibility to ICU medical professionals, (3) continued role of geneticists to assess phenotype, and (4) include genetic counselors (GCs) and neonatal nurse practitioners to enhance workflow and care. All geneticists supported shifting decisions regarding eligibility for rGS to the ICU team to minimize time cost for the genetics workforce. Exploring models of geneticist-led phenotyping, intensivist-led phenotyping for some indications, and/or inclusion of a dedicated inpatient GC may help offset the time burden of consenting and other tasks associated with rGS.
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Affiliation(s)
- Kristen P Fishler
- Munroe-Meyer Institute for Genetics & Rehabilitation, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Hannah S Steber
- Munroe-Meyer Institute for Genetics & Rehabilitation, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Luca Brunelli
- Division of Neonatology, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Ronald J Shope
- College of Allied Health Professions, University of Nebraska Medical Center, Omaha, Nebraska, USA
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Chung CCY, Hue SPY, Ng NYT, Doong PHL, Chu ATW, Chung BHY. Meta-analysis of the diagnostic and clinical utility of exome and genome sequencing in pediatric and adult patients with rare diseases across diverse populations. Genet Med 2023; 25:100896. [PMID: 37191093 DOI: 10.1016/j.gim.2023.100896] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 05/07/2023] [Accepted: 05/10/2023] [Indexed: 05/17/2023] Open
Abstract
PURPOSE This meta-analysis aims to compare the diagnostic and clinical utility of exome sequencing (ES) vs genome sequencing (GS) in pediatric and adult patients with rare diseases across diverse populations. METHODS A meta-analysis was conducted to identify studies from 2011 to 2021. RESULTS One hundred sixty-one studies across 31 countries/regions were eligible, featuring 50,417 probands of diverse populations. Diagnostic rates of ES (0.38, 95% CI 0.36-0.40) and GS (0.34, 95% CI 0.30-0.38) were similar (P = .1). Within-cohort comparison illustrated 1.2-times odds of diagnosis by GS over ES (95% CI 0.79-1.83, P = .38). GS studies discovered a higher range of novel genes than ES studies; yet, the rate of variant of unknown significance did not differ (P = .78). Among high-quality studies, clinical utility of GS (0.77, 95% CI 0.64-0.90) was higher than that of ES (0.44, 95% CI 0.30-0.58) (P < .01). CONCLUSION This meta-analysis provides an important update to demonstrate the similar diagnostic rates between ES and GS and the higher clinical utility of GS over ES. With the newly published recommendations for clinical interpretation of variants found in noncoding regions of the genome and the trend of decreasing variant of unknown significance and GS cost, it is expected that GS will be more widely used in clinical settings.
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Affiliation(s)
| | - Shirley P Y Hue
- Hong Kong Genome Institute, Hong Kong Special Administrative Region
| | - Nicole Y T Ng
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Phoenix H L Doong
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Annie T W Chu
- Hong Kong Genome Institute, Hong Kong Special Administrative Region.
| | - Brian H Y Chung
- Hong Kong Genome Institute, Hong Kong Special Administrative Region; Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region.
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Wojcik MH, Reuter CM, Marwaha S, Mahmoud M, Duyzend MH, Barseghyan H, Yuan B, Boone PM, Groopman EE, Délot EC, Jain D, Sanchis-Juan A, Starita LM, Talkowski M, Montgomery SB, Bamshad MJ, Chong JX, Wheeler MT, Berger SI, O'Donnell-Luria A, Sedlazeck FJ, Miller DE. Beyond the exome: What's next in diagnostic testing for Mendelian conditions. Am J Hum Genet 2023; 110:1229-1248. [PMID: 37541186 PMCID: PMC10432150 DOI: 10.1016/j.ajhg.2023.06.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 08/06/2023] Open
Abstract
Despite advances in clinical genetic testing, including the introduction of exome sequencing (ES), more than 50% of individuals with a suspected Mendelian condition lack a precise molecular diagnosis. Clinical evaluation is increasingly undertaken by specialists outside of clinical genetics, often occurring in a tiered fashion and typically ending after ES. The current diagnostic rate reflects multiple factors, including technical limitations, incomplete understanding of variant pathogenicity, missing genotype-phenotype associations, complex gene-environment interactions, and reporting differences between clinical labs. Maintaining a clear understanding of the rapidly evolving landscape of diagnostic tests beyond ES, and their limitations, presents a challenge for non-genetics professionals. Newer tests, such as short-read genome or RNA sequencing, can be challenging to order, and emerging technologies, such as optical genome mapping and long-read DNA sequencing, are not available clinically. Furthermore, there is no clear guidance on the next best steps after inconclusive evaluation. Here, we review why a clinical genetic evaluation may be negative, discuss questions to be asked in this setting, and provide a framework for further investigation, including the advantages and disadvantages of new approaches that are nascent in the clinical sphere. We present a guide for the next best steps after inconclusive molecular testing based upon phenotype and prior evaluation, including when to consider referral to research consortia focused on elucidating the underlying cause of rare unsolved genetic disorders.
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Affiliation(s)
- Monica H Wojcik
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Division of Newborn Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Chloe M Reuter
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Shruti Marwaha
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Medhat Mahmoud
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Michael H Duyzend
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Hayk Barseghyan
- Center for Genetics Medicine Research, Children's National Research Institute, Children's National Hospital, Washington, DC 20010, USA; Department of Genomics and Precision Medicine, School of Medicine and Health Sciences, George Washington University, Washington, DC 20037, USA
| | - Bo Yuan
- Department of Molecular and Human Genetics and Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Philip M Boone
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Emily E Groopman
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Emmanuèle C Délot
- Department of Genomics and Precision Medicine, School of Medicine and Health Sciences, George Washington University, Washington, DC 20037, USA; Center for Genetics Medicine Research, Children's National Research and Innovation Campus, Washington, DC, USA; Department of Pediatrics, George Washington University, School of Medicine and Health Sciences, George Washington University, Washington, DC 20037, USA
| | - Deepti Jain
- Department of Biostatistics, School of Public Health, University of Washington, Seattle, WA 98195, USA
| | - Alba Sanchis-Juan
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Lea M Starita
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Michael Talkowski
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Stephen B Montgomery
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Michael J Bamshad
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195, USA
| | - Jessica X Chong
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195, USA; Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195, USA
| | - Matthew T Wheeler
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Seth I Berger
- Center for Genetics Medicine Research and Rare Disease Institute, Children's National Hospital, Washington, DC 20010, USA
| | - Anne O'Donnell-Luria
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Department of Computer Science, Rice University, 6100 Main Street, Houston, TX 77005, USA
| | - Danny E Miller
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195, USA; Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195, USA; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA.
