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Li W, Li H, Lu C, Zhao J, Xu H, Xu Z, Mitchell B, Jiang Y, Gu HQ, Xu Q, Wang A, Meng X, Lin J, Jing J, Li Z, Zhu W, Liang Z, Wang M, Wang Y. Neglected Mendelian causes of stroke in adult Chinese patients who had an ischaemic stroke or transient ischaemic attack. Stroke Vasc Neurol 2024; 9:194-201. [PMID: 37495379 PMCID: PMC11221298 DOI: 10.1136/svn-2022-002158] [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: 11/11/2022] [Accepted: 06/27/2023] [Indexed: 07/28/2023] Open
Abstract
BACKGROUND AND PURPOSE Multiple factors play important roles in the occurrence and prognosis of stroke. However, the roles of monogenic variants in all-cause ischaemic stroke have not been systematically investigated. We aim to identify underdiagnosed monogenic stroke in an adult ischaemic stroke/transient ischaemic attack (TIA) cohort (the Third China National Stroke Registry, CNSR-III). METHODS Targeted next-generation sequencing for 181 genes associated with stroke was conducted on DNA samples from 10 428 patients recruited through CNSR-III. The genetic and clinical data from electronic health records (EHRs) were reviewed for completion of the diagnostic process. We assessed the percentages of individuals with pathogenic or likely pathogenic (P/LP) variants, and the diagnostic yield of pathogenic variants in known monogenic disease genes with associated phenotypes. RESULTS In total, 1953 individuals harboured at least one P/LP variant out of 10 428 patients. Then, 792 (7.6%) individuals (comprising 759 individuals harbouring one P/LP variant in one gene, 29 individuals harbouring two or more P/LP variants in different genes and 4 individuals with two P/LP variants in ABCC6) were predicted to be at risk for one or more monogenic diseases based on the inheritance pattern. Finally, 230 of 792 individuals manifested a clinical phenotype in the EHR data to support the diagnosis of stroke with a monogenic cause. The most diagnosed Mendelian cause of stroke in the cohort was cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy. There were no relationships between age or family history and the incidence of first symptomatic monogenic stroke in patients. CONCLUSION The rate of monogenic cause of stroke was 2.2% after reviewing the clinical phenotype. Possible reasons that Mendelian causes of stroke may be missed in adult patients who had an ischaemic stroke/TIA include a late onset of stroke symptoms, combination with common vascular risks and the absence of a prominent family history.
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Affiliation(s)
- Wei Li
- China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Hao Li
- China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Chaoxia Lu
- China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Jialu Zhao
- China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Huichun Xu
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Zhe Xu
- China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Braxton Mitchell
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Yong Jiang
- China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Hong-Qiu Gu
- China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Qin Xu
- China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Anxin Wang
- China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Xia Meng
- China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Jinxi Lin
- China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Jing Jing
- China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Zixiao Li
- China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Wanlin Zhu
- China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Zhigang Liang
- Department of Neurology, Qindao University Medical College Affiliated Yantai Yuhuangding Hospital, Yantai, Shandong, China
| | - Mengxing Wang
- China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yongjun Wang
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- Clinical Center for Precision Medicine in Stroke, Capital Medical University, Beijing, China
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León P, Franco P, Hinojosa N, Torres K, Moreano A, Romero VI. TTN novel splice variant in familial dilated cardiomyopathy and splice variants review: a case report. Front Cardiovasc Med 2024; 11:1387063. [PMID: 38938651 PMCID: PMC11210389 DOI: 10.3389/fcvm.2024.1387063] [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: 02/16/2024] [Accepted: 05/03/2024] [Indexed: 06/29/2024] Open
Abstract
This case report details the identification of a novel likely pathogenic splicing variant in the TTN gene, associated with dilated cardiomyopathy (DCM), in a 42-year-old male patient presenting with early-onset heart failure and reduced ejection fraction. DCM is a nonischemic heart condition characterized by left biventricular dilation and systolic dysfunction, with approximately one-third of cases being familial and often linked to genetic mutations. The TTN gene, encoding the largest human protein essential for muscle contraction and sarcomere structure, is implicated in about 25% of DCM cases through mutations, especially truncating variants. Our investigation revealed a previously unreported G > C mutation at the splice acceptor site in intron 356 of TTN, confirmed by Sanger sequencing and not found in population databases, suggesting a novel contribution to the understanding of DCM etiology. The case emphasizes the critical role of the TTN gene in cardiac function and the genetic complexity underlying DCM. A comprehensive literature review highlighted the prevalence and significance of splice variants in the TTN gene, particularly those affecting the titin A-band, which is known for its role in muscle contraction and stability. This variant's identification underscores the importance of genetic screening in patients with DCM, offering insights into the disease's familial transmission and potential therapeutic targets. Our findings contribute to the expanding knowledge of genetic factors in DCM, demonstrating the necessity of integrating genetic diagnostics in cardiovascular medicine. This case supports the growing evidence linking splicing mutations in specific regions of the TTN gene to DCM development and underscores the importance of genetic counseling and testing in managing heart disease.
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Affiliation(s)
- Paul León
- College of Biological and Environmental Sciences, Universidad San Francisco de Quito, Quito, Ecuador
| | - Paula Franco
- School of Medicine, Universidad San Francisco de Quito, Quito, Ecuador
| | - Nicole Hinojosa
- School of Medicine, Universidad San Francisco de Quito, Quito, Ecuador
| | - Kevin Torres
- School of Medicine, Universidad San Francisco de Quito, Quito, Ecuador
| | - Andrés Moreano
- Department of Cardiology, Universidad de Sao Paulo, Sao Paulo, Brazil
| | - Vanessa I. Romero
- College of Biological and Environmental Sciences, Universidad San Francisco de Quito, Quito, Ecuador
- School of Medicine, Universidad San Francisco de Quito, Quito, Ecuador
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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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Mancl N, Myers MF, Miller EM, Jackson F, Widmeyer K. Preparedness and training of genetic counselors practicing in inpatient settings. J Genet Couns 2024; 33:539-553. [PMID: 37528675 DOI: 10.1002/jgc4.1754] [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: 04/21/2023] [Revised: 07/05/2023] [Accepted: 07/15/2023] [Indexed: 08/03/2023]
Abstract
As rapid genomic testing technology increasingly allows for real-time answers that could alter management for acutely ill patients, opportunities for genetic counselors to work in inpatient settings will increase. However, genetic counselors' preparedness and the training provided by graduate programs to work in inpatient settings are unknown. We conducted semi-structured interviews with 13 genetic counselors who provided services in varied inpatient settings to assess genetic counselors' readiness for inpatient positions. We also surveyed members of the Association of Genetic Counseling Program Directors (AGCPD) about inpatient training practices of genetic counseling graduate programs. Genetic counselors were recruited through the National Society of Genetic Counselors (NSGC) Inpatient Special Interest Group listserv and graduate program faculty were recruited through the AGCPD listserv. Some challenges reported by genetic counselors in inpatient settings included working in a fast-paced hospital environment which necessitated focused interactions with patients; collaborating with diverse providers who may not understand the role of genetic counselors; and navigating grief experiences of families and of themselves as a provider. Although genetic counselors felt that many of their skills developed in graduate school were transferrable to the inpatient setting, those who had minimal or no inpatient exposure in graduate school often described feeling unprepared for working in the inpatient setting. The majority of AGCPD respondents (23/28) indicated their program provided some type of exposure to the inpatient setting for students, the most common (22/23) being an inpatient clinical rotation, which suggests many graduate programs are already recognizing the importance of providing inpatient training. Our findings indicate that while many skills are transferrable to inpatient positions, genetic counselors face unique challenges in inpatient settings. Our results suggest that graduate exposure to the inpatient setting and professional support of inpatient genetic counselors are beneficial to support genetic counselors' preparedness to take on inpatient positions.
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Affiliation(s)
- Nelliann Mancl
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
- College of Medicine, University of Cincinnati, Cincinnati, Ohio, USA
| | - Melanie F Myers
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
- College of Medicine, University of Cincinnati, Cincinnati, Ohio, USA
| | - Erin M Miller
- College of Medicine, University of Cincinnati, Cincinnati, Ohio, USA
- Division of Cardiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Farrah Jackson
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Kimberly Widmeyer
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
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Vuocolo B, German RJ, Lalani SR, Murali CN, Bacino CA, Baskin S, Littlejohn R, Odom JD, McLean S, Schmid C, Nutter M, Stuebben M, Magness E, Juarez O, El Achi D, Mitchell B, Glinton KE, Robak L, Nagamani SCS, Saba L, Ritenour A, Zhang L, Streff H, Chan K, Kemere KJ, Carter K, Owen N, Vossaert L, Liu P, Bellen H, Wangler MF. Improving access to exome sequencing in a medically underserved population through the Texome Project. Genet Med 2024; 26:101102. [PMID: 38431799 PMCID: PMC11161315 DOI: 10.1016/j.gim.2024.101102] [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: 09/26/2023] [Revised: 02/16/2024] [Accepted: 02/21/2024] [Indexed: 03/05/2024] Open
Abstract
PURPOSE Genomic medicine can end diagnostic odysseys for patients with complex phenotypes; however, limitations in insurance coverage and other systemic barriers preclude individuals from accessing comprehensive genetics evaluation and testing. METHODS The Texome Project is a 4-year study that reduces barriers to genomic testing for individuals from underserved and underrepresented populations. Participants with undiagnosed, rare diseases who have financial barriers to obtaining exome sequencing (ES) clinically are enrolled in the Texome Project. RESULTS We highlight the Texome Project process and describe the outcomes of the first 60 ES results for study participants. Participants received a genetic evaluation, ES, and return of results at no cost. We summarize the psychosocial or medical implications of these genetic diagnoses. Thus far, ES provided molecular diagnoses for 18 out of 60 (30%) of Texome participants. Plus, in 11 out of 60 (18%) participants, a partial or probable diagnosis was identified. Overall, 5 participants had a change in medical management. CONCLUSION To date, the Texome Project has recruited a racially, ethnically, and socioeconomically diverse cohort. The diagnostic rate and medical impact in this cohort support the need for expanded access to genetic testing and services. The Texome Project will continue reducing barriers to genomic care throughout the future study years.
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Affiliation(s)
- Blake Vuocolo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX
| | - Ryan J German
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX
| | - Seema R Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Chaya N Murali
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Carlos A Bacino
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Stephanie Baskin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Department of Pediatrics, Baylor College of Medicine, San Antonio, TX
| | | | - John D Odom
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Department of Pediatrics, Baylor College of Medicine, San Antonio, TX
| | - Scott McLean
- Department of Pediatrics, Baylor College of Medicine, San Antonio, TX
| | - Carrie Schmid
- Department of Pediatrics, Baylor College of Medicine, San Antonio, TX
| | - Morgan Nutter
- Department of Pediatrics, Baylor College of Medicine, San Antonio, TX
| | - Melissa Stuebben
- Department of Pediatrics, Baylor College of Medicine, San Antonio, TX
| | - Emily Magness
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Olivia Juarez
- Department of Pediatrics, Baylor College of Medicine, San Antonio, TX
| | - Dina El Achi
- Department of Pediatrics, Baylor College of Medicine, San Antonio, TX
| | - Bailey Mitchell
- Department of Pediatrics, Baylor College of Medicine, San Antonio, TX
| | - Kevin E Glinton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Laurie Robak
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Sandesh C S Nagamani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Texas Children's Hospital Department of Pathology, Houston, TX
| | - Lisa Saba
- Texas Children's Hospital Department of Pathology, Houston, TX
| | - Adasia Ritenour
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Lilei Zhang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Haley Streff
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Texas Children's Hospital Department of Pathology, Houston, TX
| | - Katie Chan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - K Jordan Kemere
- Department of Internal Medicine, Section Transition Medicine, Baylor College of Medicine and Texas Children's Hospital, Houston, TX
| | - Kent Carter
- Department of Pediatrics, University of Texas Rio Grande Valley, Harlingen, TX
| | | | | | | | - Hugo Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX
| | - Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX.
