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Lin L, Zhang Y, Pan H, Wang J, Qi Y, Ma Y. Inconsistencies between prenatal diagnostic and genetic testing laboratories on variant validation of rare monogenic diseases. Prenat Diagn 2024; 44:1053-1061. [PMID: 38898598 DOI: 10.1002/pd.6628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 05/14/2024] [Accepted: 06/10/2024] [Indexed: 06/21/2024]
Abstract
BACKGROUND The advent of next-generation sequencing (NGS) has enhanced the diagnostic efficacy for monogenic diseases, while presenting challenges in achieving consistent diagnoses. METHOD We retrospectively analyzed the concordance rate and reasons for the inconsistency between the original diagnostic result from the genetic testing laboratory and the variant validation result from the prenatal diagnostic center. The validation procedure comprised three stages: validation of variant detection, reevaluation of variant classification, and assessment of recurrence risk, which involved verifying the mode of inheritance and parental carriage. RESULT In total, 17 (6%) of the 286 families affected by rare monogenic diseases showed different results during the variant validation procedure. These cases comprised four (23.5%) with variant detection errors, 12 (70.5%) with inconsistent interpretation, and one (6%) with non-Mendelian inheritance patterns. False-positive NGS results confirmed by Sanger sequencing were related to pseudogenes and GC-rich regions. The classification of the 17 variants was altered in the 12 cases owing to various factors. The case with an atypical inheritance pattern was originally considered autosomal recessive inheritance, but was diagnosed as maternal uniparental disomy after additional genetic analysis. CONCLUSION We underscored the significance of variant validation by prenatal diagnostic centers. Families affected by monogenic diseases with reproductive plans should be referred to prenatal genetic centers as early as possible to avoid different results that may postpone subsequent prenatal diagnosis.
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Affiliation(s)
- Liling Lin
- Department of Central Laboratory, Peking University First Hospital, Beijing, China
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Beijing, China
| | - Ying Zhang
- Department of Central Laboratory, Peking University First Hospital, Beijing, China
| | - Hong Pan
- Department of Central Laboratory, Peking University First Hospital, Beijing, China
| | - Jingmin Wang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Yu Qi
- Department of Central Laboratory, Peking University First Hospital, Beijing, China
| | - Yinan Ma
- Department of Central Laboratory, Peking University First Hospital, Beijing, China
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2
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Lee S, Kang M, So KH, Jang R, Shin YW, Jang SS, Yoon JG, Kim S, Kim M, Chu K, Lee SK, Kim KJ, Baek ST, Lim BC, Moon J. Broadening the scope of multigene panel analysis for adult epilepsy patients. Epilepsia Open 2024; 9:1538-1549. [PMID: 38946282 PMCID: PMC11296137 DOI: 10.1002/epi4.12993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 05/13/2024] [Accepted: 05/28/2024] [Indexed: 07/02/2024] Open
Abstract
OBJECTIVE Epilepsy is a suitable target for gene panel sequencing because a considerable portion of epilepsy is now explained by genetic components, especially in syndromic cases. However, previous gene panel studies on epilepsy have mostly focused on pediatric patients. METHODS We enrolled adult epilepsy patients meeting any of the following criteria: family history of epilepsy, seizure onset age ≤ 19 years, neuronal migration disorder, and seizure freedom not achieved by dual anti-seizure medications. We sequenced the exonic regions of 211 epilepsy genes in these patients. To confirm the pathogenicity of a novel MTOR truncating variant, we electroporated vectors with different MTOR variants into developing mouse brains. RESULTS A total of 92 probands and 4 affected relatives were tested, and the proportion of intellectual disability (ID) and/or developmental disability (DD) was 21.7%. As a result, twelve probands (13.0%) had pathogenic or likely pathogenic variants in the following genes or regions: DEPDC5, 15q12-q13 duplication (n = 2), SLC6A1, SYNGAP1, EEF1A2, LGI1, MTOR, KCNQ2, MEF2C, and TSC1 (n = 1). We confirmed the functional impact of a novel truncating mutation in the MTOR gene (c.7570C > T, p.Gln2524Ter) that disrupted neuronal migration in a mouse model. The diagnostic yield was higher in patients with ID/DD or childhood-onset seizures. We also identified additional candidate variants in 20 patients that could be reassessed by further studies. SIGNIFICANCE Our findings underscore the clinical utility of gene panel sequencing in adult epilepsy patients suspected of having genetic etiology, especially those with ID/DD or early-onset seizures. Gene panel sequencing could not only lead to genetic diagnosis in a substantial portion of adult epilepsy patients but also inform more precise therapeutic decisions based on their genetic background. PLAIN LANGUAGE SUMMARY This study demonstrated the effectiveness of gene panel sequencing in adults with epilepsy, revealing pathogenic or likely pathogenic variants in 13.0% of patients. Higher diagnostic yields were observed in those with neurodevelopmental disorders or childhood-onset seizures. Additionally, we have shown that expanding genetic studies into adult patients would uncover new types of pathogenic variants for epilepsy, contributing to the advancement of precision medicine for individuals with epilepsy. In conclusion, our results highlight the practical value of employing gene panel sequencing in adult epilepsy patients, particularly when genetic etiology is clinically suspected.
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Affiliation(s)
- Seungbok Lee
- Department of Genomic MedicineSeoul National University HospitalSeoulKorea
- Department of PediatricsSeoul National University College of Medicine, Seoul National University Children's HospitalSeoulKorea
| | - Mi‐Kyoung Kang
- Department of NeurologySeoul National University College of Medicine, Seoul National University HospitalSeoulKorea
| | - Ki Hurn So
- Department of Life SciencesPohang University of Science and Technology (POSTECH)PohangKorea
| | - Riyul Jang
- Department of Life SciencesPohang University of Science and Technology (POSTECH)PohangKorea
| | - Yong Woo Shin
- Department of NeurologySeoul National University College of Medicine, Seoul National University HospitalSeoulKorea
| | - Se Song Jang
- Department of PediatricsSeoul National University College of Medicine, Seoul National University Children's HospitalSeoulKorea
| | - Jihoon G. Yoon
- Department of Genomic MedicineSeoul National University HospitalSeoulKorea
| | - Sheehyun Kim
- Department of Genomic MedicineSeoul National University HospitalSeoulKorea
| | - Manjin Kim
- Department of Genomic MedicineSeoul National University HospitalSeoulKorea
- Department of Laboratory MedicineSeoul National University College of Medicine, Seoul National University HospitalSeoulKorea
| | - Kon Chu
- Department of NeurologySeoul National University College of Medicine, Seoul National University HospitalSeoulKorea
| | - Sang Kun Lee
- Department of NeurologySeoul National University College of Medicine, Seoul National University HospitalSeoulKorea
| | - Ki Joong Kim
- Department of PediatricsSeoul National University College of Medicine, Seoul National University Children's HospitalSeoulKorea
| | - Seung Tae Baek
- Department of Life SciencesPohang University of Science and Technology (POSTECH)PohangKorea
| | - Byung Chan Lim
- Department of PediatricsSeoul National University College of Medicine, Seoul National University Children's HospitalSeoulKorea
| | - Jangsup Moon
- Department of Genomic MedicineSeoul National University HospitalSeoulKorea
- Department of NeurologySeoul National University College of Medicine, Seoul National University HospitalSeoulKorea
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3
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Jiao K, Cheng N, Huan X, Zhang J, Ding Y, Luan X, Liu L, Wang X, Zhu B, Du K, Fan J, Gao M, Xia X, Wang N, Wang T, Xi J, Luo S, Lu J, Zhao C, Yue D, Zhu W. Pseudoexon activation by deep intronic variation in GNE myopathy with thrombocytopenia. Muscle Nerve 2024; 69:708-718. [PMID: 38558464 DOI: 10.1002/mus.28092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 03/07/2024] [Accepted: 03/16/2024] [Indexed: 04/04/2024]
Abstract
INTRODUCTION/AIMS GNE myopathy is a rare autosomal recessive disorder caused by pathogenic variants in the GNE gene, which is essential for the sialic acid biosynthesis pathway. Although over 300 GNE variants have been reported, some patients remain undiagnosed with monoallelic pathogenic variants. This study aims to analyze the entire GNE genomic region to identify novel pathogenic variants. METHODS Patients with clinically compatible GNE myopathy and monoallelic pathogenic variants in the GNE gene were enrolled. The other GNE pathogenic variant was verified using comprehensive methods including exon 2 quantitative polymerase chain reaction and nanopore long-read single-molecule sequencing (LRS). RESULTS A deep intronic GNE variant, c.862+870C>T, was identified in nine patients from eight unrelated families. This variant generates a cryptic splice site, resulting in the activation of a novel pseudoexon between exons 5 and 6. It results in the insertion of an extra 146 nucleotides into the messengerRNA (mRNA), which is predicted to result in a truncated humanGNE1(hGNE1) protein. Peanut agglutinin(PNA) lectin staining of muscle tissues showed reduced sialylation of mucin O-glycans on sarcolemmal glycoproteins. Notably, a third of patients with the c.862+870C>T variant exhibited thrombocytopenia. A common core haplotype harboring the deep intronic GNE variant was found in all these patients. DISCUSSION The transcript with pseudoexon activation potentially affects sialic acid biosynthesis via nonsense-mediated mRNA decay, or resulting in a truncated hGNE1 protein, which interferes with normal enzyme function. LRS is expected to be more frequently incorporated in genetic analysis given its efficacy in detecting hard-to-find pathogenic variants.
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Affiliation(s)
- Kexin Jiao
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China
- Huashan Rare Disease Center, Shanghai Medical College, Huashan Hospital, Fudan University, Shanghai, China
- National Center for Neurological Disorders (NCND), Shanghai, China
| | - Nachuan Cheng
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China
- Huashan Rare Disease Center, Shanghai Medical College, Huashan Hospital, Fudan University, Shanghai, China
- National Center for Neurological Disorders (NCND), Shanghai, China
| | - Xiao Huan
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China
- Huashan Rare Disease Center, Shanghai Medical College, Huashan Hospital, Fudan University, Shanghai, China
- National Center for Neurological Disorders (NCND), Shanghai, China
| | - Jialong Zhang
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China
- Huashan Rare Disease Center, Shanghai Medical College, Huashan Hospital, Fudan University, Shanghai, China
- National Center for Neurological Disorders (NCND), Shanghai, China
| | - Yu Ding
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Xinghua Luan
- Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - LingChun Liu
- The First People's Hospital of Yunnan Province, Kunming, China
| | - Xilu Wang
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Bochen Zhu
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China
- Huashan Rare Disease Center, Shanghai Medical College, Huashan Hospital, Fudan University, Shanghai, China
- National Center for Neurological Disorders (NCND), Shanghai, China
| | - Kunzhao Du
- Jinshan Hospital Center for Neurosurgery, Jinshan Hospital, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
| | - Jiale Fan
- The State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, The Institutes of Brain Science, Shanghai, China
| | - Mingshi Gao
- Department of Pathology, Huashan Hospital, Fudan University, Shanghai, China
| | - Xingyu Xia
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China
- Huashan Rare Disease Center, Shanghai Medical College, Huashan Hospital, Fudan University, Shanghai, China
- National Center for Neurological Disorders (NCND), Shanghai, China
| | - Ningning Wang
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China
- Huashan Rare Disease Center, Shanghai Medical College, Huashan Hospital, Fudan University, Shanghai, China
- National Center for Neurological Disorders (NCND), Shanghai, China
| | - Tao Wang
- Department of Anesthesiology, Zhongshan Hospital, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
| | - Jianying Xi
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China
- Huashan Rare Disease Center, Shanghai Medical College, Huashan Hospital, Fudan University, Shanghai, China
- National Center for Neurological Disorders (NCND), Shanghai, China
| | - Sushan Luo
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China
- Huashan Rare Disease Center, Shanghai Medical College, Huashan Hospital, Fudan University, Shanghai, China
- National Center for Neurological Disorders (NCND), Shanghai, China
| | - Jiahong Lu
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China
- Huashan Rare Disease Center, Shanghai Medical College, Huashan Hospital, Fudan University, Shanghai, China
- National Center for Neurological Disorders (NCND), Shanghai, China
| | - Chongbo Zhao
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China
- Huashan Rare Disease Center, Shanghai Medical College, Huashan Hospital, Fudan University, Shanghai, China
- National Center for Neurological Disorders (NCND), Shanghai, China
| | - Dongyue Yue
- Department of Neurology, Jing'an District Center Hospital of Shanghai, Shanghai, China
| | - Wenhua Zhu
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China
- Huashan Rare Disease Center, Shanghai Medical College, Huashan Hospital, Fudan University, Shanghai, China
- National Center for Neurological Disorders (NCND), Shanghai, China
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Wilke MVMB, Klee EW, Dhamija R, Fervenza FC, Thomas B, Leung N, Hogan MC, Hager MM, Kolbert KJ, Kemppainen JL, Loftus EC, Leitzen KM, Vitek CR, McAllister T, Lazaridis KN, Pinto E Vairo F. Diagnostic yield of exome and genome sequencing after non-diagnostic multi-gene panels in patients with single-system diseases. Orphanet J Rare Dis 2024; 19:216. [PMID: 38790019 PMCID: PMC11127317 DOI: 10.1186/s13023-024-03213-x] [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: 01/30/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024] Open
Abstract
BACKGROUND Though next-generation sequencing (NGS) tests like exome sequencing (ES), genome sequencing (GS), and panels derived from exome and genome data (EGBP) are effective for rare diseases, the ideal diagnostic approach is debated. Limited research has explored reanalyzing raw ES and GS data post-negative EGBP results for diagnostics. RESULTS We analyzed complete ES/GS raw sequencing data from Mayo Clinic's Program for Rare and Undiagnosed Diseases (PRaUD) patients to assess whether supplementary findings could augment diagnostic yield. ES data from 80 patients (59 adults) and GS data from 20 patients (10 adults), averaging 43 years in age, were analyzed. Most patients had renal (n=44) and auto-inflammatory (n=29) phenotypes. Ninety-six cases had negative findings and in four cases additional genetic variants were found, including a variant related to a recently described disease (RRAGD-related hypomagnesemia), a variant missed due to discordant inheritance pattern (COL4A3), a variant with high allelic frequency (NPHS2) in the general population, and a variant associated with an initially untargeted phenotype (HNF1A). CONCLUSION ES and GS show diagnostic yields comparable to EGBP for single-system diseases. However, EGBP's limitations in detecting new disease-associated genes underscore the necessity for periodic updates.
