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Gippert S, Wagner M, Brunet T, Berruti R, Brugger M, Schwaibold EMC, Haack TB, Hoffmann GF, Bettendorf M, Choukair D. Exome sequencing (ES) of a pediatric cohort with chronic endocrine diseases: a single-center study (within the framework of the TRANSLATE-NAMSE project). Endocrine 2024; 85:444-453. [PMID: 37940764 PMCID: PMC11246252 DOI: 10.1007/s12020-023-03581-7] [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: 07/24/2023] [Accepted: 10/18/2023] [Indexed: 11/10/2023]
Abstract
BACKGROUND Endocrine disorders are heterogeneous and include a significant number of rare monogenic diseases. METHODS We performed exome sequencing (ES) in 106 children recruited from a single center within the TRANSLATE‑NAMSE project. They were categorized into subgroups: proportionate short stature (PSS), disproportionate short stature (DSS), hypopituitarism (H), differences in sexual development (DSD), syndromic diseases (SD) and others. RESULTS The overall diagnostic yield was 34.9% (n = 37/106), including 5 patients with variants in candidate genes, which have contributed to collaborations to identify gene-disease associations. The diagnostic yield varied significantly between subgroups: PSS: 16.6% (1/6); DSS: 18.8% (3/16); H: 17.1% (6/35); DSD: 37.5% (3/8); SD: 66.6% (22/33); others: 25% (2/8). Confirmed diagnoses included 75% ultrarare diseases. Three patients harbored more than one disease-causing variant, resulting in dual diagnoses. CONCLUSIONS ES is an effective tool for genetic diagnosis in pediatric patients with complex endocrine diseases. An accurate phenotypic description, including comprehensive endocrine diagnostics, as well as the evaluation of variants in multidisciplinary case conferences involving geneticists, are necessary for personalized diagnostic care. Here, we illustrate the broad spectrum of genetic endocrinopathies that have led to the initiation of specific treatment, surveillance, and family counseling.
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Affiliation(s)
- Sebastian Gippert
- Division of Pediatric Endocrinology and Diabetes, Center for Pediatrics and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany and Center for Rare Diseases, University Hospital Heidelberg, Heidelberg, Germany
| | - Matias Wagner
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
- Institute for Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Theresa Brunet
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
- Department of Pediatric Neurology and Developmental Medicine, Hauner Children's Hospital, Ludwig Maximilian University of Munich, Munich, Germany
| | - Riccardo Berruti
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Melanie Brugger
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | | | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tübingen, Germany and Centre for Rare Diseases, University of Tuebingen, Tübingen, Germany
| | - Georg F Hoffmann
- Division of Pediatric Endocrinology and Diabetes, Center for Pediatrics and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany and Center for Rare Diseases, University Hospital Heidelberg, Heidelberg, Germany
| | - Markus Bettendorf
- Division of Pediatric Endocrinology and Diabetes, Center for Pediatrics and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany and Center for Rare Diseases, University Hospital Heidelberg, Heidelberg, Germany
| | - Daniela Choukair
- Division of Pediatric Endocrinology and Diabetes, Center for Pediatrics and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany and Center for Rare Diseases, University Hospital Heidelberg, Heidelberg, Germany.
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Lee B, Nasanovsky L, Shen L, Maglinte DT, Pan Y, Gai X, Schmidt RJ, Raca G, Biegel JA, Roytman M, An P, Saunders CJ, Farrow EG, Shams S, Ji J. Significance Associated with Phenotype Score Aids in Variant Prioritization for Exome Sequencing Analysis. J Mol Diagn 2024; 26:337-348. [PMID: 38360210 DOI: 10.1016/j.jmoldx.2024.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 12/04/2023] [Accepted: 01/29/2024] [Indexed: 02/17/2024] Open
Abstract
Several in silico annotation-based methods have been developed to prioritize variants in exome sequencing analysis. This study introduced a novel metric Significance Associated with Phenotypes (SAP) score, which generates a statistical score by comparing an individual's observed phenotypes against existing gene-phenotype associations. To evaluate the SAP score, a retrospective analysis was performed on 219 exomes. Among them, 82 family-based and 35 singleton exomes had at least one disease-causing variant that explained the patient's clinical features. SAP scores were calculated, and the rank of the disease-causing variant was compared with a known method, Exomiser. Using the SAP score, the known causative variant was ranked in the top 10 retained variants for 94% (77 of 82) of the family-based exomes and in first place for 73% of these cases. For singleton exomes, the SAP score analysis ranked the known pathogenic variants within the top 10 for 80% (28 of 35) of cases. The SAP score, which is independent of detected variants, demonstrates comparable performance with Exomiser, which considers both phenotype and variant-level evidence simultaneously. Among 102 cases with negative results or variants of uncertain significance, SAP score analysis revealed two cases with a potential new diagnosis based on rank. The SAP score, a phenotypic quantitative metric, can be used in conjunction with standard variant filtration and annotation to enhance variant prioritization in exome analysis.
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Affiliation(s)
- Brian Lee
- Bionano Genomics, San Diego, California
| | | | - Lishuang Shen
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California
| | - Dennis T Maglinte
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California
| | - Yachen Pan
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California
| | - Xiaowu Gai
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Ryan J Schmidt
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Gordana Raca
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Jaclyn A Biegel
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, California
| | | | - Paul An
- Bionano Genomics, San Diego, California
| | - Carol J Saunders
- Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, Missouri; University of Missouri-Kansas City School of Medicine, Kansas City, Missouri
| | - Emily G Farrow
- Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, Missouri; University of Missouri-Kansas City School of Medicine, Kansas City, Missouri
| | | | - Jianling Ji
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, California.
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Zhang X, Han Y, Yang L, Xu N, Zhu L, Qiu S, Li Y, Xu L, Yu X. Clinical phenotype and genetic characteristics of SZT2 related diseases: A case report and literature review. Seizure 2024; 114:111-120. [PMID: 38134649 DOI: 10.1016/j.seizure.2023.12.008] [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: 05/30/2023] [Revised: 12/11/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023] Open
Abstract
PURPOSE Seizure threshold 2 protein homolog gene (SZT2, MIM: 615463) related diseases are extremely rare autosomal recessive disorders with a wide spectrum of clinical phenotypes ranging from mild intellectual impairment to severe developmental epileptic encephalopathy (DEE). Most SZT2 related diseases are accompanied by craniofacial malformation and corpus callosum malformation. This study attempts to analyze and summarize the clinical phenotype and genetic characteristics of SZT2 related diseases, providing a basis for early diagnosis, treatment, and prognosis. METHOD We analyzed the clinical characteristics of a Chinese child with pathogenic variants of SZT2. We also performed whole-exome sequencing (WES) on the patient. In addition, we conducted a literature review of previously reported patients with pathogenic mutations in the SZT2 gene. RESULT The proband was a boy aged 1 year and 9 months with severe global developmental delay, transient drug-controlled focal epilepsy, cluster epilepsy, autism spectrum disorder, craniofacial deformity, hypotonia, focal EEG discharge, corpus callosum malformation, and persistent cavum septum pellucidum. WES revealed that the patient carried the SZT2 gene c.7584dupA and c.6302A>C complex heterozygous variants; the former being Likely Pathogenic (LP) and the latter Uncertain Significance (VUS) according to ACMG classification guidelines. According to our literature review, 43 cases of SZT2 related diseases have been reported so far; these include 15 cases with homozygous variations and 28 cases with complex heterozygous variations. A total of 57 types of variation were found, including 47 genetic variants, 2 de novo variants, and 8 unknown genetic modes. In addition, 2 high-frequency variants were found (c.5949_5951delTGT and c.6553C>T). The main clinical manifestations of the 40 patients were global developmental delay (GDD) of varying degrees (38/40, 95.00 %), seizures (36/40, 90.00 %), cranial deformity (27/40, 67.50 %), facial deformity (22/40, 55.00 %), hypotonia (22/40, 55.00 %), abnormal interseizure EEG discharge (26/40, 65.00 %), slow background activity (20/40, 50.00 %), corpus callosum deformity (18/40, 45.00 %). There was also one case of sudden unexpected death in epilepsy (SUDEP) and 3 cases of death from infection. In addition, three fetuses with the same variant had hydrocephalus and encephalocele. CONCLUSION The compound heterozygous mutation of c.7584dupA and c.6302A>C in the SZT2 gene is the genetic etiology of this patient, expanding the mutation spectrum of SZT2 related diseases. Early genetic testing is the best choice for clear diagnosis, treatment, and prognosis.
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Affiliation(s)
- Xin Zhang
- Postgrad Training Base Jinzhou Med Univ, Department of Pediatrics, Linyi People's Hospital, Linyi, Shandong 276003, PR China; Department of Pediatrics, Linyi People's Hospital, Linyi, Shandong 276003, PR China
| | - Yuzeng Han
- Department of Pediatrics, Linyi People's Hospital, Linyi, Shandong 276003, PR China
| | - Li Yang
- Postgrad Training Base Jinzhou Med Univ, Department of Pediatrics, Linyi People's Hospital, Linyi, Shandong 276003, PR China; Department of Pediatrics, Linyi People's Hospital, Linyi, Shandong 276003, PR China.
| | - Na Xu
- Department of Pediatrics, Linyi People's Hospital, Linyi, Shandong 276003, PR China
| | - Liping Zhu
- Department of Pediatrics, Linyi People's Hospital, Linyi, Shandong 276003, PR China
| | - Shiyan Qiu
- Department of Pediatrics, Linyi People's Hospital, Linyi, Shandong 276003, PR China
| | - Yufen Li
- Department of Pediatrics, Linyi People's Hospital, Linyi, Shandong 276003, PR China
| | - Liyun Xu
- Department of Pediatrics, Linyi People's Hospital, Linyi, Shandong 276003, PR China
| | - Xixi Yu
- Department of Pediatrics, Linyi People's Hospital, Linyi, Shandong 276003, PR China
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Shen L, Falk MJ, Gai X. MSeqDR Quick-Mitome (QM): Combining Phenotype-Guided Variant Interpretation and Machine Learning Classifiers to Aid Primary Mitochondrial Disease Genetic Diagnosis. Curr Protoc 2024; 4:e955. [PMID: 38284225 PMCID: PMC11046528 DOI: 10.1002/cpz1.955] [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] [Indexed: 01/30/2024]
Abstract
The international Mitochondrial Disease Sequence Data Resource Consortium (MSeqDR) Quick-Mitome (QM) is a web-based platform enabling automated variant interpretation of whole-exome sequencing (WES) datasets for the genetic diagnosis of primary mitochondrial diseases (PMD). Designed specifically to address the unique dual genome nature of PMD etiologies, QM includes features for both nuclear and mitochondrial DNA (mtDNA) genome analysis. QM requires VCF variant lists, HPO ID clinical phenotypes, and pedigree files for multiple-sample VCF inputs. QM maps phenotypes to HPO terms before analysis. QM analysis requires 2 to 20 min for 100,000 variants on an 8-vCPU AWS server using Exomiser's "PASS_ONLY" mode for nuclear variants. QM ranks variants based on allele frequency, phenotype-gene association, functional impact, and inheritance mode. Variants are further annotated with multiple data sources such as OMIM, ClinVar, dbNSFP, gnoMAD, MITOMAP, and MSeqDR. In addition to standard Exomiser results, QM generates an Analysis Report and QM Integrated Report with add-on mtDNA-specific analyses, including haplogroup prediction with Phy-Mer, heteroplasmy calculation, and mvTool annotations. We developed the Mitochondrial Disease Variant (MDV) classifier using XGBoost to predict variant pathogenicity for PMD. The MDV classifier was trained on >120 features and performance benchmarking showed that it correctly classified >98% of nuclear gene variants as being pathogenic or benign, and predicted PMD-causing variants with 94% precision. The MSeqDR QM server is an open-access resource for phenotype-driven dual-genome analyses for PMD diagnosis by the global mitochondrial disease community. It is publicly available for non-commercial, non-clinical research use at https://mseqdr.org/quickmitome.php. © 2024 Wiley Periodicals LLC. Basic Protocol 1: Standardizing clinical phenotypes into human phenotype ontology (HPO) terms as the phenotype input for Quick-Mitome (QM) Basic Protocol 2: Prepare the pedigree input for multiple-sample VCF Basic Protocol 3: Quick-Mitome (QM) analysis Basic Protocol 4: Reviewing and understanding the QM Integrated Report and Analysis Report.