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Gallaway KA, Cann K, Oetting K, Rothenberger M, Raibulet A, Slaven JE, Suhrie K, Tillman EM. The Potential Impact of Preemptive Pharmacogenetic Genotyping in the Neonatal Intensive Care Unit. J Pediatr 2023; 259:113489. [PMID: 37201679 DOI: 10.1016/j.jpeds.2023.113489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 04/26/2023] [Accepted: 05/10/2023] [Indexed: 05/20/2023]
Abstract
OBJECTIVE To evaluate the use of drugs with pharmacogenomic (PGx) guidelines from the Clinical Pharmacogenetics Implementation Consortium in early childhood. STUDY DESIGN A retrospective observational study of patients admitted to the neonatal intensive care (NICU) between 2005 and 2018 with at least 1 subsequent hospitalization at or after 5 years of age was performed to determine PGx drug exposure. Data regarding hospitalizations, drug exposures, gestational age, birth weight, and congenital anomalies and/or a primary genetic diagnosis were collected. Incidence of PGx drug and drug class exposures was determined and patient specific factors predictive of exposure were investigated. RESULTS During the study, 19 195 patients received NICU care and 4196 (22%) met study inclusion; 67% received 1-2, 28% 3-4, and 5% 5 or more PGx-drugs in early childhood. Preterm gestation, low birth weight (<2500 g), and the presence of any congenital anomalies and/or a primary genetic diagnosis were statistically significant predictors of Clinical Pharmacogenetics Implementation Consortium drug exposures (P < .01, P < .01, P < .01, respectively). CONCLUSIONS Preemptive PGx testing in patients in the NICU could have a significant impact on medical management during the NICU stay and throughout early childhood.
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Affiliation(s)
- Katherine A Gallaway
- Division of Pediatric Critical Care, Indiana University School of Medicine, Indianapolis, IN
| | - Kayla Cann
- Purdue University College of Pharmacy, Purdue University, West Lafayette, IN
| | - Katherine Oetting
- Purdue University College of Pharmacy, Purdue University, West Lafayette, IN
| | - Mary Rothenberger
- Purdue University College of Pharmacy, Purdue University, West Lafayette, IN
| | - Andra Raibulet
- College of Pharmacy and Health Sciences, Butler University, Indianapolis, IN
| | - James E Slaven
- Department of Biostatistics and Health Data Science, Indiana University School of Medicine, Indianapolis, IN
| | - Kristen Suhrie
- Division of Neonatology, Department of Pediatrics, and Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN
| | - Emma M Tillman
- Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, IN.
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Smith HS, Ferket BS, Gelb BD, Hindorff L, Ferar KD, Norton ME, Sahin-Hodoglugil N, Slavotinek A, Lich KH, Berg JS, Russell HV. Parent-Reported Clinical Utility of Pediatric Genomic Sequencing. Pediatrics 2023; 152:e2022060318. [PMID: 37470118 PMCID: PMC10812387 DOI: 10.1542/peds.2022-060318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/12/2023] [Indexed: 07/21/2023] Open
Abstract
BACKGROUND AND OBJECTIVES Genomic sequencing (GS) is increasingly used for diagnostic evaluation, yet follow-up care is not well understood. We assessed clinicians' recommendations after GS, parent-reported follow-up, and actions parents initiated in response to learning their child's GS results. METHODS We surveyed parents of children who received GS through the Clinical Sequencing Evidence Generating Research consortium ∼5 to 7 months after return of results. We compared the proportion of parents who reported discussing their child's result with a clinician, clinicians' recommendations, and parents' follow-up actions by GS result type using χ2 tests. RESULTS A total of 1188 respondents completed survey measures on recommended medical actions (n = 1187) and/or parent-initiated actions (n = 913). Most parents who completed recommended medical actions questions (n = 833, 70.3%) reported having discussed their child's GS results with clinicians. Clinicians made recommendations to change current care for patients with positive GS results (n = 79, 39.1%) more frequently than for those with inconclusive (n = 31, 12.4%) or negative results (n = 44, 11.9%; P < .001). Many parents discussed (n = 152 completed, n = 135 planned) implications of GS results for future pregnancies with a clinician. Aside from clinical recommendations, 13.0% (n = 119) of parents initiated changes to their child's health or lifestyle. CONCLUSIONS In diverse pediatric clinical contexts, GS results can lead to recommendations for follow-up care, but they likely do not prompt large increases in the quantity of care received.
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Affiliation(s)
- Hadley Stevens Smith
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX USA
- Precision Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, USA
| | - Bart S. Ferket
- Institute for Healthcare Delivery Science, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bruce D. Gelb
- Mindich Child Health and Development Institute, Departments of Pediatrics and Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lucia Hindorff
- Training, Diversity and Health Equity Office, National Human Genome Research Institute, National Institutes of Health
| | - Kathleen D. Ferar
- Department of Biomedical Informatics and Medical Education, Division of Biomedical Informatics, University of Washington, Seattle, WA, USA
| | - Mary E. Norton
- University of California, San Francisco, San Francisco, CA, USA
| | | | - Anne Slavotinek
- University of California, San Francisco, San Francisco, CA, USA
| | - Kristen Hasmiller Lich
- Department of Health Policy and Management, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jonathan S. Berg
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill NC, USA
| | - Heidi V. Russell
- Department of Pediatrics, Baylor College of Medicine, Houston TX, USA
- Department of Management, Policy, and Community Health, UTHealth School of Public Health, Houston, TX, USA
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Dulmovits BM, Wild KT, Flibotte J, Lambert MP, Kwiatkowski J, Thom CS. Neonatal Thrombocytopenia as a Presenting Finding in de novo Pyruvate Kinase Deficiency. Neonatology 2023; 120:661-665. [PMID: 37473739 PMCID: PMC11027091 DOI: 10.1159/000531242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 05/22/2023] [Indexed: 07/22/2023]
Abstract
Thrombocytopenia is a common laboratory abnormality encountered in critically ill neonates. The broad differential for thrombocytopenia, and its association with potentially severe neonatal pathology, often presents a diagnostic dilemma prompting extensive evaluation. Hemolysis due to red cell enzymopathies is a rare cause of neonatal thrombocytopenia that is typically brief and self-limiting. Here, we present a case of thrombocytopenia, refractory to transfusion, associated with anemia and hyperbilirubinemia in a neonate with pyruvate kinase deficiency (PKD) arising from compound heterozygous PKLR mutations. The nature of the thrombocytopenia in this patient created considerable diagnostic uncertainty, which was ultimately resolved by whole-exome sequencing. This case emphasizes that inherited red cell defects, such as PKD, are important to consider in cases of neonatal thrombocytopenia.