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Du J, Li L, Fu D. Whole-exome-based single nucleotide variants and copy number analysis for prenatal diagnosis of compound heterozygosity of SMPD4. Psychiatr Genet 2024; 34:74-80. [PMID: 38690959 DOI: 10.1097/ypg.0000000000000369] [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: 05/03/2024]
Abstract
BACKGROUND Biallelic loss-of-function variants in SMPD4 cause a rare and severe neurodevelopmental disorder. These variants have been identified in a group of children with neurodevelopmental disorders with microcephaly, arthrogryposis, and structural brain anomalies. SMPD4 encodes a sphingomyelinase that hydrolyzes sphingomyelin into ceramide at neutral pH and can thereby affect membrane lipid homeostasis. SMPD4 localizes to the membranes of the endoplasmic reticulum and nuclear envelope and interacts with nuclear pore complexes. MATERIALS AND METHODS For the efficient prenatal diagnosis of rare and undiagnosed diseases, the parallel detection of copy number variants (CNVs) and single nucleotide variants using whole-exome analysis is required. A physical examination of the parents was performed. Karyotype and whole-exome analysis were performed for the fetus and the parents. RESULTS A fetus with microcephaly and arthrogryposis; biallelic null variants (c.387-1G>A; Chr2[GRCh38]: g.130142742_130202459del) were detected by whole-exome sequencing (WES). We have reported for the first time the biallelic loss-of-function mutations in SMPD4 in patients born to unrelated parents in China. CONCLUSION WES could replace chromosomal microarray analysis and copy number variation sequencing as a more cost-effective genetic test for detecting CNVs and diagnosing highly heterogeneous conditions.
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Affiliation(s)
| | - Lin Li
- Department of Ultrasound, Renmin Hospital, Hubei University of Medicine, Shiyan, People's Republic of China
| | - Dinghu Fu
- Department of Ultrasound, Renmin Hospital, Hubei University of Medicine, Shiyan, People's Republic of China
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Hahn JW, Lee H, Shin M, Seong MW, Moon JS, Ko JS. Diagnostic algorithm for neonatal intrahepatic cholestasis integrating single-gene testing and next-generation sequencing in East Asia. J Gastroenterol Hepatol 2024; 39:964-974. [PMID: 38323732 DOI: 10.1111/jgh.16505] [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: 09/13/2023] [Revised: 01/04/2024] [Accepted: 01/17/2024] [Indexed: 02/08/2024]
Abstract
BACKGROUND AND AIM Advances in molecular genetics have uncovered causative genes responsible for neonatal cholestasis. Panel-based next-generation sequencing has been used clinically in infants with neonatal cholestasis. We aimed to evaluate the clinical application of single-gene testing and next-generation sequencing and to develop a diagnostic algorithm for neonatal intrahepatic cholestasis. METHODS From January 2010 to July 2021, patients suspected of having neonatal intrahepatic cholestasis were tested at the Seoul National University Hospital. If there was a clinically suspected disease, single-gene testing was performed. Alternatively, if it was clinically difficult to differentiate, a neonatal cholestasis gene panel test containing 34 genes was performed. RESULTS Of the total 148 patients examined, 49 (33.1%) were received a confirmed genetic diagnosis, including 14 with Alagille syndrome, 14 with neonatal intrahepatic cholestasis caused by citrin deficiency, 7 with Dubin-Johnson syndrome, 5 with arthrogryposis-renal dysfunction-cholestasis syndrome, 5 with progressive familial intrahepatic cholestasis type II, 1 with Rotor syndrome, 1 with Niemann-Pick disease type C, 1 with Kabuki syndrome, and 1 with Phenylalanyl-tRNA synthetase subunit alpha mutation. Sixteen novel pathogenic or likely pathogenic variants of neonatal cholestasis were observed in this study. Based on the clinical characteristics and laboratory findings, we developed a diagnostic algorithm for neonatal intrahepatic cholestasis by integrating single-gene testing and next-generation sequencing. CONCLUSIONS Alagille syndrome and neonatal intrahepatic cholestasis caused by citrin deficiency were the most common diseases associated with genetic neonatal cholestasis. Single-gene testing and next-generation sequencing are important and complementary tools for the diagnosis of genetic neonatal cholestasis.
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Affiliation(s)
- Jong Woo Hahn
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, Korea
- Department of Pediatrics, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Heerah Lee
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - MinSoo Shin
- Department of Pediatrics, Korea University College of Medicine, Seoul, Korea
| | - Moon Woo Seong
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Jin Soo Moon
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, Korea
| | - Jae Sung Ko
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, Korea
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Donoghue S, Wright J, Voss AK, Lockhart PJ, Amor DJ. The Mendelian disorders of chromatin machinery: Harnessing metabolic pathways and therapies for treatment. Mol Genet Metab 2024; 142:108360. [PMID: 38428378 DOI: 10.1016/j.ymgme.2024.108360] [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: 08/29/2023] [Revised: 02/25/2024] [Accepted: 02/26/2024] [Indexed: 03/03/2024]
Abstract
The Mendelian disorders of chromatin machinery (MDCMs) represent a distinct subgroup of disorders that present with neurodevelopmental disability. The chromatin machinery regulates gene expression by a range of mechanisms, including by post-translational modification of histones, responding to histone marks, and remodelling nucleosomes. Some of the MDCMs that impact on histone modification may have potential therapeutic interventions. Two potential treatment strategies are to enhance the intracellular pool of metabolites that can act as substrates for histone modifiers and the use of medications that may inhibit or promote the modification of histone residues to influence gene expression. In this article we discuss the influence and potential treatments of histone modifications involving histone acetylation and histone methylation. Genomic technologies are facilitating earlier diagnosis of many Mendelian disorders, providing potential opportunities for early treatment from infancy. This has parallels with how inborn errors of metabolism have been afforded early treatment with newborn screening. Before this promise can be fulfilled, we require greater understanding of the biochemical fingerprint of these conditions, which may provide opportunities to supplement metabolites that can act as substrates for chromatin modifying enzymes. Importantly, understanding the metabolomic profile of affected individuals may also provide disorder-specific biomarkers that will be critical for demonstrating efficacy of treatment, as treatment response may not be able to be accurately assessed by clinical measures.
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Affiliation(s)
- Sarah Donoghue
- Murdoch Children's Research Institute, Parkville 3052, Australia; Department of Biochemical Genetics, Victorian Clinical Genetics Services, Parkville 3052, Australia; Department of Paediatrics, The University of Melbourne, Parkville 3052, Australia.
| | - Jordan Wright
- Murdoch Children's Research Institute, Parkville 3052, Australia; Department of Paediatrics, The University of Melbourne, Parkville 3052, Australia
| | - Anne K Voss
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville 3052, Australia
| | - Paul J Lockhart
- Murdoch Children's Research Institute, Parkville 3052, Australia; Department of Paediatrics, The University of Melbourne, Parkville 3052, Australia
| | - David J Amor
- Murdoch Children's Research Institute, Parkville 3052, Australia; Department of Paediatrics, The University of Melbourne, Parkville 3052, Australia
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Sloper E, Jezkova J, Thomas J, Dawson K, Halstead J, Gardner J, Burke K, Oruganti S, Calvert J, Evans J, Anderson S, Corrin S, Pottinger C, Murch O. Wales Infants' and childreN's Genome Service (WINGS): providing rapid genetic diagnoses for unwell children. Arch Dis Child 2024; 109:409-413. [PMID: 38320813 DOI: 10.1136/archdischild-2023-326579] [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: 11/06/2023] [Accepted: 01/24/2024] [Indexed: 04/20/2024]
Abstract
INTRODUCTION This study reviews the first 3 years of delivery of the first National Health Service (NHS)-commissioned trio rapid whole genome sequencing (rWGS) service for acutely unwell infants and children in Wales. METHODS Demographic and phenotypic data were prospectively collected as patients and their families were enrolled in the Wales Infants' and childreN's Genome Service (WINGS). These data were reviewed alongside trio rWGS results. RESULTS From April 2020 to March 2023, 82 families underwent WINGS, with a diagnostic yield of 34.1%. The highest diagnostic yields were noted in skeletal dysplasias, neurological or metabolic phenotypes. Mean time to reporting was 9 days. CONCLUSION This study demonstrates that trio rWGS is having a positive impact on the care of acutely unwell infants and children in an NHS setting. In particular, the study shows that rWGS can be applied in an NHS setting, achieving a diagnostic yield comparable with the previously published diagnostic yields achieved in research settings, while also helping to improve patient care and management.
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Affiliation(s)
- Emily Sloper
- All Wales Medical Genomics Service, University Hospital of Wales Healthcare NHS Trust, Cardiff, UK
| | - Jana Jezkova
- All Wales Medical Genomics Service, University Hospital of Wales Healthcare NHS Trust, Cardiff, UK
| | - Joanne Thomas
- Faculty of Life Science and Education, University of South Wales, Pontypridd, UK
| | | | - Joseph Halstead
- All Wales Medical Genomics Service, University Hospital of Wales Healthcare NHS Trust, Cardiff, UK
| | - Jennifer Gardner
- All Wales Medical Genomics Service, University Hospital of Wales Healthcare NHS Trust, Cardiff, UK
| | - Katherine Burke
- Neonatal Intensive Care Unit, Singleton Hospital, Swansea, UK
| | - Sivakumar Oruganti
- Paediatric Critical Care Unit, Noah's Ark Children's Hospital for Wales, Cardiff, UK
- College of Biomedical and Life Sciences, Cardiff University, Cardiff, UK
| | - Jennifer Calvert
- Neonatal Intensive Care Unit, University Hospital of Wales Healthcare NHS Trust, Cardiff, UK
| | - Jennifer Evans
- Child Health, Children's Hospital for Wales, Cardiff, UK
| | - Sarah Anderson
- All Wales Medical Genomics Service, University Hospital of Wales Healthcare NHS Trust, Cardiff, UK
| | - Sian Corrin
- All Wales Medical Genomics Service, University Hospital of Wales Healthcare NHS Trust, Cardiff, UK
| | - Caroline Pottinger
- All Wales Medical Genomics Service, University Hospital of Wales Healthcare NHS Trust, Cardiff, UK
| | - Oliver Murch
- All Wales Medical Genomics Service, University Hospital of Wales Healthcare NHS Trust, Cardiff, UK
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10
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Bhatia S, Pal S, Kulshrestha S, Gupta D, Soni A, Saxena R, Bijarnia-Mahay S, Verma IC, Puri RD. Role of next generation sequencing in diagnosis and management of critically ill children with suspected monogenic disorder. Eur J Hum Genet 2024:10.1038/s41431-024-01569-z. [PMID: 38605122 DOI: 10.1038/s41431-024-01569-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 01/19/2024] [Accepted: 02/12/2024] [Indexed: 04/13/2024] Open
Abstract
Next generation sequencing based diagnosis has emerged as a promising tool for evaluating critically ill neonates and children. However, there is limited data on its utility in developing countries. We assessed its diagnostic rate and clinical impact on management of pediatric patients with a suspected genetic disorder requiring critical care. The study was conducted at a single tertiary hospital in Northern India. We analyzed 70 children with an illness requiring intensive care and obtained a precise molecular diagnosis in 32 of 70 probands (45.3%) using diverse sequencing techniques such as clinical exome, whole exome, and whole genome. A significant change in clinical outcome was observed in 13 of 32 (40.6%) diagnosed probands with a change in medication in 11 subjects and redirection to palliative care in two subjects. Additional benefits included specific dietary management (three cases), avoidance of a major procedure (one case) and better reproductive counseling. Dramatic therapeutic responses were observed in three cases with SCN1A, SCN2A and KCNQ2-related epileptic encephalopathy. A delayed turn-around for sequencing results was perceived as a major limiting factor in the study, as rapid and ultra-rapid sequencing was not available. Achieving a precise molecular diagnosis has great utility in managing critically ill patients with suspected genetic disorders in developing countries.
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Affiliation(s)
- Sameer Bhatia
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Swasti Pal
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Samarth Kulshrestha
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Dhiren Gupta
- Department of Paediatrics, Institute of Child Health, Sir Ganga Ram Hospital, New Delhi, India
| | - Arun Soni
- Department of Neonatology, Institute of Child Health, Sir Ganga Ram Hospital, New Delhi, India
| | - Renu Saxena
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Sunita Bijarnia-Mahay
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Ishwar Chander Verma
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Ratna Dua Puri
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India.