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Affiliation(s)
| | - Eric W Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Radhika Dhamija
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | | | | | - Nelson Leung
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
| | - Marie C Hogan
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
| | | | - Kayla J Kolbert
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | | | - Elle C Loftus
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Katie M Leitzen
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Carolyn R Vitek
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Tammy McAllister
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Konstantinos N Lazaridis
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
- Division of Gastroenterology & Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Filippo Pinto E Vairo
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA.
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA.
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5
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Forrest IS, Duffy Á, Park JK, Vy HMT, Pasquale LR, Nadkarni GN, Cho JH, Do R. Genome-first evaluation with exome sequence and clinical data uncovers underdiagnosed genetic disorders in a large healthcare system. Cell Rep Med 2024; 5:101518. [PMID: 38642551 PMCID: PMC11148562 DOI: 10.1016/j.xcrm.2024.101518] [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: 11/04/2022] [Revised: 05/01/2023] [Accepted: 03/26/2024] [Indexed: 04/22/2024]
Abstract
Population-based genomic screening may help diagnose individuals with disease-risk variants. Here, we perform a genome-first evaluation for nine disorders in 29,039 participants with linked exome sequences and electronic health records (EHRs). We identify 614 individuals with 303 pathogenic/likely pathogenic or predicted loss-of-function (P/LP/LoF) variants, yielding 644 observations; 487 observations (76%) lack a corresponding clinical diagnosis in the EHR. Upon further investigation, 75 clinically undiagnosed observations (15%) have evidence of symptomatic untreated disease, including familial hypercholesterolemia (3 of 6 [50%] undiagnosed observations with disease evidence) and breast cancer (23 of 106 [22%]). These genetic findings enable targeted phenotyping that reveals new diagnoses in previously undiagnosed individuals. Disease yield is greater with variants in penetrant genes for which disease is observed in carriers in an independent cohort. The prevalence of P/LP/LoF variants exceeds that of clinical diagnoses, and some clinically undiagnosed carriers are discovered to have disease. These results highlight the potential of population-based genomic screening.
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Affiliation(s)
- Iain S Forrest
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Medical Scientist Training Program, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Áine Duffy
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Joshua K Park
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Medical Scientist Training Program, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ha My T Vy
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Center for Genomic Data Analytics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Louis R Pasquale
- Department of Ophthalmology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Eye and Vision Research Institute, New York Eye and Ear Infirmary of Mount Sinai, New York, NY 10003, USA
| | - Girish N Nadkarni
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Division of Data-driven and Digital Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Judy H Cho
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ron Do
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Center for Genomic Data Analytics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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6
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Sakaue S, Weinand K, Isaac S, Dey KK, Jagadeesh K, Kanai M, Watts GFM, Zhu Z, Brenner MB, McDavid A, Donlin LT, Wei K, Price AL, Raychaudhuri S. Tissue-specific enhancer-gene maps from multimodal single-cell data identify causal disease alleles. Nat Genet 2024; 56:615-626. [PMID: 38594305 DOI: 10.1038/s41588-024-01682-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 02/07/2024] [Indexed: 04/11/2024]
Abstract
Translating genome-wide association study (GWAS) loci into causal variants and genes requires accurate cell-type-specific enhancer-gene maps from disease-relevant tissues. Building enhancer-gene maps is essential but challenging with current experimental methods in primary human tissues. Here we developed a nonparametric statistical method, SCENT (single-cell enhancer target gene mapping), that models association between enhancer chromatin accessibility and gene expression in single-cell or nucleus multimodal RNA sequencing and ATAC sequencing data. We applied SCENT to 9 multimodal datasets including >120,000 single cells or nuclei and created 23 cell-type-specific enhancer-gene maps. These maps were highly enriched for causal variants in expression quantitative loci and GWAS for 1,143 diseases and traits. We identified likely causal genes for both common and rare diseases and linked somatic mutation hotspots to target genes. We demonstrate that application of SCENT to multimodal data from disease-relevant human tissue enables the scalable construction of accurate cell-type-specific enhancer-gene maps, essential for defining noncoding variant function.
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Affiliation(s)
- Saori Sakaue
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kathryn Weinand
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Shakson Isaac
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Kushal K Dey
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Karthik Jagadeesh
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Masahiro Kanai
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Gerald F M Watts
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Zhu Zhu
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Michael B Brenner
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Andrew McDavid
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY, USA
| | - Laura T Donlin
- Hospital for Special Surgery, New York, NY, USA
- Weill Cornell Medicine, New York, NY, USA
| | - Kevin Wei
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Alkes L Price
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Soumya Raychaudhuri
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
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7
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Liu K, Fu J, Guo K, Maghsoudloo M, Cheng J, Fu J. The ENG/VEGFα Pathway Is Likely Affected by a Nonsense Variant of Endoglin (ENG)/CD105, Causing Hereditary Hemorrhagic Telangiectasia Type 1 (HHT1) in a Chinese Family. Genes (Basel) 2024; 15:304. [PMID: 38540362 PMCID: PMC10970080 DOI: 10.3390/genes15030304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 02/20/2024] [Accepted: 02/23/2024] [Indexed: 06/14/2024] Open
Abstract
Hereditary hemorrhagic telangiectasia (HHT), also called Rendu-Osler syndrome, is a group of rare genetic diseases characterized by autosomal dominance, multisystemic vascular dysplasia, and age-related penetrance. This includes arteriovenous malformations (AVMs) in the skin, brain, lung, liver, and mucous membranes. The correlations between the phenotype and genotype for HHT are not clear. An HHT Chinese pedigree was recruited. Whole exome sequencing (WES) analysis, Sanger verification, and co-segregation were conducted. Western blotting was performed for monitoring ENG/VEGFα signaling. As a result, a nonsense, heterozygous variant for ENG/CD105: c.G1169A:p. Trp390Ter of the proband with hereditary hemorrhagic telangiectasia type 1 (HHT1) was identified, which co-segregated with the disease in the M666 pedigree. Western blotting found that, compared with the normal levels associated with non-carrier family members, the ENG protein levels in the proband showed approximately a one-half decrease (47.4% decrease), while levels of the VEGFα protein, in the proband, showed approximately a one-quarter decrease (25.6% decrease), implying that ENG haploinsufficiency, displayed in the carrier of this variant, may affect VEGFα expression downregulation. Pearson and Spearman correlation analyses further supported TGFβ/ENG/VEGFα signaling, implying ENG regulation in the blood vessels. Thus, next-generation sequencing including WES should provide an accurate strategy for gene diagnosis, therapy, genetic counseling, and clinical management for rare genetic diseases including that in HHT1 patients.
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Affiliation(s)
- Kemeng Liu
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou 646000, China; (K.L.); (J.F.); (K.G.); (M.M.); (J.C.)
| | - Jiewen Fu
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou 646000, China; (K.L.); (J.F.); (K.G.); (M.M.); (J.C.)
- School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, China
| | - Kan Guo
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou 646000, China; (K.L.); (J.F.); (K.G.); (M.M.); (J.C.)
| | - Mazaher Maghsoudloo
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou 646000, China; (K.L.); (J.F.); (K.G.); (M.M.); (J.C.)
| | - Jingliang Cheng
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou 646000, China; (K.L.); (J.F.); (K.G.); (M.M.); (J.C.)
| | - Junjiang Fu
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou 646000, China; (K.L.); (J.F.); (K.G.); (M.M.); (J.C.)
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8
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Jeon E, Koo B, Kim S, Kim J, Yu Y, Jang H, Lee M, Kim SH, Kang T, Kim SK, Kwak R, Shin Y, Lee J. Biporous silica nanostructure-induced nanovortex in microfluidics for nucleic acid enrichment, isolation, and PCR-free detection. Nat Commun 2024; 15:1366. [PMID: 38355558 PMCID: PMC10866868 DOI: 10.1038/s41467-024-45467-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 01/24/2024] [Indexed: 02/16/2024] Open
Abstract
Efficient pathogen enrichment and nucleic acid isolation are critical for accurate and sensitive diagnosis of infectious diseases, especially those with low pathogen levels. Our study introduces a biporous silica nanofilms-embedded sample preparation chip for pathogen and nucleic acid enrichment/isolation. This chip features unique biporous nanostructures comprising large and small pore layers. Computational simulations confirm that these nanostructures enhance the surface area and promote the formation of nanovortex, resulting in improved capture efficiency. Notably, the chip demonstrates a 100-fold lower limit of detection compared to conventional methods used for nucleic acid detection. Clinical validations using patient samples corroborate the superior sensitivity of the chip when combined with the luminescence resonance energy transfer assay. The enhanced sample preparation efficiency of the chip, along with the facile and straightforward synthesis of the biporous nanostructures, offers a promising solution for polymer chain reaction-free detection of nucleic acids.
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Affiliation(s)
- Eunyoung Jeon
- Department of Chemistry, Hanyang University, Seoul, 04763, Republic of Korea
- Research Institute for Natural Science, Hanyang University, Seoul, 04763, Republic of Korea
- Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul, 04763, Republic of Korea
| | - Bonhan Koo
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Suyeon Kim
- Department of Chemistry, Hanyang University, Seoul, 04763, Republic of Korea
- Research Institute for Natural Science, Hanyang University, Seoul, 04763, Republic of Korea
- Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul, 04763, Republic of Korea
| | - Jieun Kim
- Department of Mechanical Convergence Engineering, Hanyang University, Seoul, 04763, Republic of Korea
| | - Yeonuk Yu
- Department of Mechanical Convergence Engineering, Hanyang University, Seoul, 04763, Republic of Korea
| | - Hyowon Jang
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Minju Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Sung-Han Kim
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, Republic of Korea
| | - Taejoon Kang
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Sang Kyung Kim
- Center for Augmented Safety Systems with Intelligence, Sensing and Tracking (ASSIST), Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea
| | - Rhokyun Kwak
- Department of Mechanical Convergence Engineering, Hanyang University, Seoul, 04763, Republic of Korea.
| | - Yong Shin
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea.
| | - Joonseok Lee
- Department of Chemistry, Hanyang University, Seoul, 04763, Republic of Korea.
- Research Institute for Natural Science, Hanyang University, Seoul, 04763, Republic of Korea.
- Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul, 04763, Republic of Korea.
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9
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Mudau MM, Seymour H, Nevondwe P, Kerr R, Spencer C, Feben C, Lombard Z, Honey E, Krause A, Carstens N. A feasible molecular diagnostic strategy for rare genetic disorders within resource-constrained environments. J Community Genet 2024; 15:39-48. [PMID: 37815686 PMCID: PMC10858011 DOI: 10.1007/s12687-023-00674-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 09/19/2023] [Indexed: 10/11/2023] Open
Abstract
Timely and accurate diagnosis of rare genetic disorders is critical, as it enables improved patient management and prognosis. In a resource-constrained environment such as the South African State healthcare system, the challenge is to design appropriate and cost-effective assays that will enable accurate genetic diagnostic services in patients of African ancestry across a broad disease spectrum. Next-generation sequencing (NGS) has transformed testing approaches for many Mendelian disorders, but this technology is still relatively new in our setting and requires cost-effective ways to implement. As a proof of concept, we describe a feasible diagnostic strategy for genetic disorders frequently seen in our genetics clinics (RASopathies, Cornelia de Lange syndrome, Treacher Collins syndrome, and CHARGE syndrome). The custom-designed targeted NGS gene panel enabled concurrent variant screening for these disorders. Samples were batched during sequencing and analyzed selectively based on the clinical phenotype. The strategy employed in the current study was cost-effective, with sequencing and analysis done at USD849.68 per sample and achieving an overall detection rate of 54.5%. The strategy employed is cost-effective as it allows batching of samples from patients with different diseases in a single run, an approach that can be utilized with rare and less frequently ordered molecular diagnostic tests. The subsequent selective analysis pipeline allowed for timeous reporting back of patients results. This is feasible with a reasonable yield and can be employed for the molecular diagnosis of a wide range of rare monogenic disorders in a resource-constrained environment.
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Affiliation(s)
- Maria Mabyalwa Mudau
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Heather Seymour
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Patracia Nevondwe
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Robyn Kerr
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Careni Spencer
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Candice Feben
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Zané Lombard
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Engela Honey
- Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa
| | - Amanda Krause
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nadia Carstens
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Genomics Platform, South African Medical Research Council, Cape Town, South Africa
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10
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Sim B, Ng JWZ, Sim DY, Goh J, Kam S, Teo JX, Lim WW, Lieviant J, Lim WK, Lim SA, Tang PH, Ling S, Ng SWL, Roca X, Jamuar SS. A novel intronic variant in ROBO3 associated with horizontal gaze palsy with progressive scoliosis: case report and literature review. J AAPOS 2023; 27:359-363. [PMID: 37931836 DOI: 10.1016/j.jaapos.2023.08.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/31/2023] [Accepted: 08/03/2023] [Indexed: 11/08/2023]
Abstract
Horizontal gaze palsy with progressive scoliosis (HGPPS) is a rare, autosomal recessive inherited disorder caused by mutations in ROBO3 gene. The clinical features of HGPPS include horizontal gaze palsy, progressive scoliosis, other oculomotor abnormalities such as strabismus and nystagmus. Whole-exome sequencing (WES) is used to diagnose rare Mendelian disorders, when routine standard tests have failed to make a formal pathological diagnosis. However, WES may identify variants of uncertain significance (VUS) that may add further ambiguity to the diagnosis. We report the case of a 4-year-old boy with horizontal gaze palsy, progressive scoliosis, microcephaly, and mild developmental delay. WES identified an intronic VUS in ROBO3 gene. We performed minigene splicing functional analysis to confirm the pathogenicity of this VUS. This report illustrates that WES data analysis with supportive functional analysis provides an effective approach to improve the diagnostic yield for unsolved clinical cases. This case also highlights the phenotypic heterogeneity in patients with HGPPS.