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Affiliation(s)
- Lishuang Shen
- Center for Personalized Medicine, Department of Pathology & Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, California, USA
| | - Marni J. Falk
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, Department of Pediatrics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Xiaowu Gai
- Center for Personalized Medicine, Department of Pathology & Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, California, USA
- Keck School of Medicine, University of Southern California, California, USA
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Pachchek S, Landoulsi Z, Pavelka L, Schulte C, Buena-Atienza E, Gross C, Hauser AK, Reddy Bobbili D, Casadei N, May P, Krüger R. Accurate long-read sequencing identified GBA1 as major risk factor in the Luxembourgish Parkinson's study. NPJ Parkinsons Dis 2023; 9:156. [PMID: 37996455 PMCID: PMC10667262 DOI: 10.1038/s41531-023-00595-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 10/24/2023] [Indexed: 11/25/2023] Open
Abstract
Heterozygous variants in the glucocerebrosidase GBA1 gene are an increasingly recognized risk factor for Parkinson's disease (PD). Due to the GBAP1 pseudogene, which shares 96% sequence homology with the GBA1 coding region, accurate variant calling by array-based or short-read sequencing methods remains a major challenge in understanding the genetic landscape of GBA1-associated PD. We analyzed 660 patients with PD, 100 patients with Parkinsonism and 808 healthy controls from the Luxembourg Parkinson's study, sequenced using amplicon-based long-read DNA sequencing technology. We found that 12.1% (77/637) of PD patients carried GBA1 variants, with 10.5% (67/637) of them carrying known pathogenic variants (including severe, mild, risk variants). In comparison, 5% (34/675) of the healthy controls carried GBA1 variants, and among them, 4.3% (29/675) were identified as pathogenic variant carriers. We found four GBA1 variants in patients with atypical parkinsonism. Pathogenic GBA1 variants were 2.6-fold more frequently observed in PD patients compared to controls (OR = 2.6; CI = [1.6,4.1]). Three novel variants of unknown significance (VUS) were identified. Using a structure-based approach, we defined a potential risk prediction method for VUS. This study describes the full landscape of GBA1-related parkinsonism in Luxembourg, showing a high prevalence of GBA1 variants as the major genetic risk for PD. Although the long-read DNA sequencing technique used in our study may be limited in its effectiveness to detect potential structural variants, our approach provides an important advancement for highly accurate GBA1 variant calling, which is essential for providing access to emerging causative therapies for GBA1 carriers.
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Grants
- FNR/NCER13/BM/11264123 Fonds National de la Recherche Luxembourg (National Research Fund)
- funded by the Luxembourg National Research (FNR/NCER13/BM/11264123), the PEARL program (FNR/P13/6682797 to RK), MotaSYN (12719684 to RK), MAMaSyn (to RK), MiRisk‐PD (C17/BM/11676395 to RK, PM), the FNR/DFG Core INTER (ProtectMove, FNR11250962 to PM), and the PARK-QC DTU (PRIDE17/12244779/PARK-QC to RK, SP)
- Luxembourg National Research Fund (FNR/NCER13/BM/11264123), the PEARL program (FNR/P13/6682797), MotaSYN (12719684), MAMaSyn, MiRisk‐PD (C17/BM/11676395), and the PARK-QC DTU (PRIDE17/12244779/PARK-QC)
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Affiliation(s)
- Sinthuja Pachchek
- LCSB, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-Sur-Alzette, Luxembourg.
| | - Zied Landoulsi
- LCSB, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-Sur-Alzette, Luxembourg
| | - Lukas Pavelka
- Parkinson Research Clinic, Centre Hospitalier de Luxembourg (CHL), Luxembourg, Luxembourg
- Transversal Translational Medicine, Luxembourg Institute of Health (LIH), Strassen, Luxembourg
| | - Claudia Schulte
- Department of Neurodegeneration, Center of Neurology, Hertie Institute for Clinical Brain Research, German Center for Neurodegenerative Diseases, University of Tübingen, Tübingen, Germany
| | - Elena Buena-Atienza
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- NGS Competence Center Tübingen (NCCT), University of Tübingen, Tübingen, Germany
| | - Caspar Gross
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- NGS Competence Center Tübingen (NCCT), University of Tübingen, Tübingen, Germany
| | - Ann-Kathrin Hauser
- Department of Neurodegeneration, Center of Neurology, Hertie Institute for Clinical Brain Research, German Center for Neurodegenerative Diseases, University of Tübingen, Tübingen, Germany
| | - Dheeraj Reddy Bobbili
- LCSB, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-Sur-Alzette, Luxembourg
| | - Nicolas Casadei
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- NGS Competence Center Tübingen (NCCT), University of Tübingen, Tübingen, Germany
| | - Patrick May
- LCSB, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-Sur-Alzette, Luxembourg.
| | - Rejko Krüger
- LCSB, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-Sur-Alzette, Luxembourg.
- Parkinson Research Clinic, Centre Hospitalier de Luxembourg (CHL), Luxembourg, Luxembourg.
- Transversal Translational Medicine, Luxembourg Institute of Health (LIH), Strassen, Luxembourg.
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Li Q, Chen Z, Wang J, Xu K, Fan X, Gong C, Wu Z, Zhang TJ, Wu N. Molecular Diagnostic Yield of Exome Sequencing and Chromosomal Microarray in Short Stature: A Systematic Review and Meta-Analysis. JAMA Pediatr 2023; 177:1149-1157. [PMID: 37695591 PMCID: PMC10495925 DOI: 10.1001/jamapediatrics.2023.3566] [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: 04/14/2023] [Accepted: 06/21/2023] [Indexed: 09/12/2023]
Abstract
Importance Currently, the diagnostic yield of exome sequencing (ES) and chromosomal microarray analysis (CMA) for short stature cohorts is uncertain. Despite previous studies reporting the widespread use of ES and CMA, a definitive diagnostic yield has not been established. Objective To investigate the diagnostic yield of ES and CMA in short stature. Data Sources A systematic literature search was conducted using relevant keywords in 3 databases (PubMed, Embase, and Web of Science) in February 2023. Study Selection Eligible studies for meta-analysis were those that had at least 10 participants with short stature who were diagnosed using either ES or CMA and the number of diagnosed patients was reported. Of 5222 identified studies, 20 were eventually included in the study. Data Extraction and Synthesis Two independent investigators extracted relevant information from each study, which was then synthesized using proportional meta-analysis to obtain the overall diagnostic yield of ES and CMA. Main Outcomes and Measures The primary outcome measure was to determine the overall diagnostic yield of ES and CMA. A subgroup meta-analysis was also performed to assess if the diagnostic yield varied depending on whether ES was used as a first-tier or last-resort test. Additionally, a meta-regression was carried out to investigate how the diagnostic yield varied over time. Results Twenty studies were included, comprising 1350 patients with short stature who underwent ES and 1070 patients who completed CMA. The overall diagnostic yield of ES among the cohorts and CMA among the cohorts was found to be 27.1% (95% CI, 18.1%-37.2%) and 13.6% (95% CI, 9.2%-18.7%), respectively. No statistically significant difference was observed between the first-tier (27.8%; 95% CI, 15.7%-41.8%) and last-resort groups (25.6%; 95% CI, 13.6%-39.6%) (P = .83) or in the percentage of positively diagnosed patients over time. No statistically significant difference was observed between the first-tier (27.8%; 95% CI, 15.7%-41.8%) and last-resort groups (25.6%; 95% CI, 13.6%-39.6%) (P = .83) or in the percentage of positively diagnosed patients over time. Conclusion and Relevance This systematic review and meta-analysis provides high-level evidence supporting the diagnostic efficacy of ES and CMA in patients with short stature. The findings serve as a solid reference for clinicians when making informed decisions about recommending these genetic tests.
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Affiliation(s)
- Qing Li
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences; Beijing, 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity; Beijing, China
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences; Beijing, China
| | - Zefu Chen
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences; Beijing, 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity; Beijing, China
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences; Beijing, China
- Division of Spine Surgery, Department of Orthopedics, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jie Wang
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences; Beijing, 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity; Beijing, China
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences; Beijing, China
| | - Kexin Xu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences; Beijing, 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity; Beijing, China
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences; Beijing, China
| | - Xin Fan
- Department of Pediatric, The second affiliated hospital of Guangxi Medical University, Guangxi, China
| | - Chunxiu Gong
- Department of Endocrinology, Genetics and Metabolism, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Zhihong Wu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences; Beijing, 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity; Beijing, China
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences; Beijing, China
| | - Terry Jianguo Zhang
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences; Beijing, 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity; Beijing, China
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences; Beijing, China
| | - Nan Wu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences; Beijing, 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity; Beijing, China
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences; Beijing, China
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Ke X, Yang H, Pan H, Jiang Y, Li M, Zhang H, Hao N, Zhu H. The Application of Optical Genome Mapping (OGM) in Severe Short Stature Caused by Duplication of 15q14q21.3. Genes (Basel) 2023; 14:genes14051016. [PMID: 37239376 DOI: 10.3390/genes14051016] [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: 03/28/2023] [Revised: 04/26/2023] [Accepted: 04/27/2023] [Indexed: 05/28/2023] Open
Abstract
(1) Background: Optical genome mapping (OGM) is a novel approach to identifying genomic structural variations with high accuracy and resolution. We report a proband with severe short stature caused by 46, XY, der (16) ins (16;15) (q23; q21.3q14) that was detected by OGM combined with other tests and review the clinical features of patients with duplication within 15q14q21.3; (2) Methods: OGM, whole exon sequencing (WES), copy number variation sequencing (CNV-seq), and karyotyping were used; (3) Results: The proband was a 10.7-year-old boy with a complaint of severe short stature (-3.41SDS) and abnormal gait. He had growth hormone deficiency, lumbar lordosis, and epiphyseal dysplasia of both femurs. WES and CNV-seq showed a 17.27 Mb duplication of chromosome 15, and there was an insertion in chromosome 16 found by karyotyping. Furthermore, OGM revealed that duplication of 15q14q21.3 was inversely inserted into 16q23.1, resulting in two fusion genes. A total of fourteen patients carried the duplication of 15q14q21.3, with thirteen previously reported and one from our center, 42.9% of which were de novo. In addition, neurologic symptoms (71.4%,10/14) were the most common phenotypes; (4) Conclusions: OGM combined with other genetic methods can reveal the genetic etiology of patients with the clinical syndrome, presenting great potential for use in properly diagnosing in the genetic cause of the clinical syndrome.
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Affiliation(s)
- Xiaoan Ke
- State Key Laboratory of Complex Severe and Rare Diseases, Chinese Research Center for Behavior Medicine in Growth and Development, Department of Endocrinology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China
| | - Hongbo Yang
- State Key Laboratory of Complex Severe and Rare Diseases, Chinese Research Center for Behavior Medicine in Growth and Development, Department of Endocrinology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China
| | - Hui Pan
- State Key Laboratory of Complex Severe and Rare Diseases, Chinese Research Center for Behavior Medicine in Growth and Development, Department of Endocrinology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China
| | - Yulin Jiang
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetric and Gynecologic Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Mengmeng Li
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetric and Gynecologic Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Hanzhe Zhang
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetric and Gynecologic Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Na Hao
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetric and Gynecologic Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Huijuan Zhu
- State Key Laboratory of Complex Severe and Rare Diseases, Chinese Research Center for Behavior Medicine in Growth and Development, Department of Endocrinology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China
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8
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Aslan D, Akgun-Dogan O, Ay B, Çamurdan MO, Mancılar H, Alanay Y. DNAJC21-related thrombocytopenia in a young adult female. AMERICAN JOURNAL OF MEDICAL GENETICS. PART C, SEMINARS IN MEDICAL GENETICS 2023. [PMID: 37186482 DOI: 10.1002/ajmg.c.32043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 04/04/2023] [Accepted: 04/15/2023] [Indexed: 05/17/2023]
Abstract
Bone marrow failure type 3 (BMFS3) (MIM:617052) is a subtype of inherited bone marrow failure syndromes (IBMFS) caused by homozygous pathogenic variants in DNAJC21. It was first defined in 2016, and to date, 19 patients have been reported. Here we report the first adult patient; a 20-year-old female with a novel frameshift variant in DNAJC21 presents with thrombocytopenia, dysmorphic findings, and ovarian agenesis. Our patient expands the clinical spectrum to the milder end and suggests that DNAJC21-related disorders can have relatively mild presentations. Investigation of DNAJC21 variants in both childhood and adult patients with persistent, non-progressive thrombocytopenia will allow to broaden the gene-related phenotypic and genotypic spectrum and elucidate the pathophysiology. Therefore, we encourage revisiting undiagnosed patients to offer whole exome sequencing (WES) in adulthood.
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Affiliation(s)
- Deniz Aslan
- Faculty of Medicine, Department of Pediatrics, Division of Hematology, Gazi University, Ankara, Turkey
| | - Ozlem Akgun-Dogan
- School of Medicine, Department of Pediatrics, Division of Genetics, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
- Acibadem Mehmet Ali Aydinlar University Rare Diseases and Orphan Drugs Application and Research Center (ACURARE), Istanbul, Turkey
| | - Beril Ay
- School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Mahmut Orhun Çamurdan
- Faculty of Medicine, Department of Pediatrics, Division of Endocrinology, Gazi University, Ankara, Turkey
| | | | - Yasemin Alanay
- School of Medicine, Department of Pediatrics, Division of Genetics, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
- Acibadem Mehmet Ali Aydinlar University Rare Diseases and Orphan Drugs Application and Research Center (ACURARE), Istanbul, Turkey
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9
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Fan Y, Zhou Y, Liu H, Luo X, Xu T, Sun Y, Yang T, Chen L, Gu X, Yu Y. Improving variant prioritization in exome analysis by entropy-weighted ensemble of multiple tools. Clin Genet 2023; 103:190-199. [PMID: 36309956 DOI: 10.1111/cge.14257] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 10/09/2022] [Accepted: 10/22/2022] [Indexed: 01/07/2023]
Abstract
Variant prioritization is a crucial step in the analysis of exome and genome sequencing. Multiple phenotype-driven tools have been developed to automate the variant prioritization process, but the efficacy of these tools in clinical setting with fuzzy phenotypic information and whether ensemble of these tools could outperform single algorithm remains to be assessed. A large rare disease cohort with heterogeneous phenotypic information, including a primary cohort of 1614 patients and a replication cohort of 1904 patients referred to exome sequencing, were recruited to assess the efficacy of variant prioritization and their ensemble. Three freely available tools-Exomiser, Xrare, and DeepPVP-and their ensemble were evaluated. The performance of all three tools was influenced by the attributes of phenotypic input. When combining these three tools by weighted-sum entropy method (EWE3), the ensemble outperformed any single algorithm, achieving a rate of 78% diagnostic variants in top 3 (13% improvement over current best performer, compared to Exomiser: 63%, Xrare: 65%, and DeepPVP: 51%), 88% in top 10 and 96% in top 30. The results were replicated in another independent cohort. Our study supports using entropy-weighted ensemble of multiple tools to improve variant prioritization and accelerate molecular diagnosis in exome/genome sequencing.