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MESH Headings
- Infant, Newborn
- Humans
- Thrombocytopenia, Neonatal Alloimmune
- Anemia, Hemolytic, Congenital Nonspherocytic/complications
- Anemia, Hemolytic, Congenital Nonspherocytic/diagnosis
- Anemia, Hemolytic, Congenital Nonspherocytic/genetics
- Pyruvate Metabolism, Inborn Errors/diagnosis
- Pyruvate Metabolism, Inborn Errors/genetics
- Pyruvate Metabolism, Inborn Errors/complications
- Pyruvate Kinase/genetics
- Anemia
- Infant, Newborn, Diseases
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Affiliation(s)
- Brian M Dulmovits
- Division of Neonatology, Children’s Hospital of Philadelphia, Philadelphia, PA
| | - K Taylor Wild
- Division of Neonatology, Children’s Hospital of Philadelphia, Philadelphia, PA
- Division of Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA
| | - John Flibotte
- Division of Neonatology, Children’s Hospital of Philadelphia, Philadelphia, PA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Michele P Lambert
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
- Division of Hematology, Children’s Hospital of Philadelphia, Philadelphia, PA
| | - Janet Kwiatkowski
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
- Division of Hematology, Children’s Hospital of Philadelphia, Philadelphia, PA
| | - Christopher S Thom
- Division of Neonatology, Children’s Hospital of Philadelphia, Philadelphia, PA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
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36
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Maron JL, Kingsmore S, Gelb BD, Vockley J, Wigby K, Bragg J, Stroustrup A, Poindexter B, Suhrie K, Kim JH, Diacovo T, Powell CM, Trembath A, Guidugli L, Ellsworth KA, Reed D, Kurfiss A, Breeze JL, Trinquart L, Davis JM. Rapid Whole-Genomic Sequencing and a Targeted Neonatal Gene Panel in Infants With a Suspected Genetic Disorder. JAMA 2023; 330:161-169. [PMID: 37432431 PMCID: PMC10336625 DOI: 10.1001/jama.2023.9350] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 05/12/2023] [Indexed: 07/12/2023]
Abstract
Importance Genomic testing in infancy guides medical decisions and can improve health outcomes. However, it is unclear whether genomic sequencing or a targeted neonatal gene-sequencing test provides comparable molecular diagnostic yields and times to return of results. Objective To compare outcomes of genomic sequencing with those of a targeted neonatal gene-sequencing test. Design, Setting, and Participants The Genomic Medicine for Ill Neonates and Infants (GEMINI) study was a prospective, comparative, multicenter study of 400 hospitalized infants younger than 1 year of age (proband) and their parents, when available, suspected of having a genetic disorder. The study was conducted at 6 US hospitals from June 2019 to November 2021. Exposure Enrolled participants underwent simultaneous testing with genomic sequencing and a targeted neonatal gene-sequencing test. Each laboratory performed an independent interpretation of variants guided by knowledge of the patient's phenotype and returned results to the clinical care team. Change in clinical management, therapies offered, and redirection of care was provided to families based on genetic findings from either platform. Main Outcomes and Measures Primary end points were molecular diagnostic yield (participants with ≥1 pathogenic variant or variant of unknown significance), time to return of results, and clinical utility (changes in patient care). Results A molecular diagnostic variant was identified in 51% of participants (n = 204; 297 variants identified with 134 being novel). Molecular diagnostic yield of genomic sequencing was 49% (95% CI, 44%-54%) vs 27% (95% CI, 23%-32%) with the targeted gene-sequencing test. Genomic sequencing did not report 19 variants found by the targeted neonatal gene-sequencing test; the targeted gene-sequencing test did not report 164 variants identified by genomic sequencing as diagnostic. Variants unidentified by the targeted genomic-sequencing test included structural variants longer than 1 kilobase (25.1%) and genes excluded from the test (24.6%) (McNemar odds ratio, 8.6 [95% CI, 5.4-14.7]). Variant interpretation by laboratories differed by 43%. Median time to return of results was 6.1 days for genomic sequencing and 4.2 days for the targeted genomic-sequencing test; for urgent cases (n = 107) the time was 3.3 days for genomic sequencing and 4.0 days for the targeted gene-sequencing test. Changes in clinical care affected 19% of participants, and 76% of clinicians viewed genomic testing as useful or very useful in clinical decision-making, irrespective of a diagnosis. Conclusions and Relevance The molecular diagnostic yield for genomic sequencing was higher than a targeted neonatal gene-sequencing test, but the time to return of routine results was slower. Interlaboratory variant interpretation contributes to differences in molecular diagnostic yield and may have important consequences for clinical management.
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Affiliation(s)
- Jill L. Maron
- Women and Infants Hospital of Rhode Island, Providence
| | - Stephen Kingsmore
- Rady Children’s Institute for Genomic Medicine, San Diego, California
| | - Bruce D. Gelb
- Mindich Child Health and Development Institute and Departments of Pediatrics and Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jerry Vockley
- University of Pittsburgh Medical Center Children’s Hospital, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Kristen Wigby
- Rady Children’s Institute for Genomic Medicine, San Diego, California
- Department of Pediatrics, University of California San Diego, San Diego
| | - Jennifer Bragg
- Mindich Child Health and Development Institute and Departments of Pediatrics and Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Annemarie Stroustrup
- Division of Neonatology, Department of Pediatrics, Cohen Children’s Medical Center at Northwell Health, New Hyde Park, New York, New York
| | - Brenda Poindexter
- Children’s Healthcare of Atlanta, Department of Pediatrics, Emory University, Atlanta, Georgia
| | - Kristen Suhrie
- Indiana University School of Medicine, Department of Pediatrics and Medical and Molecular Genetics, Indianapolis
| | - Jae H. Kim
- Perinatal Institute, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Thomas Diacovo
- University of Pittsburgh Medical Center Children’s Hospital, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Cynthia M. Powell
- University of North Carolina Children’s Research Institute, University of North Carolina Children’s Hospital, Chapel Hill
| | - Andrea Trembath
- University of North Carolina Children’s Research Institute, University of North Carolina Children’s Hospital, Chapel Hill
| | - Lucia Guidugli
- Rady Children’s Institute for Genomic Medicine, San Diego, California
| | | | - Dallas Reed
- Department of Pediatrics, Tufts Medical Center, Boston, Massachusetts
| | - Anne Kurfiss
- Department of Pediatrics, Tufts Medical Center, Boston, Massachusetts
| | - Janis L. Breeze
- Tufts Clinical and Translational Science Institute, Tufts University, and Institute for Clinical Research and Health Policy Studies, Tufts Medical Center, Boston, Massachusetts
| | - Ludovic Trinquart
- Tufts Clinical and Translational Science Institute, Tufts University, and Institute for Clinical Research and Health Policy Studies, Tufts Medical Center, Boston, Massachusetts
| | - Jonathan M. Davis
- Department of Pediatrics, Tufts Medical Center, Boston, Massachusetts
- Tufts Clinical and Translational Science Institute, Tufts University, and Institute for Clinical Research and Health Policy Studies, Tufts Medical Center, Boston, Massachusetts
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37
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D'Gama AM, Agrawal PB. Role of genomic medicine and implementing equitable access for critically ill infants in neonatal intensive care units. J Perinatol 2023; 43:963-967. [PMID: 36774516 PMCID: PMC9918837 DOI: 10.1038/s41372-023-01630-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 01/27/2023] [Accepted: 01/31/2023] [Indexed: 02/13/2023]
Abstract
Genetic disorders are a leading cause of morbidity and mortality in infants admitted to neonatal intensive care units. This population has immense potential to benefit from genomic medicine, as early precision diagnosis is critical to early personalized management. However, the implementation of genomic medicine in neonatology thus far has arguably worsened health inequities, and strategies are urgently needed to achieve equitable access to genomics in neonatal care. In this perspective, we demonstrate the utility of genomic sequencing in critically ill infants and highlight three key recommendations to advance equitable access: recruitment of underrepresented populations, education of non-genetics providers to empower practice of genomic medicine, and development of innovative infrastructure to implement genomic medicine across diverse settings.