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Affiliation(s)
- Bryan Sim
- Neuro-Ophthalmology Service, KKH Eye Centre, KK Women's and Children's Hospital, Singapore; Myopia Service, Singapore National Eye Centre (SNEC), Singapore
| | - Janice Wan Zhen Ng
- School of Biological Sciences, Nanyang Technological University Singapore
| | - Donald Yuhui Sim
- School of Biological Sciences, Nanyang Technological University Singapore
| | - Jeannette Goh
- Genetics Service, Department of Paediatrics, KK Women's and Children's Hospital, Singapore; SingHealth Duke-NUS Genomic Medicine Centre, Singapore
| | - Sylvia Kam
- Genetics Service, Department of Paediatrics, KK Women's and Children's Hospital, Singapore; SingHealth Duke-NUS Genomic Medicine Centre, Singapore
| | - Jing Xian Teo
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore
| | - Wan Wan Lim
- Cancer & Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Jane Lieviant
- Cancer & Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Weng Khong Lim
- SingHealth Duke-NUS Genomic Medicine Centre, Singapore; SingHealth Duke-NUS Institute of Precision Medicine, Singapore; Cancer & Stem Cell Biology Program, Duke-NUS Medical School, Singapore; Laboratory of Genome Variation Analytics, Genome Institute of Singapore, Singapore
| | - Su Ann Lim
- Neuro-Ophthalmology Service, KKH Eye Centre, KK Women's and Children's Hospital, Singapore; Department of Ophthalmology, Tan Tock Seng Hospital, Singapore
| | - Phua Hwee Tang
- Department of Radiology, KK Women's and Children's Hospital, Singapore
| | - Simon Ling
- Neurology Service, Department of Paediatrics, KK Women's and Children's Hospital, Singapore
| | - Stacy Wei Ling Ng
- Department of Orthopaedics, KK Women's and Children's Hospital, Singapore
| | - Xavier Roca
- School of Biological Sciences, Nanyang Technological University Singapore
| | - Saumya Shekhar Jamuar
- Genetics Service, Department of Paediatrics, KK Women's and Children's Hospital, Singapore; SingHealth Duke-NUS Genomic Medicine Centre, Singapore; SingHealth Duke-NUS Institute of Precision Medicine, Singapore.
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11
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Yadav D, Patil-Takbhate B, Khandagale A, Bhawalkar J, Tripathy S, Khopkar-Kale P. Next-Generation sequencing transforming clinical practice and precision medicine. Clin Chim Acta 2023; 551:117568. [PMID: 37839516 DOI: 10.1016/j.cca.2023.117568] [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: 07/08/2023] [Revised: 09/27/2023] [Accepted: 09/27/2023] [Indexed: 10/17/2023]
Abstract
Next-generation sequencing (NGS) has revolutionized the field of genomics and is rapidly transforming clinical diagnosis and precision medicine. This advanced sequencing technology enables the rapid and cost-effective analysis of large-scale genomic data, allowing comprehensive exploration of the genetic landscape of diseases. In clinical diagnosis, NGS has proven to be a powerful tool for identifying disease-causing variants, enabling accurate and early detection of genetic disorders. Additionally, NGS facilitates the identification of novel disease-associated genes and variants, aiding in the development of targeted therapies and personalized treatment strategies. NGS greatly benefits precision medicine by enhancing our understanding of disease mechanisms and enabling the identification of specific molecular markers for disease subtypes, thus enabling tailored medical interventions based on individual characteristics. Furthermore, NGS contributes to the development of non-invasive diagnostic approaches, such as liquid biopsies, which can monitor disease progression and treatment response. The potential of NGS in clinical diagnosis and precision medicine is vast, yet challenges persist in data analysis, interpretation, and protocol standardization. This review highlights NGS applications in disease diagnosis, prognosis, and personalized treatment strategies, while also addressing challenges and future prospects in fully harnessing genomic potential within clinical practice.
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Affiliation(s)
- Deepali Yadav
- Central Research Facility, Dr. D.Y Patil Medical College, Hospital & Research Centre, Dr. D. Y. Patil Vidyapeeth, Pimpri Pune 411018, India; Department of Biotechnology, Dr. D. Y. Patil Arts Science and Commerce College, Pimpri Pune 411018, India
| | - Bhagyashri Patil-Takbhate
- Central Research Facility, Dr. D.Y Patil Medical College, Hospital & Research Centre, Dr. D. Y. Patil Vidyapeeth, Pimpri Pune 411018, India
| | - Anil Khandagale
- Department of Biotechnology, Dr. D. Y. Patil Arts Science and Commerce College, Pimpri Pune 411018, India
| | - Jitendra Bhawalkar
- Department of Community Medicine, Dr. D.Y Patil Medical College, Hospital & Research Centre, Dr. D. Y. Patil Vidyapeeth, Pimpri Pune 411018, India
| | - Srikanth Tripathy
- Central Research Facility, Dr. D.Y Patil Medical College, Hospital & Research Centre, Dr. D. Y. Patil Vidyapeeth, Pimpri Pune 411018, India.
| | - Priyanka Khopkar-Kale
- Central Research Facility, Dr. D.Y Patil Medical College, Hospital & Research Centre, Dr. D. Y. Patil Vidyapeeth, Pimpri Pune 411018, India.
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12
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Deshmukh R, Ong ZZ, Rampat R, Alió del Barrio JL, Barua A, Ang M, Mehta JS, Said DG, Dua HS, Ambrósio R, Ting DSJ. Management of keratoconus: an updated review. Front Med (Lausanne) 2023; 10:1212314. [PMID: 37409272 PMCID: PMC10318194 DOI: 10.3389/fmed.2023.1212314] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 05/30/2023] [Indexed: 07/07/2023] Open
Abstract
Keratoconus is the most common corneal ectatic disorder. It is characterized by progressive corneal thinning with resultant irregular astigmatism and myopia. Its prevalence has been estimated at 1:375 to 1:2,000 people globally, with a considerably higher rate in the younger populations. Over the past two decades, there was a paradigm shift in the management of keratoconus. The treatment has expanded significantly from conservative management (e.g., spectacles and contact lenses wear) and penetrating keratoplasty to many other therapeutic and refractive modalities, including corneal cross-linking (with various protocols/techniques), combined CXL-keratorefractive surgeries, intracorneal ring segments, anterior lamellar keratoplasty, and more recently, Bowman's layer transplantation, stromal keratophakia, and stromal regeneration. Several recent large genome-wide association studies (GWAS) have identified important genetic mutations relevant to keratoconus, facilitating the development of potential gene therapy targeting keratoconus and halting the disease progression. In addition, attempts have been made to leverage the power of artificial intelligence-assisted algorithms in enabling earlier detection and progression prediction in keratoconus. In this review, we provide a comprehensive overview of the current and emerging treatment of keratoconus and propose a treatment algorithm for systematically guiding the management of this common clinical entity.
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Affiliation(s)
- Rashmi Deshmukh
- Department of Cornea and Refractive Surgery, LV Prasad Eye Institute, Hyderabad, India
| | - Zun Zheng Ong
- Department of Ophthalmology, Queen’s Medical Centre, Nottingham, United Kingdom
| | - Radhika Rampat
- Department of Ophthalmology, Royal Free London NHS Foundation Trust, London, United Kingdom
| | - Jorge L. Alió del Barrio
- Cornea, Cataract and Refractive Surgery Unit, Vissum (Miranza Group), Alicante, Spain
- Division of Ophthalmology, School of Medicine, Universidad Miguel Hernández, Alicante, Spain
| | - Ankur Barua
- Birmingham and Midland Eye Centre, Birmingham, United Kingdom
| | - Marcus Ang
- Singapore National Eye Centre, Singapore Eye Research Institute, Singapore, Singapore
| | - Jodhbir S. Mehta
- Singapore National Eye Centre, Singapore Eye Research Institute, Singapore, Singapore
| | - Dalia G. Said
- Department of Ophthalmology, Queen’s Medical Centre, Nottingham, United Kingdom
- Academic Ophthalmology, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Harminder S. Dua
- Department of Ophthalmology, Queen’s Medical Centre, Nottingham, United Kingdom
- Academic Ophthalmology, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Renato Ambrósio
- Department of Cornea and Refractive Surgery, Instituto de Olhos Renato Ambrósio, Rio de Janeiro, Brazil
- Department of Ophthalmology, Federal University of the State of Rio de Janeiro (UNIRIO), Rio de Janeiro, Brazil
- Federal University of São Paulo (UNIFESP), São Paulo, Brazil
| | - Darren Shu Jeng Ting
- Birmingham and Midland Eye Centre, Birmingham, United Kingdom
- Academic Ophthalmology, School of Medicine, University of Nottingham, Nottingham, United Kingdom
- Academic Unit of Ophthalmology, Institute of Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
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13
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Fu S, Fu J, Mobasher-Jannat A, Jadidi K, Li Y, Chen R, Imani S, Cheng J. Novel pathogenic CERKL variant in Iranian familial with inherited retinal dystrophies: genotype-phenotype correlation. 3 Biotech 2023; 13:166. [PMID: 37162806 PMCID: PMC10163994 DOI: 10.1007/s13205-023-03535-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 03/28/2023] [Indexed: 05/11/2023] Open
Abstract
Inherited retinal dystrophies (IRDs) include a large chronic heterogeneity genetic disease. While many disease-causing pathogenic variants were involved in the progression of IRD, the Ceramide Kinase Like (CERKL) gene variant in Iranian patients is not well characterized. In this study, a consanguineous Iranian family with three generations was recruited whom presented with the clinical diagnosis of autosomal recessive IRD. By targeted next-generation sequencing (TGS) and Sanger sequencing, the proband was found to have a novel, pathological homozygous deletion variant c.560_568del (p.187_190del) of the CERKL gene (NM_001030311.2) that co-segregated with the disease in all affected family members. The Cerkl is highly expressed in the later four developmental retinal stages, playing a vital role in retina degeneration. Therefore, the identification of a novel, homozygous deletion CERKL variant c.560_568del (p.187_190del) in an IRD familial cohort descent provides insights into the molecular pathogenesis of IRD and facilitates genetic counseling and disease prediction.
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Affiliation(s)
- Shangyi Fu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
- School of Medicine, Baylor College of Medicine, Houston, TX USA
| | - Jiewen Fu
- Key Laboratory of Epigenetics and Oncology, Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, Sichuan 646000 People’s Republic of China
| | | | - Khosrow Jadidi
- Department of Ophthalmology, Bina Eye Hospital Research Center, Tehran, Iran
| | - Yumei Li
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - Rui Chen
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - Saber Imani
- Key Laboratory of Epigenetics and Oncology, Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, Sichuan 646000 People’s Republic of China
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, Zhejiang China
| | - Jingliang Cheng
- Key Laboratory of Epigenetics and Oncology, Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, Sichuan 646000 People’s Republic of China
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14
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Banerjee J, Taroni JN, Allaway RJ, Prasad DV, Guinney J, Greene C. Machine learning in rare disease. Nat Methods 2023:10.1038/s41592-023-01886-z. [PMID: 37248386 DOI: 10.1038/s41592-023-01886-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 04/22/2023] [Indexed: 05/31/2023]
Abstract
High-throughput profiling methods (such as genomics or imaging) have accelerated basic research and made deep molecular characterization of patient samples routine. These approaches provide a rich portrait of genes, molecular pathways and cell types involved in disease phenotypes. Machine learning (ML) can be a useful tool for extracting disease-relevant patterns from high-dimensional datasets. However, depending upon the complexity of the biological question, machine learning often requires many samples to identify recurrent and biologically meaningful patterns. Rare diseases are inherently limited in clinical cases, leading to few samples to study. In this Perspective, we outline the challenges and emerging solutions for using ML for small sample sets, specifically in rare diseases. Advances in ML methods for rare diseases are likely to be informative for applications beyond rare diseases for which few samples exist with high-dimensional data. We propose that the method community prioritize the development of ML techniques for rare disease research.
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Affiliation(s)
| | - Jaclyn N Taroni
- Childhood Cancer Data Lab, Alex's Lemonade Stand Foundation, Philadelphia, PA, USA
| | | | | | | | - Casey Greene
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, USA.
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15
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Liu Y, Mao L, Huang H, Li W, Man J, Zhang W, Wang L, Li L, Sun Y, Zhai T, Guo X, Du L, Huang J, Li H, Wan Y, Wei X. Clinical diagnosis of genetic disorders at both single-nucleotide and chromosomal levels based on BGISEQ-500 platform. Hum Genome Var 2023; 10:15. [PMID: 37217505 PMCID: PMC10203365 DOI: 10.1038/s41439-023-00238-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 02/05/2023] [Accepted: 02/19/2023] [Indexed: 05/24/2023] Open
Abstract
Most variations in the human genome refer to single-nucleotide variation (SNV), small fragment insertions and deletions, and genomic copy number variation (CNV). Many human diseases including genetic disorders are associated with variations in the genome. These disorders are often difficult to be diagnosed because of their complex clinical conditions, therefore, an effective detection method is needed to facilitate clinical diagnosis and prevent birth defects. With the development of high-throughput sequencing technology, the method of targeted sequence capture chip has been extensively used owing to its high throughput, high accuracy, fast speed, and low cost. In this study, we designed a chip that potentially captured the coding region of 3043 genes associated with 4013 monogenic diseases, with an addition of 148 chromosomal abnormalities that can be identified by targeting specific regions. To assess the efficiency, a strategy of combining the BGISEQ500 sequencing platform with the designed chip was utilized to screen variants in 63 patients. Eventually, 67 disease-associated variants were found, 31 of which were novel. The results of the evaluation test also show that this combined strategy complies with the requirements of clinical testing and has proper clinical application value.
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Affiliation(s)
- Yanqiu Liu
- Department of Genetics, Jiangxi Maternal and Child Health Hospital, 330006, Nanchang, China
| | - Liangwei Mao
- BGI-Anhui Clinical Laboratory, BGI-Shenzhen, 236000, Fuyang, China
- The State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, 430062, Wuhan, China
| | - Hui Huang
- BGI Genomics, BGI-Shenzhen, 518083, Shenzhen, China
| | - Wei Li
- BGI Genomics, BGI-Shenzhen, 518083, Shenzhen, China
| | - Jianfen Man
- BGI-Wuhan Clinical Laboratory, BGI-Shenzhen, 430074, Wuhan, China
| | - Wenqian Zhang
- BGI Genomics, BGI-Shenzhen, 518083, Shenzhen, China
- BGI-Wuhan Clinical Laboratory, BGI-Shenzhen, 430074, Wuhan, China
- Department of Biology, University of Copenhagen, Copenhagen, DK-2200, Denmark
| | - Lina Wang
- BGI-Wuhan Clinical Laboratory, BGI-Shenzhen, 430074, Wuhan, China
| | - Long Li
- BGI-Wuhan Clinical Laboratory, BGI-Shenzhen, 430074, Wuhan, China
| | - Yan Sun
- BGI Genomics, BGI-Shenzhen, 518083, Shenzhen, China
| | - Teng Zhai
- BGI Genomics, BGI-Shenzhen, 518083, Shenzhen, China
| | - Xueqin Guo
- BGI-Wuhan Clinical Laboratory, BGI-Shenzhen, 430074, Wuhan, China
| | - Lique Du
- BGI-Wuhan Clinical Laboratory, BGI-Shenzhen, 430074, Wuhan, China
| | - Jin Huang
- BGI-Wuhan Clinical Laboratory, BGI-Shenzhen, 430074, Wuhan, China
| | - Hao Li
- BGI-Anhui Clinical Laboratory, BGI-Shenzhen, 236000, Fuyang, China
| | - Yang Wan
- Department of Obstetrics and Gynecology, Fuyang People's Hospital, 236000, Fuyang, China.
| | - Xiaoming Wei
- BGI-Wuhan Clinical Laboratory, BGI-Shenzhen, 430074, Wuhan, China.