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Affiliation(s)
- Yanjie Fan
- Shanghai Institute of Pediatric Research, Xinhua Hospital affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
| | | | - Huili Liu
- Shanghai Institute of Pediatric Research, Xinhua Hospital affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Xiaomei Luo
- Shanghai Institute of Pediatric Research, Xinhua Hospital affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Ting Xu
- Shanghai Institute of Pediatric Research, Xinhua Hospital affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yu Sun
- Shanghai Institute of Pediatric Research, Xinhua Hospital affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Tingting Yang
- Shanghai Institute of Pediatric Research, Xinhua Hospital affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Linlin Chen
- Shanghai Institute of Pediatric Research, Xinhua Hospital affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Xuefan Gu
- Shanghai Institute of Pediatric Research, Xinhua Hospital affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yongguo Yu
- Shanghai Institute of Pediatric Research, Xinhua Hospital affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
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10
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Morais CG, Quental R, Lourenço L, Guardiano M, Silva C, Leão M. Detection of a de novo heterozygous ANK2 variant in a child with autism spectrum disorder and epilepsy: a case report. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2023. [DOI: 10.1186/s43042-023-00389-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Abstract
Background
The pathogenesis of autism spectrum disorder (ASD) is not fully clarified. Next-generation sequencing technologies have greatly enhanced the identification of new genes associated with ASD. Variants in ANK2 gene are known to correlate with a broad spectrum of clinical cardiac phenotypes, but, more recently, it has also been pointed out as a candidate gene for the etiology of ASD.
Case presentation
We report the case of a female patient with ASD and epilepsy in whom clinical exome sequencing was performed for etiological enlightenment. A heterozygous variant of uncertain significance was identified in the ANK2 gene: c.3412C > T p.(Arg1138Ter). The child was submitted to a formal cardiac evaluation, ruling out cardiovascular abnormalities. The genetic variant was searched in her parents and was negative in both, suggesting a de novo variant, which favors its pathogenicity.
Conclusions
We recognize the challenge of assessing variant pathogenicity in candidate genes for ASD, and ANK2 gene is currently not associated with neurodevelopmental disorders in the Online Mendelian Inheritance in Man database. Nonetheless, our case can be added to other published reports of de novo ANK2 variants in children with ASD and neurological phenotypes (including seizures), some without cardiac impairment. Hopefully, this study provides a more detailed phenotypical description that is often lacking, and it may contribute to a better understanding of the association between ANK2 and ASD.
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11
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Lázaro-Guevara JM, Flores-Robles BJ, Garrido-Lopez KM, McKeown RJ, Flores-Morán AE, Labrador-Sánchez E, Pinillos-Aransay V, Trasahedo EA, López-Martín JA, Soberanis LSR, Melgar MY, Téllez-Arreola JL, Thébault SC. Identification of RP1 as the genetic cause of retinitis pigmentosa in a multi-generational pedigree using Extremely Low-Coverage Whole Genome Sequencing (XLC-WGS). Gene X 2023; 851:146956. [DOI: 10.1016/j.gene.2022.146956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 09/25/2022] [Accepted: 10/03/2022] [Indexed: 11/04/2022] Open
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12
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Feurstein S. Emerging bone marrow failure syndromes- new pieces to an unsolved puzzle. Front Oncol 2023; 13:1128533. [PMID: 37091189 PMCID: PMC10119586 DOI: 10.3389/fonc.2023.1128533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 03/22/2023] [Indexed: 04/25/2023] Open
Abstract
Inherited bone marrow failure (BMF) syndromes are genetically diverse - more than 100 genes have been associated with those syndromes and the list is rapidly expanding. Risk assessment and genetic counseling of patients with recently discovered BMF syndromes is inherently difficult as disease mechanisms, penetrance, genotype-phenotype associations, phenotypic heterogeneity, risk of hematologic malignancies and clonal markers of disease progression are unknown or unclear. This review aims to shed light on recently described BMF syndromes with sparse concise data and with an emphasis on those associated with germline variants in ADH5/ALDH2, DNAJC21, ERCC6L2 and MECOM. This will provide important data that may help to individualize and improve care for these patients.
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13
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Jacobsen JOB, Kelly C, Cipriani V, Research Consortium GE, Mungall CJ, Reese J, Danis D, Robinson PN, Smedley D. Phenotype-driven approaches to enhance variant prioritization and diagnosis of rare disease. Hum Mutat 2022; 43:1071-1081. [PMID: 35391505 PMCID: PMC9288531 DOI: 10.1002/humu.24380] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 01/25/2022] [Accepted: 04/03/2022] [Indexed: 11/20/2022]
Abstract
Rare disease diagnostics and disease gene discovery have been revolutionized by whole-exome and genome sequencing but identifying the causative variant(s) from the millions in each individual remains challenging. The use of deep phenotyping of patients and reference genotype-phenotype knowledge, alongside variant data such as allele frequency, segregation, and predicted pathogenicity, has proved an effective strategy to tackle this issue. Here we review the numerous tools that have been developed to automate this approach and demonstrate the power of such an approach on several thousand diagnosed cases from the 100,000 Genomes Project. Finally, we discuss the challenges that need to be overcome if we are going to improve detection rates and help the majority of patients that still remain without a molecular diagnosis after state-of-the-art genomic interpretation.
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Affiliation(s)
- Julius O. B. Jacobsen
- William Harvey Research Institute, Charterhouse Square, Barts and the London School of Medicine and Dentistry QueenQueen Mary University of LondonLondonUK
| | - Catherine Kelly
- William Harvey Research Institute, Charterhouse Square, Barts and the London School of Medicine and Dentistry QueenQueen Mary University of LondonLondonUK
| | - Valentina Cipriani
- William Harvey Research Institute, Charterhouse Square, Barts and the London School of Medicine and Dentistry QueenQueen Mary University of LondonLondonUK
| | | | - Christopher J. Mungall
- Environmental Genomics and Systems Biology, Lawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
| | - Justin Reese
- Environmental Genomics and Systems Biology, Lawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
| | - Daniel Danis
- The Jackson Laboratory for Genomic MedicineFarmingtonConnecticutUSA
| | | | - Damian Smedley
- William Harvey Research Institute, Charterhouse Square, Barts and the London School of Medicine and Dentistry QueenQueen Mary University of LondonLondonUK
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14
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Cai T, Huang J, Ma X, Hu S, Zhu L, Zhu J, Feng Z. Case Report: Identification of Two Variants of ALG13 in Families With or Without Seizure and Binocular Strabismus: Phenotypic Spectrum Analysis. Front Genet 2022; 13:892940. [PMID: 35899201 PMCID: PMC9310169 DOI: 10.3389/fgene.2022.892940] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 06/07/2022] [Indexed: 11/28/2022] Open
Abstract
Background: Genetic causes in most affected children with intellectual disability and/or development delay remain unknown. Methods: To identify potential variants responsible for these disorders, we recruited 161 affected families and performed whole-exome sequencing and associated bioinformatics analysis. Results: In the present study, we report the identification of variants in the ALG13 gene in two of the families. In family 1, a known pathogenic missense variant (c.23T > C; p.V8A) of ALG13 was identified in a boy and his mother. In family 2, a novel missense variant (c.862C > G; p.L288V) of the same gene was identified in the affected boy and his phenotypically normal mother. Genotype-phenotype correlation analysis by comparing reported 28 different variants (HGMD) showed that three major phenotypes, including various seizures/epilepsy, intellectual disability, and development delay (such as growth, speech, motor, etc.), are present in most affected individuals. However, other phenotypes, such as strabismus and absence of seizure in our second patient, are not reported if any, which may represent a unique case of X-linked recessive nonsyndromic disorder caused by a mutation in ALG13. Conclusion: We identified two missense variants in ALG13 in a cohort of 161 families with affected individuals diagnosed as intellectual disability and/or development delay. A novel c.862C > G mutation may represent a case of X-linked recessive.
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Affiliation(s)
- Tao Cai
- Senior Department of Pediatrics, the Seventh Medical Center of PLA General Hospital, Beijing, China,Experimental Medicine Section, National Institutes of Health/National Institute of Dental and Craniofacial Research, Bethesda, MD, United States,*Correspondence: Tao Cai, ; Zhichun Feng,
| | - Jieting Huang
- Senior Department of Pediatrics, the Seventh Medical Center of PLA General Hospital, Beijing, China,Beijing Key Laboratory of Pediatric Organ Failure, Beijing, China
| | - Xiuwei Ma
- Senior Department of Pediatrics, the Seventh Medical Center of PLA General Hospital, Beijing, China
| | - Siqi Hu
- Senior Department of Pediatrics, the Seventh Medical Center of PLA General Hospital, Beijing, China,The National Engineering Laboratory for Birth Defects Prevention and Control of Key Technology, Beijing, China
| | - Lina Zhu
- Senior Department of Pediatrics, the Seventh Medical Center of PLA General Hospital, Beijing, China
| | - Jinwen Zhu
- Angen Gene Medicine Technology, Beijing, China
| | - Zhichun Feng
- Senior Department of Pediatrics, the Seventh Medical Center of PLA General Hospital, Beijing, China,Beijing Key Laboratory of Pediatric Organ Failure, Beijing, China,The National Engineering Laboratory for Birth Defects Prevention and Control of Key Technology, Beijing, China,*Correspondence: Tao Cai, ; Zhichun Feng,
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15
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Cohen ASA, Farrow EG, Abdelmoity AT, Alaimo JT, Amudhavalli SM, Anderson JT, Bansal L, Bartik L, Baybayan P, Belden B, Berrios CD, Biswell RL, Buczkowicz P, Buske O, Chakraborty S, Cheung WA, Coffman KA, Cooper AM, Cross LA, Curran T, Dang TTT, Elfrink MM, Engleman KL, Fecske ED, Fieser C, Fitzgerald K, Fleming EA, Gadea RN, Gannon JL, Gelineau-Morel RN, Gibson M, Goldstein J, Grundberg E, Halpin K, Harvey BS, Heese BA, Hein W, Herd SM, Hughes SS, Ilyas M, Jacobson J, Jenkins JL, Jiang S, Johnston JJ, Keeler K, Korlach J, Kussmann J, Lambert C, Lawson C, Le Pichon JB, Leeder JS, Little VC, Louiselle DA, Lypka M, McDonald BD, Miller N, Modrcin A, Nair A, Neal SH, Oermann CM, Pacicca DM, Pawar K, Posey NL, Price N, Puckett LMB, Quezada JF, Raje N, Rowell WJ, Rush ET, Sampath V, Saunders CJ, Schwager C, Schwend RM, Shaffer E, Smail C, Soden S, Strenk ME, Sullivan BR, Sweeney BR, Tam-Williams JB, Walter AM, Welsh H, Wenger AM, Willig LK, Yan Y, Younger ST, Zhou D, Zion TN, Thiffault I, Pastinen T. Genomic answers for children: Dynamic analyses of >1000 pediatric rare disease genomes. Genet Med 2022; 24:1336-1348. [PMID: 35305867 DOI: 10.1016/j.gim.2022.02.007] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 02/05/2022] [Accepted: 02/07/2022] [Indexed: 12/17/2022] Open
Abstract
PURPOSE This study aimed to provide comprehensive diagnostic and candidate analyses in a pediatric rare disease cohort through the Genomic Answers for Kids program. METHODS Extensive analyses of 960 families with suspected genetic disorders included short-read exome sequencing and short-read genome sequencing (srGS); PacBio HiFi long-read genome sequencing (HiFi-GS); variant calling for single nucleotide variants (SNV), structural variant (SV), and repeat variants; and machine-learning variant prioritization. Structured phenotypes, prioritized variants, and pedigrees were stored in PhenoTips database, with data sharing through controlled access the database of Genotypes and Phenotypes. RESULTS Diagnostic rates ranged from 11% in patients with prior negative genetic testing to 34.5% in naive patients. Incorporating SVs from genome sequencing added up to 13% of new diagnoses in previously unsolved cases. HiFi-GS yielded increased discovery rate with >4-fold more rare coding SVs compared with srGS. Variants and genes of unknown significance remain the most common finding (58% of nondiagnostic cases). CONCLUSION Computational prioritization is efficient for diagnostic SNVs. Thorough identification of non-SNVs remains challenging and is partly mitigated using HiFi-GS sequencing. Importantly, community research is supported by sharing real-time data to accelerate gene validation and by providing HiFi variant (SNV/SV) resources from >1000 human alleles to facilitate implementation of new sequencing platforms for rare disease diagnoses.