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Affiliation(s)
- Alissa M D'Gama
- Epilepsy Genetics Program, Division of Epilepsy and Neurophysiology, Department of Neurology, Boston Children's Hospital, Boston, MA, USA
- Neonatal Genomics Program, Division of Newborn Medicine, 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
| | - Pankaj B Agrawal
- Neonatal Genomics Program, Division of Newborn Medicine, 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.
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38
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Shen W, Sellers HL, Choate LA, Stein MI, Tandale PP, Tan J, Setlem R, Sakai Y, Fadra N, Sosa C, McClelland SP, Barnett SS, Rasmussen KJ, Runke CK, Smoley SA, Tillmans LS, Marcou CA, Rowsey RA, Thorland EC, Boczek NJ, Kearney HM. Clinical Validation of Tagmentation-Based Genome Sequencing for Germline Disorders. J Mol Diagn 2023; 25:524-531. [PMID: 37088140 DOI: 10.1016/j.jmoldx.2023.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 03/09/2023] [Accepted: 04/04/2023] [Indexed: 04/25/2023] Open
Abstract
Genome sequencing (GS) is a powerful clinical tool used for the comprehensive diagnosis of germline disorders. GS library preparation typically involves mechanical DNA fragmentation, end repair, and bead-based library size selection followed by adapter ligation, which can require a large amount of input genomic DNA. Tagmentation using bead-linked transposomes can simplify the library preparation process and reduce the DNA input requirement. Here we describe the clinical validation of tagmentation-based PCR-free GS as a clinical test for rare germline disorders. Compared with the Genome-in-a-Bottle Consortium benchmark variant sets, GS had a recall >99.7% and a precision of 99.8% for single nucleotide variants and small insertion-deletions. GS also exhibited 100% sensitivity for clinically reported sequence variants and the copy number variants examined. Furthermore, GS detected mitochondrial sequence variants above 5% heteroplasmy and showed reliable detection of disease-relevant repeat expansions and SMN1 homozygous loss. Our results indicate that while lowering DNA input requirements and reducing library preparation time, GS enables uniform coverage across the genome as well as robust detection of various types of genetic alterations. With the advantage of comprehensive profiling of multiple types of genetic alterations, GS is positioned as an ideal first-tier diagnostic test for germline disorders.
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Affiliation(s)
- Wei Shen
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota.
| | - Heidi L Sellers
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Lauren A Choate
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Mariam I Stein
- Division of Computational Biology, Mayo Clinic Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Pratyush P Tandale
- Division of Computational Biology, Mayo Clinic Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Jiayu Tan
- Division of Computational Biology, Mayo Clinic Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Rohit Setlem
- Division of Computational Biology, Mayo Clinic Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Yuta Sakai
- Division of Computational Biology, Mayo Clinic Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Numrah Fadra
- Division of Computational Biology, Mayo Clinic Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Carlos Sosa
- Division of Computational Biology, Mayo Clinic Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Shawn P McClelland
- Division of Computational Biology, Mayo Clinic Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Sarah S Barnett
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Kristen J Rasmussen
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Cassandra K Runke
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Stephanie A Smoley
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Lori S Tillmans
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Cherisse A Marcou
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Ross A Rowsey
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Erik C Thorland
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Nicole J Boczek
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Hutton M Kearney
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota.
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39
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Nurchis MC, Altamura G, Riccardi MT, Radio FC, Chillemi G, Bertini ES, Garlasco J, Tartaglia M, Dallapiccola B, Damiani G. Whole genome sequencing diagnostic yield for paediatric patients with suspected genetic disorders: systematic review, meta-analysis, and GRADE assessment. Arch Public Health 2023; 81:93. [PMID: 37231492 DOI: 10.1186/s13690-023-01112-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Accepted: 05/18/2023] [Indexed: 05/27/2023] Open
Abstract
BACKGROUND About 80% of the roughly 7,000 known rare diseases are single gene disorders, about 85% of which are ultra-rare, affecting less than one in one million individuals. NGS technologies, in particular whole genome sequencing (WGS) in paediatric patients suffering from severe disorders of likely genetic origin improve the diagnostic yield allowing targeted, effective care and management. The aim of this study is to perform a systematic review and meta-analysis to assess the effectiveness of WGS, with respect to whole exome sequencing (WES) and/or usual care, for the diagnosis of suspected genetic disorders among the paediatric population. METHODS A systematic review of the literature was conducted querying relevant electronic databases, including MEDLINE, EMBASE, ISI Web of Science, and Scopus from January 2010 to June 2022. A random-effect meta-analysis was run to inspect the diagnostic yield of different techniques. A network meta-analysis was also performed to directly assess the comparison between WGS and WES. RESULTS Of the 4,927 initially retrieved articles, thirty-nine met the inclusion criteria. Overall results highlighted a significantly higher pooled diagnostic yield for WGS, 38.6% (95% CI: [32.6 - 45.0]), in respect to WES, 37.8% (95% CI: [32.9 - 42.9]) and usual care, 7.8% (95% CI: [4.4 - 13.2]). The meta-regression output suggested a higher diagnostic yield of the WGS compared to WES after controlling for the type of disease (monogenic vs non-monogenic), with a tendency to better diagnostic performances for Mendelian diseases. The network meta-analysis showed a higher diagnostic yield for WGS compared to WES (OR = 1.54, 95%CI: [1.11 - 2.12]). CONCLUSIONS Although whole genome sequencing for the paediatric population with suspected genetic disorders provided an accurate and early genetic diagnosis in a high proportion of cases, further research is needed for evaluating costs, effectiveness, and cost-effectiveness of WGS and achieving an informed decision-making process. TRIAL REGISTRATION This systematic review has not been registered.