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16
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Wright CF, Campbell P, Eberhardt RY, Aitken S, Perrett D, Brent S, Danecek P, Gardner EJ, Chundru VK, Lindsay SJ, Andrews K, Hampstead J, Kaplanis J, Samocha KE, Middleton A, Foreman J, Hobson RJ, Parker MJ, Martin HC, FitzPatrick DR, Hurles ME, Firth HV. Genomic Diagnosis of Rare Pediatric Disease in the United Kingdom and Ireland. N Engl J Med 2023; 388:1559-1571. [PMID: 37043637 PMCID: PMC7614484 DOI: 10.1056/nejmoa2209046] [Citation(s) in RCA: 57] [Impact Index Per Article: 57.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
BACKGROUND Pediatric disorders include a range of highly penetrant, genetically heterogeneous conditions amenable to genomewide diagnostic approaches. Finding a molecular diagnosis is challenging but can have profound lifelong benefits. METHODS We conducted a large-scale sequencing study involving more than 13,500 families with probands with severe, probably monogenic, difficult-to-diagnose developmental disorders from 24 regional genetics services in the United Kingdom and Ireland. Standardized phenotypic data were collected, and exome sequencing and microarray analyses were performed to investigate novel genetic causes. We developed an iterative variant analysis pipeline and reported candidate variants to clinical teams for validation and diagnostic interpretation to inform communication with families. Multiple regression analyses were performed to evaluate factors affecting the probability of diagnosis. RESULTS A total of 13,449 probands were included in the analyses. On average, we reported 1.0 candidate variant per parent-offspring trio and 2.5 variants per singleton proband. Using clinical and computational approaches to variant classification, we made a diagnosis in approximately 41% of probands (5502 of 13,449). Of 3599 probands in trios who received a diagnosis by clinical assertion, approximately 76% had a pathogenic de novo variant. Another 22% of probands (2997 of 13,449) had variants of uncertain significance in genes that were strongly linked to monogenic developmental disorders. Recruitment in a parent-offspring trio had the largest effect on the probability of diagnosis (odds ratio, 4.70; 95% confidence interval [CI], 4.16 to 5.31). Probands were less likely to receive a diagnosis if they were born extremely prematurely (i.e., 22 to 27 weeks' gestation; odds ratio, 0.39; 95% CI, 0.22 to 0.68), had in utero exposure to antiepileptic medications (odds ratio, 0.44; 95% CI, 0.29 to 0.67), had mothers with diabetes (odds ratio, 0.52; 95% CI, 0.41 to 0.67), or were of African ancestry (odds ratio, 0.51; 95% CI, 0.31 to 0.78). CONCLUSIONS Among probands with severe, probably monogenic, difficult-to-diagnose developmental disorders, multimodal analysis of genomewide data had good diagnostic power, even after previous attempts at diagnosis. (Funded by the Health Innovation Challenge Fund and Wellcome Sanger Institute.).
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Affiliation(s)
- Caroline F. Wright
- Department of Clinical and Biomedical Sciences, University of Exeter Medical School, RILD Building, Royal Devon & Exeter Hospital, Barrack Road, Exeter UK, EX2 5DW
| | - Patrick Campbell
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
- Cambridge University Hospitals Foundation Trust, Addenbrooke’s Hospital, Cambridge UK, CB2 0QQ
| | - Ruth Y. Eberhardt
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
| | - Stuart Aitken
- MRC Human Genetics Unit, Institute of Genetic and Cancer, University of Edinburgh, Edinburgh UK, EH4 2XU
| | - Daniel Perrett
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SD
| | - Simon Brent
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SD
| | - Petr Danecek
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
| | - Eugene J. Gardner
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
| | - V. Kartik Chundru
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
| | - Sarah J. Lindsay
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
| | - Katrina Andrews
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
| | - Juliet Hampstead
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
| | - Joanna Kaplanis
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
| | - Kaitlin E. Samocha
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
| | - Anna Middleton
- Wellcome Connecting Science, Wellcome Genome Campus, Hinxton, Cambridge, UK, CB10 1SA
| | - Julia Foreman
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SD
| | - Rachel J. Hobson
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
| | - Michael J. Parker
- Wellcome Centre for Ethics and Humanities/Ethox Centre, Oxford Population Health, University of Oxford, Big Data Institute, Old Road Campus, Oxford, UK, OX3 7LF
| | - Hilary C. Martin
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
| | - David R. FitzPatrick
- MRC Human Genetics Unit, Institute of Genetic and Cancer, University of Edinburgh, Edinburgh UK, EH4 2XU
| | - Matthew E. Hurles
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
| | - Helen V. Firth
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
- Cambridge University Hospitals Foundation Trust, Addenbrooke’s Hospital, Cambridge UK, CB2 0QQ
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17
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Yang L, Fu J, Cheng J, Zhou B, Chen M, Anuchapreeda S, Fu J. Novel, heterozygous, de novo pathogenic variant (c.4963delA: p.Thr1656Glnfs*42) of the NF1 gene in a Chinese family with neurofibromatosis type 1. BMC Med Genomics 2023; 16:85. [PMID: 37095468 PMCID: PMC10123994 DOI: 10.1186/s12920-023-01514-x] [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: 10/26/2022] [Accepted: 04/09/2023] [Indexed: 04/26/2023] Open
Abstract
Neurofibromatosis type 1 (NF1) presents an autosomal dominant, haploinsufficient, and multisystemic disorder with patches of skin café-au-lait spots, lisch nodules in the iris, even tumors in the peripheral nervous system or fibromatous skin. In this study, a Chinese young woman who suffered from NF1 disease with first-trimester spontaneous abortion was recruited. Analysis for whole exome sequencing (WES), Sanger sequencing, short tandem repeat (STR), and co-segregation was carried out. As results, a novel, heterozygous, de novo pathogenic variant (c.4963delA:p.Thr1656Glnfs*42) of the NF1 gene in the proband was identified. This pathogenic variant of the NF1 gene produced a truncated protein that lost more than one-third of the NF1 protein at the C-terminus including half of the CRAL-TRIO lipid-binding domain and nuclear localization signal (NLS), thus leading to pathogenicity (ACMG criteria: PVS1 + PM2 + PM2). Analysis for NF1 conservation in species revealed high conservation in different species. Analysis of NF1 mRNA levels in different human tissues showed low tissue specificity, which may affect multiple organs presenting other symptoms or phenotypes. Moreover, prenatal NF1 gene diagnosis showed both alleles as wild types. Thus, this NF1 novel variant probably underlays the NF1 pathogenesis in this pedigree, which would help for the diagnosis, genetic counseling, and clinical management of this disorder.
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Affiliation(s)
- Lisha Yang
- Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, 3-319, Zhongshan Rd, Luzhou, Sichuan, 646000, China
- Department of Obstetrics, the Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, 646000, China
| | - Jiewen Fu
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, 3-319, Zhongshan Rd, Luzhou, Sichuan, 646000, China
| | - Jingliang Cheng
- Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, 3-319, Zhongshan Rd, Luzhou, Sichuan, 646000, China
| | - Baixu Zhou
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, 3-319, Zhongshan Rd, Luzhou, Sichuan, 646000, China
- Department of Gynecology and Obstetrics, Guangdong Women and Children Hospital, Guangzhou, Guangdong, China
| | - Maomei Chen
- Department of Obstetrics, the Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, 646000, China
| | - Songyot Anuchapreeda
- Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand.
- Research Center of Pharmaceutical Nanotechnology, Chiang Mai University, Chiang Mai, 50200, Thailand.
| | - Junjiang Fu
- Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand.
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, 3-319, Zhongshan Rd, Luzhou, Sichuan, 646000, China.
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18
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Yauy K, Van Goethem C, Pégeot H, Baux D, Guignard T, Thèze C, Ardouin O, Roux AF, Koenig M, Bergougnoux A, Cossée M. Evaluating the Transition from Targeted to Exome Sequencing: A Guide for Clinical Laboratories. Int J Mol Sci 2023; 24:ijms24087330. [PMID: 37108493 PMCID: PMC10138641 DOI: 10.3390/ijms24087330] [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: 03/15/2023] [Revised: 04/03/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
The transition from targeted to exome or genome sequencing in clinical contexts requires quality standards, such as targeted sequencing, in order to be fully adopted. However, no clear recommendations or methodology have emerged for evaluating this technological evolution. We developed a structured method based on four run-specific sequencing metrics and seven sample-specific sequencing metrics for evaluating the performance of exome sequencing strategies to replace targeted strategies. The indicators include quality metrics and coverage performance on gene panels and OMIM morbid genes. We applied this general strategy to three different exome kits and compared them with a myopathy-targeted sequencing method. After having achieved 80 million reads, all-tested exome kits generated data suitable for clinical diagnosis. However, significant differences in the coverage and PCR duplicates were observed between the kits. These are two main criteria to consider for the initial implementation with high-quality assurance. This study aims to assist molecular diagnostic laboratories in adopting and evaluating exome sequencing kits in a diagnostic context compared to the strategy used previously. A similar strategy could be used to implement whole-genome sequencing for diagnostic purposes.
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Affiliation(s)
- Kevin Yauy
- Laboratoire de Génétique Moléculaire, LGM, Centre Hospitalier Universitaire de Montpellier, IURC-Institut Universitaire de Recherche Clinique, 641 Avenue du Doyen G. Giraud, 34090 Montpellier, France
- Service de Génétique Médicale, CHU Montpellier, 371 Avenue du Doyen G. Giraud, 34090 Montpellier, France
| | - Charles Van Goethem
- Laboratoire de Génétique Moléculaire, LGM, Centre Hospitalier Universitaire de Montpellier, IURC-Institut Universitaire de Recherche Clinique, 641 Avenue du Doyen G. Giraud, 34090 Montpellier, France
| | - Henri Pégeot
- Laboratoire de Génétique Moléculaire, LGM, Centre Hospitalier Universitaire de Montpellier, IURC-Institut Universitaire de Recherche Clinique, 641 Avenue du Doyen G. Giraud, 34090 Montpellier, France
| | - David Baux
- Laboratoire de Génétique Moléculaire, LGM, Centre Hospitalier Universitaire de Montpellier, IURC-Institut Universitaire de Recherche Clinique, 641 Avenue du Doyen G. Giraud, 34090 Montpellier, France
- INM, Université de Montpellier, INSERM, Hôpital Saint Eloi-Bâtiment INM 80, rue Augustin Fliche-BP 74103, 34090 Montpellier, France
| | - Thomas Guignard
- Unité de Génétique Chromosomique, Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, Hôpital Arnaud de Villeneuve, CHU de Montpellier, 371 Av. du Doyen Gaston Giraud, 34090 Montpellier, France
| | - Corinne Thèze
- Laboratoire de Génétique Moléculaire, LGM, Centre Hospitalier Universitaire de Montpellier, IURC-Institut Universitaire de Recherche Clinique, 641 Avenue du Doyen G. Giraud, 34090 Montpellier, France
| | - Olivier Ardouin
- Plateau de Médecine Moléculaire et Génomique, Hôpital Arnaud de Villeneuve, CHU de Montpellier, 34090 Montpellier, France
| | - Anne-Françoise Roux
- Laboratoire de Génétique Moléculaire, LGM, Centre Hospitalier Universitaire de Montpellier, IURC-Institut Universitaire de Recherche Clinique, 641 Avenue du Doyen G. Giraud, 34090 Montpellier, France
- INM, Université de Montpellier, INSERM, Hôpital Saint Eloi-Bâtiment INM 80, rue Augustin Fliche-BP 74103, 34090 Montpellier, France
| | - Michel Koenig
- Laboratoire de Génétique Moléculaire, LGM, Centre Hospitalier Universitaire de Montpellier, IURC-Institut Universitaire de Recherche Clinique, 641 Avenue du Doyen G. Giraud, 34090 Montpellier, France
- PhyMedExp-Physiologie et Médecine Expérimentale du Cœur et des Muscles, Université de Montpellier, Inserm U1046, CNRS UMR 9214, 371 Avenue du Doyen G. Giraud, 34090 Montpellier, France
| | - Anne Bergougnoux
- Laboratoire de Génétique Moléculaire, LGM, Centre Hospitalier Universitaire de Montpellier, IURC-Institut Universitaire de Recherche Clinique, 641 Avenue du Doyen G. Giraud, 34090 Montpellier, France
- PhyMedExp-Physiologie et Médecine Expérimentale du Cœur et des Muscles, Université de Montpellier, Inserm U1046, CNRS UMR 9214, 371 Avenue du Doyen G. Giraud, 34090 Montpellier, France
| | - Mireille Cossée
- Laboratoire de Génétique Moléculaire, LGM, Centre Hospitalier Universitaire de Montpellier, IURC-Institut Universitaire de Recherche Clinique, 641 Avenue du Doyen G. Giraud, 34090 Montpellier, France
- PhyMedExp-Physiologie et Médecine Expérimentale du Cœur et des Muscles, Université de Montpellier, Inserm U1046, CNRS UMR 9214, 371 Avenue du Doyen G. Giraud, 34090 Montpellier, France
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19
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Tariq Z, Qadeer MI, Anjum I, Hano C, Anjum S. Thalassemia and Nanotheragnostics: Advanced Approaches for Diagnosis and Treatment. BIOSENSORS 2023; 13:bios13040450. [PMID: 37185525 PMCID: PMC10136341 DOI: 10.3390/bios13040450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/20/2023] [Accepted: 03/27/2023] [Indexed: 05/17/2023]
Abstract
Thalassemia is a monogenic autosomal recessive disorder caused by mutations, which lead to abnormal or reduced production of hemoglobin. Ineffective erythropoiesis, hemolysis, hepcidin suppression, and iron overload are common manifestations that vary according to genotypes and dictate, which diagnosis and therapeutic modalities, including transfusion therapy, iron chelation therapy, HbF induction, gene therapy, and editing, are performed. These conventional therapeutic methods have proven to be effective, yet have several disadvantages, specifically iron toxicity, associated with them; therefore, there are demands for advanced therapeutic methods. Nanotechnology-based applications, such as the use of nanoparticles and nanomedicines for theragnostic purposes have emerged that are simple, convenient, and cost-effective methods. The therapeutic potential of various nanoparticles has been explored by developing artificial hemoglobin, nano-based iron chelating agents, and nanocarriers for globin gene editing by CRISPR/Cas9. Au, Ag, carbon, graphene, silicon, porous nanoparticles, dendrimers, hydrogels, quantum dots, etc., have been used in electrochemical biosensors development for diagnosis of thalassemia, quantification of hemoglobin in these patients, and analysis of conventional iron chelating agents. This review summarizes the potential of nanotechnology in the development of various theragnostic approaches to determine thalassemia-causing gene mutations using various nano-based biosensors along with the employment of efficacious nano-based therapeutic procedures, in contrast to conventional therapies.