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11
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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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12
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Ma M, Ganapathi M, Zheng Y, Tan KL, Kanca O, Bove KE, Quintanilla N, Sag SO, Temel SG, LeDuc CA, McPartland AJ, Pereira EM, Shen Y, Hagen J, Thomas CP, Nguyen Galván NT, Pan X, Lu S, Rosenfeld JA, Calame DG, Wangler MF, Lupski JR, Pehlivan D, Hertel PM, Chung WK, Bellen HJ. Homozygous missense variants in YKT6 result in loss of function and are associated with developmental delay, with or without severe infantile liver disease and risk for hepatocellular carcinoma. Genet Med 2024; 26:101125. [PMID: 38522068 DOI: 10.1016/j.gim.2024.101125] [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: 09/21/2023] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 03/26/2024] Open
Abstract
PURPOSE YKT6 plays important roles in multiple intracellular vesicle trafficking events but has not been associated with Mendelian diseases. METHODS We report 3 unrelated individuals with rare homozygous missense variants in YKT6 who exhibited neurological disease with or without a progressive infantile liver disease. We modeled the variants in Drosophila. We generated wild-type and variant genomic rescue constructs of the fly ortholog dYkt6 and compared their ability in rescuing the loss-of-function phenotypes in mutant flies. We also generated a dYkt6KozakGAL4 allele to assess the expression pattern of dYkt6. RESULTS Two individuals are homozygous for YKT6 [NM_006555.3:c.554A>G p.(Tyr185Cys)] and exhibited normal prenatal course followed by failure to thrive, developmental delay, and progressive liver disease. Haplotype analysis identified a shared homozygous region flanking the variant, suggesting a common ancestry. The third individual is homozygous for YKT6 [NM_006555.3:c.191A>G p.(Tyr64Cys)] and exhibited neurodevelopmental disorders and optic atrophy. Fly dYkt6 is essential and is expressed in the fat body (analogous to liver) and central nervous system. Wild-type genomic rescue constructs can rescue the lethality and autophagic flux defects, whereas the variants are less efficient in rescuing the phenotypes. CONCLUSION The YKT6 variants are partial loss-of-function alleles, and the p.(Tyr185Cys) is more severe than p.(Tyr64Cys).
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Affiliation(s)
- Mengqi Ma
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX
| | - Mythily Ganapathi
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY
| | - Yiming Zheng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX
| | - Kai-Li Tan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX
| | - Oguz Kanca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX
| | - Kevin E Bove
- Department of Pathology and Laboratory Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Norma Quintanilla
- Department of Pathology and Immunology, Texas Children's Hospital, Baylor College of Medicine, Houston, TX
| | - Sebnem O Sag
- Department of Medical Genetics, Faculty of Medicine, Uludag University, Bursa, Turkey
| | - Sehime G Temel
- Department of Medical Genetics, Faculty of Medicine, Uludag University, Bursa, Turkey
| | | | | | | | - Yufeng Shen
- Department of Systems Biology, Columbia University Medical Center, New York, NY
| | - Jacob Hagen
- Department of Systems Biology, Columbia University Medical Center, New York, NY
| | - Christie P Thomas
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, IA
| | | | - Xueyang Pan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX
| | - Shenzhao Lu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Baylor Genetics Laboratories, Houston, TX
| | - Daniel G Calame
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Division of Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX; Texas Children's Hospital, Houston, TX
| | - Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Texas Children's Hospital, Houston, TX; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX; Division of Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX; Texas Children's Hospital, Houston, TX
| | - Paula M Hertel
- Texas Children's Hospital, Houston, TX; Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Baylor College of Medicine, Houston, TX
| | - Wendy K Chung
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA.
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX.
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13
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D'Souza EE, Findley TO, Hu R, Khazal ZSH, Signorello R, Dash C, D'Gama AM, Feldman HA, Agrawal PB, Wojcik MH, Morton SU. Genomic testing and molecular diagnosis among infants with congenital heart disease in the neonatal intensive care unit. J Perinatol 2024:10.1038/s41372-024-01935-1. [PMID: 38499751 DOI: 10.1038/s41372-024-01935-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 03/07/2024] [Accepted: 03/11/2024] [Indexed: 03/20/2024]
Abstract
OBJECTIVE To evaluate patterns of genetic testing among infants with CHD at a tertiary care center. STUDY DESIGN We conducted a retrospective observational cohort study of infants in the NICU with suspicion of a genetic disorder. 1075 of 7112 infants admitted to BCH had genetic evaluation including 329 with CHD and 746 without CHD. 284 of 525 infants with CHD admitted to CMHH had genetic evaluation. Patterns of testing and diagnoses were compared. RESULTS The rate of diagnosis after testing was similar for infants with or without CHD (38% [121/318] vs. 36% [246/676], p = 0.14). In a multiple logistic regression, atrioventricular septal defects were most high associated with genetic diagnosis (odds ratio 29.99, 95% confidence interval 2.69-334.12, p < 0.001). CONCLUSIONS Infants with suspicion of a genetic disorder with CHD had similar rates of molecular diagnosis as those without CHD. These results support a role for genetic testing among NICU infants with CHD.
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Affiliation(s)
- Erica E D'Souza
- Division of Newborn Medicine, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Tina O Findley
- Division of Neonatal-Perinatal Medicine, Department of Pediatrics, McGovern Medical School at the University of Texas Health Science Center at Houston and Children's Memorial Hermann Hospital, Houston, TX, 77030, USA
| | - Rachel Hu
- Division of Newborn Medicine, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Zahra S H Khazal
- Division of Newborn Medicine, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Rachel Signorello
- Division of Newborn Medicine, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Camille Dash
- Division of Newborn Medicine, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Alissa M D'Gama
- Division of Newborn Medicine, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Henry A Feldman
- Division of Newborn Medicine, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Pankaj B Agrawal
- Division of Newborn Medicine, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, 02115, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, 02115, USA
- Division of Neonatology, Department of Pediatrics, University of Miami Miller School of Medicine and Holtz Children's Hospital, Jackson Health System, Miami, FL, USA
| | - Monica H Wojcik
- Division of Newborn Medicine, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, 02115, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Sarah U Morton
- Division of Newborn Medicine, Boston Children's Hospital, Boston, MA, 02115, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA.
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, 02115, USA.
- Fetal-Neonatal Neuroimaging and Developmental Science Center, Boston Children's Hospital, Boston, MA, 02115, USA.
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14
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Popova L, Carabetta VJ. The use of next-generation sequencing in personalized medicine. ARXIV 2024:arXiv:2403.03688v1. [PMID: 38495572 PMCID: PMC10942477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
The revolutionary progress in development of next-generation sequencing (NGS) technologies has made it possible to deliver accurate genomic information in a timely manner. Over the past several years, NGS has transformed biomedical and clinical research and found its application in the field of personalized medicine. Here we discuss the rise of personalized medicine and the history of NGS. We discuss current applications and uses of NGS in medicine, including infectious diseases, oncology, genomic medicine, and dermatology. We provide a brief discussion of selected studies where NGS was used to respond to wide variety of questions in biomedical research and clinical medicine. Finally, we discuss the challenges of implementing NGS into routine clinical use.
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Affiliation(s)
- Liya Popova
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden NJ, 08103
| | - Valerie J. Carabetta
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden NJ, 08103
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15
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Liu Y, Qian S. Current situation and prospect for the diagnosis and treatment of pediatric critical rare diseases in China. Pediatr Investig 2024; 8:66-71. [PMID: 38516143 PMCID: PMC10951483 DOI: 10.1002/ped4.12419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 01/16/2024] [Indexed: 03/23/2024] Open
Abstract
The onset of critical rare diseases (RDs) in children is rapid and dangerous, accompanied by a high mortality rate, which brings a heavy burden to both families and society. Multiple malformations, neuromuscular diseases, metabolic diseases, and heart diseases are the most common types of RDs in children of China, often manifesting with multiple organ dysfunction. At present, the diagnosis and treatment of critical RDs in children face challenges such as prolonged diagnosis time, a high misdiagnosis rate, limited treatment modalities, and a significant disease burden. However, with the progress in genetic testing technology, the establishment of multidisciplinary diagnosis and treatment platforms, and the implementation of relevant RD policies in China, children with critical RDs will received enhanced medical services, experience improved prognoses, and reintegrate into social life.
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Affiliation(s)
- Yingchao Liu
- Pediatric Intensive Care Unit, Beijing Children's Hospital, Capital Medical UniversityNational Center for Children's HealthBeijingChina
| | - Suyun Qian
- Pediatric Intensive Care Unit, Beijing Children's Hospital, Capital Medical UniversityNational Center for Children's HealthBeijingChina
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16
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Chen CL, Lee NC, Chien YH, Hwu WL, Hung MZ, Lin YL, Lin SY, Lee CN. Ethnically unique disease burden and limitations of current expanded carrier screening panels. Int J Gynaecol Obstet 2024; 164:918-924. [PMID: 37681470 DOI: 10.1002/ijgo.15072] [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: 03/23/2023] [Revised: 07/28/2023] [Accepted: 08/17/2023] [Indexed: 09/09/2023]
Abstract
OBJECTIVES The purpose of the study is to identify the recessive diseases currently affecting real-world pediatric patients in Taiwan, and whether current extended carrier screening panels have the coverage and detective power to identify the pathogenic variants in the carrier parents. METHODS A total of 132 trio-samples were collected from May 2017 to March 2022. The participants were parents of pediatric intensive care unit patients who were critically ill or infants with abnormal newborn screening results. A retrospective carrier screening scheme was applied to analyze only the carrier status of pathogenic or likely pathogenic recessive variants resulting in diseases in their children. The recessive disorders diagnosed in our cohort were compared with the gene content in commercial panels. RESULTS Mutations in COQ4, PEX1, OTC, and IKBKG were the most frequently identified. In the parents of 44 children with confirmed diagnoses of recessive diseases, 47 (53.40%) screened positive for being the carriers of the same recessive disorders diagnosed in their children. The commercial panels covered 35.13% to 54.05% of the disorders diagnosed in this cohort. CONCLUSION Clinicians and genetic counselors should be aware of the limitations of current extended carrier screening and interpret negative screening results with caution. Future panels should also consider genes with ethnically unique mutations such as pathogenic variants of the COQ4 gene in the East Asian population.
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Affiliation(s)
- Chih-Ling Chen
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
- Department of Obstetrics and Gynecology, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Ni-Chung Lee
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
- Department of Pediatrics, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Yin-Hsiu Chien
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
- Department of Pediatrics, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Wuh-Liang Hwu
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
- Department of Pediatrics, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Miao-Zi Hung
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Yi-Lin Lin
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Shin-Yu Lin
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
- Department of Obstetrics and Gynecology, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Chien-Nan Lee
- Department of Obstetrics and Gynecology, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
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17
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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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18
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Ahmad RN, Zhang LT, Morita R, Tani H, Wu Y, Chujo T, Ogawa A, Harada R, Shigeta Y, Tomizawa K, Wei FY. Pathological mutations promote proteolysis of mitochondrial tRNA-specific 2-thiouridylase 1 (MTU1) via mitochondrial caseinolytic peptidase (CLPP). Nucleic Acids Res 2024; 52:1341-1358. [PMID: 38113276 PMCID: PMC10853782 DOI: 10.1093/nar/gkad1197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 11/22/2023] [Accepted: 12/01/2023] [Indexed: 12/21/2023] Open
Abstract
MTU1 controls intramitochondrial protein synthesis by catalyzing the 2-thiouridine modification of mitochondrial transfer RNAs (mt-tRNAs). Missense mutations in the MTU1 gene are associated with life-threatening reversible infantile hepatic failure. However, the molecular pathogenesis is not well understood. Here, we investigated 17 mutations associated with this disease, and our results showed that most disease-related mutations are partial loss-of-function mutations, with three mutations being particularly severe. Mutant MTU1 is rapidly degraded by mitochondrial caseinolytic peptidase (CLPP) through a direct interaction with its chaperone protein CLPX. Notably, knockdown of CLPP significantly increased mutant MTU1 protein expression and mt-tRNA 2-thiolation, suggesting that accelerated proteolysis of mutant MTU1 plays a role in disease pathogenesis. In addition, molecular dynamics simulations demonstrated that disease-associated mutations may lead to abnormal intermolecular interactions, thereby impairing MTU1 enzyme activity. Finally, clinical data analysis underscores a significant correlation between patient prognosis and residual 2-thiolation levels, which is partially consistent with the AlphaMissense predictions. These findings provide a comprehensive understanding of MTU1-related diseases, offering prospects for modification-based diagnostics and novel therapeutic strategies centered on targeting CLPP.