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Grants
- RF-2018-12,366,391, 2018 Ministero della Salute
- RF-2018-12,366,391, 2018 Ministero della Salute
- RF-2018-12,366,391, 2018 Ministero della Salute
- RF-2018-12,366,391, 2018 Ministero della Salute
- RF-2018-12,366,391, 2018 Ministero della Salute
- RF-2018-12,366,391, 2018 Ministero della Salute
- RF-2018-12,366,391, 2018 Ministero della Salute
- RF-2018-12,366,391, 2018 Ministero della Salute
- RF-2018-12,366,391, 2018 Ministero della Salute
- RF-2018-12,366,391, 2018 Ministero della Salute
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Affiliation(s)
- Mario Cesare Nurchis
- Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168, Rome, Italy
- School of Economics, Università Cattolica del Sacro Cuore, 00168, Rome, Italy
| | - Gerardo Altamura
- Department of Health Sciences and Public Health, Section of Hygiene, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168, Rome, Italy.
| | - Maria Teresa Riccardi
- Department of Health Sciences and Public Health, Section of Hygiene, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168, Rome, Italy
| | - Francesca Clementina Radio
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù IRCCS, 00146, Rome, Italy
| | - Giovanni Chillemi
- Department for Innovation in Biological Agro-Food and Forest Systems (DIBAF), University of Tuscia, 01100, Viterbo, Italy
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Centro Nazionale Delle Ricerche, 70126, Bari, Italy
| | - Enrico Silvio Bertini
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù IRCCS, 00146, Rome, Italy
| | - Jacopo Garlasco
- Department of Public Health Sciences and Paediatrics, University of Turin, 10126, Turin, Italy
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù IRCCS, 00146, Rome, Italy
| | - Bruno Dallapiccola
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù IRCCS, 00146, Rome, Italy
| | - Gianfranco Damiani
- Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168, Rome, Italy
- Department of Health Sciences and Public Health, Section of Hygiene, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168, Rome, Italy
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40
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von Hardenberg S, Wallaschek H, Du C, Schmidt G, Auber B. A holistic approach to maximise diagnostic output in trio exome sequencing. Front Pediatr 2023; 11:1183891. [PMID: 37274821 PMCID: PMC10238563 DOI: 10.3389/fped.2023.1183891] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 05/02/2023] [Indexed: 06/07/2023] Open
Abstract
Introduction Rare genetic diseases are a major cause for severe illness in children. Whole exome sequencing (WES) is a powerful tool for identifying genetic causes of rare diseases. For a better and faster assessment of the vast number of variants that are identified in the index patient in WES, parental sequencing can be applied ("trio WES"). Methods We assessed the diagnostic rate of routine trio WES including analysis of copy number variants in 224 pediatric patients during an evaluation period of three years. Results Trio WES provided a diagnosis in 67 (30%) of all 224 analysed children. The turnaround time of trio WES analysis has been reduced significantly from 41 days in 2019 to 23 days in 2021. Copy number variants could be identified to be causative in 10 cases (4.5%), underlying the importance of copy number variant analysis. Variants in three genes which were previously not associated with a clinical condition (GAD1, TMEM222 and ZNFX1) were identified using the matching tool GeneMatcher and were part of the first description of a new syndrome. Discussion Trio WES has proven to have a high diagnostic yield and to shorten the process of identifying the correct diagnosis in paediatric patients. Re-evaluation of all 224 trio WES 1-3 years after initial analysis did not establish new diagnoses. Initiating (trio) WES as a first-tier diagnostics including copy number variant detection should be considered as early as possible, especially for children treated in ICU, if a monogenetic disease is suspected.
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Affiliation(s)
| | | | | | | | - Bernd Auber
- Correspondence: Sandra von Hardenberg Bernd Auber
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41
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Hamvas A, Chaudhari BP, Nogee LM. Genetic testing for diffuse lung diseases in children. Pediatr Pulmonol 2023. [PMID: 37191361 DOI: 10.1002/ppul.26447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 04/04/2023] [Accepted: 04/23/2023] [Indexed: 05/17/2023]
Abstract
Newly developing genomic technologies are an increasingly important part of clinical care and thus, it is not only important to understand the technologies and their limitations, but to also interpret the findings in an actionable fashion. Clinical geneticists and genetic counselors are now an integral part of the clinical team and are able to bridge the complexities of this rapidly changing science between the bedside clinicians and patients. This manuscript reviews the terminology, the current technology, some of the known genetic disorders that result in lung disease, and indications for genetic testing with associated caveats. Because this field is evolving quickly, we also provide links to websites that provide continuously updated information important for integrating genomic technology results into clinical decision-making.
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Affiliation(s)
- Aaron Hamvas
- Department of Pediatrics, Division of Neonatology, Ann and Robert H. Lurie Children's Hospital of Chicago and Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Bimal P Chaudhari
- Divisions of Genetics and Genomic Medicine, Neonatology, Nationwide Children's Hospital, The Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Lawrence M Nogee
- Department of Pediatrics, Eudowood Neonatal Pulmonary Division, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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42
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Sergi MM, Keinath MC, Fanaroff J, Miller KE. Ethical Considerations of Genome Sequencing for Pediatric Patients. Semin Pediatr Neurol 2023; 45:101039. [PMID: 37003628 DOI: 10.1016/j.spen.2023.101039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 02/20/2023] [Accepted: 02/23/2023] [Indexed: 04/03/2023]
Abstract
Advancements in genetic testing in the healthcare setting, most recently genomic sequencing, has enhanced our ability to diagnose genetic conditions. These advances include increased accessibility and affordability of genomic technologies. With expanded use comes the potential for significant ethical challenges for clinicians, particularly considering the implications of testing a child for one condition and incidentally finding a different condition or health risk. In this focused review, we address various ethical considerations from informed consent to the rights of a child undergoing genetic testing.
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Affiliation(s)
- Michelle M Sergi
- From theUniversity Hospitals Rainbow Babies & Children's Hospital, Cleveland, OH; Case Western Reserve University School of Medicine, Cleveland, OH; University Hospitals Cleveland Medical Center, Cleveland, OH; MacLean Center for Clinical Medical Ethics, University of Chicago, Chicago, IL.
| | - Melissa C Keinath
- Case Western Reserve University School of Medicine, Cleveland, OH; University Hospitals Cleveland Medical Center, Cleveland, OH
| | - Jonathan Fanaroff
- From theUniversity Hospitals Rainbow Babies & Children's Hospital, Cleveland, OH; Case Western Reserve University School of Medicine, Cleveland, OH
| | - Kathryn E Miller
- From theUniversity Hospitals Rainbow Babies & Children's Hospital, Cleveland, OH
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43
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Olde Keizer RACM, Marouane A, Kerstjens-Frederikse WS, Deden AC, Lichtenbelt KD, Jonckers T, Vervoorn M, Vreeburg M, Henneman L, de Vries LS, Sinke RJ, Pfundt R, Stevens SJC, Andriessen P, van Lingen RA, Nelen M, Scheffer H, Stemkens D, Oosterwijk C, van Amstel HKP, de Boode WP, van Zelst-Stams WAG, Frederix GWJ, Vissers LELM. Rapid exome sequencing as a first-tier test in neonates with suspected genetic disorder: results of a prospective multicenter clinical utility study in the Netherlands. Eur J Pediatr 2023:10.1007/s00431-023-04909-1. [PMID: 36997769 PMCID: PMC10257607 DOI: 10.1007/s00431-023-04909-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 02/21/2023] [Accepted: 02/26/2023] [Indexed: 04/01/2023]
Abstract
The introduction of rapid exome sequencing (rES) for critically ill neonates admitted to the neonatal intensive care unit has made it possible to impact clinical decision-making. Unbiased prospective studies to quantify the impact of rES over routine genetic testing are, however, scarce. We performed a clinical utility study to compare rES to conventional genetic diagnostic workup for critically ill neonates with suspected genetic disorders. In a multicenter prospective parallel cohort study involving five Dutch NICUs, we performed rES in parallel to routine genetic testing for 60 neonates with a suspected genetic disorder and monitored diagnostic yield and the time to diagnosis. To assess the economic impact of rES, healthcare resource use was collected for all neonates. rES detected more conclusive genetic diagnoses than routine genetic testing (20% vs. 10%, respectively), in a significantly shorter time to diagnosis (15 days (95% CI 10-20) vs. 59 days (95% CI 23-98, p < 0.001)). Moreover, rES reduced genetic diagnostic costs by 1.5% (€85 per neonate). CONCLUSION Our findings demonstrate the clinical utility of rES for critically ill neonates based on increased diagnostic yield, shorter time to diagnosis, and net healthcare savings. Our observations warrant the widespread implementation of rES as first-tier genetic test in critically ill neonates with disorders of suspected genetic origin. WHAT IS KNOWN • Rapid exome sequencing (rES) enables diagnosing rare genetic disorders in a fast and reliable manner, but retrospective studies with neonates admitted to the neonatal intensive care unit (NICU) indicated that genetic disorders are likely underdiagnosed as rES is not routinely used. • Scenario modeling for implementation of rES for neonates with presumed genetic disorders indicated an expected increase in costs associated with genetic testing. WHAT IS NEW • This unique prospective national clinical utility study of rES in a NICU setting shows that rES obtained more and faster diagnoses than conventional genetic tests. • Implementation of rES as replacement for all other genetic tests does not increase healthcare costs but in fact leads to a reduction in healthcare costs.