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Affiliation(s)
- Ana S A Cohen
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO; UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO
| | - Emily G Farrow
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO; UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | | | - Joseph T Alaimo
- Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO; UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO
| | - Shivarajan M Amudhavalli
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Division of Genetics, Children's Mercy Kansas City, Kansas City, MO
| | - John T Anderson
- Department of Orthopaedic Surgery, Children's Mercy Kansas City, Kansas City, MO
| | - Lalit Bansal
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Lauren Bartik
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Division of Genetics, Children's Mercy Kansas City, Kansas City, MO
| | | | - Bradley Belden
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO
| | | | - Rebecca L Biswell
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO
| | | | | | | | - Warren A Cheung
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO
| | - Keith A Coffman
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Ashley M Cooper
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Laura A Cross
- Division of Genetics, Children's Mercy Kansas City, Kansas City, MO
| | - Tom Curran
- Children's Mercy Research Institute, Kansas City, MO
| | - Thuy Tien T Dang
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Mary M Elfrink
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO
| | | | - Erin D Fecske
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Cynthia Fieser
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Keely Fitzgerald
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Emily A Fleming
- Division of Genetics, Children's Mercy Kansas City, Kansas City, MO
| | - Randi N Gadea
- Division of Genetics, Children's Mercy Kansas City, Kansas City, MO
| | | | - Rose N Gelineau-Morel
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Margaret Gibson
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO
| | - Jeffrey Goldstein
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Elin Grundberg
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO
| | - Kelsee Halpin
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Brian S Harvey
- Department of Orthopaedic Surgery, Children's Mercy Kansas City, Kansas City, MO
| | - Bryce A Heese
- Division of Genetics, Children's Mercy Kansas City, Kansas City, MO
| | - Wendy Hein
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Suzanne M Herd
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO
| | - Susan S Hughes
- Division of Genetics, Children's Mercy Kansas City, Kansas City, MO
| | - Mohammed Ilyas
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Jill Jacobson
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Janda L Jenkins
- Division of Genetics, Children's Mercy Kansas City, Kansas City, MO
| | | | | | - Kathryn Keeler
- Department of Orthopaedic Surgery, Children's Mercy Kansas City, Kansas City, MO
| | - Jonas Korlach
- Pacific Biosciences of California, Inc, Menlo Park, CA
| | | | | | - Caitlin Lawson
- Division of Genetics, Children's Mercy Kansas City, Kansas City, MO
| | | | | | - Vicki C Little
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | | | | | | | - Neil Miller
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO; UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Division of Allergy Immunology Pulmonary and Sleep Medicine, Children's Mercy Kansas City, Kansas City, MO
| | - Ann Modrcin
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Annapoorna Nair
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO
| | - Shelby H Neal
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO
| | | | - Donna M Pacicca
- Department of Orthopaedic Surgery, Children's Mercy Kansas City, Kansas City, MO
| | - Kailash Pawar
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Nyshele L Posey
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO
| | - Nigel Price
- Department of Orthopaedic Surgery, Children's Mercy Kansas City, Kansas City, MO
| | - Laura M B Puckett
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO
| | - Julio F Quezada
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Nikita Raje
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Division of Neonatology, Children's Mercy Kansas City, Kansas City, MO
| | | | - Eric T Rush
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Division of Genetics, Children's Mercy Kansas City, Kansas City, MO; Department of Internal Medicine, University of Kansas School of Medicine, Kansas City, MO
| | - Venkatesh Sampath
- Division of Neonatology, Children's Mercy Hospital Kansas City, Kansas City, MO
| | - Carol J Saunders
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO; UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO
| | - Caitlin Schwager
- Division of Genetics, Children's Mercy Kansas City, Kansas City, MO
| | - Richard M Schwend
- Department of Orthopaedic Surgery, Children's Mercy Kansas City, Kansas City, MO
| | - Elizabeth Shaffer
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Craig Smail
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO
| | - Sarah Soden
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Meghan E Strenk
- Division of Genetics, Children's Mercy Kansas City, Kansas City, MO
| | | | - Brooke R Sweeney
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | | | - Adam M Walter
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO
| | - Holly Welsh
- Division of Genetics, Children's Mercy Kansas City, Kansas City, MO
| | | | - Laurel K Willig
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Yun Yan
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Scott T Younger
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO
| | - Dihong Zhou
- Division of Genetics, Children's Mercy Kansas City, Kansas City, MO
| | - Tricia N Zion
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO; UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO; Division of Genetics, Children's Mercy Kansas City, Kansas City, MO
| | - Isabelle Thiffault
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO; UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO.
| | - Tomi Pastinen
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO; UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Children's Mercy Research Institute, Kansas City, MO.
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16
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Jacobsen JOB, Kelly C, Cipriani V, Robinson PN, Smedley D. Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases. Brief Bioinform 2022; 23:6589867. [PMID: 35595299 PMCID: PMC9487604 DOI: 10.1093/bib/bbac188] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/18/2022] [Accepted: 04/25/2022] [Indexed: 11/14/2022] Open
Abstract
Yuan et al. recently described an independent evaluation of several phenotype-driven gene prioritization methods for Mendelian disease on two separate, clinical datasets. Although they attempted to use default settings for each tool, we describe three key differences from those we currently recommend for our Exomiser and PhenIX tools. These influence how variant frequency, quality and predicted pathogenicity are used for filtering and prioritization. We propose that these differences account for much of the discrepancy in performance between that reported by them (15–26% diagnoses ranked top by Exomiser) and previously published reports by us and others (72–77%). On a set of 161 singleton samples, we show using these settings increases performance from 34% to 72% and suggest a reassessment of Exomiser and PhenIX on their datasets using these would show a similar uplift.
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Affiliation(s)
- Julius O B Jacobsen
- William Harvey Research Institute, Charterhouse Square, Barts and the London School of Medicine and Dentistry Queen, Queen Mary University of London, EC1M 6BQ London, UK
| | - Catherine Kelly
- William Harvey Research Institute, Charterhouse Square, Barts and the London School of Medicine and Dentistry Queen, Queen Mary University of London, EC1M 6BQ London, UK
| | - Valentina Cipriani
- William Harvey Research Institute, Charterhouse Square, Barts and the London School of Medicine and Dentistry Queen, Queen Mary University of London, EC1M 6BQ London, UK
| | - Peter N Robinson
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032, USA
| | - Damian Smedley
- William Harvey Research Institute, Charterhouse Square, Barts and the London School of Medicine and Dentistry Queen, Queen Mary University of London, EC1M 6BQ London, UK
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17
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Austin-Tse CA, Jobanputra V, Perry DL, Bick D, Taft RJ, Venner E, Gibbs RA, Young T, Barnett S, Belmont JW, Boczek N, Chowdhury S, Ellsworth KA, Guha S, Kulkarni S, Marcou C, Meng L, Murdock DR, Rehman AU, Spiteri E, Thomas-Wilson A, Kearney HM, Rehm HL. Best practices for the interpretation and reporting of clinical whole genome sequencing. NPJ Genom Med 2022; 7:27. [PMID: 35395838 PMCID: PMC8993917 DOI: 10.1038/s41525-022-00295-z] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 02/17/2022] [Indexed: 01/19/2023] Open
Abstract
Whole genome sequencing (WGS) shows promise as a first-tier diagnostic test for patients with rare genetic disorders. However, standards addressing the definition and deployment practice of a best-in-class test are lacking. To address these gaps, the Medical Genome Initiative, a consortium of leading health care and research organizations in the US and Canada, was formed to expand access to high quality clinical WGS by convening experts and publishing best practices. Here, we present best practice recommendations for the interpretation and reporting of clinical diagnostic WGS, including discussion of challenges and emerging approaches that will be critical to harness the full potential of this comprehensive test.
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Affiliation(s)
- Christina A Austin-Tse
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Vaidehi Jobanputra
- Molecular Diagnostics Laboratory, New York Genome Center, New York, NY, USA
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | | | - David Bick
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | | | - Eric Venner
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Ted Young
- Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | - Sarah Barnett
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | | | - Nicole Boczek
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Shimul Chowdhury
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | | | - Saurav Guha
- Molecular Diagnostics Laboratory, New York Genome Center, New York, NY, USA
| | - Shashikant Kulkarni
- Baylor Genetics and Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Cherisse Marcou
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Linyan Meng
- Baylor Genetics and Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - David R Murdock
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Atteeq U Rehman
- Molecular Diagnostics Laboratory, New York Genome Center, New York, NY, USA
| | - Elizabeth Spiteri
- Department of Pathology, Stanford Medicine, Stanford University, Stanford, CA, USA
| | | | - Hutton M Kearney
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Heidi L Rehm
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
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18
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Chirita-Emandi A, Petrescu CAM, Zimbru CG, Stoica F, Marian C, Ciubotaru A, Bataneant M, Puiu M. Case Report: Novel Biallelic Variants in DNAJC21 Causing an Inherited Bone Marrow Failure Spectrum Phenotype: An Odyssey to Diagnosis. Front Genet 2022; 13:870233. [PMID: 35464845 PMCID: PMC9023866 DOI: 10.3389/fgene.2022.870233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 02/28/2022] [Indexed: 11/13/2022] Open
Abstract
Bone marrow failure represents an umbrella diagnosis for several life-threatening disorders. In many people, the etiology remains unknown for a long time, leading to an odyssey to diagnosis, with numerous tests performed and sometimes inappropriate treatment. Biallelic pathogenic variants in the DNAJC21 gene were recently discovered to cause bone marrow failure syndrome type 3, having phenotypic overlap with Fanconi anemia, dyskeratosis congenita, Shwachman–Diamond syndrome, and Diamond–Blackfan anemia. Herein, we report an 8-year-old boy, with normal intellect, presenting bone marrow failure; growth retardation; failure to thrive; recurrent infections (including sepsis); cryptorchidia; skeletal, skin, teeth, and hair abnormalities; joint hypermobility; eczema; palpebral ptosis; high myopia; rod–cone retinal dystrophy; and short telomeres. He underwent several tests and evaluations, including genetic investigations (panel and exome sequencing), before the DNAJC21 gene was known to cause disease. Whole-genome sequencing performed at the age of 7 years, identified two novel, pathogenic, and compound heterozygous variants in the DNAJC21 gene: NM_001012339.3:c.148C>T (stopgain-maternal origin), p.Gln50∗ and c.643_644delinsTTT (frameshift paternal origin), and p.Lys215Phefs∗71. He received aggressive treatments for his multisystem disease: blood cell transfusions, high-dose corticosteroids, immunoglobulins, multiple antibiotics, vitamins, growth hormone, and others. However, allogeneic hematopoietic stem cell transplantation was avoided. The clinical evolution of bone marrow failure and recurrent infections stabilized with age, yet the myopia progressed. Exocrine pancreatic insufficiency was not detected. This report widens the molecular and clinical understanding of bone marrow failure syndrome type 3. Genome sequencing directed a precise diagnosis that improved patient management and enabled family genetic counseling.
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Affiliation(s)
- Adela Chirita-Emandi
- Department of Genetics, Center of Genomic Medicine, “Victor Babes” University of Medicine and Pharmacy, Timisoara, Romania
- Regional Center of Medical Genetics Timis, Clinical Emergency Hospital for Children “Louis Turcanu”, Timisoara, Romania
- *Correspondence: Adela Chirita-Emandi,
| | - Carmen-Angela-Maria Petrescu
- Department of Pediatrics, “Victor Babes” University of Medicine and Pharmacy, Timisoara, Romania
- Department of Oncology and Hematology, Clinical Emergency Hospital for Children “Louis Turcanu”, Timisoara, Romania
| | - Cristian G. Zimbru
- Department of Genetics, Center of Genomic Medicine, “Victor Babes” University of Medicine and Pharmacy, Timisoara, Romania
- Department of Automation and Applied Informatics, Politehnica University of Timisoara, Timisoara, Romania
| | - Florina Stoica
- Department of Ophthalmology, Municipal Clinical Emergency Hospital of Timisoara, Timisoara, Romania
| | - Catalin Marian
- Department of Biochemistry, “Victor Babes” University of Medicine and Pharmacy, Timisoara, Romania
- Center for Complex Networks Science, “Victor Babes” University of Medicine and Pharmacy, Timisoara, Romania
| | | | - Mihaela Bataneant
- Department of Pediatrics, “Victor Babes” University of Medicine and Pharmacy, Timisoara, Romania
- Department of Oncology and Hematology, Clinical Emergency Hospital for Children “Louis Turcanu”, Timisoara, Romania
| | - Maria Puiu
- Department of Genetics, Center of Genomic Medicine, “Victor Babes” University of Medicine and Pharmacy, Timisoara, Romania
- Regional Center of Medical Genetics Timis, Clinical Emergency Hospital for Children “Louis Turcanu”, Timisoara, Romania
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19
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Methods to Improve Molecular Diagnosis in Genomic Cold Cases in Pediatric Neurology. Genes (Basel) 2022; 13:genes13020333. [PMID: 35205378 PMCID: PMC8871714 DOI: 10.3390/genes13020333] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 02/06/2022] [Accepted: 02/07/2022] [Indexed: 02/04/2023] Open
Abstract
During the last decade, genetic testing has emerged as an important etiological diagnostic tool for Mendelian diseases, including pediatric neurological conditions. A genetic diagnosis has a considerable impact on disease management and treatment; however, many cases remain undiagnosed after applying standard diagnostic sequencing techniques. This review discusses various methods to improve the molecular diagnostic rates in these genomic cold cases. We discuss extended analysis methods to consider, non-Mendelian inheritance models, mosaicism, dual/multiple diagnoses, periodic re-analysis, artificial intelligence tools, and deep phenotyping, in addition to integrating various omics methods to improve variant prioritization. Last, novel genomic technologies, including long-read sequencing, artificial long-read sequencing, and optical genome mapping are discussed. In conclusion, a more comprehensive molecular analysis and a timely re-analysis of unsolved cases are imperative to improve diagnostic rates. In addition, our current understanding of the human genome is still limited due to restrictions in technologies. Novel technologies are now available that improve upon some of these limitations and can capture all human genomic variation more accurately. Last, we recommend a more routine implementation of high molecular weight DNA extraction methods that is coherent with the ability to use and/or optimally benefit from these novel genomic methods.