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Affiliation(s)
- Raja Norazireen Raja Ahmad
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Kumamoto, 860-8556, Japan
- Department of Modomics Biology and Medicine, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Miyagi, 980-8575, Japan
| | - Long-Teng Zhang
- Department of Modomics Biology and Medicine, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Miyagi, 980-8575, Japan
| | - Rikuri Morita
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8577, Japan
| | - Haruna Tani
- Department of Modomics Biology and Medicine, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Miyagi, 980-8575, Japan
| | - Yong Wu
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Kumamoto, 860-8556, Japan
| | - Takeshi Chujo
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Kumamoto, 860-8556, Japan
| | - Akiko Ogawa
- Department of Modomics Biology and Medicine, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Miyagi, 980-8575, Japan
| | - Ryuhei Harada
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8577, Japan
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8577, Japan
| | - Kazuhito Tomizawa
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Kumamoto, 860-8556, Japan
| | - Fan-Yan Wei
- Department of Modomics Biology and Medicine, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Miyagi, 980-8575, Japan
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19
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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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20
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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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21
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Cheung C, Berger SM, Ross M, Kramer T, Li Y, Andrews C, Dergham KR, Spitz E, Florido ME, Ahimaz P. Assessing management practices for variants of uncertain significance among genetic counselors in pediatrics. J Genet Couns 2024. [PMID: 38217320 DOI: 10.1002/jgc4.1860] [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: 02/14/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 01/15/2024]
Abstract
Increased utilization of genomic sequencing in pediatric medicine has increased the detection of variants of uncertain significance (VUS). Periodic VUS reinterpretation can clarify clinical significance and increase diagnostic yield, highlighting the importance of systematic VUS tracking and reinterpretation. There are currently no standardized guidelines or established best practices for VUS management, and our understanding of how genetic counselors (GCs) track and manage VUS results for pediatric patients is limited. In this exploratory study, GCs in pediatric clinics in North America were surveyed about their VUS management practices. A total of 124 responses were included in the analysis. The majority (n = 115, 92.7%) of GCs reported that VUS management workflows were at the discretion of each individual provider in their workplace. Approximately half (n = 65, 52%) kept track of patient VUS results over time, and GCs with lower patient volumes were more likely to do so (p = 0.04). While 95% (n = 114) of GCs had requested VUS reinterpretation at least once, only 5% (n = 6) requested it routinely. Most (n = 80, 86%) GCs notified patients when a VUS was reclassified, although methods of recontact differed when the reclassification was an upgrade versus a downgrade. GCs who asked patients to stay in touch through periodic recontact or follow-up appointments were more likely to request VUS reinterpretation (p = 0.01). The most frequently reported barriers to requesting reinterpretation regularly were patients being lost to follow-up (n = 39, 33.1%), insufficient bandwidth (n = 27, 22.9%), and lack of standardized guidelines (n = 25, 21.2%). GCs had consistent overall practices around VUS management around investigation, disclosure, reinterpretation, and recontact, but specific methods used differed and were at the discretion of each provider. These results showcase the current landscape of VUS management workflows in pediatrics and the challenges associated with adopting more uniform practices. The study findings can help inform future strategies to develop standardized guidelines surrounding VUS management.
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Affiliation(s)
- Chloe Cheung
- Genetic Counseling Graduate Program, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
- Clinical Trials Office, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Sara M Berger
- Department of Pediatrics, Division of Clinical Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - Meredith Ross
- Department of Pediatrics, Division of Clinical Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - Tamar Kramer
- Department of Pediatrics, Division of Clinical Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - Yuhuan Li
- Department of Biostatistics, Columbia University, New York, New York, USA
| | - Carli Andrews
- Department of Pediatrics, Division of Clinical Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - Katia R Dergham
- Department of Pediatrics, Division of Clinical Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
- School of Pharmacy and Health Sciences, Keck Graduate Insititute, Claremont, California, USA
| | - Elana Spitz
- Department of Pediatrics, Division of Clinical Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
- Department of Hematology Oncology, University of Carlifornia, Los Angeles Health, Los Angeles, California, USA
| | - Michelle E Florido
- Genetic Counseling Graduate Program, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
- Department of Genetics and Development, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - Priyanka Ahimaz
- Genetic Counseling Graduate Program, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
- Department of Pediatrics, Division of Clinical Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
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22
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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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23
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Cao Z, He X, Wang D, Gu M, Suo F, Qiang R, Zhang R, Song C, Wang X, Zhu B, Cao D, Yu H, Qu Y, Shen G, Wu J, Wang P, Wang J, Zhang H, Yan Z, Yu G, Zou L. Targeted exome sequencing strategy (NeoEXOME) for Chinese newborns using a pilot study with 3423 neonates. Mol Genet Genomic Med 2024; 12:e2357. [PMID: 38284445 PMCID: PMC10795095 DOI: 10.1002/mgg3.2357] [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: 02/01/2023] [Revised: 09/15/2023] [Accepted: 12/26/2023] [Indexed: 01/30/2024] Open
Abstract
BACKGROUND Newborn screening (NBS) aims to detect congenital anomalies, and next-generation sequencing (NGS) has shown promise in this aspect. However, the NBS strategy for monogenic inherited diseases in China remains insufficient. METHODS We developed a NeoEXOME panel comprising 601 genes that are relevant to the Chinese population found through extensive research on available databases. An interpretation system to grade the results into positive (high-risk, moderate-risk, and low-risk genotypes), negative, and carrier according to the American College of Medical Genetics (ACMG) guidelines was also developed. We validated the panel to evaluate its efficacy by using data from the "1000 Genomes Project" and conducted a pilot multicenter study involving 3423 neonates. RESULTS The NGS positive rate in the 1000 Genomes Project was 7.6% (23/301), whereas the rate was 12.0% in the multicenter study, including 3249 recruited neonates. Notably, in 200 neonates, positive per conventional NBS, 58.5% (69/118) showed results consistent with NGS. In the remaining 3049 neonates showing negative results in conventional NBS, 271 (8.9%) were positive per NGS, and nine of them were clinically diagnosed with diseases in the follow-up. CONCLUSION We successfully designed a NeoEXOME panel for targeted sequencing of monogenic inherited diseases in NBS. The panel demonstrated high performance in the Chinese population, particularly for the early detection of diseases with no biochemical markers.
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Affiliation(s)
- Ziyang Cao
- Clinical Research Unit, Shanghai Children's HospitalShanghai Jiao Tong University Medical SchoolShanghaiChina
- Institute of Pediatric Infection, Immunity, and Critical Care MedicineShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Xiaoyan He
- Center for Clinical Molecular Laboratory Medicine of Children's Hospital of Chongqing Medical UniversityChongqingChina
| | - Dongjuan Wang
- Center for Clinical Molecular Laboratory Medicine of Children's Hospital of Chongqing Medical UniversityChongqingChina
| | - Maosheng Gu
- Center of Medical GeneticsXuzhou Maternal and Child Health Care HospitalXuzhouChina
| | - Feng Suo
- Center of Medical GeneticsXuzhou Maternal and Child Health Care HospitalXuzhouChina
| | - Rong Qiang
- Center of Medical GeneticsNorthwest Women and Children's HospitalXi'anChina
| | - Ruixue Zhang
- Center of Medical GeneticsNorthwest Women and Children's HospitalXi'anChina
| | - Chengrong Song
- Center of Medical GeneticsNorthwest Women and Children's HospitalXi'anChina
| | - Xiaohua Wang
- Center of Medical GeneticsInner Mongolia Maternal and Child Health Care HospitalHohhotChina
| | - Bo Zhu
- Center of Medical GeneticsInner Mongolia Maternal and Child Health Care HospitalHohhotChina
| | - Donghua Cao
- Medical Genetic LaboratoryDalian Municipal Women and Children's Medical Center (Group)DalianChina
- Genetic LaboratoryShenyang Jinghua Hospital Co., LtdShenyangChina
| | - Haihua Yu
- Medical Genetic LaboratoryDalian Municipal Women and Children's Medical Center (Group)DalianChina
| | - Yiping Qu
- Newborn Screening Center of Children's Hospital of Zhejiang University School of MedicineHangzhouChina
| | - Guosong Shen
- Medical Laboratory Center of Huzhou Maternal and Child Health Care HospitalHuzhouChina
| | - Jian Wu
- Research and Development DepartmentMyGenostics Inc.BeijingChina
| | - Pengpeng Wang
- Research and Development DepartmentMyGenostics Inc.BeijingChina
| | - Jinxia Wang
- Clinical Research Unit, Shanghai Children's HospitalShanghai Jiao Tong University Medical SchoolShanghaiChina
- Institute of Pediatric Infection, Immunity, and Critical Care MedicineShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Hongyang Zhang
- Clinical Research Unit, Shanghai Children's HospitalShanghai Jiao Tong University Medical SchoolShanghaiChina
- Institute of Pediatric Infection, Immunity, and Critical Care MedicineShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Zijun Yan
- Clinical Research Unit, Shanghai Children's HospitalShanghai Jiao Tong University Medical SchoolShanghaiChina
- Institute of Pediatric Infection, Immunity, and Critical Care MedicineShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Guangjun Yu
- Clinical Research Unit, Shanghai Children's HospitalShanghai Jiao Tong University Medical SchoolShanghaiChina
- Institute of Pediatric Infection, Immunity, and Critical Care MedicineShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Lin Zou
- Clinical Research Unit, Shanghai Children's HospitalShanghai Jiao Tong University Medical SchoolShanghaiChina
- Institute of Pediatric Infection, Immunity, and Critical Care MedicineShanghai Jiao Tong University School of MedicineShanghaiChina
- Center for Clinical Molecular Laboratory Medicine of Children's Hospital of Chongqing Medical UniversityChongqingChina
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24
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Wild KT, Miquel-Verges F, Rintoul NE, DiGeronimo R, Keene S, Hamrick SE, Mahmood B, Rao R, Carr NR. Current Practices for Genetic Testing in Neonatal Extracorporeal Membrane Oxygenation: Findings from a National survey. Perfusion 2024; 39:116-123. [PMID: 36169593 DOI: 10.1177/02676591221130178] [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] [Indexed: 11/15/2022]
Abstract
Introduction: Comprehensive genetic testing with whole-exome (WES) or whole-genome (WGS) sequencing facilitates diagnosis, can optimize treatment, and may improve outcomes in critically ill neonates, including those requiring extracorporeal membrane oxygenation (ECMO) for respiratory failure. Our objective was to describe practice variation and barriers to the utilization of comprehensive genetic testing for neonates on ECMO.Methods: We performed a cross-sectional survey of Level IV neonatal intensive care units in the United States across the Children's Hospitals Neonatal Consortium (CHNC).Results: Common indications for WES and WGS included concerning phenotype, severity of disease, unexpected postnatal clinical course, and inability to wean from ECMO support. Unexpected severity of disease on ECMO was the most common indication for rapid genetic testing. Cost of utilization was the primary barrier to testing. If rapid WES or WGS were readily available, 63% of centers would consider incorporating universal screening for neonates upon ECMO cannulation.Conclusion: Despite variation in the use of WES and WGS, universal testing may offer earlier diagnosis and influence the treatment course among neonates on ECMO. Cost is the primary barrier to utilization and most centers would consider incorporating universal screening on ECMO if readily available.