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Affiliation(s)
- Zahra Tariq
- Department of Biotechnology, Kinnaird College for Women, 92-Jail Road, Lahore 54000, Pakistan
| | | | - Iram Anjum
- Department of Biotechnology, Kinnaird College for Women, 92-Jail Road, Lahore 54000, Pakistan
| | - Christophe Hano
- Department of Chemical Biology, Eure & Loir Campus, University of Orleans, 28000 Chartres, France
| | - Sumaira Anjum
- Department of Biotechnology, Kinnaird College for Women, 92-Jail Road, Lahore 54000, Pakistan
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20
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Geladari E, Vallianou N, Geladari C, Aronis K, Vlachos K, Andreadis E, Theocharopoulos I, Dourakis S. "Failing kidneys in a failing planet; CKD of unknown origin". REVIEWS ON ENVIRONMENTAL HEALTH 2023; 38:125-135. [PMID: 34881546 DOI: 10.1515/reveh-2021-0109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 11/22/2021] [Indexed: 06/13/2023]
Abstract
The 'alarm clock' for human beings in the era of climate medicine has rung. Original diseases have appeared, that could not be explained and attributed to common causes, which are suggested to be linked to global warming and environmental factors. Such an indolent disease is the chronic kidney disease of unknown cause (CKDu), introduced also as Mesoamerican or Uddanam nephropathy. Scientists equate the climate impact on kidneys with the canary in the coal mine; coal miners used to carry caged canaries with them, so that if poisonous gases, such as methane or carbon monoxide leaked into the mine-shaft, the gases would kill the canary before killing the miners; similarly, kidneys are injured before devastating and lethal complications occur in humans. In some regions of Central America, the deaths due to chronic kidney disease increased by 177% with a death toll being as high as over 20,000. It was first documented in animals that periodic heat and dehydration have a major role in causing chronic kidney disease. Based on that observation, it is advocated that young male agricultural workers in Central America and South Asia, develop renal disease by getting exposed to extreme heat repeatedly. The clinico-pathological characteristics of this type of kidney injury, do not belong to an existing classification, even though a form of tubulo-interstitial renal disease has been proposed. In this review, we will discuss about CKDu, its epidemiology and pathophysiological mechanisms, clinical presentation and diagnostic biomarkers and examine potential therapeutic options.
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Affiliation(s)
- Eleni Geladari
- National and Kapodistrian University of Athens, Athens, Attica, Greece
| | | | | | | | | | | | | | - Spyros Dourakis
- National and Kapodistrian University of Athens, Athens, Attica, Greece
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21
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Martínez-Barrios E, Grassi S, Brión M, Toro R, Cesar S, Cruzalegui J, Coll M, Alcalde M, Brugada R, Greco A, Ortega-Sánchez ML, Barberia E, Oliva A, Sarquella-Brugada G, Campuzano O. Molecular autopsy: Twenty years of post-mortem diagnosis in sudden cardiac death. Front Med (Lausanne) 2023; 10:1118585. [PMID: 36844202 PMCID: PMC9950119 DOI: 10.3389/fmed.2023.1118585] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 01/30/2023] [Indexed: 02/12/2023] Open
Abstract
In the forensic medicine field, molecular autopsy is the post-mortem genetic analysis performed to attempt to unravel the cause of decease in cases remaining unexplained after a comprehensive forensic autopsy. This negative autopsy, classified as negative or non-conclusive, usually occurs in young population. In these cases, in which the cause of death is unascertained after a thorough autopsy, an underlying inherited arrhythmogenic syndrome is the main suspected cause of death. Next-generation sequencing allows a rapid and cost-effectives genetic analysis, identifying a rare variant classified as potentially pathogenic in up to 25% of sudden death cases in young population. The first symptom of an inherited arrhythmogenic disease may be a malignant arrhythmia, and even sudden death. Early identification of a pathogenic genetic alteration associated with an inherited arrhythmogenic syndrome may help to adopt preventive personalized measures to reduce risk of malignant arrhythmias and sudden death in the victim's relatives, at risk despite being asymptomatic. The current main challenge is a proper genetic interpretation of variants identified and useful clinical translation. The implications of this personalized translational medicine are multifaceted, requiring the dedication of a specialized team, including forensic scientists, pathologists, cardiologists, pediatric cardiologists, and geneticists.
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Affiliation(s)
- Estefanía Martínez-Barrios
- Pediatric Arrhythmias, Inherited Cardiac Diseases and Sudden Death Unit, Cardiology Department, Sant Joan de Déu Hospital de Barcelona, Barcelona, Spain,European Reference Network for Rare, Low Prevalence and Complex Diseases of the Heart, Amsterdam, Netherlands,Arrítmies Pediàtriques, Cardiologia Genètica i Mort Sobtada, Malalties Cardiovasculars en el Desenvolupament, Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
| | - Simone Grassi
- Forensic Medical Sciences, Department of Health Science, University of Florence, Florence, Italy
| | - María Brión
- Family Heart Disease Unit, Cardiology Service, Santiago de Compostela University Hospital, Santiago de Compostela, Spain,Cardiovascular Genetics, Santiago de Compostela Health Research Institute, Santiago de Compostela, Spain,Genomic Medicine Group, Universidade de Santiago de Compostela, Santiago de Compostela, Spain,Centro de Investigación Biomédica en Red en Enfermedades Cardiovasculares, Madrid, Spain
| | - Rocío Toro
- Medicine Department, School of Medicine, University of Cádiz, Cádiz, Spain
| | - Sergi Cesar
- Pediatric Arrhythmias, Inherited Cardiac Diseases and Sudden Death Unit, Cardiology Department, Sant Joan de Déu Hospital de Barcelona, Barcelona, Spain,European Reference Network for Rare, Low Prevalence and Complex Diseases of the Heart, Amsterdam, Netherlands,Arrítmies Pediàtriques, Cardiologia Genètica i Mort Sobtada, Malalties Cardiovasculars en el Desenvolupament, Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
| | - José Cruzalegui
- Pediatric Arrhythmias, Inherited Cardiac Diseases and Sudden Death Unit, Cardiology Department, Sant Joan de Déu Hospital de Barcelona, Barcelona, Spain,European Reference Network for Rare, Low Prevalence and Complex Diseases of the Heart, Amsterdam, Netherlands,Arrítmies Pediàtriques, Cardiologia Genètica i Mort Sobtada, Malalties Cardiovasculars en el Desenvolupament, Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
| | - Mònica Coll
- Medical Science Department, School of Medicine, University of Girona, Girona, Spain,Cardiovascular Genetics Center, Institut d’Investigacions Biomèdiques de Girona (IDIBGI), University of Girona, Girona, Spain
| | - Mireia Alcalde
- Medical Science Department, School of Medicine, University of Girona, Girona, Spain,Cardiovascular Genetics Center, Institut d’Investigacions Biomèdiques de Girona (IDIBGI), University of Girona, Girona, Spain
| | - Ramon Brugada
- Centro de Investigación Biomédica en Red en Enfermedades Cardiovasculares, Madrid, Spain,Medical Science Department, School of Medicine, University of Girona, Girona, Spain,Cardiovascular Genetics Center, Institut d’Investigacions Biomèdiques de Girona (IDIBGI), University of Girona, Girona, Spain,Cardiology Department, Hospital Josep Trueta, Girona, Spain
| | - Andrea Greco
- Arrítmies Pediàtriques, Cardiologia Genètica i Mort Sobtada, Malalties Cardiovasculars en el Desenvolupament, Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain,Department of Medical and Surgical Sciences of the Mother, Children and Adults, University of Modena and Reggio Emilia, Modena, Italy
| | - María Luisa Ortega-Sánchez
- Forensic Pathology Department, Institut de Medicina Legal i Ciències Forenses de Catalunya (IMLCFC), Barcelona, Spain,School of Medicine, Universitat Autònoma de Barcelona, Cerdanyola del Vallés, Spain
| | - Eneko Barberia
- Forensic Pathology Department, Institut de Medicina Legal i Ciències Forenses de Catalunya (IMLCFC), Barcelona, Spain,School of Medicine and Health Sciences, Universitat Rovira i Virgili, Reus, Spain
| | - Antonio Oliva
- Section of Legal Medicine, Department of Health Surveillance and Bioethics, Fondazione Policlinico A. Gemelli IRCCS, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Georgia Sarquella-Brugada
- Pediatric Arrhythmias, Inherited Cardiac Diseases and Sudden Death Unit, Cardiology Department, Sant Joan de Déu Hospital de Barcelona, Barcelona, Spain,European Reference Network for Rare, Low Prevalence and Complex Diseases of the Heart, Amsterdam, Netherlands,Arrítmies Pediàtriques, Cardiologia Genètica i Mort Sobtada, Malalties Cardiovasculars en el Desenvolupament, Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain,Medical Science Department, School of Medicine, University of Girona, Girona, Spain,*Correspondence: Georgia Sarquella-Brugada,
| | - Oscar Campuzano
- Centro de Investigación Biomédica en Red en Enfermedades Cardiovasculares, Madrid, Spain,Medical Science Department, School of Medicine, University of Girona, Girona, Spain,Cardiovascular Genetics Center, Institut d’Investigacions Biomèdiques de Girona (IDIBGI), University of Girona, Girona, Spain,Oscar Campuzano,
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22
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Watanabe H, Goto S, Hosojima M, Kabasawa H, Imai N, Ito Y, Narita I. Pathogenic variants of Alport syndrome and monogenic diabetes identified by exome sequencing in a family. Hum Genome Var 2023; 10:5. [PMID: 36732323 PMCID: PMC9894847 DOI: 10.1038/s41439-023-00233-0] [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: 11/14/2022] [Revised: 12/30/2022] [Accepted: 01/03/2023] [Indexed: 02/04/2023] Open
Abstract
We present a family of two female Alport syndrome patients with a family history of impaired glucose tolerance. Whole exome sequencing identified a novel heterozygous variant of COL4A5 NM_033380.3: c.2636 C > A (p.S879*) and a rare variant of GCK NM_001354800.1: c.1135 G > A (p.A379T) as the causes of Alport syndrome and monogenic diabetes, respectively. Two independent pathogenic variants affected the clinical phenotypes. Clinical next-generation sequencing is helpful for identifying the causes of patients' manifestations.
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Affiliation(s)
- Hirofumi Watanabe
- Division of Clinical Nephrology and Rheumatology, Kidney Research Center, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan.
| | - Shin Goto
- Division of Clinical Nephrology and Rheumatology, Kidney Research Center, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Michihiro Hosojima
- Department of Clinical Nutrition Science, Kidney Research Center, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Hideyuki Kabasawa
- Department of Clinical Nutrition Science, Kidney Research Center, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Naofumi Imai
- Division of Clinical Nephrology and Rheumatology, Kidney Research Center, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Yumi Ito
- Division of Clinical Nephrology and Rheumatology, Kidney Research Center, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
- Department of Health Promotion Medicine, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Ichiei Narita
- Division of Clinical Nephrology and Rheumatology, Kidney Research Center, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
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Novel, heterozygous, pathogenic variant (c.4272delA: p.I1426Ffs*2) for the NF1 gene in a large Chinese family with neurofibromatosis type 1. Mol Biol Rep 2023; 50:1117-1123. [PMID: 36401065 DOI: 10.1007/s11033-022-08096-4] [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: 07/22/2022] [Accepted: 11/07/2022] [Indexed: 11/19/2022]
Abstract
BACKGROUND Neurofibromatosis type 1 (NF1) is an autosomal dominant with haploinsufficient, and multisystemic disorder including patches of skin Café-au-lait spots, Lisch nodules in the iris, and tumors in the peripheral nervous systems or fibromatous skin. METHODS Blood samples were collected and DNA was extracted from a large Chinese pedigree suffering from NF1 disease with three spontaneous abortions or death for proband. Analysis for whole exome sequencing (WES), Sanger sequencing, and co-segregation was carried out. Prenatal gene diagnosis was also carried out in amniotic fluid DNA. The expression of NF1 was conducted by bioinformatics. RESULTS A large Chinese pedigree with NF1 was recruited and a novel, heterozygous, variant (c.4272delA: p.I1426Ffs*2) for the NF1 gene in the proband was identified. This variant of NF1 produced a truncated protein that losses half of NF1 protein at the C-terminus including the CRAL-TRIO lipid-binding domain, NLS, and a small portion of Ras-GAP domain, thus leading to pathogenicity (ACMG criteria: PVS1 + PM2). NF1 expressions in different human tissues showed low tissue specificity, which may affect multiple organs presenting different phenotypes. Moreover, prenatal gene diagnosis for NF1 showed both alleles as wild types in the fetus of the proband. CONCLUSION We thus successfully identified a novel, pathogenic, heterozygous variant (c.4272delA:p.I1426Ffs*2) in the NF1 gene of NF1 disorder, expanding the NF1 mutation spectrum, that will help elucidate the molecular pathogenesis of NF1 disease and to contribute to the NF1 diagnosis, genetic counseling, clinical management in this large Chinese family.