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20
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Abstract
Hearing loss (HL) is an etiologically heterogeneous disorder that affects around 5% of the world's population. There has been an exponential increase in the identification of genes and variants responsible for hereditary HL over recent years. Iran, a country located in the Middle East, has a high prevalence of consanguineous marriages, so heterogeneous diseases such as HL are more common. Comprehensive studies using different strategies from linkage analysis to next-generation sequencing, especially exome-sequencing, have achieved significant success in identifying possible pathogens in deaf Iranian families. About 12% of non-syndromic autosomal recessive HL genes investigated to date, were first identified in families from Iran. Variations of 56 genes have been observed in families with NSHL in Iran. Variants in GJB2, SLC26A4, MYO15A, MYO7A, CDH23, and TMC1 account for 16.5%, 16.25%, 13.5%, 9.35%, 6.9% and 4.92%, cases of NSHL, respectively. In summary, there are also different diagnostic rates between studies conducted in Iran. In the comprehensive investigations conducted by the Genetic Research Center of the University of Social Welfare and Rehabilitation Sciences over the past 20 years, the overall diagnosis rate is about 80% while there are other studies with lower diagnostic rates which could reflect differences in project designs, sampling, and accuracy and validity of the methods used. Furthermore, there are several syndromic HHLs in Iran including, Waardenburg syndrome, BOR syndrome, Brown-Vialetto-Van Laere syndrome, Wolfram syndrome, among which Pendred and Usher syndromes are well-studied. These results are of importance for further investigation and elucidation of the molecular basis of HHL in Iran.
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21
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Zampaglione E, Maher M, Place EM, Wagner NE, DiTroia S, Chao KR, England E, Cmg B, Catomeris A, Nassiri S, Himes S, Pagliarulo J, Ferguson C, Galdikaité-Braziené E, Cole B, Pierce EA, Bujakowska KM. The importance of automation in genetic diagnosis: Lessons from analyzing an inherited retinal degeneration cohort with the Mendelian Analysis Toolkit (MATK). Genet Med 2021; 24:332-343. [PMID: 34906470 DOI: 10.1016/j.gim.2021.09.015] [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: 05/07/2021] [Revised: 08/02/2021] [Accepted: 09/21/2021] [Indexed: 10/19/2022] Open
Abstract
PURPOSE In Mendelian disease diagnosis, variant analysis is a repetitive, error-prone, and time consuming process. To address this, we have developed the Mendelian Analysis Toolkit (MATK), a configurable, automated variant ranking program. METHODS MATK aggregates variant information from multiple annotation sources and uses expert-designed rules with parameterized weights to produce a ranked list of potentially causal solutions. MATK performance was measured by a comparison between MATK-aided and human-domain expert analyses of 1060 families with inherited retinal degeneration (IRD), analyzed using an IRD-specific gene panel (589 individuals) and exome sequencing (471 families). RESULTS When comparing MATK-assisted analysis with expert curation in both the IRD-specific gene panel and exome sequencing (1060 subjects), 97.3% of potential solutions found by experts were also identified by the MATK-assisted analysis (541 solutions identified with MATK of 556 solutions found by conventional analysis). Furthermore, MATK-assisted analysis identified 114 additional potential solutions from the 504 cases unsolved by conventional analysis. CONCLUSION MATK expedites the process of identification of likely solving variants in Mendelian traits, and reduces variability stemming from human error and researcher bias. MATK facilitates data reanalysis to keep up with the constantly improving annotation sources and next-generation sequencing processing pipelines. The software is open source and available at https://gitlab.com/matthew_maher/mendelanalysis.
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Affiliation(s)
- Erin Zampaglione
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary and Harvard Medical School, Boston, MA
| | - Matthew Maher
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary and Harvard Medical School, Boston, MA
| | - Emily M Place
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary and Harvard Medical School, Boston, MA
| | - Naomi E Wagner
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary and Harvard Medical School, Boston, MA; Invitae Corporation, San Francisco, CA
| | - Stephanie DiTroia
- Center for Mendelian Genomics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA
| | - Katherine R Chao
- Center for Mendelian Genomics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA
| | - Eleina England
- Center for Mendelian Genomics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA
| | - Broad Cmg
- Center for Mendelian Genomics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA
| | | | - Sherwin Nassiri
- Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL
| | - Seraphim Himes
- Touro University College of Osteopathic Medicine in California, Vallejo, CA
| | - Joey Pagliarulo
- Department of Genetic Counseling, School of Health and Rehab Sciences, MGH Institute of Health Professions, Boston, MA
| | - Charles Ferguson
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary and Harvard Medical School, Boston, MA
| | - Eglé Galdikaité-Braziené
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary and Harvard Medical School, Boston, MA
| | - Brian Cole
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary and Harvard Medical School, Boston, MA
| | - Eric A Pierce
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary and Harvard Medical School, Boston, MA
| | - Kinga M Bujakowska
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary and Harvard Medical School, Boston, MA.
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22
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Melas M, Mathew MT, Mori M, Jayaraman V, Wilson SA, Martin C, Jacobson-Kelly AE, Kelly BJ, Magrini V, Mardis ER, Cottrell CE, Lee K. Somatic Variation as an Incidental Finding in the Pediatric Next Generation Sequencing Era. Cold Spring Harb Mol Case Stud 2021; 7:mcs.a006135. [PMID: 34716204 PMCID: PMC8751410 DOI: 10.1101/mcs.a006135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 10/27/2021] [Indexed: 11/28/2022] Open
Abstract
The methodologic approach used in next-generation sequencing (NGS) affords a high depth of coverage in genomic analysis. Inherent in the nature of genomic testing, there exists potential for identifying genomic findings that are incidental or secondary to the indication for clinical testing, with the frequency dependent on the breadth of analysis and the tissue sample under study. The interpretation and management of clinically meaningful incidental genomic findings is a pressing issue particularly in the pediatric population. Our study describes a 16-mo-old male who presented with profound global delays, brain abnormality, progressive microcephaly, and growth deficiency, as well as metopic craniosynostosis. Clinical exome sequencing (ES) trio analysis revealed the presence of two variants in the proband. The first was a de novo variant in the PPP2R1A gene (c.773G > A, p.Arg258His), which is associated with autosomal dominant (AD) intellectual disability, accounting for the proband's clinical phenotype. The second was a recurrent hotspot variant in the CBL gene (c.1111T > C, p.Tyr371His), which was present at a variant allele fraction of 11%, consistent with somatic variation in the peripheral blood sample. Germline pathogenic variants in CBL are associated with AD Noonan syndrome–like disorder with or without juvenile myelomonocytic leukemia. Molecular analyses using a different tissue source, buccal epithelial cells, suggest that the CBL alteration may represent a clonal population of cells restricted to leukocytes. This report highlights the laboratory methodologic and interpretative processes and clinical considerations in the setting of acquired variation detected during clinical ES in a pediatric patient.
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Affiliation(s)
- Marilena Melas
- The Steve and Cindy Rasmussen Inst for Genomic Medicine, Nationwide Children's Hospital
| | - Mariam T Mathew
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital; Dept of Pathology, The Ohio State Univ; Dept of Pediatrics, The Ohio State University
| | - Mari Mori
- Dept of Pediatrics, The Ohio State University; Genetic and Genomic Medicine, Nationwide Children's Hospital
| | - Vijayakumar Jayaraman
- The Steve and Cindy Rasmussen Inst for Genomic Medicine, Nationwide Children's Hospital
| | - Sarah A Wilson
- The Steve and Cindy Rasmussen Inst for Genomic Medicine, Nationwide Children's Hospital
| | | | - Amanda E Jacobson-Kelly
- Dept of Pediatrics, The Ohio State University; Division of Hematology/Oncology/BMT, Nationwide Children's Hospital
| | - Ben J Kelly
- The Steve and Cindy Rasmussen Inst for Genomic Medicine, Nationwide Children's Hospital
| | - Vincent Magrini
- The Steve and Cindy Rasmussen Inst for Genomic Medicine, Nationwide Children's Hospital; Dept of Pediatrics, The Ohio State University
| | - Elaine R Mardis
- The Steve and Cindy Rasmussen Inst for Genomic Medicine, Nationwide Children's Hospital; Dept of Pediatrics, The Ohio State University
| | - Catherine E Cottrell
- The Steve and Cindy Rasmussen Inst for Genomic Medicine, Nationwide Children's Hospital; Dept of Pathology, The Ohio State University; Dept of Pediatrics, The Ohio State University
| | - Kristy Lee
- The Steve and Cindy Rasmussen Inst for Genomic Medicine, Nationwide Children's Hospital; Dept of Pathology, The Ohio State University; Dept of Pediatrics, The Ohio State University
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23
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Shickh S, Mighton C, Uleryk E, Pechlivanoglou P, Bombard Y. The clinical utility of exome and genome sequencing across clinical indications: a systematic review. Hum Genet 2021; 140:1403-1416. [PMID: 34368901 DOI: 10.1007/s00439-021-02331-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 07/31/2021] [Indexed: 12/15/2022]
Abstract
Exome sequencing and genome sequencing have the potential to improve clinical utility for patients undergoing genetic investigations. However, evidence of clinical utility is limited to pediatric populations; we aimed to fill this gap by conducting a systematic review of the literature on the clinical utility of exome/genome sequencing across disease indications in pediatric and adult populations. MEDLINE, EMBASE and Cochrane Library were searched between 2016 and 2020. Quantitative studies evaluating diagnostic yield were included; other measures of clinical utility such as changes to clinical management were documented if reported. Two reviewers screened, extracted data, and appraised risk of bias. Fifty studies met our inclusion criteria. All studies reported diagnostic yield, which ranged from 3 to 70%, with higher range of yields reported for neurological indications and acute illness ranging from 22 to 68% and 37-70%, respectively. Diagnoses triggered a range of clinical management changes including surveillance, reproductive-risk counseling, and identifying at-risk relatives in 4-100% of patients, with higher frequencies reported for acute illness ranging from 67 to 95%. The frequency of variants of uncertain significance ranged from 5 to 85% across studies with a potential trend of decreasing frequency over time and higher rates identified in patients of non-European ancestry. This review provides evidence for a higher range of diagnostic yield of exome/genome sequencing compared to standard genetic tests, particularly in neurological and acute indications. However, we identified significant heterogeneity in study procedures and outcomes, precluding a meaningful meta-analysis and certainty in the evidence available for decision-making. Future research that incorporates a comprehensive and consistent approach in capturing clinical utility of exome/genome sequencing across broader ancestral groups is necessary to improve diagnostic accuracy and yield and allow for analysis of trends over time.Prospero registration CRD42019094101.
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Affiliation(s)
- Salma Shickh
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada.,Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, Unity Health Toronto, Toronto, ON, Canada
| | - Chloe Mighton
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada.,Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, Unity Health Toronto, Toronto, ON, Canada
| | | | - Petros Pechlivanoglou
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada.,The Hospital for Sick Children, Toronto, ON, Canada
| | - Yvonne Bombard
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada. .,Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, Unity Health Toronto, Toronto, ON, Canada. .,Li Ka Shing Knowledge Institute of St. Michael's Hospital, University of Toronto, 30 Bond Street, Toronto, ON, M5B 1W8, Canada.
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24
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Abstract
PURPOSE OF REVIEW Short stature is a common clinical manifestation in children. Yet, a cause is often unidentifiable in the majority of children with short stature by a routine screening approach. The purpose of this review is to describe the optimal genetic approach for evaluating short stature, challenges of genetic testing, and recent advances in genetic testing for short stature. RECENT FINDINGS Genetic testing, such as karyotype, chromosomal microarray, targeted gene sequencing, or exome sequencing, has served to identify the underlying genetic causes of short stature. When determining which short stature patient would benefit from genetic evaluation, it is important to consider whether the patient would have a single identifiable genetic cause. Specific diagnoses permit clinicians to predict responses to growth hormone treatment, to understand the phenotypic spectrum, and to understand any associated co-morbidities. SUMMARY The continued progress in the field of genetics and enhanced capabilities provided by genetic testing methods expands the ability of physicians to evaluate children with short stature for underlying genetic defects. Continued effort is needed to elaborate new genetic causes of linear growth disorders, therefore, we expand the list of known genes for short stature, which will subsequently increase the rate of genetic diagnosis for children with short stature.
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Affiliation(s)
- Elaine Zhou
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States of America
| | - Benjamin Hauser
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States of America
| | - Youn Hee Jee
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States of America
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25
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Sundercombe SL, Berbic M, Evans CA, Cliffe C, Elakis G, Temple SEL, Selvanathan A, Ewans L, Quayum N, Nixon CY, Dias KR, Lang S, Richards A, Goh S, Wilson M, Mowat D, Sachdev R, Sandaradura S, Walsh M, Farrar MA, Walsh R, Fletcher J, Kirk EP, Teunisse GM, Schofield D, Buckley MF, Zhu Y, Roscioli T. Clinically Responsive Genomic Analysis Pipelines: Elements to Improve Detection Rate and Efficiency. J Mol Diagn 2021; 23:894-905. [PMID: 33962052 DOI: 10.1016/j.jmoldx.2021.04.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 03/27/2021] [Accepted: 04/21/2021] [Indexed: 11/25/2022] Open
Abstract
Massively parallel sequencing has markedly improved mendelian diagnostic rates. This study assessed the effects of custom alterations to a diagnostic genomic bioinformatic pipeline in response to clinical need and derived practice recommendations relative to diagnostic rates and efficiency. The Genomic Annotation and Interpretation Application (GAIA) bioinformatics pipeline was designed to detect panel, exome, and genome sample integrity and prioritize gene variants in mendelian disorders. Reanalysis of selected negative cases was performed after improvements to the pipeline. GAIA improvements and their effect on sensitivity are described, including addition of a PubMed search for gene-disease associations not in the Online Mendelian Inheritance of Man database, inclusion of a process for calling low-quality variants (known as QPatch), and gene symbol nomenclature consistency checking. The new pipeline increased the diagnostic rate and reduced staff costs, resulting in a saving of US$844.34 per additional diagnosis. Recommendations for genomic analysis pipeline requirements are summarized. Clinically responsive bioinformatics pipeline improvements increase diagnostic sensitivity and increase cost-effectiveness.