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Affiliation(s)
- K Taylor Wild
- Children's Hospital of Philadelphia, Perelman School of Medicine at University of Pennsylvania, Philadelphia, PA, USA
| | | | - Natalie E Rintoul
- Children's Hospital of Philadelphia, Perelman School of Medicine at University of Pennsylvania, Philadelphia, PA, USA
| | - Robert DiGeronimo
- Seattle Children's Hospital, University of Washington, Seattle WA, USA
| | - Sarah Keene
- Children's Healthcare of Atlanta, School of Medicine, Emory University, Atlanta, GA, USA
| | - Shannon E Hamrick
- Children's Healthcare of Atlanta, School of Medicine, Emory University, Atlanta, GA, USA
| | - Burhan Mahmood
- UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, USA
| | - Rakesh Rao
- St. Louis Children's Hospital, Washington University School of Medicine, St. Louis, MO, USA
| | - Nicholas R Carr
- Primary Children's Hospital, University of Utah School of Medicine, Salt Lake City, UT, USA
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25
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Tian W, Li H, Li Y, Guo J, Wang H, Yang B, Li P, Cui X, Liu L. A novel missense variant in OTUD5 causes X-linked multiple congenital anomalies-neurodevelopmental syndrome. Mol Genet Genomic Med 2024; 12:e2325. [PMID: 38037881 PMCID: PMC10767676 DOI: 10.1002/mgg3.2325] [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: 07/13/2023] [Revised: 10/13/2023] [Accepted: 11/10/2023] [Indexed: 12/02/2023] Open
Abstract
BACKGROUND The OTUD5 gene encodes a deubiquitinating enzyme (DUB) of the OTU family. Variants of OTUD5 are associated with X-linked multiple congenital anomalies-neurodevelopmental syndrome (MCAND). The case described in this study expands the clinical and molecular spectrum of OTUD5. METHODS Trio-based clinical exome sequencing (trio-CES) was performed on a Chinese boy with a clinical phenotype and both of his parents. Sanger sequencing was employed for validation of the variant detected. RESULTS The patient presented with characteristic facial features, intellectual disability, motor/language/cognitive, and global developmental delays, limb contractures, and kidney abnormalities, and trio-CES identified a de novo missense variant, c.1305T>A, of the OTUD5 gene. DISCUSSION We describe OTUD5 gene variation in the Chinese population, with the first report of this variant. Additionally, we provide a comprehensive summary of all published cases of MCAND to date, in order to elucidate the primary clinical features of the syndrome and the variability in phenotype severity. This case expands the genetic and clinical phenotypic spectrum of OTUD5-associated MCAND.
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Affiliation(s)
- Weifang Tian
- Prenatal Diagnosis Center, The Third Affiliated Hospital of Zhengzhou University, Maternal and Child Health Hospital of Henan ProvinceZhengzhouChina
| | - Haiyu Li
- Prenatal Diagnosis Center, The Third Affiliated Hospital of Zhengzhou University, Maternal and Child Health Hospital of Henan ProvinceZhengzhouChina
| | - Ying Li
- Prenatal Diagnosis Center, The Third Affiliated Hospital of Zhengzhou University, Maternal and Child Health Hospital of Henan ProvinceZhengzhouChina
| | - Jing Guo
- Prenatal Diagnosis Center, The Third Affiliated Hospital of Zhengzhou University, Maternal and Child Health Hospital of Henan ProvinceZhengzhouChina
| | - Handuo Wang
- Prenatal Diagnosis Center, The Third Affiliated Hospital of Zhengzhou University, Maternal and Child Health Hospital of Henan ProvinceZhengzhouChina
| | - Bo Yang
- Prenatal Diagnosis Center, The Third Affiliated Hospital of Zhengzhou University, Maternal and Child Health Hospital of Henan ProvinceZhengzhouChina
| | - Pengyun Li
- Prenatal Diagnosis Center, The Third Affiliated Hospital of Zhengzhou University, Maternal and Child Health Hospital of Henan ProvinceZhengzhouChina
| | - Xueyin Cui
- Prenatal Diagnosis Center, The Third Affiliated Hospital of Zhengzhou University, Maternal and Child Health Hospital of Henan ProvinceZhengzhouChina
| | - Ling Liu
- Prenatal Diagnosis Center, The Third Affiliated Hospital of Zhengzhou University, Maternal and Child Health Hospital of Henan ProvinceZhengzhouChina
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26
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Kim S, Pistawka C, Langlois S, Osiovich H, Virani A, Kitchin V, Elliott AM. Genetic counselling considerations with genetic/genomic testing in Neonatal and Pediatric Intensive Care Units: A scoping review. Clin Genet 2024; 105:13-33. [PMID: 37927209 DOI: 10.1111/cge.14446] [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: 07/28/2023] [Revised: 09/23/2023] [Accepted: 10/15/2023] [Indexed: 11/07/2023]
Abstract
Genetic and genomic technologies can effectively diagnose numerous genetic disorders. Patients benefit when genetic counselling accompanies genetic testing and international guidelines recommend pre- and post-test genetic counselling with genome-wide sequencing. However, there is a gap in knowledge regarding the unique genetic counselling considerations with different types of genetic testing in the Neonatal Intensive Care Unit (NICU) and the Pediatric Intensive Care Unit (PICU). This scoping review was conducted to identify the gaps in care with respect to genetic counselling for infants/pediatric patients undergoing genetic and genomic testing in NICUs and PICUs and understand areas in need of improvement in order to optimize clinical care for patients, caregivers, and healthcare providers. Five databases (MEDLINE [Ovid], Embase [Ovid], PsycINFO [Ebsco], CENTRAL [Ovid], and CINHAL [Ebsco]) and grey literature were searched. A total of 170 studies were included and used for data extraction and analysis. This scoping review includes descriptive analysis, followed by a narrative account of the extracted data. Results were divided into three groups: pre-test, post-test, and comprehensive (both pre- and post-test) genetic counselling considerations based on indication for testing. More studies were conducted in the NICU than the PICU. Comprehensive genetic counselling was discussed in only 31% of all the included studies demonstrating the need for both pre-test and post-test genetic counselling for different clinical indications in addition to the need to account for different cultural aspects based on ethnicity and geographic factors.
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Affiliation(s)
- Sunu Kim
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Carly Pistawka
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sylvie Langlois
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada
- Women's Health Research Institute, Vancouver, British Columbia, Canada
| | - Horacio Osiovich
- BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada
- Women's Health Research Institute, Vancouver, British Columbia, Canada
- Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alice Virani
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- Ethics Service, Provincial Health Services Authority, Vancouver, British Columbia, Canada
| | - Vanessa Kitchin
- Woodward Library, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alison M Elliott
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada
- Women's Health Research Institute, Vancouver, British Columbia, Canada
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27
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Huth EA, Zhao X, Owen N, Luna PN, Vogel I, Dorf ILH, Joss S, Clayton-Smith J, Parker MJ, Louw JJ, Gewillig M, Breckpot J, Kraus A, Sasaki E, Kini U, Burgess T, Tan TY, Armstrong R, Neas K, Ferrero GB, Brusco A, Kerstjens-Frederikse WS, Rankin J, Helvaty LR, Landis BJ, Geddes GC, McBride KL, Ware SM, Shaw CA, Lalani SR, Rosenfeld JA, Scott DA. Clinical exome sequencing efficacy and phenotypic expansions involving anomalous pulmonary venous return. Eur J Hum Genet 2023; 31:1430-1439. [PMID: 37673932 PMCID: PMC10689790 DOI: 10.1038/s41431-023-01451-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 08/08/2023] [Accepted: 08/24/2023] [Indexed: 09/08/2023] Open
Abstract
Anomalous pulmonary venous return (APVR) frequently occurs with other congenital heart defects (CHDs) or extra-cardiac anomalies. While some genetic causes have been identified, the optimal approach to genetic testing in individuals with APVR remains uncertain, and the etiology of most cases of APVR is unclear. Here, we analyzed molecular data from 49 individuals to determine the diagnostic yield of clinical exome sequencing (ES) for non-isolated APVR. A definitive or probable diagnosis was made for 8 of those individuals yielding a diagnostic efficacy rate of 16.3%. We then analyzed molecular data from 62 individuals with APVR accrued from three databases to identify novel APVR genes. Based on data from this analysis, published case reports, mouse models, and/or similarity to known APVR genes as revealed by a machine learning algorithm, we identified 3 genes-EFTUD2, NAA15, and NKX2-1-for which there is sufficient evidence to support phenotypic expansion to include APVR. We also provide evidence that 3 recurrent copy number variants contribute to the development of APVR: proximal 1q21.1 microdeletions involving RBM8A and PDZK1, recurrent BP1-BP2 15q11.2 deletions, and central 22q11.2 deletions involving CRKL. Our results suggest that ES and chromosomal microarray analysis (or genome sequencing) should be considered for individuals with non-isolated APVR for whom a genetic etiology has not been identified, and that genetic testing to identify an independent genetic etiology of APVR is not warranted in individuals with EFTUD2-, NAA15-, and NKX2-1-related disorders.
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Affiliation(s)
- Emily A Huth
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Xiaonan Zhao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Baylor Genetics, Houston, TX, USA
| | - Nichole Owen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Baylor Genetics, Houston, TX, USA
| | - Pamela N Luna
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ida Vogel
- Department of Clinical Medicine, Aarhus University, 8000, Aarhus, C, Denmark
| | - Inger L H Dorf
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | - Shelagh Joss
- West of Scotland Genomics Service, Queen Elizabeth University Hospital, Glasgow, G51 4TF, UK
| | - Jill Clayton-Smith
- Manchester Centre For Genomic Medicine, Manchester University Hospitals, Manchester, M13 9WL, UK
- University of Manchester, Manchester, M13 9PL, UK
| | - Michael J Parker
- Department of Clinical Genetics, Sheffield, Children's Hospital, UK
| | - Jacoba J Louw
- Pediatric Cardiology Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Marc Gewillig
- Department of Cardiovascular Sciences KU Leuven, Leuven, Belgium
- Pediatric Cardiology University Hospitals Leuven, Leuven, Belgium
| | - Jeroen Breckpot
- Center for Human Genetics, University Hospitals Leuven, Catholic University, Leuven, Belgium
| | - Alison Kraus
- Yorkshire Regional Genetics Service, Chapel Allerton Hospital, Leeds, LS7 4SA, UK
| | - Erina Sasaki
- Oxford Centre for Genomic Medicine, Oxford University Hospital, Oxford, OX3 7HE, UK
| | - Usha Kini
- Oxford Centre for Genomic Medicine, Oxford University Hospital, Oxford, OX3 7HE, UK
- Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DU, UK
| | - Trent Burgess
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Tiong Y Tan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Ruth Armstrong
- East Anglian Medical Genetics Service, Addenbrooke's Treatment Centre, Addenbrooke's Hospital, Cambridge, CB2 0QQ, UK
| | | | - Giovanni B Ferrero
- Department of Clinical and Biological Sciences, University of Torino, Orbassano, Italy
| | - Alfredo Brusco
- Department of Medical Sciences, University of Torino, Torino, Italy
- Città della Salute e della Scienza University Hospital, Torino, Italy
| | | | | | | | | | - Gabrielle C Geddes
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Kim L McBride
- Department of Medical Genetics, University of Calgary, Calgary, Alberta, Canada
- Center for Cardiovascular Research, Nationwide Children's Hospital, Columbus, OH, USA
| | - Stephanie M Ware
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Chad A Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Seema R Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Daryl A Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA.
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28
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Bilal M, Haack TB, Buchert R, Peralta S, Ahmad I, Faisal, Abbasi S, Ahmad W. Sequence Variants in the WNT10B Underlying Non-Syndromic Split-Hand/Foot Malformation. Mol Syndromol 2023; 14:469-476. [PMID: 38058757 PMCID: PMC10697732 DOI: 10.1159/000531069] [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: 04/20/2023] [Accepted: 05/10/2023] [Indexed: 12/08/2023] Open
Abstract
Introduction Split hand and foot malformation (SHFM) or ectrodactyly is a rare limb deformity characterized by median cleft of the hand and foot with impaired or missing central rays. It can occur as an isolated anomaly or in association with abnormalities of other body parts. Methods After delineating the clinical features of two families (A-B), with non-syndromic SHFM, exome and Sanger sequencing were employed to search for the disease-causing variants. Results Analysis of exome and Sanger sequencing data revealed two causative variants in the WNT10B gene in affected members of the two families. This included a novel missense change [c.338G>C; p.(Gly113Ala)] in family A and a previously reported frameshift variant [c.884-896delTCCAGCCCCGTCT; p.(Phe295Cysfs*87)] in family B. Conclusion Our findings add a novel variant in WNT10B gene as the underlying cause of SHFM. The finding adds to the growing body of knowledge about the genetic basis of developmental disorders and provides valuable insights into the molecular mechanisms that regulate limb development.