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Abstract
Exome sequencing (ES) and genome sequencing (GS) have radically transformed the diagnostic approach to undiagnosed rare/ultrarare Mendelian diseases. Next-generation sequencing (NGS), the technology integral for ES, GS, and most large (100+) gene panels, has enabled previously unimaginable diagnoses, changes in medical management, new treatments, and accurate reproductive risk assessments for patients, as well as new disease gene discoveries. Yet, challenges remain, as most individuals remain undiagnosed with current NGS. Improved NGS technology has resulted in long-read sequencing, which may resolve diagnoses in some patients who do not obtain a diagnosis with current short-read ES and GS, but its effectiveness is unclear, and it is expensive. Other challenges that persist include the resolution of variants of uncertain significance, the urgent need for patients with ultrarare disorders to have access to therapeutics, the need for equity in patient access to NGS-based testing, and the study of ethical concerns. However, the outlook for undiagnosed disease resolution is bright, due to continual advancements in the field.
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Affiliation(s)
- Jennifer A Sullivan
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, USA;
| | - Kelly Schoch
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, USA;
| | - Rebecca C Spillmann
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, USA;
| | - Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, USA;
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Genetic Predisposition to Colorectal Cancer: How Many and Which Genes to Test? Int J Mol Sci 2023; 24:ijms24032137. [PMID: 36768460 PMCID: PMC9916931 DOI: 10.3390/ijms24032137] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/11/2023] [Accepted: 01/16/2023] [Indexed: 01/25/2023] Open
Abstract
Colorectal cancer is one of the most common tumors, and genetic predisposition is one of the key risk factors in the development of this malignancy. Lynch syndrome and familial adenomatous polyposis are the best-known genetic diseases associated with hereditary colorectal cancer. However, some other genetic disorders confer an increased risk of colorectal cancer, such as Li-Fraumeni syndrome (TP53 gene), MUTYH-associated polyposis (MUTYH gene), Peutz-Jeghers syndrome (STK11 gene), Cowden syndrome (PTEN gene), and juvenile polyposis syndrome (BMPR1A and SMAD4 genes). Moreover, the recent advances in molecular techniques, in particular Next-Generation Sequencing, have led to the identification of many new genes involved in the predisposition to colorectal cancers, such as RPS20, POLE, POLD1, AXIN2, NTHL1, MSH3, RNF43 and GREM1. In this review, we summarized the past and more recent findings in the field of cancer predisposition genes, with insights into the role of the encoded proteins and into the associated genetic disorders. Furthermore, we discussed the possible clinical utility of genetic testing in terms of prevention protocols and therapeutic approaches.
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D4Z4 Methylation Levels Combined with a Machine Learning Pipeline Highlight Single CpG Sites as Discriminating Biomarkers for FSHD Patients. Cells 2022; 11:cells11244114. [PMID: 36552879 PMCID: PMC9777431 DOI: 10.3390/cells11244114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 11/18/2022] [Accepted: 12/16/2022] [Indexed: 12/23/2022] Open
Abstract
The study describes a protocol for methylation analysis integrated with Machine Learning (ML) algorithms developed to classify Facio-Scapulo-Humeral Dystrophy (FSHD) subjects. The DNA methylation levels of two D4Z4 regions (DR1 and DUX4-PAS) were assessed by an in-house protocol based on bisulfite sequencing and capillary electrophoresis, followed by statistical and ML analyses. The study involved two independent cohorts, namely a training group of 133 patients with clinical signs of FSHD and 150 healthy controls (CTRL) and a testing set of 27 FSHD patients and 25 CTRL. As expected, FSHD patients showed significantly reduced methylation levels compared to CTRL. We utilized single CpG sites to develop a ML pipeline able to discriminate FSHD subjects. The model identified four CpGs sites as the most relevant for the discrimination of FSHD subjects and showed high metrics values (accuracy: 0.94, sensitivity: 0.93, specificity: 0.96). Two additional models were developed to differentiate patients with lower D4Z4 size and patients who might carry pathogenic variants in FSHD genes, respectively. Overall, the present model enables an accurate classification of FSHD patients, providing additional evidence for DNA methylation as a powerful disease biomarker that could be employed for prioritizing subjects to be tested for FSHD.
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Soucy M, Tanaka AJ, Dharmadhikari A. Molecular Genetic Testing Approaches for Retinitis Pigmentosa. Methods Mol Biol 2022; 2560:41-66. [PMID: 36481882 DOI: 10.1007/978-1-0716-2651-1_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Retinitis pigmentosa (RP) affects approximately 1 in 4000 individuals. It has many different genetic etiologies and therefore diagnosis can be challenging. Understanding the different testing methodologies is beneficial for clinicians and researchers in order to select the best testing method, whether it be panel testing, whole exome sequencing, or whole genome sequencing for individuals affected with RP. The Methods section also outlines the steps required to complete a WES assay, which has become a popular method for identifying the molecular diagnosis for individuals with RP.
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Affiliation(s)
- Megan Soucy
- Columbia University Irving Medical Center, New York, NY, USA.
| | - Akemi Joy Tanaka
- Genetics and Genomics, Columbia University Irving Medical Center, New York, NY, USA
| | - Avinash Dharmadhikari
- Clinical Genomics, Department of Clinical Pathology, Children's Hospital Los Angeles, Los Angeles, CA, USA
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Liu LY, Lu Q, Wang QH, Wang YY, Zhang B, Zou LP. Diagnostic yield of a multi-strategy genetic testing procedure in a nationwide cohort of 728 patients with infantile spasms in China. Seizure 2022; 103:51-57. [DOI: 10.1016/j.seizure.2022.10.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 10/10/2022] [Accepted: 10/12/2022] [Indexed: 11/27/2022] Open
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Hopkins CE, Brock T, Caulfield TR, Bainbridge M. Phenotypic screening models for rapid diagnosis of genetic variants and discovery of personalized therapeutics. Mol Aspects Med 2022; 91:101153. [PMID: 36411139 PMCID: PMC10073243 DOI: 10.1016/j.mam.2022.101153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/22/2022] [Accepted: 10/23/2022] [Indexed: 11/19/2022]
Abstract
Precision medicine strives for highly individualized treatments for disease under the notion that each individual's unique genetic makeup and environmental exposures imprints upon them not only a disposition to illness, but also an optimal therapeutic approach. In the realm of rare disorders, genetic predisposition is often the predominant mechanism driving disease presentation. For such, mostly, monogenic disorders, a causal gene to phenotype association is likely. As a result, it becomes important to query the patient's genome for the presence of pathogenic variations that are likely to cause the disease. Determining whether a variant is pathogenic or not is critical to these analyses and can be challenging, as many disease-causing variants are novel and, ergo, have no available functional data to help categorize them. This problem is exacerbated by the need for rapid evaluation of pathogenicity, since many genetic diseases present in young children who will experience increased morbidity and mortality without rapid diagnosis and therapeutics. Here, we discuss the utility of animal models, with a focus mainly on C. elegans, as a contrast to tissue culture and in silico approaches, with emphasis on how these systems are used in determining pathogenicity of variants with uncertain significance and then used to screen for novel therapeutics.
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Affiliation(s)
| | | | - Thomas R Caulfield
- Mayo Clinic, Department of Neuroscience, Department of Computational Biology, Department of Clinical Genomics, Jacksonville, FL, 32224, Rochester, MN, 55905, USA
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Conlin LK, Aref-Eshghi E, McEldrew DA, Luo M, Rajagopalan R. Long-read sequencing for molecular diagnostics in constitutional genetic disorders. Hum Mutat 2022; 43:1531-1544. [PMID: 36086952 PMCID: PMC9561063 DOI: 10.1002/humu.24465] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 09/03/2022] [Accepted: 09/06/2022] [Indexed: 11/11/2022]
Abstract
Long-read sequencing (LRS) has been around for more than a decade, but widespread adoption of the technology has been slow due to the perceived high error rates and high sequencing cost. This is changing due to the recent advancements to produce highly accurate sequences and the reducing costs. LRS promises significant improvement over short read sequencing in four major areas: (1) better detection of structural variation (2) better resolution of highly repetitive or nonunique regions (3) accurate long-range haplotype phasing and (4) the detection of base modifications natively from the sequencing data. Several successful applications of LRS have demonstrated its ability to resolve molecular diagnoses where short-read sequencing fails to identify a cause. However, the argument for increased diagnostic yield from LRS remains to be validated. Larger cohort studies may be required to establish the realistic boundaries of LRS's clinical utility and analytical validity, as well as the development of standards for clinical applications. We discuss the limitations of the current standard of care, and contrast with the applications and advantages of two major LRS platforms, PacBio and Oxford Nanopore, for molecular diagnostics of constitutional disorders, and present a critical argument about the potential of LRS in diagnostic settings.
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Affiliation(s)
- Laura K. Conlin
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Erfan Aref-Eshghi
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
| | - Deborah A. McEldrew
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
| | - Minjie Luo
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Ramakrishnan Rajagopalan
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
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Soriano-Sexto A, Gallego D, Leal F, Castejón-Fernández N, Navarrete R, Alcaide P, Couce ML, Martín-Hernández E, Quijada-Fraile P, Peña-Quintana L, Yahyaoui R, Correcher P, Ugarte M, Rodríguez-Pombo P, Pérez B. Identification of Clinical Variants beyond the Exome in Inborn Errors of Metabolism. Int J Mol Sci 2022; 23:ijms232112850. [PMID: 36361642 PMCID: PMC9654865 DOI: 10.3390/ijms232112850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/13/2022] [Accepted: 10/21/2022] [Indexed: 11/24/2022] Open
Abstract
Inborn errors of metabolism (IEM) constitute a huge group of rare diseases affecting 1 in every 1000 newborns. Next-generation sequencing has transformed the diagnosis of IEM, leading to its proposed use as a second-tier technology for confirming cases detected by clinical/biochemical studies or newborn screening. The diagnosis rate is, however, still not 100%. This paper reports the use of a personalized multi-omics (metabolomic, genomic and transcriptomic) pipeline plus functional genomics to aid in the genetic diagnosis of six unsolved cases, with a clinical and/or biochemical diagnosis of galactosemia, mucopolysaccharidosis type I (MPS I), maple syrup urine disease (MSUD), hyperphenylalaninemia (HPA), citrullinemia, or urea cycle deficiency. Eight novel variants in six genes were identified: six (four of them deep intronic) located in GALE, IDUA, PTS, ASS1 and OTC, all affecting the splicing process, and two located in the promoters of IDUA and PTS, thus affecting these genes’ expression. All the new variants were subjected to functional analysis to verify their pathogenic effects. This work underscores how the combination of different omics technologies and functional analysis can solve elusive cases in clinical practice.
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Affiliation(s)
- Alejandro Soriano-Sexto
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Departamento de Biología Molecular, Universidad Autónoma de Madrid, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), IdiPAZ, 28049 Madrid, Spain
| | - Diana Gallego
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Departamento de Biología Molecular, Universidad Autónoma de Madrid, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), IdiPAZ, 28049 Madrid, Spain
| | - Fátima Leal
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Departamento de Biología Molecular, Universidad Autónoma de Madrid, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), IdiPAZ, 28049 Madrid, Spain
| | - Natalia Castejón-Fernández
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Departamento de Biología Molecular, Universidad Autónoma de Madrid, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), IdiPAZ, 28049 Madrid, Spain
| | - Rosa Navarrete
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Departamento de Biología Molecular, Universidad Autónoma de Madrid, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), IdiPAZ, 28049 Madrid, Spain
| | - Patricia Alcaide
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Departamento de Biología Molecular, Universidad Autónoma de Madrid, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), IdiPAZ, 28049 Madrid, Spain
| | - María L. Couce
- Unit for the Diagnosis and Treatment of Congenital Metabolic Diseases, Clinical University Hospital of Santiago de Compostela, Health Research Institute of Santiago de Compostela, University of Santiago de Compostela, CIBERER, MetabERN, 15706 Santiago de Compostela, Spain
| | - Elena Martín-Hernández
- Unidad de Enfermedades Mitocondriales-Metabólicas Hereditarias, Servicio de Pediatría, Centro de Referencia Nacional (CSUR) y Europeo (MetabERN) para Enfermedades Metabólicas Hereditarias, Hospital Universitario 12 de Octubre, 28041 Madrid, Spain
| | - Pilar Quijada-Fraile
- Unidad de Enfermedades Mitocondriales-Metabólicas Hereditarias, Servicio de Pediatría, Centro de Referencia Nacional (CSUR) y Europeo (MetabERN) para Enfermedades Metabólicas Hereditarias, Hospital Universitario 12 de Octubre, 28041 Madrid, Spain
| | - Luis Peña-Quintana
- Pediatric Gastroenterology, Hepatology and Nutrition Unit, Complejo Hospitalario Universitario Insular Materno-Infantil (CHUIMI), Universidad de Las Palmas de Gran Canaria, Asociación Canaria para La Investigación Pediátrica, Centro de Investigación Biomédica en Red de la Fisiopatología de la Obesidad y la Nutrición (CIBEROBN) ISCIII, 35016 Gran Canaria, Spain
| | - Raquel Yahyaoui
- Laboratory of Metabolic Disorders and Newborn Screening, Institute of Biomedical Research in Málaga (IBIMA-Plafatorma BIONAND), IBIMA-RARE, Málaga Regional University Hospital, 29010 Málaga, Spain
| | - Patricia Correcher
- Nutrition and Metabolophaties Unit, Hospital Universitario La Fe, 46026 Valencia, Spain
| | - Magdalena Ugarte
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Departamento de Biología Molecular, Universidad Autónoma de Madrid, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), IdiPAZ, 28049 Madrid, Spain
| | - Pilar Rodríguez-Pombo
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Departamento de Biología Molecular, Universidad Autónoma de Madrid, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), IdiPAZ, 28049 Madrid, Spain
| | - Belén Pérez
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Departamento de Biología Molecular, Universidad Autónoma de Madrid, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), IdiPAZ, 28049 Madrid, Spain
- Correspondence:
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Sturm J, Milera H, Essmann S, Fruth A, Jahn-Eimermacher A, Selig M, Winter J, Seidmann L, Kampmann C, Kidszun A, Mildenberger E, Whybra C. A single center experience in 90 cases with nonimmune hydrops fetalis: diagnostic categories ‒ mostly aneuploidy and still often idiopathic. J Perinat Med 2022; 50:985-992. [PMID: 35405041 DOI: 10.1515/jpm-2022-0005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 03/10/2022] [Indexed: 11/15/2022]
Abstract
OBJECTIVES The prognosis of nonimmune hydrops fetalis (NIHF) is still poor with a high mortality and morbidity rate despite progress in perinatal care. This study was designed to investigate etiology and outcome of NIHF. METHODS A retrospective review of 90 NIHF cases from 2007 to 2019 was conducted at University Medical Center of the Johannes Gutenberg University, Mainz, Germany. Demographics, genetic results, prenatal and postnatal outcomes including one year survival as well as autopsy data were extracted. Etiology of hydrops was classified using 13 previously established categories. In 4 patients observed between 2016 and 2019, we used a next-generation-sequencing (NGS) panel for genetic evaluation. RESULTS Ninety NIHF cases were identified, with a median gestational age (GA) at diagnosis of 14 weeks. There were 25 live-born infants with a median GA of 34 weeks at birth, 15 patients survived to one year. There was aneuploidy in more than one third of the cases. All 90 cases were subclassified into etiologic categories with chromosomal 35, idiopathic 15, syndromic 11, cardiovascular 9, inborn errors of metabolism 6, lymphatic dysplasia 3, thoracic 3, infections 3, gastrointestinal 3 and hematologic 2. The NGS panel was used in 4 cases and 4 diagnoses were made. CONCLUSIONS In 90 cases with NIHF we identified an aneuploidy in more than one third of the cases. Improved techniques, such as possibly specific genetic analysis, could reduce the high rate of unexplained cases of NIHF.