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Grants
- 843002608, 846002003 ZonMw
- 843002608, 846002003 ZonMw
- 843002608, 846002003 ZonMw
- 843002608, 846002003 ZonMw
- 843002608, 846002003 ZonMw
- 843002608, 846002003 ZonMw
- 843002608, 846002003 ZonMw
- 843002608, 846002003 ZonMw
- 843002608, 846002003 ZonMw
- 843002608, 846002003 ZonMw
- 843002608, 846002003 ZonMw
- 843002608, 846002003 ZonMw
- 779257 Horizon 2020 Framework Programme
- 779257 Horizon 2020 Framework Programme
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Affiliation(s)
- Richelle A C M Olde Keizer
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Abderrahim Marouane
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, Netherlands
| | | | - A Chantal Deden
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, Netherlands
| | | | - Tinneke Jonckers
- Department of Pediatrics and Neonatology, Máxima Medical Center, Veldhoven, Netherlands
| | - Marieke Vervoorn
- Department of Pediatrics and Neonatology, Máxima Medical Center, Veldhoven, Netherlands
| | - Maaike Vreeburg
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, Netherlands
| | - Lidewij Henneman
- Department of Human Genetics and Amsterdam Reproduction and Development Research Institute, Amsterdam UMC, Vrije Universiteit, Amsterdam, Netherlands
| | - Linda S de Vries
- Department of Neonatology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Richard J Sinke
- Department of Genetics, University Medical Center, University of Groningen, Groningen, Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, Netherlands
| | - Servi J C Stevens
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, Netherlands
| | - Peter Andriessen
- Department of Pediatrics, Máxima Medical Center, Veldhoven, Netherlands
- Department of Applied Physics, Eindhoven University of Technology, Eindhoven, Netherlands
| | | | - Marcel Nelen
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, Netherlands
| | - Hans Scheffer
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, Netherlands
| | - Daphne Stemkens
- VSOP - National Patient Alliance for Rare and Genetic Diseases, Soest, Netherlands
| | - Cor Oosterwijk
- VSOP - National Patient Alliance for Rare and Genetic Diseases, Soest, Netherlands
| | | | - Willem P de Boode
- Department of Neonatology, Radboud University Medical Center, Radboud Institute for Health Sciences, Amalia Children's Hospital, Nijmegen, Netherlands
| | - Wendy A G van Zelst-Stams
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, Netherlands.
| | - Geert W J Frederix
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
- Department of Genetics, Utrecht University Medical Center, Utrecht, Netherlands
| | - Lisenka E L M Vissers
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, Netherlands.
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44
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Staub E. Current and potential methods to assess kidney structure and morphology in term and preterm neonates. Anat Rec (Hoboken) 2023. [PMID: 36883787 DOI: 10.1002/ar.25195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 01/25/2023] [Accepted: 02/21/2023] [Indexed: 03/09/2023]
Abstract
After birth, the kidney structure in neonates adapt to the functional demands of extrauterine life. Nephrogenesis is complete in the third trimester, but glomeruli, tubuli, and vasculature mature with the rapidly increasing renal blood flow and glomerular filtration. In preterm infants, nephrogenesis remains incomplete and maturation is slower and may be aberrant. This structural and functional deficit has life-long consequences: preterm born individuals are at higher risk for chronic kidney disease and arterial hypertension later in life. This review assembles the literature on existing and potential methods to visualize neonatal kidney structure and morphology and explore their potential to longitudinally document the developmental deviation after preterm birth. X-rays with and without contrast, fluoroscopy and computed tomography (CT) involve relevant ionizing radiation exposure and, apart from CT, do not provide sufficient structural details. Ultrasound has evolved into a safe and noninvasive high-resolution imaging method which is excellent for longitudinal observations. Doppler ultrasound modes can characterize and quantify blood flow to and through the kidneys. Microvascular flow imaging has opened new possibilities of visualizing previously unseen vascular structures. Recent advances in magnetic resonance imaging display renal structure and function in unprecedented detail, but are offset by the logistical challenges of the imaging procedure and limited experience with the new techniques in neonates. Kidney biopsies visualize structure histologically, but are too invasive and remain anecdotal in newborns. All the explored methods have predominantly been examined in term newborns and require further research on longitudinal structural observation in the kidneys of preterm infants.
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Affiliation(s)
- Eveline Staub
- Department of Neonatology, Royal North Shore Hospital, St Leonards, New South Wales, Australia
- University of Sydney Northern Clinical School, Royal North Shore Hospital, St Leonards, New South Wales, Australia
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45
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Callahan KP, Radack J, Wojcik MH, Jenkins SM, Nye RT, Skraban C, Wild KT, Feudtner C. Hospital-level variation in genetic testing in children's hospitals' neonatal intensive care units from 2016 to 2021. Genet Med 2023; 25:100357. [PMID: 36521640 PMCID: PMC9991964 DOI: 10.1016/j.gim.2022.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 12/07/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022] Open
Abstract
PURPOSE This study aimed to examine variation in genetic testing between neonatal intensive care units (NICUs) across hospitals over time. METHODS We performed a multicenter large-scale retrospective cohort study using NICU discharge data from the Pediatric Hospital Information System database between 2016 and 2021. We analyzed the variation in the percentage of NICU patients who had any genetic testing across hospitals and over time. We used a multivariable multilevel logistic regression model to investigate the potential association between patient characteristics and genetic testing. RESULTS The final analysis included 207,228 neonates from 38 hospitals. Overall, 13% of patients had at least 1 genetic test sent, although this varied from 4% to 50% across hospitals. Over the study period, the proportion of patients tested increased, with the increase disproportionately borne by hospitals already testing high proportions of patients. On average, patients who received genetic testing had higher illness severity. Controlling for severity, however, only minimally reduced the degree of hospital-level variation in genetic testing. CONCLUSION The percentage of NICU patients who undergo genetic testing varies among hospitals and increasingly so over time. Variation is largely unexplained by differences in severity between hospitals. The degree of variation suggests that clearer guidelines for NICU genetic testing are warranted.