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Affiliation(s)
- Muhammad Bilal
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
- Institute for Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Tobias B. Haack
- Institute for Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Rebecca Buchert
- Institute for Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Susana Peralta
- Institute for Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Imtiaz Ahmad
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Faisal
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Sanaullah Abbasi
- Department of Biochemistry, Shah Abdul Latif, Khairpur, Pakistan
| | - Wasim Ahmad
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
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29
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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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30
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Schuler BA, Mosera M, Hatch LD, Grochowsky A, Wheeler F. Collaborative efforts to improve genetic testing in the neonatal intensive care unit. J Perinatol 2023; 43:1500-1505. [PMID: 37914812 DOI: 10.1038/s41372-023-01817-y] [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: 05/01/2023] [Revised: 09/22/2023] [Accepted: 10/23/2023] [Indexed: 11/03/2023]
Abstract
OBJECTIVE To reduce unnecessary simultaneous karyotype analysis and chromosomal microarray (CMA) testing in the neonatal intensive care unit (NICU). STUDY DESIGN This quality improvement study investigated the effect of collaborative efforts between the NICU, cytogenetics, and clinical genetics on numbers of genetic tests, rates of abnormal tests, and number of genetics consults comparing baseline and 5-month intervention periods. RESULTS Simultaneous karyotype analyses and CMAs decreased due to a decrease in karyotype testing (11.3% [68/600] vs. 0.98% [6/614], p < 0.01). Karyotype analyses were more likely to be abnormal (13.8% [12/87] vs. 64.0% [16/25], p < 0.01). Frequency of genetics consultation did not change (7.0% [42/600] vs. 9.4% [58/614], p = 0.12). CONCLUSION Collaborative efforts between the NICU, cytogenetics, and clinical genetics decreased redundant genetic testing, which demonstrated potential cost savings to our institution. Ongoing collaborative efforts could facilitate genetic testing practices in the NICU that readily evolve in tandem with genetic testing recommendations.
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Affiliation(s)
- Bryce A Schuler
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA.
| | - Mackenzie Mosera
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - L Dupree Hatch
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Angela Grochowsky
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Ferrin Wheeler
- Department of Pathology, Vanderbilt University Medical Center, Nashville, TN, USA
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31
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Campbell L, Fredericks J, Mathivha K, Moshesh P, Coovadia A, Chirwa P, Dillon B, Ghoor A, Lawrence D, Nair L, Mabaso N, Mokwele D, Novellie M, Krause A, Carstens N. The implementation and utility of clinical exome sequencing in a South African infant cohort. Front Genet 2023; 14:1277948. [PMID: 38028619 PMCID: PMC10665497 DOI: 10.3389/fgene.2023.1277948] [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: 08/15/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
Genetic disorders are significant contributors to infant hospitalization and mortality globally. The early diagnosis of these conditions in infants remains a considerable challenge. Clinical exome sequencing (CES) has shown to be a successful tool for the early diagnosis of genetic conditions, however, its utility in African infant populations has not been investigated. The impact of the under-representation of African genomic data, the cost of testing, and genomic workforce shortages, need to be investigated and evidence-based implementation strategies accounting for locally available genetics expertise and diagnostic infrastructure need to be developed. We evaluated the diagnostic utility of singleton CES in a cohort of 32 ill, South African infants from two State hospitals in Johannesburg, South Africa. We analysed the data using a series of filtering approaches, including a curated virtual gene panel consisting of genes implicated in neonatal-and early childhood-onset conditions and genes with known founder and common variants in African populations. We reported a diagnostic yield of 22% and identified seven pathogenic variants in the NPHS1, COL2A1, OCRL, SHOC2, TPRV4, MTM1 and STAC3 genes. This study demonstrates the utility value of CES in the South African State healthcare setting, providing a diagnosis to patients who would otherwise not receive one and allowing for directed management. We anticipate an increase in the diagnostic yield of our workflow with further refinement of the study inclusion criteria. This study highlights important considerations for the implementation of genomic medicine in under-resourced settings and in under-represented African populations where variant interpretation remains a challenge.
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Affiliation(s)
- L. Campbell
- Division of Human Genetics, National Health Laboratory Service andSchool of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - J. Fredericks
- Department of Paediatrics and Child Health, School of Clinical Medicine, Rahima Moosa Mother and Child Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - K. Mathivha
- Department of Paediatrics and Child Health, School of Clinical Medicine, Nelson Mandela Children’s Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - P. Moshesh
- Department of Paediatrics and Child Health, School of Clinical Medicine, Nelson Mandela Children’s Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - A. Coovadia
- Department of Paediatrics and Child Health, School of Clinical Medicine, Rahima Moosa Mother and Child Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - P. Chirwa
- Nelson Mandela Children’s Hospital, Johannesburg, South Africa
| | - B. Dillon
- Division of Human Genetics, National Health Laboratory Service andSchool of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - A. Ghoor
- Department of Paediatrics and Child Health, School of Clinical Medicine, Rahima Moosa Mother and Child Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - D. Lawrence
- Department of Paediatrics and Child Health, School of Clinical Medicine, Rahima Moosa Mother and Child Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - L. Nair
- Department of Paediatrics and Child Health, School of Clinical Medicine, Rahima Moosa Mother and Child Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - N. Mabaso
- Division of Human Genetics, National Health Laboratory Service andSchool of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - D. Mokwele
- Division of Human Genetics, National Health Laboratory Service andSchool of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - M. Novellie
- Division of Human Genetics, National Health Laboratory Service andSchool of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - A. Krause
- Division of Human Genetics, National Health Laboratory Service andSchool of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - N. Carstens
- Division of Human Genetics, National Health Laboratory Service andSchool of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Genomics Platform, South African Medical Research Council, Cape Town, South Africa
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32
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Latzer IT, Blau N, Ferreira CR, Pearl PL. Clinical and biochemical footprints of inherited metabolic diseases. XV. Epilepsies. Mol Genet Metab 2023; 140:107690. [PMID: 37659319 DOI: 10.1016/j.ymgme.2023.107690] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 08/24/2023] [Accepted: 08/25/2023] [Indexed: 09/04/2023]
Abstract
We provide a comprehensive overview of inherited metabolic disorders (IMDs) in which epilepsy is a prominent manifestation. Our unique database search has identified 256 IMDs associated with various types of epilepsies, which we classified according to the classic pathophysiology-based classification of IMDs, and according to selected seizure-related factors (neonatal seizures, infantile spasms, myoclonic seizures, and characteristic EEG patterns) and treatability for the underlying metabolic defect. Our findings indicate that inherited metabolic epilepsies are more likely to present in the neonatal period, with infantile spasms or myoclonic seizures. Additionally, the ∼20% of treatable inherited metabolic epilepsies found by our search were mainly associated with the IMD groups of "cofactor and mineral metabolism" and "Intermediary nutrient metabolism." The information provided by this study, including a comprehensive list of IMDs with epilepsy stratified according to age of onset, and seizure type and characteristics, along with an overview of the key clinical features and proposed diagnostic and therapeutic approaches, may benefit any epileptologist and healthcare provider caring for individuals with metabolic conditions.
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Affiliation(s)
- Itay Tokatly Latzer
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv, Israel.
| | - Nenad Blau
- Division of Metabolism, University Children's Hospital, Zürich, Switzerland.
| | - Carlos R Ferreira
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Phillip L Pearl
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
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33
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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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34
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Chung DH, Zheng M, Bale AE, Vilarinho S. Hepatology Genome Rounds: An interdisciplinary approach to integrate genomic data into clinical practice. J Hepatol 2023; 79:1065-1071. [PMID: 37011712 PMCID: PMC10523901 DOI: 10.1016/j.jhep.2023.03.030] [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: 12/14/2022] [Revised: 03/13/2023] [Accepted: 03/21/2023] [Indexed: 04/05/2023]
Abstract
In the last decade, the utility of whole-exome sequencing in uncovering genetic aetiologies of a variety of liver diseases has been demonstrated. These new diagnoses have guided the management, treatment, and prognostication of previously undiagnosed patients, largely thanks to improved insight into the underlying pathogenesis of their conditions. Despite its clear benefits, the uptake of genetic testing by hepatologists has been limited, in part due to limited prior genetic training and/or opportunities for continuing education. Herein, we show that Hepatology Genome Rounds, an interdisciplinary forum highlighting hepatology cases of clinical interest and educational value, are an important venue for integrating genotypic and phenotypic information to enable accurate diagnosis and appropriate management, dissemination of genomic knowledge within the field of hepatology, and ongoing education to providers and trainees in genomic medicine. We describe our single-centre experience and discuss practical considerations for clinicians interested in launching such a series. We foresee that this format will be adopted at other institutions and by additional specialties, with the aim of further incorporating genomic information into clinical medicine.
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Affiliation(s)
- David H Chung
- Department of Internal Medicine, Section of Digestive Diseases, Yale School of Medicine, New Haven, CT, USA
| | - Melanie Zheng
- Department of Internal Medicine, Section of Digestive Diseases, Yale School of Medicine, New Haven, CT, USA
| | - Allen E Bale
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Sílvia Vilarinho
- Department of Internal Medicine, Section of Digestive Diseases, Yale School of Medicine, New Haven, CT, USA; Department of Pathology, Yale School of Medicine, New Haven, CT, USA.
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35
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Slavotinek A. Genetics in Pediatric Practice: From Baby Steps to Running Fast. Pediatr Clin North Am 2023; 70:885-894. [PMID: 37704347 DOI: 10.1016/j.pcl.2023.05.003] [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] [Indexed: 09/15/2023]
Abstract
In the last few decades, medical genetics has undergone a revolution because of the development of technologies and informatics approaches that can generate and analyze large amounts of genomic data. Pediatricians have been hugely affected by these changes. The early age of presentation for birth defects and neurocognitive disorders, together with a shortage of trained genetics professionals, has increased consultations for conditions with a genetic cause, not only in pediatric practice but also in other subspecialties. In the future, genetic testing in childhood is likely to include pediatricians, who can initiate testing in partnership with trained genetics professionals.
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Affiliation(s)
- Anne Slavotinek
- Medical Genetics, Division of Human Genetics, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati School of Medicine, 3333 Burnet Avenue, Cincinnati, OH 45229, USA.
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36
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Hays T, Hernan R, Disco M, Griffin EL, Goldshtrom N, Vargas D, Krishnamurthy G, Bomback M, Rehman AU, Wilson AT, Guha S, Phadke S, Okur V, Robinson D, Felice V, Abhyankar A, Jobanputra V, Chung WK. Implementation of Rapid Genome Sequencing for Critically Ill Infants With Complex Congenital Heart Disease. CIRCULATION. GENOMIC AND PRECISION MEDICINE 2023; 16:415-420. [PMID: 37417234 DOI: 10.1161/circgen.122.004050] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 06/16/2023] [Indexed: 07/08/2023]
Abstract
BACKGROUND Rapid genome sequencing (rGS) has been shown to improve care of critically ill infants. Congenital heart disease (CHD) is a leading cause of infant mortality and is often caused by genetic disorders, yet the utility of rGS has not been prospectively studied in this population. METHODS We conducted a prospective evaluation of rGS to improve the care of infants with complex CHD in our cardiac neonatal intensive care unit. RESULTS In a cohort of 48 infants with complex CHD, rGS diagnosed 14 genetic disorders in 13 (27%) individuals and led to changes in clinical management in 8 (62%) cases with diagnostic results. These included 2 cases in whom genetic diagnoses helped avert intensive, futile interventions before cardiac neonatal intensive care unit discharge, and 3 cases in whom eye disease was diagnosed and treated in early childhood. CONCLUSIONS Our study provides the first prospective evaluation of rGS for infants with complex CHD to our knowledge. We found that rGS diagnosed genetic disorders in 27% of cases and led to changes in management in 62% of cases with diagnostic results. Our model of care depended on coordination between neonatologists, cardiologists, surgeons, geneticists, and genetic counselors. These findings highlight the important role of rGS in CHD and demonstrate the need for expanded study of how to implement this resource to a broader population of infants with CHD.