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Affiliation(s)
- Julia Sturm
- Department of Neonatology, Universitätsmedizin der Johannes Gutenberg-Universität Mainz, Mainz, Germany
| | - Heiko Milera
- Department of Neonatology, Universitätsmedizin der Johannes Gutenberg-Universität Mainz, Mainz, Germany
| | - Stephanie Essmann
- Department of Neonatology, Universitätsmedizin der Johannes Gutenberg-Universität Mainz, Mainz, Germany
| | - Anja Fruth
- Department of Obstetrics and Gynecology, Johannes Gutenberg Universitat Universitatsmedizin, Mainz, Germany
| | - Antje Jahn-Eimermacher
- Department of Mathematics and Natural Sciences, Darmstadt University of Applied Sciences, Mainz, Germany
| | - Mareike Selig
- Institute of Human Genetics, Universitätsmedizin der Johannes Gutenberg-Universität Mainz, Mainz, Germany
| | - Jennifer Winter
- Institute of Human Genetics, Universitätsmedizin der Johannes Gutenberg-Universität Mainz, Mainz, Germany
| | - Larissa Seidmann
- Institute of Pathology, Universitätsmedizin der Johannes Gutenberg-Universität Mainz, Mainz, Germany
| | - Christoph Kampmann
- Pediatric Cardiology Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - André Kidszun
- Department of Neonatology, Universitätsmedizin der Johannes Gutenberg-Universität Mainz, Mainz, Germany
| | - Eva Mildenberger
- Department of Neonatology, Universitätsmedizin der Johannes Gutenberg-Universität Mainz, Mainz, Germany
| | - Catharina Whybra
- Department of Neonatology, Universitätsmedizin der Johannes Gutenberg-Universität Mainz, Mainz, Germany
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Michaeli DT, Mills M, Kanavos P. Value and Price of Multi-indication Cancer Drugs in the USA, Germany, France, England, Canada, Australia, and Scotland. APPLIED HEALTH ECONOMICS AND HEALTH POLICY 2022; 20:757-768. [PMID: 35821360 PMCID: PMC9385843 DOI: 10.1007/s40258-022-00737-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 05/02/2022] [Indexed: 05/24/2023]
Abstract
PURPOSE Oncology drugs are often approved for multiple indications, for which their clinical benefit varies. Aligning a single price to this differing value remains a challenge. This study examines the clinical and economic value, price, and reimbursement of multi-indication cancer drugs across seven countries, representing different approaches to value assessment, pricing, and coverage decisions: the USA, Germany, France, England, Canada, Australia, and Scotland. METHODS Twenty-five multi-indication cancer drugs across 100 indications were identified with US Food and Drug Administration (FDA) approval between 2009 and 2019. For each indication data on Health Technology Assessment (HTA) recommendations, disease prevalence, and drug prices were obtained. Quality-adjusted life years (QALYs) gained, disease prevalence, list prices, and HTA outcomes were then compared across indications and regions. RESULTS First approved indications provide a higher clinical benefit whilst targeting a smaller patient group than indication extensions. Quality-adjusted life year gains were higher for first (0.99, 95% CI 0.05-3.25) compared to second (0.51, 95% CI 0.02-1.63, p < 0.001) and third (0.58, 95% CI 0.05-2.07, p < 0.01) approved indications. Disease prevalence per 100,000 inhabitants was 20.7 (95% CI 0.2-63.3) for first compared to 27.1 (95% CI 1.5-109.6, p = 0.907) for second and 128.3 (95% CI 3.1-720.1, p < 0.001) for third approved indications. With each approved indication drug prices declined in Germany and France, remained constant in the UK, Canada, and Australia, whilst they increased in the USA. Negative HTA outcomes, clinical restrictions, and managed entry agreements (MEAs) were more frequently observed for indication extensions. CONCLUSIONS Results suggest that indication development is prioritised according to clinical value and disease prevalence. Countries employ different mechanisms to account for each indication's differential benefit, e.g., weighted-average prices (Germany, France, Australia), differential discounts (England, Scotland), clinical restrictions, and MEAs (England, Scotland, Australia, Canada). Value-based indication-specific pricing can help to align the benefit and price for multi-indication cancer drugs.
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Affiliation(s)
- Daniel Tobias Michaeli
- Fifth Department of Medicine, University Hospital Mannheim, Heidelberg University, Mannheim, Germany.
- Department of Personalized Oncology, University Hospital Mannheim, Heidelberg University, Mannheim, Germany.
- Department of Health Policy and Medical Technology Research Group LSE Health, London School of Economics and Political Science, London, UK.
| | - Mackenzie Mills
- Department of Health Policy and Medical Technology Research Group LSE Health, London School of Economics and Political Science, London, UK
| | - Panos Kanavos
- Department of Health Policy and Medical Technology Research Group LSE Health, London School of Economics and Political Science, London, UK.
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van der Made CI, Netea MG, van der Veerdonk FL, Hoischen A. Clinical implications of host genetic variation and susceptibility to severe or critical COVID-19. Genome Med 2022; 14:96. [PMID: 35986347 PMCID: PMC9390103 DOI: 10.1186/s13073-022-01100-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 08/03/2022] [Indexed: 01/08/2023] Open
Abstract
Since the start of the coronavirus disease 2019 (COVID-19) pandemic, important insights have been gained into virus biology and the host factors that modulate the human immune response against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). COVID-19 displays a highly variable clinical picture that ranges from asymptomatic disease to lethal pneumonia. Apart from well-established general risk factors such as advanced age, male sex and chronic comorbidities, differences in host genetics have been shown to influence the individual predisposition to develop severe manifestations of COVID-19. These differences range from common susceptibility loci to rare genetic variants with strongly predisposing effects, or proven pathogenic variants that lead to known or novel inborn errors of immunity (IEI), which constitute a growing group of heterogeneous Mendelian disorders with increased susceptibility to infectious disease, auto-inflammation, auto-immunity, allergy or malignancies. The current genetic findings point towards a convergence of common and rare genetic variants that impact the interferon signalling pathways in patients with severe or critical COVID-19. Monogenic risk factors that impact IFN-I signalling have an expected prevalence between 1 and 5% in young, previously healthy individuals (<60 years of age) with critical COVID-19. The identification of these IEI such as X-linked TLR7 deficiency indicates a possibility for targeted genetic screening and personalized clinical management. This review aims to provide an overview of our current understanding of the host genetic factors that predispose to severe manifestations of COVID-19 and focuses on rare variants in IFN-I signalling genes and their potential clinical implications.
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Affiliation(s)
- Caspar I van der Made
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands
- Radboud Institute of Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands
- Radboud Institute of Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands
- Department for Immunology and Metabolism, Life and Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany
| | - Frank L van der Veerdonk
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands
- Radboud Institute of Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands
| | - Alexander Hoischen
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands.
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands.
- Radboud Institute of Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands.
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Variants of uncertain significance in the era of next-generation sequencing. J Am Assoc Nurse Pract 2022; 34:1018-1021. [PMID: 35731603 DOI: 10.1097/jxx.0000000000000745] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 05/05/2022] [Indexed: 02/04/2023]
Abstract
ABSTRACT Next-generation sequencing (NGS) is now widely used in diagnosing rare diseases. However, it has some limitations, such as variants of uncertain significance (VUS). This can present difficulties even for nurse practitioners involved in clinical genetics. We present three cases from our clinical practice: two targeted panel testing and one exome sequencing. Whole blood samples were collected and sent for NGS analysis. In case 1, a VUS was found in the LITAF gene, which is associated with autosomal dominant Charcot-Marie-Tooth disease type 1C. In case 2, a VUS was reported in the MEFV gene, which is associated with autosomal recessive and autosomal dominant familial Mediterranean fever. In these cases, the reported VUS corresponded to the clinical diagnosis. In case 3, two variants in the heterozygous state were found in the ATP7B gene, which is associated with Wilson disease, and the disorder was later clinically recognized. According to the published guidelines, VUSs should not be discussed as a cause for an observed genetic condition. Nevertheless, if the reported variant is in a gene associated with the clinically diagnosed disorder, and there is a strong genotype-phenotype correlation, it could be suggestive of the etiological role of this variant.
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Phenotypic Variation in Two Siblings Affected with Shwachman-Diamond Syndrome: The Use of Expert Variant Interpreter (eVai) Suggests Clinical Relevance of a Variant in the KMT2A Gene. Genes (Basel) 2022; 13:genes13081314. [PMID: 35893049 PMCID: PMC9394309 DOI: 10.3390/genes13081314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/14/2022] [Accepted: 07/20/2022] [Indexed: 12/04/2022] Open
Abstract
Introduction. Shwachman-Diamond Syndrome (SDS) is an autosomal-recessive disorder characterized by neutropenia, pancreatic exocrine insufficiency, skeletal dysplasia, and an increased risk for leukemic transformation. Biallelic mutations in the SBDS gene have been found in about 90% of patients. The clinical spectrum of SDS in patients is wide, and variability has been noticed between different patients, siblings, and even within the same patient over time. Herein, we present two SDS siblings (UPN42 and UPN43) carrying the same SBDS mutations and showing relevant differences in their phenotypic presentation. Study aim. We attempted to understand whether other germline variants, in addition to SBDS, could explain some of the clinical variability noticed between the siblings. Methods. Whole-exome sequencing (WES) was performed. Human Phenotype Ontology (HPO) terms were defined for each patient, and the WES data were analyzed using the eVai and DIVAs platforms. Results. In UPN43, we found and confirmed, using Sanger sequencing, a novel de novo variant (c.10663G > A, p.Gly3555Ser) in the KMT2A gene that is associated with autosomal-dominant Wiedemann−Steiner Syndrome. The variant is classified as pathogenic according to different in silico prediction tools. Interestingly, it was found to be related to some of the HPO terms that describe UPN43. Conclusions. We postulate that the KMT2A variant found in UPN43 has a concomitant and co-occurring clinical effect, in addition to SBDS mutation. This dual molecular effect, supported by in silico prediction, could help to understand some of the clinical variations found among the siblings. In the future, these new data are likely to be useful for personalized medicine and therapy for selected cases.
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Panikker P, Roy S, Ghosh A, Poornachandra B, Ghosh A. Advancing precision medicines for ocular disorders: Diagnostic genomics to tailored therapies. Front Med (Lausanne) 2022; 9:906482. [PMID: 35911417 PMCID: PMC9334564 DOI: 10.3389/fmed.2022.906482] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 06/29/2022] [Indexed: 11/20/2022] Open
Abstract
Successful sequencing of the human genome and evolving functional knowledge of gene products has taken genomic medicine to the forefront, soon combining broadly with traditional diagnostics, therapeutics, and prognostics in patients. Recent years have witnessed an extraordinary leap in our understanding of ocular diseases and their respective genetic underpinnings. As we are entering the age of genomic medicine, rapid advances in genome sequencing, gene delivery, genome surgery, and computational genomics enable an ever-increasing capacity to provide a precise and robust diagnosis of diseases and the development of targeted treatment strategies. Inherited retinal diseases are a major source of blindness around the world where a large number of causative genes have been identified, paving the way for personalized diagnostics in the clinic. Developments in functional genetics and gene transfer techniques has also led to the first FDA approval of gene therapy for LCA, a childhood blindness. Many such retinal diseases are the focus of various clinical trials, making clinical diagnoses of retinal diseases, their underlying genetics and the studies of natural history important. Here, we review methodologies for identifying new genes and variants associated with various ocular disorders and the complexities associated with them. Thereafter we discuss briefly, various retinal diseases and the application of genomic technologies in their diagnosis. We also discuss the strategies, challenges, and potential of gene therapy for the treatment of inherited and acquired retinal diseases. Additionally, we discuss the translational aspects of gene therapy, the important vector types and considerations for human trials that may help advance personalized therapeutics in ophthalmology. Retinal disease research has led the application of precision diagnostics and precision therapies; therefore, this review provides a general understanding of the current status of precision medicine in ophthalmology.