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Affiliation(s)
| | - Marina Berbic
- NSW Health Pathology Randwick Genomics, Prince of Wales Hospital, Randwick, New South Wales, Australia; School of Women's and Children's Health, University of New South Wales Sydney, Kensington, New South Wales, Australia
| | - Carey-Anne Evans
- Neuroscience Research Australia (NeuRA), Randwick, New South Wales, Australia
| | - Corrina Cliffe
- NSW Health Pathology Randwick Genomics, Prince of Wales Hospital, Randwick, New South Wales, Australia
| | - George Elakis
- NSW Health Pathology Randwick Genomics, Prince of Wales Hospital, Randwick, New South Wales, Australia
| | - Suzanna E L Temple
- NSW Health Pathology Randwick Genomics, Prince of Wales Hospital, Randwick, New South Wales, Australia; Neuroscience Research Australia (NeuRA), Randwick, New South Wales, Australia; Centre for Clinical Genetics, Sydney Children's Hospital, Sydney, Randwick, New South Wales, Australia
| | - Arthavan Selvanathan
- NSW Health Pathology Randwick Genomics, Prince of Wales Hospital, Randwick, New South Wales, Australia; Neuroscience Research Australia (NeuRA), Randwick, New South Wales, Australia; Discipline of Child and Adolescent Health, The University of Sydney, New South Wales, Australia
| | - Lisa Ewans
- Department of Medical Genomics, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia; Central Clinical School, Sydney Medical School, The University of Sydney, New South Wales, Australia
| | - Nila Quayum
- NSW Health Pathology Randwick Genomics, Prince of Wales Hospital, Randwick, New South Wales, Australia
| | - Cheng-Yee Nixon
- NSW Health Pathology Randwick Genomics, Prince of Wales Hospital, Randwick, New South Wales, Australia; Neuroscience Research Australia (NeuRA), Randwick, New South Wales, Australia
| | - Kerith-Rae Dias
- Neuroscience Research Australia (NeuRA), Randwick, New South Wales, Australia; Prince of Wales Clinical School, Faculty of Medicine, University of New South Wales Sydney, Kensington, New South Wales, Australia
| | - Sarah Lang
- NSW Health Pathology Randwick Genomics, Prince of Wales Hospital, Randwick, New South Wales, Australia
| | - Anna Richards
- NSW Health Pathology Randwick Genomics, Prince of Wales Hospital, Randwick, New South Wales, Australia
| | - Shuxiang Goh
- NSW Health Pathology Randwick Genomics, Prince of Wales Hospital, Randwick, New South Wales, Australia; Neuroscience Research Australia (NeuRA), Randwick, New South Wales, Australia
| | - Meredith Wilson
- Department of Clinical Genetics, Children's Hospital at Westmead, Sydney, Westmead, New South Wales, Australia
| | - David Mowat
- Centre for Clinical Genetics, Sydney Children's Hospital, Sydney, Randwick, New South Wales, Australia
| | - Rani Sachdev
- Centre for Clinical Genetics, Sydney Children's Hospital, Sydney, Randwick, New South Wales, Australia
| | - Sarah Sandaradura
- Department of Clinical Genetics, Children's Hospital at Westmead, Sydney, Westmead, New South Wales, Australia
| | - Maie Walsh
- Genetic Medicine Department, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Michelle A Farrar
- School of Women's and Children's Health, University of New South Wales Sydney, Kensington, New South Wales, Australia; Neurology Department, Sydney Children's Hospital, Sydney, Randwick, New South Wales, Australia
| | - Rebecca Walsh
- NSW Health Pathology Randwick Genomics, Prince of Wales Hospital, Randwick, New South Wales, Australia
| | - Janice Fletcher
- NSW Health Pathology Randwick Genomics, Prince of Wales Hospital, Randwick, New South Wales, Australia
| | - Edwin P Kirk
- NSW Health Pathology Randwick Genomics, Prince of Wales Hospital, Randwick, New South Wales, Australia; School of Women's and Children's Health, University of New South Wales Sydney, Kensington, New South Wales, Australia; Centre for Clinical Genetics, Sydney Children's Hospital, Sydney, Randwick, New South Wales, Australia
| | - Guus M Teunisse
- Neuroscience Research Australia (NeuRA), Randwick, New South Wales, Australia
| | - Deborah Schofield
- Centre for Economic Impacts of Genomic Medicine, Macquarie Business School, Macquarie University, Macquarie Park, New South Wales, Australia
| | - Michael Francis Buckley
- NSW Health Pathology Randwick Genomics, Prince of Wales Hospital, Randwick, New South Wales, Australia
| | - Ying Zhu
- NSW Health Pathology Randwick Genomics, Prince of Wales Hospital, Randwick, New South Wales, Australia; Neuroscience Research Australia (NeuRA), Randwick, New South Wales, Australia; Genetics of Learning Disability Service, Hunter Genetics, Waratah Newcastle, New South Wales, Australia
| | - Tony Roscioli
- NSW Health Pathology Randwick Genomics, Prince of Wales Hospital, Randwick, New South Wales, Australia; Neuroscience Research Australia (NeuRA), Randwick, New South Wales, Australia; Centre for Clinical Genetics, Sydney Children's Hospital, Sydney, Randwick, New South Wales, Australia.
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26
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Klee EW, Cousin MA, Pinto E Vairo F, Morales-Rosado JA, Macke EL, Jenkinson WG, Ferrer A, Schultz-Rogers LE, Olson RJ, Oliver GR, Sigafoos AN, Schwab TL, Zimmermann MT, Urrutia RA, Kaiwar C, Gupta A, Blackburn PR, Boczek NJ, Prochnow CA, Lowy RJ, Mulvihill LA, McAllister TM, Aoudia SL, Kruisselbrink TM, Gunderson LB, Kemppainen JL, Fisher LJ, Tarnowski JM, Hager MM, Kroc SA, Bertsch NL, Agre KE, Jackson JL, Macklin-Mantia SK, Murphree MI, Rust LM, Summer Bolster JM, Beck SA, Atwal PS, Ellingson MS, Barnett SS, Rasmussen KJ, Lahner CA, Niu Z, Hasadsri L, Ferber MJ, Marcou CA, Clark KJ, Pichurin PN, Deyle DR, Morava-Kozicz E, Gavrilova RH, Dhamija R, Wierenga KJ, Lanpher BC, Babovic-Vuksanovic D, Farrugia G, Schimmenti LA, Stewart AK, Lazaridis KN. Impact of integrated translational research on clinical exome sequencing. Genet Med 2021; 23:498-507. [PMID: 33144682 DOI: 10.1038/s41436-020-01005-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 09/30/2020] [Accepted: 10/01/2020] [Indexed: 02/07/2023] Open
Abstract
PURPOSE Exome sequencing often identifies pathogenic genetic variants in patients with undiagnosed diseases. Nevertheless, frequent findings of variants of uncertain significance necessitate additional efforts to establish causality before reaching a conclusive diagnosis. To provide comprehensive genomic testing to patients with undiagnosed disease, we established an Individualized Medicine Clinic, which offered clinical exome testing and included a Translational Omics Program (TOP) that provided variant curation, research activities, or research exome sequencing. METHODS From 2012 to 2018, 1101 unselected patients with undiagnosed diseases received exome testing. Outcomes were reviewed to assess impact of the TOP and patient characteristics on diagnostic rates through descriptive and multivariate analyses. RESULTS The overall diagnostic yield was 24.9% (274 of 1101 patients), with 174 (15.8% of 1101) diagnosed on the basis of clinical exome sequencing alone. Four hundred twenty-three patients with nondiagnostic or without access to clinical exome sequencing were evaluated by the TOP, with 100 (9% of 1101) patients receiving a diagnosis, accounting for 36.5% of the diagnostic yield. The identification of a genetic diagnosis was influenced by the age at time of testing and the disease phenotype of the patient. CONCLUSION Integration of translational research activities into clinical practice of a tertiary medical center can significantly increase the diagnostic yield of patients with undiagnosed disease.
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Affiliation(s)
- Eric W Klee
- Department of Health Sciences Research, College of Medicine, Mayo Clinic, Rochester, MN, USA. .,Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA. .,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA.
| | - Margot A Cousin
- Department of Health Sciences Research, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Filippo Pinto E Vairo
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Joel A Morales-Rosado
- Department of Health Sciences Research, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Erica L Macke
- Department of Health Sciences Research, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - W Garrett Jenkinson
- Department of Health Sciences Research, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Alejandro Ferrer
- Department of Health Sciences Research, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Laura E Schultz-Rogers
- Department of Health Sciences Research, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Rory J Olson
- Department of Health Sciences Research, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Gavin R Oliver
- Department of Health Sciences Research, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Ashley N Sigafoos
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Tanya L Schwab
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Michael T Zimmermann
- Bioinformatics Research and Development Laboratory, Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Raul A Urrutia
- Division of Research, Department of Surgery and the Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Charu Kaiwar
- Center for Individualized Medicine, Mayo Clinic, Scottsdale, AZ, USA
| | - Aditi Gupta
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Patrick R Blackburn
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Nicole J Boczek
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Carri A Prochnow
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Rebecca J Lowy
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Lindsay A Mulvihill
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Tammy M McAllister
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Stacy L Aoudia
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Teresa M Kruisselbrink
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | | | - Jennifer L Kemppainen
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Laura J Fisher
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | | | - Megan M Hager
- Department of Clinical Genomics, Mayo Clinic, Scottsdale, AZ, USA
| | - Sarah A Kroc
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Nicole L Bertsch
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Katherine E Agre
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | | | | | | | - Laura M Rust
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | | | - Scott A Beck
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Paldeep S Atwal
- Department of Clinical Genomics, Mayo Clinic, Jacksonville, FL, USA.,Center for Individualized Medicine, Mayo Clinic, Jacksonville, FL, USA
| | - Marissa S Ellingson
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Sarah S Barnett
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Kristen J Rasmussen
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Carrie A Lahner
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Zhiyv Niu
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA.,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Linda Hasadsri
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Matthew J Ferber
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Cherisse A Marcou
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Karl J Clark
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Pavel N Pichurin
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - David R Deyle
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Eva Morava-Kozicz
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Ralitza H Gavrilova
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Radhika Dhamija
- Center for Individualized Medicine, Mayo Clinic, Scottsdale, AZ, USA.,Department of Clinical Genomics, Mayo Clinic, Scottsdale, AZ, USA
| | - Klaas J Wierenga
- Department of Clinical Genomics, Mayo Clinic, Jacksonville, FL, USA.,Center for Individualized Medicine, Mayo Clinic, Jacksonville, FL, USA
| | - Brendan C Lanpher
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Dusica Babovic-Vuksanovic
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Gianrico Farrugia
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Division of Gastroenterology and Hepatology, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Lisa A Schimmenti
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | | | - Konstantinos N Lazaridis
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA. .,Division of Gastroenterology and Hepatology, College of Medicine, Mayo Clinic, Rochester, MN, USA.
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27
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Dilated cardiomyopathy in a patient with autosomal dominant EEF1A2-related neurodevelopmental disorder. Eur J Med Genet 2020; 64:104121. [PMID: 33307280 DOI: 10.1016/j.ejmg.2020.104121] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 10/28/2020] [Accepted: 12/03/2020] [Indexed: 12/27/2022]
Abstract
The EEF1A2 gene encodes eukaryotic translation elongation factor 1α2, an integral component of the elongation factor complex. Heterozygous pathogenic variants in EEF1A2 are associated with neurodevelopmental disorders characterized by epilepsy, global developmental delay, and autism. To date, dilated cardiomyopathy has only been reported in two siblings with neurodevelopmental phenotypes and a homozygous missense variant in EEF1A2. This report describes a nine-year-old female patient who presented with neurodevelopmental phenotypes and dilated cardiomyopathy. Analysis of 193 epilepsy genes by focused exome sequencing revealed a novel heterozygous variant c.46G > C (p.Val16Leu; NM_001958.3) in EEF1A2. The variant was not detected in either parent, confirming its de novo origin. No additional variants that explain the patient's phenotypes were found by subsequent whole exome analysis. Copy number analysis of the exome data and exon-level microarray excluded a deletion in the other allele of EEF1A2. We present the first patient with a heterozygous pathogenic EEF1A2 variant who had dilated cardiomyopathy as well as neurodevelopmental phenotypes, suggesting that this cardiac phenotype may be associated with the autosomal dominant form of the EEF1A2-related disorder.