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Affiliation(s)
- Thomas Hays
- Division of Neonatology, Department of Pediatrics (T.H., N.G., D.V., G.K.), Columbia University Irving Medical Center, New York, NY
| | - Rebecca Hernan
- Division of Genetics, Department of Pediatrics (R.H., M.D., E.L.G., W.K.C.), Columbia University Irving Medical Center, New York, NY
| | - Michele Disco
- Division of Genetics, Department of Pediatrics (R.H., M.D., E.L.G., W.K.C.), Columbia University Irving Medical Center, New York, NY
| | - Emily L Griffin
- Division of Genetics, Department of Pediatrics (R.H., M.D., E.L.G., W.K.C.), Columbia University Irving Medical Center, New York, NY
| | - Nimrod Goldshtrom
- Division of Neonatology, Department of Pediatrics (T.H., N.G., D.V., G.K.), Columbia University Irving Medical Center, New York, NY
| | - Diana Vargas
- Division of Neonatology, Department of Pediatrics (T.H., N.G., D.V., G.K.), Columbia University Irving Medical Center, New York, NY
| | - Ganga Krishnamurthy
- Division of Neonatology, Department of Pediatrics (T.H., N.G., D.V., G.K.), Columbia University Irving Medical Center, New York, NY
| | - Miles Bomback
- Feinberg School of Medicine, Northwestern University, Chicago, IL (M.B.)
| | - Atteeq U Rehman
- New York Genome Center, New York, NY (A.U.R., A.T.W., S.G., S.P., V.O., D.R., V.F., A.A., V.J.)
| | - Amanda T Wilson
- New York Genome Center, New York, NY (A.U.R., A.T.W., S.G., S.P., V.O., D.R., V.F., A.A., V.J.)
| | - Saurav Guha
- New York Genome Center, New York, NY (A.U.R., A.T.W., S.G., S.P., V.O., D.R., V.F., A.A., V.J.)
| | - Shruti Phadke
- New York Genome Center, New York, NY (A.U.R., A.T.W., S.G., S.P., V.O., D.R., V.F., A.A., V.J.)
| | - Volkan Okur
- New York Genome Center, New York, NY (A.U.R., A.T.W., S.G., S.P., V.O., D.R., V.F., A.A., V.J.)
| | - Dino Robinson
- New York Genome Center, New York, NY (A.U.R., A.T.W., S.G., S.P., V.O., D.R., V.F., A.A., V.J.)
| | - Vanessa Felice
- New York Genome Center, New York, NY (A.U.R., A.T.W., S.G., S.P., V.O., D.R., V.F., A.A., V.J.)
| | - Avinash Abhyankar
- New York Genome Center, New York, NY (A.U.R., A.T.W., S.G., S.P., V.O., D.R., V.F., A.A., V.J.)
| | - Vaidehi Jobanputra
- Department of Pathology & Cell Biology (V.J.), Columbia University Irving Medical Center, New York, NY
- New York Genome Center, New York, NY (A.U.R., A.T.W., S.G., S.P., V.O., D.R., V.F., A.A., V.J.)
| | - Wendy K Chung
- Division of Genetics, Department of Pediatrics (R.H., M.D., E.L.G., W.K.C.), Columbia University Irving Medical Center, New York, NY
- Department of Medicine (W.K.C.), Columbia University Irving Medical Center, New York, NY
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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: 13] [Impact Index Per Article: 13.0] [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: 18] [Impact Index Per Article: 18.0] [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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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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Kurzlechner LM, Kishnani S, Chowdhury S, Atkins SL, Moya-Mendez ME, Parker LE, Rosamilia MB, Tadros HJ, Pace LA, Patel V, Chahal CAA, Landstrom AP. DiscoVari: A Web-Based Precision Medicine Tool for Predicting Variant Pathogenicity in Cardiomyopathy- and Channelopathy-Associated Genes. CIRCULATION. GENOMIC AND PRECISION MEDICINE 2023; 16:317-327. [PMID: 37409478 PMCID: PMC10527712 DOI: 10.1161/circgen.122.003911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 05/30/2023] [Indexed: 07/07/2023]
Abstract
BACKGROUND With genetic testing advancements, the burden of incidentally identified cardiac disease-associated gene variants is rising. These variants may carry a risk of sudden cardiac death, highlighting the need for accurate diagnostic interpretation. We sought to identify pathogenic hotspots in sudden cardiac death-associated genes using amino acid-level signal-to-noise (S:N) analysis and develop a web-based precision medicine tool, DiscoVari, to improve variant evaluation. METHODS The minor allele frequency of putatively pathogenic variants was derived from cohort-based cardiomyopathy and channelopathy studies in the literature. We normalized disease-associated minor allele frequencies to rare variants in an ostensibly healthy population (Genome Aggregation Database) to calculate amino acid-level S:N. Amino acids with S:N above the gene-specific threshold were defined as hotspots. DiscoVari was built using JavaScript ES6 and using open-source JavaScript library ReactJS, web development framework Next.js, and JavaScript runtime NodeJS. We validated the ability of DiscoVari to identify pathogenic variants using variants from ClinVar and individuals clinically evaluated at the Duke University Hospitals with cardiac genetic testing. RESULTS We developed DiscoVari as an internet-based tool for S:N-based variant hotspots. Upon validation, a higher proportion of ClinVar likely pathogenic/pathogenic variants localized to DiscoVari hotspots (43.1%) than likely benign/benign variants (17.8%; P<0.0001). Further, 75.3% of ClinVar variants reclassified to likely pathogenic/pathogenic were in hotspots, compared with 41.3% of those reclassified as variants of uncertain significance (P<0.0001) and 23.4% of those reclassified as likely benign/benign (P<0.0001). Of the clinical cohort variants, 73.1% of likely pathogenic/pathogenic were in hotspots, compared with 0.0% of likely benign/benign (P<0.01). CONCLUSIONS DiscoVari reliably identifies disease-susceptible amino acid residues to evaluate variants by searching amino acid-specific S:N ratios.
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Affiliation(s)
| | - Sujata Kishnani
- Dept of Pediatrics, Division of Pediatric Cardiology, Durham, NC
| | - Shawon Chowdhury
- Dept of Pediatrics, Division of Pediatric Cardiology, Durham, NC
| | - Sage L. Atkins
- Dept of Pediatrics, Division of Pediatric Cardiology, Durham, NC
| | | | - Lauren E. Parker
- Dept of Pediatrics, Division of Pediatric Cardiology, Durham, NC
| | | | - Hanna J. Tadros
- Dept of Pediatrics, Section of Pediatric Cardiology, Baylor College of Medicine, Houston, TX
| | - Leslie A. Pace
- Dept of Pediatrics, Division of Pediatric Cardiology, Durham, NC
| | - Viraj Patel
- North West Thames Regional Genetics Service, St Mark’s Hospital, London, United Kingdom
| | - C. Anwar A. Chahal
- Center for Inherited Cardiovascular Diseases, WellSpan Health, Lancaster, PA
- Barts Heart Centre, St Bartholomew’s Hospital, Barts Health NHS Trust, London, United Kingdom
- Cardiac Electrophysiology, Cardiovascular Division, Hospital of the Univ of Pennsylvania, Philadelphia, PA
- Dept of Cardiovascular Medicine, Mayo Clinic, Rochester, MN
| | - Andrew P. Landstrom
- Dept of Pediatrics, Division of Pediatric Cardiology, Durham, NC
- Dept of Cell Biology, Duke Univ School of Medicine, Durham, NC
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Tang S, You J, Liu L, Ouyang H, Jiang N, Duan J, Li C, Luo Y, Zhang W, Zhan M, Liu C, Lyu G, Zhang VW, Zhao H. Expanding the mutational spectrum of ZTTK syndrome: A de novo variant with global developmental delay and malnutrition in a Chinese patient. Mol Genet Genomic Med 2023; 11:e2188. [PMID: 37488749 PMCID: PMC10422072 DOI: 10.1002/mgg3.2188] [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: 06/18/2022] [Revised: 10/23/2022] [Accepted: 02/22/2023] [Indexed: 07/26/2023] Open
Abstract
BACKGROUND Zhu-Tokita-Takenouchi-Kim (ZTTK, OMIM 617140) syndrome is a severe multisystem developmental disorder characterized by intellectual disability, developmental delay, cortical malformations, epilepsy, visual problems, musculoskeletal abnormalities, and congenital malformations. ZTTK syndrome is caused by a heterozygous pathogenic variant of the SON gene (NM_138927) at chromosome 21q22.1. The purpose of this study was to investigate the pathogenesis of a 6-month-old Chinese child who exhibited global developmental delay, muscle weakness, malnutrition, weight loss, and strabismus, brain abnormality, immunological system abnormalities. METHODS The little girl was tested for medical exome sequencing (MES) and mtDNA sequencing in trio. And, the mutation was validated by Sanger sequencing. RESULTS A novel de novo frameshift variant, c.1845_1870del26 (p.G616Sfs*61), in the SON gene was found in the proband. CONCLUSION We described a 6-month-old Chinese child with global developmental delay caused by pathogenic de novo mutation c.1845_1870del26 (p.G616Sfs*61) in the SON. Apart from a founder mutation, we reviewed the phenotypic abnormalities and genotypes in 79 individuals. The data showed that global developmental delay is accompanied by other system disorders. Our findings expanded the mutational spectrum of ZTTK syndrome and provide genetic counseling of baby with global developmental delay.
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Affiliation(s)
- Shuo Tang
- Department of Digestive System DiseasesHunan Children's HospitalChangshaChina
| | - Jieyu You
- Department of Digestive System DiseasesHunan Children's HospitalChangshaChina
| | - Li Liu
- Department of Digestive System DiseasesHunan Children's HospitalChangshaChina
| | - Hongjuan Ouyang
- Department of Digestive System DiseasesHunan Children's HospitalChangshaChina
| | - Na Jiang
- Department of Digestive System DiseasesHunan Children's HospitalChangshaChina
| | - Jiaqi Duan
- Department of Digestive System DiseasesHunan Children's HospitalChangshaChina
| | - Canlin Li
- Department of Digestive System DiseasesHunan Children's HospitalChangshaChina
| | - Yanhong Luo
- Department of Digestive System DiseasesHunan Children's HospitalChangshaChina
| | - Wenting Zhang
- Department of Digestive System DiseasesHunan Children's HospitalChangshaChina
| | - Meizheng Zhan
- Department of Digestive System DiseasesHunan Children's HospitalChangshaChina
| | - Chenxi Liu
- Department of Digestive System DiseasesHunan Children's HospitalChangshaChina
| | | | | | - Hongmei Zhao
- Department of Digestive System DiseasesHunan Children's HospitalChangshaChina
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Kadıoğlu Yılmaz B, Akgül AH. Inherited Metabolic Diseases from Past to Present: A Bibliometric Analysis (1968-2023). CHILDREN (BASEL, SWITZERLAND) 2023; 10:1205. [PMID: 37508702 PMCID: PMC10378490 DOI: 10.3390/children10071205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/09/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023]
Abstract
Bibliometric studies on inherited metabolic diseases (IMDs) do not exist in the literature. Therefore, our research aims to conduct a bibliometric study to determine the current status, trending topics, and missing points of publications on IMDs. Between 1968 and 2023, we conducted a literature search with the keyword "inherited metabolic disease" in the SCOPUS database. We included research articles in medicine written in English and published in the final section. We created our data pool using VOSviewer, SciMAT, and Rstudio software programs for the bibliometric parameters of the articles that met the inclusion criteria. We performed a bibliometric analysis of the data with the R package "bibliometrix" and BibExcel programs. We included 2702 research articles published on IMDs. The top three countries that have written the most articles in this field are the USA (n = 501), the United Kingdom (n = 182), and China (n = 172). The most preferred keywords by the authors were: newborn screening (n = 54), mutation (n = 43), phenylketonuria (n = 42), children (n = 35), genetics (n = 34), and maple syrup urine disease (n = 32). Trending topics were osteoporosis, computed tomography, bone marrow transplantation in the early years of the study, chronic kidney disease, urea cycle disorders, next-generation sequencing, newborn screening, and familial hypercholesterolemia in the final years of the study. This study provides clinicians with a new perspective, showing that molecular and genetic studies of inherited metabolic diseases will play an essential role in diagnosis and treatment in the future.