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Affiliation(s)
- Katharine Press Callahan
- Division of Neonatology, Children's Hospital of Philadelphia Philadelphia, PA; Department of Medical Ethics and Health Policy, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA.
| | - Joshua Radack
- Division of Neonatology, Children's Hospital of Philadelphia Philadelphia, PA
| | - Monica H Wojcik
- Divisions of Newborn Medicine and Genetics and Genomics, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Sabrina Malone Jenkins
- Division of Neonatology, Department of Pediatrics, School of Medicine, Health University of Utah, Salt Lake City, UT
| | - Russell T Nye
- Division of Neonatology, Children's Hospital of Philadelphia Philadelphia, PA
| | - Cara Skraban
- Division of Neonatology, Children's Hospital of Philadelphia Philadelphia, PA
| | | | - Chris Feudtner
- Division of Neonatology, Children's Hospital of Philadelphia Philadelphia, PA; Department of Medical Ethics and Health Policy, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
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46
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Price ME, Fishler KP, Muff-Luett M, Mauch TJ, Brunelli L, Euteneuer JC. Variants in AQP11 may result in autosomal recessive bilateral cystic renal dysgenesis. Am J Med Genet A 2023; 191:612-616. [PMID: 36420936 DOI: 10.1002/ajmg.a.63056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/01/2022] [Accepted: 11/02/2022] [Indexed: 11/25/2022]
Abstract
Congenital renal cystic dysplasia is a rare disease that occurs in approximately 1 in 4000 children and is often discovered in the antenatal period by ultrasound. It is commonly associated with oligohydramnios in utero and/or renal insufficiency or failure in the postnatal period. Aquaporins are membrane proteins that serve as transport channels in the transfer of water or small solutes across cell membranes. They play a role in the development of renal cysts. Aquaporin 11 (AQP11) deficient mice develop polycystic kidney disease in utero due to disruption of polycystin-1. Here we describe a case of bilateral cystic kidney disease in a patient with novel compound heterozygous variants in AQP11: c.780G>T (p. Trp260Cys) and c.472C>T (p.Pro158Ser) (NM_173039.2) identified by whole genome sequencing. These findings suggest, for the first time, the potential role of AQP11 in congenital renal cystic dysplasia.
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Affiliation(s)
- Michael E Price
- University of Nebraska Medical Center, College of Medicine, Omaha, Nebraska, USA
| | - Kristen P Fishler
- Munroe-Meyer Institute of Genetics and Rehabilitation, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Melissa Muff-Luett
- Department of Pediatrics, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Teri J Mauch
- Department of Pediatrics, University of Nebraska Medical Center, Omaha, Nebraska, USA.,Department of Pediatrics, University of Utah, Salt Lake City, Utah, USA
| | - Luca Brunelli
- Department of Pediatrics, University of Nebraska Medical Center, Omaha, Nebraska, USA.,Department of Pediatrics, University of Utah, Salt Lake City, Utah, USA
| | - Joshua C Euteneuer
- Department of Pediatrics, University of Nebraska Medical Center, Omaha, Nebraska, USA
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47
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Reactive gene curation to support interpretation and reporting of a clinical genome test for rare disease: Experience from over 1,000 cases. CELL GENOMICS 2023; 3:100258. [PMID: 36819666 PMCID: PMC9932986 DOI: 10.1016/j.xgen.2023.100258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 09/13/2022] [Accepted: 01/06/2023] [Indexed: 02/04/2023]
Abstract
Current standards in clinical genetics recognize the need to establish the validity of gene-disease relationships as a first step in the interpretation of sequence variants. We describe our experience incorporating the ClinGen Gene-Disease Clinical Validity framework in our interpretation and reporting workflow for a clinical genome sequencing (cGS) test for individuals with rare and undiagnosed genetic diseases. This "reactive" gene curation is completed upon identification of candidate variants during active case analysis and within the test turn-around time by focusing on the most impactful evidence and taking advantage of the broad applicability of the framework to cover a wide range of disease areas. We demonstrate that reactive gene curation can be successfully implemented in support of cGS in a clinical laboratory environment, enabling robust clinical decision making and allowing all variants to be fully and appropriately considered and their clinical significance confidently interpreted.
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48
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Wojcik MH, Reuter CM, Marwaha S, Mahmoud M, Duyzend MH, Barseghyan H, Yuan B, Boone PM, Groopman EE, Délot EC, Jain D, Sanchis-Juan A, Starita LM, Talkowski M, Montgomery SB, Bamshad MJ, Chong JX, Wheeler MT, Berger SI, O’Donnell-Luria A, Sedlazeck FJ, Miller DE. Beyond the exome: what's next in diagnostic testing for Mendelian conditions. ARXIV 2023:arXiv:2301.07363v1. [PMID: 36713248 PMCID: PMC9882576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Despite advances in clinical genetic testing, including the introduction of exome sequencing (ES), more than 50% of individuals with a suspected Mendelian condition lack a precise molecular diagnosis. Clinical evaluation is increasingly undertaken by specialists outside of clinical genetics, often occurring in a tiered fashion and typically ending after ES. The current diagnostic rate reflects multiple factors, including technical limitations, incomplete understanding of variant pathogenicity, missing genotype-phenotype associations, complex gene-environment interactions, and reporting differences between clinical labs. Maintaining a clear understanding of the rapidly evolving landscape of diagnostic tests beyond ES, and their limitations, presents a challenge for non-genetics professionals. Newer tests, such as short-read genome or RNA sequencing, can be challenging to order and emerging technologies, such as optical genome mapping and long-read DNA or RNA sequencing, are not available clinically. Furthermore, there is no clear guidance on the next best steps after inconclusive evaluation. Here, we review why a clinical genetic evaluation may be negative, discuss questions to be asked in this setting, and provide a framework for further investigation, including the advantages and disadvantages of new approaches that are nascent in the clinical sphere. We present a guide for the next best steps after inconclusive molecular testing based upon phenotype and prior evaluation, including when to consider referral to a consortium such as GREGoR, which is focused on elucidating the underlying cause of rare unsolved genetic disorders.