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28
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McNulty SN, Evenson MJ, Riley M, Yoest JM, Corliss MM, Heusel JW, Duncavage EJ, Pfeifer JD. A Next-Generation Sequencing Test for Severe Congenital Neutropenia: Utility in a Broader Clinicopathologic Spectrum of Disease. J Mol Diagn 2020; 23:200-211. [PMID: 33217554 DOI: 10.1016/j.jmoldx.2020.10.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 09/24/2020] [Accepted: 10/22/2020] [Indexed: 10/24/2022] Open
Abstract
Severe congenital neutropenia (SCN) is a collection of diverse disorders characterized by chronically low absolute neutrophil count in the peripheral blood, increased susceptibility to infection, and a significant predisposition to the development of myeloid malignancies. SCN can be acquired or inherited. Inherited forms have been linked to variants in a group of diverse genes involved in the neutrophil-differentiation process. Variants that promote resistance to treatment have also been identified. Thus, genetic testing is important for the diagnosis, prognosis, and management of SCN. Herein we describe clinically validated assay developed for assessing patients with suspected SCN. The assay is performed from a whole-exome backbone. Variants are called across all coding exons, and results are filtered to focus on 48 genes that are clinically relevant to SCN. Validation results indicated 100% analytical sensitivity and specificity for the detection of constitutional variants among the 48 reportable genes. To date, 34 individuals have been referred for testing (age range: birth to 67 years). Several pathogenic and likely pathogenic variants have been identified, including one in a patient with late-onset disease. The pattern of cases referred for testing suggests that this assay has clinical utility in a broader spectrum of patients beyond those in the pediatric population who have classic early-onset symptoms characteristic of SCN.
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Affiliation(s)
- Samantha N McNulty
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri
| | - Michael J Evenson
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri
| | - Meaghan Riley
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri; Summit Pathology, Loveland, Colorado
| | - Jennifer M Yoest
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Meagan M Corliss
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri
| | - Jonathan W Heusel
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri; Department of Genetics, Washington University School of Medicine, St. Louis, Missouri
| | - Eric J Duncavage
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri
| | - John D Pfeifer
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri.
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29
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Velasco HM, Ullah E, Martin AM, Hufnagel RB, Prada CE. Novel progressive acrodysostosis-like skeletal dysplasia, cerebellar atrophy, and ichthyosis. Am J Med Genet A 2020; 182:2214-2221. [PMID: 32783359 DOI: 10.1002/ajmg.a.61782] [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: 02/24/2020] [Revised: 05/09/2020] [Accepted: 06/22/2020] [Indexed: 11/07/2022]
Abstract
Acrodysostosis refers to a rare heterogeneous group of bone dysplasias that share skeletal features, hormone resistance, and intellectual disability. Two genes have been associated with acrodysostosis with or without hormone resistance (PRKAR1A and PDE4D). Severe intellectual disability has been reported with acrodysostosis but brain malformations and ichthyosis have not been reported in these syndromes. Here we describe a female patient with acrodysostosis, intellectual disability, cerebellar hypoplasia, and lamellar ichthyosis. The patient has an evolving distinctive facial phenotype and childhood onset ataxia. X-rays showed generalized osteopenia, shortening of middle and distal phalanges, and abnormal distal epiphysis of the ulna and radius. Brain magnetic resonance imaging showed cerebellar atrophy without other brainstem abnormalities. Genetic workup included nondiagnostic chromosomal microarray and skeletal dysplasia molecular panels. These clinical findings are different from any recognized form of acrodysostosis syndrome. Whole exome sequencing did not identify rare or predicted pathogenic variants in genes associated with known acrodysostosis, lamellar ichthyosis, and other overlapping disorders. A broader search for rare alleles absent in healthy population databases and controls identified two heterozygous truncating alleles in FBNL7 and PPM1M genes, and one missense allele in the NPEPPS gene. Identification of additional patients is required to delineate the mechanism of this unique disorder.
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Affiliation(s)
- Harvy M Velasco
- Master of Science in Human Genetics Program, Department of Morphology, Universidad Nacional de Colombia, Cundinamarca, Colombia
| | - Ehsan Ullah
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Angela M Martin
- Master of Science in Human Genetics Program, Department of Morphology, Universidad Nacional de Colombia, Cundinamarca, Colombia
| | - Robert B Hufnagel
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Carlos E Prada
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
- Fundación Cardiovascular de Colombia, Bucaramanga, Colombia
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
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30
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Kozyra EJ, Pastor VB, Lefkopoulos S, Sahoo SS, Busch H, Voss RK, Erlacher M, Lebrecht D, Szvetnik EA, Hirabayashi S, Pasaulienė R, Pedace L, Tartaglia M, Klemann C, Metzger P, Boerries M, Catala A, Hasle H, de Haas V, Kállay K, Masetti R, De Moerloose B, Dworzak M, Schmugge M, Smith O, Starý J, Mejstrikova E, Ussowicz M, Morris E, Singh P, Collin M, Derecka M, Göhring G, Flotho C, Strahm B, Locatelli F, Niemeyer CM, Trompouki E, Wlodarski MW. Synonymous GATA2 mutations result in selective loss of mutated RNA and are common in patients with GATA2 deficiency. Leukemia 2020; 34:2673-2687. [PMID: 32555368 PMCID: PMC7515837 DOI: 10.1038/s41375-020-0899-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 05/19/2020] [Accepted: 05/29/2020] [Indexed: 02/08/2023]
Abstract
Deficiency of the transcription factor GATA2 is a highly penetrant genetic disorder predisposing to myelodysplastic syndromes (MDS) and immunodeficiency. It has been recognized as the most common cause underlying primary MDS in children. Triggered by the discovery of a recurrent synonymous GATA2 variant, we systematically investigated 911 patients with phenotype of pediatric MDS or cellular deficiencies for the presence of synonymous alterations in GATA2. In total, we identified nine individuals with five heterozygous synonymous mutations: c.351C>G, p.T117T (N = 4); c.649C>T, p.L217L; c.981G>A, p.G327G; c.1023C>T, p.A341A; and c.1416G>A, p.P472P (N = 2). They accounted for 8.2% (9/110) of cases with GATA2 deficiency in our cohort and resulted in selective loss of mutant RNA. While for the hotspot mutation (c.351C>G) a splicing error leading to RNA and protein reduction was identified, severe, likely late stage RNA loss without splicing disruption was found for other mutations. Finally, the synonymous mutations did not alter protein function or stability. In summary, synonymous GATA2 substitutions are a new common cause of GATA2 deficiency. These findings have broad implications for genetic counseling and pathogenic variant discovery in Mendelian disorders.
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Affiliation(s)
- Emilia J Kozyra
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Faculty of Biology, University of Freiburg, Schänzlestraße 1, 79104, Freiburg, Germany
| | - Victor B Pastor
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Stylianos Lefkopoulos
- Faculty of Biology, University of Freiburg, Schänzlestraße 1, 79104, Freiburg, Germany.,Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Sushree S Sahoo
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Department of Hematology, St. Jude Children´s Research Hospital, Memphis, USA
| | - Hauke Busch
- Institute of Molecular Medicine and Cell Research, University of Freiburg, Freiburg, Germany.,Lübeck Institute of Experimental Dermatology and Institute of Cardiogenetics, University of Lübeck, Lübeck, Germany.,Comprehensive Cancer Center Freiburg (CCCF), University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Rebecca K Voss
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Miriam Erlacher
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,German Cancer Consortium (DKTK), Freiburg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dirk Lebrecht
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Enikoe A Szvetnik
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Shinsuke Hirabayashi
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Department of Pediatrics, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Ramunė Pasaulienė
- Vilnius University Hospital Santaros Klinikos, Center for Pediatric Oncology and Hematology, Bone Marrow Transplantations Unit, Vilnius, Lithuania
| | - Lucia Pedace
- Department of Pediatric Hematology and Oncology, Istituto di Ricovero e Cura a Carattere Scientifico Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Istituto di Ricovero e Cura a Carattere Scientifico Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Christian Klemann
- Department of Pediatric Pneumology, Allergy and Neonatology, Hannover Medical School, Hannover, Germany
| | - Patrick Metzger
- Faculty of Biology, University of Freiburg, Schänzlestraße 1, 79104, Freiburg, Germany.,Institute of Medical Bioinformatics and Systems Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Melanie Boerries
- German Cancer Consortium (DKTK), Freiburg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Institute of Medical Bioinformatics and Systems Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Albert Catala
- Department of Hematology and Oncology, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Henrik Hasle
- Department of Pediatrics, Aarhus University Hospital Skejby, Aarhus, Denmark
| | - Valerie de Haas
- Dutch Childhood Oncology Group (DCOG), Princess Máxima Centre, Utrecht, The Netherlands
| | - Krisztián Kállay
- Central Hospital of Southern Pest-National Institute of Hematology and Infectious Diseases, Budapest, Hungary
| | - Riccardo Masetti
- Department of Pediatric Oncology and Hematology, University of Bologna, Bologna, Italy
| | - Barbara De Moerloose
- Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium
| | - Michael Dworzak
- St. Anna Children´s Hospital and Cancer Research Institute, Pediatric Clinic, Medical University of Vienna, Vienna, Austria
| | - Markus Schmugge
- Department of Hematology and Oncology, University Children's Hospital, Zurich, Switzerland
| | - Owen Smith
- Paediatric Oncology and Haematology, Our Lady's Children's Hospital Crumlin, Dublin, Ireland
| | - Jan Starý
- Department of Pediatric Hematology and Oncology, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Ester Mejstrikova
- Department of Pediatric Hematology and Oncology, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Marek Ussowicz
- Department of Paediatric Bone Marrow Transplantation, Oncology and Hematology, Medical University of Wroclaw, Wroclaw, Poland
| | - Emma Morris
- Institute of Immunity and Transplantation, University College London (UCL), London, UK.,Bone Marrow Transplant (BMT) Programme, UCL Hospital National Health Service Foundation Trust (NHS FT), London, UK.,Department of Immunology, Royal Free London NHS FT, London, UK
| | - Preeti Singh
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK.,NIHR Newcastle Biomedical Research Centre at Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Matthew Collin
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK.,NIHR Newcastle Biomedical Research Centre at Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Marta Derecka
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Gudrun Göhring
- Institute of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Christian Flotho
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,German Cancer Consortium (DKTK), Freiburg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Brigitte Strahm
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Franco Locatelli
- Department of Pediatric Hematology and Oncology, Istituto di Ricovero e Cura a Carattere Scientifico Ospedale Pediatrico Bambino Gesù, Rome, Italy.,Department of Pediatrics, Sapienza University of Rome, Rome, Italy
| | - Charlotte M Niemeyer
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,German Cancer Consortium (DKTK), Freiburg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Eirini Trompouki
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.,CIBSS-Centre for Integrative Biological Signaling Studies, Freiburg, Germany
| | - Marcin W Wlodarski
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany. .,Department of Hematology, St. Jude Children´s Research Hospital, Memphis, USA.
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Shefchek KA, Harris NL, Gargano M, Matentzoglu N, Unni D, Brush M, Keith D, Conlin T, Vasilevsky N, Zhang XA, Balhoff JP, Babb L, Bello SM, Blau H, Bradford Y, Carbon S, Carmody L, Chan LE, Cipriani V, Cuzick A, Della Rocca M, Dunn N, Essaid S, Fey P, Grove C, Gourdine JP, Hamosh A, Harris M, Helbig I, Hoatlin M, Joachimiak M, Jupp S, Lett KB, Lewis SE, McNamara C, Pendlington ZM, Pilgrim C, Putman T, Ravanmehr V, Reese J, Riggs E, Robb S, Roncaglia P, Seager J, Segerdell E, Similuk M, Storm AL, Thaxon C, Thessen A, Jacobsen JOB, McMurry JA, Groza T, Köhler S, Smedley D, Robinson PN, Mungall CJ, Haendel MA, Munoz-Torres MC, Osumi-Sutherland D. The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species. Nucleic Acids Res 2020; 48:D704-D715. [PMID: 31701156 PMCID: PMC7056945 DOI: 10.1093/nar/gkz997] [Citation(s) in RCA: 138] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 10/09/2019] [Accepted: 10/14/2019] [Indexed: 12/14/2022] Open
Abstract
In biology and biomedicine, relating phenotypic outcomes with genetic variation and environmental factors remains a challenge: patient phenotypes may not match known diseases, candidate variants may be in genes that haven’t been characterized, research organisms may not recapitulate human or veterinary diseases, environmental factors affecting disease outcomes are unknown or undocumented, and many resources must be queried to find potentially significant phenotypic associations. The Monarch Initiative (https://monarchinitiative.org) integrates information on genes, variants, genotypes, phenotypes and diseases in a variety of species, and allows powerful ontology-based search. We develop many widely adopted ontologies that together enable sophisticated computational analysis, mechanistic discovery and diagnostics of Mendelian diseases. Our algorithms and tools are widely used to identify animal models of human disease through phenotypic similarity, for differential diagnostics and to facilitate translational research. Launched in 2015, Monarch has grown with regards to data (new organisms, more sources, better modeling); new API and standards; ontologies (new Mondo unified disease ontology, improvements to ontologies such as HPO and uPheno); user interface (a redesigned website); and community development. Monarch data, algorithms and tools are being used and extended by resources such as GA4GH and NCATS Translator, among others, to aid mechanistic discovery and diagnostics.