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Affiliation(s)
- Banu Kadıoğlu Yılmaz
- Department of Pediatric Nutrition and Metabolism, Faculty of Medicine, Selçuk University, Konya 42250, Turkey
| | - Ayşe Hümeyra Akgül
- Department of Pediatrics, Faculty of Medicine, Necmettin Erbakan University, Konya 42080, Turkey
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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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Gilholm P, Gibbons K, Brüningk S, Klatt J, Vaithianathan R, Long D, Millar J, Tomaszewski W, Schlapbach LJ. Machine learning to predict poor school performance in paediatric survivors of intensive care: a population-based cohort study. Intensive Care Med 2023; 49:785-795. [PMID: 37354231 PMCID: PMC10354166 DOI: 10.1007/s00134-023-07137-1] [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] [Received: 02/23/2023] [Accepted: 06/09/2023] [Indexed: 06/26/2023]
Abstract
PURPOSE Whilst survival in paediatric critical care has improved, clinicians lack tools capable of predicting long-term outcomes. We developed a machine learning model to predict poor school outcomes in children surviving intensive care unit (ICU). METHODS Population-based study of children < 16 years requiring ICU admission in Queensland, Australia, between 1997 and 2019. Failure to meet the National Minimum Standard (NMS) in the National Assessment Program-Literacy and Numeracy (NAPLAN) assessment during primary and secondary school was the primary outcome. Routine ICU information was used to train machine learning classifiers. Models were trained, validated and tested using stratified nested cross-validation. RESULTS 13,957 childhood ICU survivors with 37,200 corresponding NAPLAN tests after a median follow-up duration of 6 years were included. 14.7%, 17%, 15.6% and 16.6% failed to meet NMS in school grades 3, 5, 7 and 9. The model demonstrated an Area Under the Receiver Operating Characteristic curve (AUROC) of 0.8 (standard deviation SD, 0.01), with 51% specificity to reach 85% sensitivity [relative Area Under the Precision Recall Curve (rel-AUPRC) 3.42, SD 0.06]. Socio-economic status, illness severity, and neurological, congenital, and genetic disorders contributed most to the predictions. In children with no comorbidities admitted between 2009 and 2019, the model achieved a AUROC of 0.77 (SD 0.03) and a rel-AUPRC of 3.31 (SD 0.42). CONCLUSIONS A machine learning model using data available at time of ICU discharge predicted failure to meet minimum educational requirements at school age. Implementation of this prediction tool could assist in prioritizing patients for follow-up and targeting of rehabilitative measures.
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Affiliation(s)
- Patricia Gilholm
- Child Health Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Kristen Gibbons
- Child Health Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Sarah Brüningk
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Juliane Klatt
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Rhema Vaithianathan
- Institute for Social Science Research, The University of Queensland, Brisbane, QLD, Australia
| | - Debbie Long
- Child Health Research Centre, The University of Queensland, Brisbane, QLD, Australia
- School of Nursing, Centre for Healthcare Transformation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Johnny Millar
- Paediatric Intensive Care Unit, The Royal Children's Hospital, Melbourne, VIC, Australia
- The Australian and New Zealand Intensive Care Society (ANZICS) Centre for Outcome and Resource Evaluation (CORE), ANZICS House, Melbourne, VIC, Australia
- Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Wojtek Tomaszewski
- Institute for Social Science Research, The University of Queensland, Brisbane, QLD, Australia
| | - Luregn J Schlapbach
- Child Health Research Centre, The University of Queensland, Brisbane, QLD, Australia.
- Department of Intensive Care and Neonatology, and Children's Research Center, University Children's Hospital Zurich, Steinwiesstrasse 75, 8032, Zurich, Switzerland.
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45
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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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46
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Huang Z, Lu W, Zhang P, Lu Y, Chen L, Kang W, Yang L, Li G, Zhu J, Wu B, Zhou W, Wang H. Early onset critically ill infants with Schaaf-Yang syndrome: a retrospective study from the China neonatal genomes project and literature review. ANNALS OF TRANSLATIONAL MEDICINE 2023; 11:312. [PMID: 37404980 PMCID: PMC10316094 DOI: 10.21037/atm-22-4396] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 02/19/2023] [Indexed: 07/06/2023]
Abstract
Background Schaaf-Yang syndrome (SYS) is a recently identified rare neurodevelopmental disorder characterized by neonatal hypotonia, feeding difficulty, joint contractures, autism spectrum disorder and development delay/intellectual disability. It is mainly caused by truncating variants in maternally imprinted gene MAGEL2 within the Prader-Willi syndrome critical region 15q11-q13. Clinical diagnosis of SYS is difficult for clinicians due to its rarity and highly variable phenotypes, while unique inheritance patterns also complicate genetic diagnosis. To date, no published papers have analyzed the clinical consequences and molecular changes in Chinese patients. Methods In this study, we retrospectively investigated the mutation spectrums and phenotypic features of 12 SYS infants. The data were from a cohort of critically ill infants from the China neonatal genomes project (CNGP), sponsored by Children's Hospital of Fudan University. We also reviewed relevant literature. Results Six previously reported mutations and six novel pathogenic variations of MAGEL2 were identified in 12 unrelated infants. Neonatal respiratory problems were the major complaint for hospitalization, which occurred in 91.7% (11/12) cases. All babies displayed feeding difficulties and a poor suck postnatally, and neonatal dystonia was present in 11 of the cases; joint contractures and multiple congenital defects were also observed. Interestingly, we found that 42.5% (57/134) of the reported SYS patients, including ours carried variants in the c.1996 site, particularly the c.1996dupC variant. The mortality rate was 17.2% (23/134), with the median age of death between 24 gestational weeks in fetuses and 1-month-old in infants. Respiratory failure was the leading cause of death in live-born patients (58.8%, 10/17), especially during the neonatal period. Conclusions Our findings expanded the genotype and phenotype spectrum of neonatal SYS patients. The results demonstrated that respiratory dysfunction was a typical characteristic among Chinese SYS neonates that should attract physicians' attention. The early identification of such disorders allows early intervention and can further provide genetic counseling as well as reproductive options for the affected families.
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Affiliation(s)
- Zhongwen Huang
- Center for Molecular Medicine, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Wei Lu
- Department of Endocrinology and Inherited Metabolic Diseases1, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Ping Zhang
- Center for Molecular Medicine, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Yulan Lu
- Center for Molecular Medicine, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Liping Chen
- Department of Neonatology, Jiangxi Provincial Children’s Hospital, Nanchang, China
| | - Wenqing Kang
- Department of Neonatology, Children’s Hospital Affiliated to Zhengzhou University, Zhengzhou, China
| | - Lin Yang
- Department of Endocrinology and Inherited Metabolic Diseases1, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Gang Li
- Center for Molecular Medicine, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Jitao Zhu
- Center for Molecular Medicine, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Bingbing Wu
- Center for Molecular Medicine, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Wenhao Zhou
- Center for Molecular Medicine, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
- Division of Neonatology, Children’s Hospital of Fudan University, National Children’s Medical Center, Key Laboratory of Neonatal Diseases, Ministry of Health, Shanghai, China
| | - Huijun Wang
- Center for Molecular Medicine, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
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47
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Lantos JD. The Future of Newborn Genomic Testing. CHILDREN (BASEL, SWITZERLAND) 2023; 10:1140. [PMID: 37508635 PMCID: PMC10378699 DOI: 10.3390/children10071140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/26/2023] [Accepted: 06/29/2023] [Indexed: 07/30/2023]
Abstract
Genome sequencing (GS) provides exciting opportunities to rapidly identify a diagnosis in critically ill newborns and children with rare genetic conditions. Nevertheless, there are reasons to remain cautious about the use of GS. Studies to date have been mostly in highly selected populations of babies with unusual clinical presentations. GS leads to diagnoses in many such infants. More rarely, it leads to beneficial changes in management. Parents and physicians whose babies meet these criteria and for whom GS is performed both find these results useful. The concern is this: we do not know how useful such testing will be in the general population. We can speculate that a number of problems will arise as the use of GS expands. First, the percentage of cases in which a valid molecular diagnosis is made will likely go down. The number of ambiguous results or false positives will rise. Genetic counseling will become more complex and challenging. We do not know the relative cost-effectiveness of whole genome, whole exome, or targeted panels in different populations. We do not know the relative contribution of a molecular diagnosis to the decision to withdraw life support. We will have to carefully evaluate the use of such testing in order to understand whether it truly improves outcome and survival or reduces symptoms in babies who are tested. Each of these concerns will require careful study of both the technology and the ethical issues to allow us to harness the potential of these new technologies while avoiding foreseeable problems. Studies are underway to see how the tests are used in general populations. These studies should generate important information to guide clinicians and policymakers. As part of informed consent, doctors should explain to parents that genetic results are not always straightforward. Sometimes, they confirm a diagnosis that was already suspected. Sometimes, they rule out a possible diagnosis. Sometimes, the results are ambiguous and difficult to interpret. Anticipatory discussions should try to give parents a realistic understanding of the likely impact of a genetic diagnosis. Diagnostic genomic testing for newborns is a science that is still in its infancy. More research is essential in order to establish how to personalize this promising but sometimes problematic tool.
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Affiliation(s)
- John D Lantos
- Department of Pediatrics, Mt Sinai School of Medicine, New York, NY 10029, USA
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48
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Monies D, Goljan E, Assoum M, Albreacan M, Binhumaid F, Subhani S, Boureggah A, Hashem M, Abdulwahab F, Abuyousef O, Temsah MH, Alsohime F, Kelaher J, Abouelhoda M, Meyer BF, Alkuraya FS. The clinical utility of rapid exome sequencing in a consanguineous population. Genome Med 2023; 15:44. [PMID: 37344829 DOI: 10.1186/s13073-023-01192-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 05/16/2023] [Indexed: 06/23/2023] Open
Abstract
BACKGROUND The clinical utility of exome sequencing is now well documented. Rapid exome sequencing (RES) is more resource-intensive than regular exome sequencing and is typically employed in specialized clinical settings wherein urgent molecular diagnosis is thought to influence acute management. Studies on the clinical utility of RES have been largely limited to outbred populations. METHODS Here, we describe our experience with rapid exome sequencing (RES) in a highly consanguineous population. Clinical settings included intensive care units, prenatal cases approaching the legal cutoff for termination, and urgent transplant decisions. RESULTS A positive molecular finding (a pathogenic or likely pathogenic variant that explains the phenotype) was observed in 80 of 189 cases (42%), while 15 (8%) and 94 (50%) received ambiguous (variant of uncertain significance (VUS)) and negative results, respectively. The consanguineous nature of the study population gave us an opportunity to observe highly unusual and severe phenotypic expressions of previously reported genes. Clinical utility was observed in nearly all (79/80) cases with positive molecular findings and included management decisions, prognostication, and reproductive counseling. Reproductive counseling is a particularly important utility in this population where the overwhelming majority (86%) of identified variants are autosomal recessive, which are more actionable in this regard than the de novo variants typically reported by RES elsewhere. Indeed, our cost-effectiveness analysis shows compelling cost savings in the study population. CONCLUSIONS This work expands the diversity of environments in which RES has a demonstrable clinical utility.
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Affiliation(s)
- Dorota Monies
- Department of Clinical Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Ewa Goljan
- Department of Clinical Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mirna Assoum
- Department of Clinical Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Muna Albreacan
- Department of Clinical Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Faisal Binhumaid
- Department of Clinical Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Shazia Subhani
- Department of Computational Science, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Abdulmlik Boureggah
- Department of Clinical Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mais Hashem
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, MBC-26, PO Box 3354, Riyadh, 11211, Saudi Arabia
| | - Firdous Abdulwahab
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, MBC-26, PO Box 3354, Riyadh, 11211, Saudi Arabia
| | - Omar Abuyousef
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, MBC-26, PO Box 3354, Riyadh, 11211, Saudi Arabia
| | - Mohamad H Temsah
- Department of Pediatrics, Pediatric Critical Care Unit, King Khalid University Hospital and College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Fahad Alsohime
- Department of Pediatrics, Pediatric Critical Care Unit, King Khalid University Hospital and College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - James Kelaher
- General Corporate Consultancy Department, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mohamed Abouelhoda
- Department of Computational Science, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.
| | - Brian F Meyer
- Department of Clinical Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, MBC-26, PO Box 3354, Riyadh, 11211, Saudi Arabia.
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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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50
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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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