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Affiliation(s)
- Monica H. Wojcik
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115 USA
- Division of Newborn Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Chloe M. Reuter
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Shruti Marwaha
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Medhat Mahmoud
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston TX 77030 USA
| | - Michael H. Duyzend
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115 USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114 USA
| | - Hayk Barseghyan
- Center for Genetics Medicine Research, Children’s National Research Institute, Children’s National Hospital, Washington, DC 20010 USA
- Department of Genomics and Precision Medicine, School of Medicine and Health Sciences, George Washington University, Washington, DC 20037 USA
| | - Bo Yuan
- Department of Molecular and Human Genetics and Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston TX 77030 USA
| | - Philip M. Boone
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115 USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114 USA
| | - Emily E. Groopman
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115 USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114 USA
| | - Emmanuèle C. Délot
- Department of Genomics and Precision Medicine, School of Medicine and Health Sciences, George Washington University, Washington, DC 20037 USA
- Center for Genetics Medicine Research, Children’s National Research and Innovation Campus, Washington, DC, USA
- Department of Pediatrics, George Washington University, School of Medicine and Health Sciences, George Washington University, Washington, DC 20037 USA
| | - Deepti Jain
- Department of Biostatistics, School of Public Health, University of Washington, Seattle WA 98195 USA
| | - Alba Sanchis-Juan
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114 USA
| | | | - Lea M. Starita
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195 USA
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195 USA
| | - Michael Talkowski
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114 USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Stephen B. Montgomery
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA 94305 USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305 USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Michael J. Bamshad
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195 USA
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195 USA
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195 USA
| | - Jessica X. Chong
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195 USA
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195 USA
| | - Matthew T. Wheeler
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Seth I. Berger
- Center for Genetics Medicine Research and Rare Disease Institute, Children’s National Hospital, Washington, DC 20010 USA
| | - Anne O’Donnell-Luria
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115 USA
- Center for Genomic Medicine, Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114 USA
| | - Fritz J. Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston TX 77030 USA
- Department of Computer Science, Rice University, 6100 Main Street, Houston, TX, 77005 USA
| | - Danny E. Miller
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195 USA
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195 USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195 USA
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49
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Bupp CP, Ames EG, Arenchild MK, Caylor S, Dimmock DP, Fakhoury JD, Karna P, Lehman A, Meghea CI, Misra V, Nolan DA, O’Shea J, Sharangpani A, Franck LS, Scheurer-Monaghan A. Breaking Barriers to Rapid Whole Genome Sequencing in Pediatrics: Michigan's Project Baby Deer. CHILDREN (BASEL, SWITZERLAND) 2023; 10:children10010106. [PMID: 36670656 PMCID: PMC9857227 DOI: 10.3390/children10010106] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 12/02/2022] [Accepted: 12/19/2022] [Indexed: 01/06/2023]
Abstract
The integration of precision medicine in the care of hospitalized children is ever evolving. However, access to new genomic diagnostics such as rapid whole genome sequencing (rWGS) is hindered by barriers in implementation. Michigan's Project Baby Deer (PBD) is a multi-center collaborative effort that sought to break down barriers to access by offering rWGS to critically ill neonatal and pediatric inpatients in Michigan. The clinical champion team used a standardized approach with inclusion and exclusion criteria, shared learning, and quality improvement evaluation of the project's impact on the clinical outcomes and economics of inpatient rWGS. Hospitals, including those without on-site geneticists or genetic counselors, noted positive clinical impacts, accelerating time to definitive treatment for project patients. Between 95-214 hospital days were avoided, net savings of $4155 per patient, and family experience of care was improved. The project spurred policy advancement when Michigan became the first state in the United States to have a Medicaid policy with carve-out payment to hospitals for rWGS testing. This state project demonstrates how front-line clinician champions can directly improve access to new technology for pediatric patients and serves as a roadmap for expanding clinical implementation of evidence-based precision medicine technologies.
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Affiliation(s)
- Caleb P. Bupp
- Corewell Health Helen DeVos Children’s Hospital, Grand Rapids, MI 49503, USA
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
- Correspondence: (C.P.B.); (A.S.-M.); Tel.: +1-616-391-2700 (C.P.B.)
| | - Elizabeth G. Ames
- Sparrow Hospital, University of Michigan Health System, Lansing, MI 48912, USA
| | | | - Sara Caylor
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - David P. Dimmock
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Joseph D. Fakhoury
- Pediatric Hospital Medicine, Bronson Children’s Hospital, Kalamazoo, MI 49007, USA
- Department of Pediatric and Adolescent Medicine, Homer Stryker School of Medicine, Western Michigan University, Kalamazoo, MI 49007, USA
| | - Padmani Karna
- Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Lansing, MI 48912, USA
| | - April Lehman
- Children’s Hospital of Michigan, Central Michigan University, Detroit, MI 48201, USA
| | - Cristian I. Meghea
- Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Lansing, MI 48912, USA
| | - Vinod Misra
- Children’s Hospital of Michigan, Central Michigan University, Detroit, MI 48201, USA
| | | | - Jessica O’Shea
- Sparrow Hospital, University of Michigan Health System, Lansing, MI 48912, USA
| | - Aditi Sharangpani
- Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Lansing, MI 48912, USA
| | - Linda S. Franck
- Department of Family Health Care Nursing, University of California, San Francisco, CA 94143, USA
| | - Andrea Scheurer-Monaghan
- Department of Pediatric and Adolescent Medicine, Homer Stryker School of Medicine, Western Michigan University, Kalamazoo, MI 49007, USA
- Neonatal Intensive Care, Bronson Children’s Hospital, Kalamazoo, MI 49007, USA
- Correspondence: (C.P.B.); (A.S.-M.); Tel.: +1-616-391-2700 (C.P.B.)
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50
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SCIP: software for efficient clinical interpretation of copy number variants detected by whole-genome sequencing. Hum Genet 2023; 142:201-216. [PMID: 36376761 PMCID: PMC9918589 DOI: 10.1007/s00439-022-02494-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 10/09/2022] [Indexed: 11/16/2022]
Abstract
Copy number variants (CNVs) represent major etiologic factors in rare genetic diseases. Current clinical CNV interpretation workflows require extensive back-and-forth with multiple tools and databases. This increases complexity and time burden, potentially resulting in missed genetic diagnoses. We present the Suite for CNV Interpretation and Prioritization (SCIP), a software package for the clinical interpretation of CNVs detected by whole-genome sequencing (WGS). The SCIP Visualization Module near-instantaneously displays all information necessary for CNV interpretation (variant quality, population frequency, inheritance pattern, and clinical relevance) on a single page-supported by modules providing variant filtration and prioritization. SCIP was comprehensively evaluated using WGS data from 1027 families with congenital cardiac disease and/or autism spectrum disorder, containing 187 pathogenic or likely pathogenic (P/LP) CNVs identified in previous curations. SCIP was efficient in filtration and prioritization: a median of just two CNVs per case were selected for review, yet it captured all P/LP findings (92.5% of which ranked 1st). SCIP was also able to identify one pathogenic CNV previously missed. SCIP was benchmarked against AnnotSV and a spreadsheet-based manual workflow and performed superiorly than both. In conclusion, SCIP is a novel software package for efficient clinical CNV interpretation, substantially faster and more accurate than previous tools (available at https://github.com/qd29/SCIP , a video tutorial series is available at https://bit.ly/SCIPVideos ).
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