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Affiliation(s)
- Kent A Shefchek
- Center for Genome Research and Biocomputing, Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA
| | - Nomi L Harris
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94710, USA
| | - Michael Gargano
- The Jackson Laboratory For Genomic Medicine, Farmington, CT 06032, USA
| | - Nicolas Matentzoglu
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Deepak Unni
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94710, USA
| | - Matthew Brush
- Oregon Clinical and Translational Research Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Daniel Keith
- Center for Genome Research and Biocomputing, Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA
| | - Tom Conlin
- Center for Genome Research and Biocomputing, Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA
| | - Nicole Vasilevsky
- Oregon Clinical and Translational Research Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | | | - James P Balhoff
- Renaissance Computing Institute at UNC, Chapel Hill, NC 27517, USA
| | - Larry Babb
- Broad Institute, Cambridge, MA 02142, USA
| | | | - Hannah Blau
- The Jackson Laboratory For Genomic Medicine, Farmington, CT 06032, USA
| | - Yvonne Bradford
- Institute of Neuroscience, University of Oregon, Eugene, OR 97401, USA
| | - Seth Carbon
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94710, USA
| | - Leigh Carmody
- The Jackson Laboratory For Genomic Medicine, Farmington, CT 06032, USA
| | - Lauren E Chan
- College of Public Health and Human Sciences, Oregon State University, Corvallis, OR 97331, USA
| | - Valentina Cipriani
- William Harvey Research Institute, Barts & The London School of Medicine & Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | | | - Maria Della Rocca
- Office of Rare Diseases Research (ORDR), National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Nathan Dunn
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94710, USA
| | - Shahim Essaid
- Oregon Clinical and Translational Research Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Petra Fey
- dictyBase, Center for Genetic Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Chris Grove
- California Institute of Technology, Pasadena, CA 91125, USA
| | - Jean-Phillipe Gourdine
- Oregon Clinical and Translational Research Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Ada Hamosh
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | | | - Ingo Helbig
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.,Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.,Department of Neuropediatrics, Christian-Albrechts-University of Kiel, 24105 Kiel, Germany.,Department of Neurology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Maureen Hoatlin
- Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Marcin Joachimiak
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94710, USA
| | - Simon Jupp
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Kenneth B Lett
- Center for Genome Research and Biocomputing, Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA
| | - Suzanna E Lewis
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94710, USA
| | | | - Zoë M Pendlington
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | | | - Tim Putman
- Center for Genome Research and Biocomputing, Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA
| | - Vida Ravanmehr
- The Jackson Laboratory For Genomic Medicine, Farmington, CT 06032, USA
| | - Justin Reese
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94710, USA
| | - Erin Riggs
- Autism & Developmental Medicine Institute, Geisinger, Danville, PA 17837, USA
| | - Sofia Robb
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Paola Roncaglia
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | | | - Erik Segerdell
- Xenbase, Cincinnati Children's Hospital, Cincinnati, OH 45229, USA
| | - Morgan Similuk
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Andrea L Storm
- Office of Rare Diseases Research (ORDR), National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Courtney Thaxon
- University of North Carolina Medical School, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA
| | - Anne Thessen
- Center for Genome Research and Biocomputing, Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA
| | - Julius O B Jacobsen
- William Harvey Research Institute, Barts & The London School of Medicine & Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Julie A McMurry
- College of Public Health and Human Sciences, Oregon State University, Corvallis, OR 97331, USA
| | | | - Sebastian Köhler
- Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Damian Smedley
- William Harvey Research Institute, Barts & The London School of Medicine & Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Peter N Robinson
- The Jackson Laboratory For Genomic Medicine, Farmington, CT 06032, USA
| | - Christopher J Mungall
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94710, USA
| | - Melissa A Haendel
- Center for Genome Research and Biocomputing, Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA.,Oregon Clinical and Translational Research Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Monica C Munoz-Torres
- Center for Genome Research and Biocomputing, Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA
| | - David Osumi-Sutherland
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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González‐Del Carmen M, Montaño S, Reyes‐Hernández OD, Vizcaíno‐Dorado PA, Leyva‐García N, Morales‐Morfín JC, Diaz‐Beltran W, Quinto‐Santiago E, Cariño‐Calvo L, Magaña JJ, Leyva‐Gómez G, Cortés H. High prevalence of autosomal recessive congenital ichthyosis in a Mexican population caused by a new mutation in the
TGM1
gene: epidemiological evidence of a founder effect. Int J Dermatol 2020; 59:969-977. [DOI: 10.1111/ijd.14952] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 04/19/2020] [Accepted: 04/24/2020] [Indexed: 12/12/2022]
Affiliation(s)
| | - Sarita Montaño
- Laboratorio de Modelado Molecular y Bioinformática Facultad de Ciencias Químico‐Biológicas Universidad Autónoma de Sinaloa Culiacán Sinaloa México
| | - Octavio D. Reyes‐Hernández
- Laboratorio de Biología Molecular del Cáncer UMIEZ Facultad de Estudios Superiores Zaragoza Universidad Nacional Autónoma de México Ciudad de México México
| | - Pablo A. Vizcaíno‐Dorado
- Laboratorio de Medicina Genómica Departamento de Genética Instituto Nacional de Rehabilitación Luis Guillermo Ibarra Ibarra Ciudad de México México
| | - Norberto Leyva‐García
- Laboratorio de Medicina Genómica Departamento de Genética Instituto Nacional de Rehabilitación Luis Guillermo Ibarra Ibarra Ciudad de México México
| | - Juan C. Morales‐Morfín
- Laboratorio de Medicina Genómica Departamento de Genética Instituto Nacional de Rehabilitación Luis Guillermo Ibarra Ibarra Ciudad de México México
| | - Wendy Diaz‐Beltran
- Facultad de Medicina Universidad Veracruzana Ciudad Mendoza, Veracruz México
| | | | | | - Jonathan J. Magaña
- Laboratorio de Medicina Genómica Departamento de Genética Instituto Nacional de Rehabilitación Luis Guillermo Ibarra Ibarra Ciudad de México México
| | - Gerardo Leyva‐Gómez
- Departamento de Farmacia Facultad de Química Universidad Nacional Autónoma de México Ciudad de México México
| | - Hernán Cortés
- Laboratorio de Medicina Genómica Departamento de Genética Instituto Nacional de Rehabilitación Luis Guillermo Ibarra Ibarra Ciudad de México México
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Cipriani V, Pontikos N, Arno G, Sergouniotis PI, Lenassi E, Thawong P, Danis D, Michaelides M, Webster AR, Moore AT, Robinson PN, Jacobsen JO, Smedley D. An Improved Phenotype-Driven Tool for Rare Mendelian Variant Prioritization: Benchmarking Exomiser on Real Patient Whole-Exome Data. Genes (Basel) 2020; 11:E460. [PMID: 32340307 PMCID: PMC7230372 DOI: 10.3390/genes11040460] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/08/2020] [Accepted: 04/16/2020] [Indexed: 02/06/2023] Open
Abstract
Next-generation sequencing has revolutionized rare disease diagnostics, but many patients remain without a molecular diagnosis, particularly because many candidate variants usually survive despite strict filtering. Exomiser was launched in 2014 as a Java tool that performs an integrative analysis of patients' sequencing data and their phenotypes encoded with Human Phenotype Ontology (HPO) terms. It prioritizes variants by leveraging information on variant frequency, predicted pathogenicity, and gene-phenotype associations derived from human diseases, model organisms, and protein-protein interactions. Early published releases of Exomiser were able to prioritize disease-causative variants as top candidates in up to 97% of simulated whole-exomes. The size of the tested real patient datasets published so far are very limited. Here, we present the latest Exomiser version 12.0.1 with many new features. We assessed the performance using a set of 134 whole-exomes from patients with a range of rare retinal diseases and known molecular diagnosis. Using default settings, Exomiser ranked the correct diagnosed variants as the top candidate in 74% of the dataset and top 5 in 94%; not using the patients' HPO profiles (i.e., variant-only analysis) decreased the performance to 3% and 27%, respectively. In conclusion, Exomiser is an effective support tool for rare Mendelian phenotype-driven variant prioritization.
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Affiliation(s)
- Valentina Cipriani
- William Harvey Research Institute, Queen Mary University of London, London EC1M 6BQ, UK; (J.O.B.J.); (D.S.)
- UCL Institute of Ophthalmology, University College London, London EC1V 9EL, UK; (N.P.); (G.A.); (M.M.); (A.R.W.); (A.T.M.)
- Moorfields Eye Hospital NHS Foundation Trust, London EC1V 2PD, UK
- UCL Genetics Institute, University College London, London WC1E 6AA, UK
| | - Nikolas Pontikos
- UCL Institute of Ophthalmology, University College London, London EC1V 9EL, UK; (N.P.); (G.A.); (M.M.); (A.R.W.); (A.T.M.)
- Moorfields Eye Hospital NHS Foundation Trust, London EC1V 2PD, UK
| | - Gavin Arno
- UCL Institute of Ophthalmology, University College London, London EC1V 9EL, UK; (N.P.); (G.A.); (M.M.); (A.R.W.); (A.T.M.)
- Moorfields Eye Hospital NHS Foundation Trust, London EC1V 2PD, UK
- North East Thames Regional Genetics Laboratory, Great Ormond Street Hospital NHS Trust, London WC1N 3BH, UK
| | | | - Eva Lenassi
- Manchester Royal Eye Hospital & University of Manchester, Manchester M13 9WL, UK; (P.I.S.); (E.L.)
| | - Penpitcha Thawong
- Department of Medical Sciences, Medical Genetics Section, National Institute of Health, Ministry of Public Health, Nonthaburi 11000, Thailand;
| | - Daniel Danis
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; (D.D.); (P.N.R.)
| | - Michel Michaelides
- UCL Institute of Ophthalmology, University College London, London EC1V 9EL, UK; (N.P.); (G.A.); (M.M.); (A.R.W.); (A.T.M.)
- Moorfields Eye Hospital NHS Foundation Trust, London EC1V 2PD, UK
| | - Andrew R. Webster
- UCL Institute of Ophthalmology, University College London, London EC1V 9EL, UK; (N.P.); (G.A.); (M.M.); (A.R.W.); (A.T.M.)
- Moorfields Eye Hospital NHS Foundation Trust, London EC1V 2PD, UK
| | - Anthony T. Moore
- UCL Institute of Ophthalmology, University College London, London EC1V 9EL, UK; (N.P.); (G.A.); (M.M.); (A.R.W.); (A.T.M.)
- Moorfields Eye Hospital NHS Foundation Trust, London EC1V 2PD, UK
- Ophthalmology Department, UCSF School of Medicine, San Francisco, CA 94143-0644, USA
| | - Peter N. Robinson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; (D.D.); (P.N.R.)
| | - Julius O.B. Jacobsen
- William Harvey Research Institute, Queen Mary University of London, London EC1M 6BQ, UK; (J.O.B.J.); (D.S.)
| | - Damian Smedley
- William Harvey Research Institute, Queen Mary University of London, London EC1M 6BQ, UK; (J.O.B.J.); (D.S.)
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34
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Kaneva K, Merkurjev D, Ostrow D, Ryutov A, Triska P, Stachelek K, Cobrinik D, Biegel JA, Gai X. Detection of mitochondrial DNA variants at low level heteroplasmy in pediatric CNS and extra-CNS solid tumors with three different enrichment methods. Mitochondrion 2020; 51:97-103. [PMID: 31972374 DOI: 10.1016/j.mito.2020.01.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 11/28/2019] [Accepted: 01/08/2020] [Indexed: 02/06/2023]
Abstract
The mitochondrial genome is small, 16.5 kb, and yet complex to study due to an abundance of mitochondria in any given cell or tissue. Mitochondrial DNA (mtDNA) mutations have been previously described in cancer, many of which were detected at low heteroplasmy. In this study we enriched the mitochondrial genome in primary pediatric tumors for detection of mtDNA variants. We completed mtDNA enrichment using REPLI-g, Agilent SureSelect, and long-range polymerase chain reaction (LRPCR) followed by next generation sequencing (NGS) on Illumina platforms. Primary tumor and germline genomic DNA from a variety of pediatric central nervous system (CNS) and extra-CNS solid tumors were analyzed by the three different methods. Although all three methods performed equally well for detecting variants at high heteroplasmy or homoplasmy, only LRPCR and SureSelect-based enrichment methods provided consistent results for variants that were present at less than five percent heteroplasmy. We then applied both LRPCR and SureSelect to three successive samples from a patient with multiply-recurrent gliofibroma and detected a low-level novel mutation as well as a change in heteroplasmy levels of a synonymous variant that was correlated with progression of disease. IMPLICATION: This study demonstrates that LRPCR and SureSelect enrichment, but not REPLI-g, followed by NGS are accurate methods for studying the mtDNA variations at low heteroplasmy, which may be applied to studying mtDNA mutations in cancer.
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Affiliation(s)
- Kristiyana Kaneva
- Division of Hematology-Oncology, Neuro-Oncology & Stem Cell Transplantation, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, United States.
| | - Daria Merkurjev
- Department of Pathology Children's Hospital Los Angeles and Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Dejerianne Ostrow
- Department of Pathology Children's Hospital Los Angeles and Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Alex Ryutov
- Department of Pathology Children's Hospital Los Angeles and Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Petr Triska
- Department of Pediatric Hematology and Oncology, Charles University, Prague, United States
| | - Kevin Stachelek
- The Vision Center and The Saban Research Institute, Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - David Cobrinik
- The Vision Center and The Saban Research Institute, Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Jaclyn A Biegel
- Department of Pathology Children's Hospital Los Angeles and Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Xiaowu Gai
- Department of Pathology Children's Hospital Los Angeles and Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
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35
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Pinto E Vairo F, Lazaridis KN. Individualized medicine comes to the liver clinic. J Hepatol 2019; 70:1057-1059. [PMID: 31000362 DOI: 10.1016/j.jhep.2019.03.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 03/25/2019] [Accepted: 03/28/2019] [Indexed: 12/04/2022]
Affiliation(s)
- Filippo Pinto E Vairo
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA; Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Konstantinos N Lazaridis
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA; Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA.
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