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Affiliation(s)
| | - Shomereeta Roy
- Grow Research Laboratory, Narayana Nethralaya Foundation, Bengaluru, India
| | - Anuprita Ghosh
- Grow Research Laboratory, Narayana Nethralaya Foundation, Bengaluru, India
| | | | - Arkasubhra Ghosh
- Grow Research Laboratory, Narayana Nethralaya Foundation, Bengaluru, India
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Demir Eksi D, Yilmaz E, Basaran AE, Erduran G, Nur B, Mihci E, Karadag B, Bingol A, Alper OM. Novel Gene Variants Associated with Primary Ciliary Dyskinesia. Indian J Pediatr 2022; 89:682-691. [PMID: 35239159 DOI: 10.1007/s12098-022-04098-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 11/24/2021] [Indexed: 11/25/2022]
Abstract
OBJECTIVES To determine the demographic, clinical, and genetic profile of Turkish Caucasian PCD cases. METHODS Targeted next-generation sequencing (t-NGS) of 46 nuclear genes was performed in 21 unrelated PCD cases. Sanger sequencing confirmed of potentially disease-related variations, and genotype-phenotype correlations were evaluated. RESULTS Disease-related variations were identified in eight different genes (CCDC39, CCDC40, CCDC151, DNAAF2, DNAAF4, DNAH11, HYDIN, RSPH4A) in 52.4% (11/21) of the cases. The frequency of variations for CCDC151, DNAH11, and DNAAF2 genes which were highly mutated genes in the cohort was 18% in 11 patients. Each of the remaining gene variations was detected once (9%) in different patients. The variants, p.R482fs*12 in CCDC151, p.E216* in DNAAF2, p.I317* in DNAAF4, p.L318P and p.R1865* in DNAH11, and p.N1505D and p.L1167P in HYDIN gene were identified as novel variations. Interestingly, varying phenotypic findings were identified even in patients with the same mutation, which once again confirmed that PCD has a high phenotypic heterogeneity and shows individual differences. CONCLUSION This t-NGS panel is potentially helpful for exact and rapid identification of reported/novel PCD-disease-causing variants to establish the molecular diagnosis of ciliary diseases.
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Affiliation(s)
- Durkadin Demir Eksi
- Department of Medical Biology and Genetics, School of Medicine, Akdeniz University, Antalya, 07070, Turkey.
- Department of Medical Biology, School of Medicine, Alanya Alaaddin Keykubat University, Antalya, 07425, Turkey.
| | - Elanur Yilmaz
- Department of Medical Biology and Genetics, School of Medicine, Akdeniz University, Antalya, 07070, Turkey
- Department of Medical Genetics & Koç University Research Center for Translational Medicine (KUTTAM), School of Medicine, Koç University, Istanbul, Turkey
| | - A Erdem Basaran
- Department of Pediatric Pulmonology, School of Medicine, Akdeniz University, Antalya, Turkey
| | - Gizem Erduran
- Department of Medical Biology and Genetics, School of Medicine, Akdeniz University, Antalya, 07070, Turkey
| | - Banu Nur
- Department of Pediatric Genetics, School of Medicine, Akdeniz University, Antalya, Turkey
| | - Ercan Mihci
- Department of Pediatric Genetics, School of Medicine, Akdeniz University, Antalya, Turkey
| | - Bulent Karadag
- Department of Pediatric Pulmonology, School of Medicine, Marmara University, Istanbul, Turkey
| | - Aysen Bingol
- Department of Pediatric Pulmonology, School of Medicine, Akdeniz University, Antalya, Turkey
| | - Ozgul M Alper
- Department of Medical Biology and Genetics, School of Medicine, Akdeniz University, Antalya, 07070, Turkey.
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Burns W, Chaudhari BP, Haffner DN. Neurogenetic and Metabolic Mimics of Common Neonatal Neurological Disorders. Semin Pediatr Neurol 2022; 42:100972. [PMID: 35868729 DOI: 10.1016/j.spen.2022.100972] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 04/05/2022] [Accepted: 04/05/2022] [Indexed: 10/18/2022]
Abstract
Neurogenetic and metabolic diseases often present in the neonatal period, masquerading as other disorders, most commonly as neonatal encephalopathy and seizures. Advancements in our understanding of inborn errors of metabolism are leading to an increasing number of therapeutic options. Many of these treatments can improve long-term neurodevelopment and seizure control. However, the treatments are frequently condition-specific. A high index of suspicion is required for prompt identification and treatment. When suspected, simultaneous metabolic and molecular testing are recommended along with concurrent treatment.
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Affiliation(s)
- William Burns
- Division of Genetics and Genomic Medicine, Nationwide Children's Hospital, Columbus, OH; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH.
| | - Bimal P Chaudhari
- Division of Genetics and Genomic Medicine, Nationwide Children's Hospital, Columbus, OH; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH; Division of Neonatology, Nationwide Children's Hospital, Columbus, OH; Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH
| | - Darrah N Haffner
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH; Division of Neurology, Nationwide Children's Hospital, Columbus, OH
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Yauy K, Lecoquierre F, Baert-Desurmont S, Trost D, Boughalem A, Luscan A, Costa JM, Geromel V, Raymond L, Richard P, Coutant S, Broutin M, Lanos R, Fort Q, Cackowski S, Testard Q, Diallo A, Soirat N, Holder JM, Duforet-Frebourg N, Bouge AL, Beaumeunier S, Bertrand D, Audoux J, Genevieve D, Mesnard L, Nicolas G, Thevenon J, Philippe N. Genome Alert!: A standardized procedure for genomic variant reinterpretation and automated gene-phenotype reassessment in clinical routine. Genet Med 2022; 24:1316-1327. [PMID: 35311657 DOI: 10.1016/j.gim.2022.02.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/07/2022] [Accepted: 02/07/2022] [Indexed: 12/12/2022] Open
Abstract
PURPOSE Retrospective interpretation of sequenced data in light of the current literature is a major concern of the field. Such reinterpretation is manual and both human resources and variable operating procedures are the main bottlenecks. METHODS Genome Alert! method automatically reports changes with potential clinical significance in variant classification between releases of the ClinVar database. Using ClinVar submissions across time, this method assigns validity category to gene-disease associations. RESULTS Between July 2017 and December 2019, the retrospective analysis of ClinVar submissions revealed a monthly median of 1247 changes in variant classification with potential clinical significance and 23 new gene-disease associations. Re-examination of 4929 targeted sequencing files highlighted 45 changes in variant classification, and of these classifications, 89% were expert validated, leading to 4 additional diagnoses. Genome Alert! gene-disease association catalog provided 75 high-confidence associations not available in the OMIM morbid list; of which, 20% became available in OMIM morbid list For more than 356 negative exome sequencing data that were reannotated for variants in these 75 genes, this elective approach led to a new diagnosis. CONCLUSION Genome Alert! (https://genomealert.univ-grenoble-alpes.fr/) enables systematic and reproducible reinterpretation of acquired sequencing data in a clinical routine with limited human resource effect.
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Affiliation(s)
- Kevin Yauy
- Institute for Advanced Biosciences, Centre de recherche UGA / Inserm U 1209 / CNRS UMR 5309, Grenoble, France; SeqOne Genomics, Montpellier, France.
| | - François Lecoquierre
- Department of Genetics and Reference Center for Developmental Disorders, Normandy Center for Genomic and Personalized Medicine, Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, F 76000, Rouen, France
| | - Stéphanie Baert-Desurmont
- Department of Genetics and Reference Center for Developmental Disorders, Normandy Center for Genomic and Personalized Medicine, Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, F 76000, Rouen, France
| | | | | | | | | | | | | | - Pascale Richard
- Unité Fonctionnelle de Cardiogénétique et Myogénétique, Centre de Génétique, Hôpitaux Universitaire Pitié Salpêtrière-Charles Foix, Paris, France
| | - Sophie Coutant
- Department of Genetics and Reference Center for Developmental Disorders, Normandy Center for Genomic and Personalized Medicine, Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, F 76000, Rouen, France
| | | | | | | | - Stenzel Cackowski
- Grenoble Institut Neurosciences, GIN, Inserm U1216, Université de Grenoble Alpes, Grenoble, France
| | - Quentin Testard
- Institute for Advanced Biosciences, Centre de recherche UGA / Inserm U 1209 / CNRS UMR 5309, Grenoble, France; Laboratoire Eurofins Biomnis, Lyon, France
| | | | | | | | | | | | | | | | | | - David Genevieve
- Medical Genetic Department for Rare Diseases and Personalized Medicine, Montpellier University Hospital, Montpellier, France
| | - Laurent Mesnard
- Soins Intensifs Néphrologiques et Rein Aigu, Hôpital Tenon, Assistance Publique des Hôpitaux de Paris, Paris, France; UMR_S1155, INSERM, Sorbonne Université, Paris, France
| | - Gael Nicolas
- Department of Genetics and Reference Center for Developmental Disorders, Normandy Center for Genomic and Personalized Medicine, Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, F 76000, Rouen, France
| | - Julien Thevenon
- Institute for Advanced Biosciences, Centre de recherche UGA / Inserm U 1209 / CNRS UMR 5309, Grenoble, France
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Sant' Ana I, Torrini R, Alves Coelho MC, Cantoni J, Madeira M, Ribeiro M. X-linked hypophosphatemic rickets: Description of seven new variants in patients followed up in reference hospitals in Rio de Janeiro. Mol Genet Genomic Med 2022; 10:e1941. [PMID: 35384411 PMCID: PMC9184672 DOI: 10.1002/mgg3.1941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 03/20/2022] [Accepted: 03/23/2022] [Indexed: 11/13/2022] Open
Abstract
Background X‐linked hypophosphatemic rickets (XLHR) is a rare genetic disease, often delayed in diagnosis due to the low degree of suspicion and limited access to sophisticated diagnostic tools that confirm the diagnosis, such as genetic testing. Methods Through a cross‐sectional and observational study, 26 patients with a previously presumptive diagnosis of X‐linked hypophosphatemic rickets (based on clinical history, laboratory findings, and physical examination), were followed for approximately 12 months. During 12 months of follow‐up, only 16 patients underwent genetic testing and enrolled in the study. Previous data were analyzed, such as clinical history (e.g., gender, current age, age of clinical diagnosis, age of admission to hospital, family history, and previous orthopedic surgery), physical exam, imaging tests (e.g., radiological changes) and laboratory tests (e.g., tubular maximum reabsorption rate of phosphate to glomerular filtration rate, alkaline phosphatase, and phosphate levels) at the time of the patient’s admission to IEDE and UFRJ, to corroborate and substantiate our research. These data were extracted from the medical records of the patients. Results Among the 16 patients analyzed by molecular biology techniques, the new generation sequencing (NGS), using DNA samples from oral swabs, we obtained seven variants never previously described, which were verified by Sanger sequencing. Among the seven variants never previously described, the most common coding impact was the nonsense mutation. We found two frameshift, one intronic splicing variant, three nonsense, and one deletion splice junction loss. Among patients with new mutations who presented data in the medical record, 100% showed a reduction in TmP/GFR (average of 1.98 mg/dl), the most sensitive laboratory parameter at the time of diagnosis, as well as serum phosphorus (100% had hypophosphatemia on arrival at the referral hospitals––average of 2.4 mg/dl and median 2.3 mg/dl). We also performed NGS on three mothers of the patients with identified mutations. Among these mothers, only one tested negative for the mutation and no family history was reported as well. This mother had serum phosphate of 3.5 mg/dl (normal range: 2.5–4.5 mg/dl) at the time of genetic test collection. The others had a positive test, low serum phosphorus at the time of the molecular test, in addition to a positive family history. Conclusion This study describes seven new variants in the PHEX gene and aims to increase the knowledge of the scientific community about the types of mutations involving this gene, increasing information on the genetic basis of this condition, enabling future considerations about genotype–phenotype correlation, in addition to diagnosis accurate and early.
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Affiliation(s)
- Iara Sant' Ana
- Instituto Estadual de Diabetes e Endocrinologia Luiz Capriglione (IEDE), Rio de Janeiro, Brazil.,Endocrinology Division, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Renato Torrini
- Instituto Estadual de Diabetes e Endocrinologia Luiz Capriglione (IEDE), Rio de Janeiro, Brazil
| | | | - Joyce Cantoni
- Instituto Estadual de Diabetes e Endocrinologia Luiz Capriglione (IEDE), Rio de Janeiro, Brazil
| | - Miguel Madeira
- Endocrinology Division, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Márcia Ribeiro
- Medical Genetic Service, Instituto de Puericultura e Pediatria Martagão Gesteira, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
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Rinaldi B, Cesaretti C, Boito S, Villa R, Guerneri S, Borzani I, Rizzuti T, Marchetti D, Conte G, Cinnante C, Triulzi F, Persico N, Iascone M, Natacci F. Family history is key to the interpretation of exome sequencing in the prenatal context: Unexpected diagnosis of Basal Cell Nevus Syndrome. Prenat Diagn 2022; 42:927-933. [PMID: 35584264 DOI: 10.1002/pd.6171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 05/13/2022] [Accepted: 05/16/2022] [Indexed: 11/10/2022]
Abstract
OBJECTIVE To reach a molecular diagnosis for a family with two consecutive fetuses presenting with multiple congenital anomalies. METHOD The two fetuses underwent prenatal ultrasound, autopsy, radiologic and genetic investigation. Genetic analysis included karyotype and array-CGH for both fetuses and trio-based whole exome sequencing (WES) only for the second fetus. RESULTS WES results, initially focusing on recessive or dominant de novo variants, were negative. However, as a result of new relevant information regarding family history, the variant c.648_651dup in the PTCH1 gene was identified as causative of the fetal phenotype. CONCLUSION This case further highlights how WES data analysis and interpretation strongly rely on family history and robust genotype-phenotype correlation. This is even more relevant in the prenatal setting, where access to fetal phenotype is limited and prenatal recognition of many morbid genes is not fully explored. We also provide a detailed description of the prenatal manifestations of Basal Cell Nevus Syndrome. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Berardo Rinaldi
- Medical Genetics Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Claudia Cesaretti
- Medical Genetics Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Simona Boito
- Fetal Medicine and Surgery Service, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Roberta Villa
- Medical Genetics Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Silvana Guerneri
- Laboratory of Medical Genetics, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Irene Borzani
- Pediatric Radiology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Tommaso Rizzuti
- Division of Pathology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Daniela Marchetti
- Laboratorio di Genetica Medica, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Giorgio Conte
- Department of Neuroradiology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy.,Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Claudia Cinnante
- Istituto Auxologico Italiano IRCCS, Dipartimento di Radiologia e Diagnostica per Immagini, Milan, Italy
| | - Fabio Triulzi
- Department of Neuroradiology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy.,Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Nicola Persico
- Fetal Medicine and Surgery Service, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy.,Department of Clinical Science and Community Health, University of Milan, Milan, Italy
| | - Maria Iascone
- Laboratorio di Genetica Medica, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Federica Natacci
- Medical Genetics Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
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Dai P, Honda A, Ewans L, McGaughran J, Burnett L, Law M, Phan TG. Recommendations for next generation sequencing data reanalysis of unsolved cases with suspected Mendelian disorders: A systematic review and meta-analysis. Genet Med 2022; 24:1618-1629. [PMID: 35550369 DOI: 10.1016/j.gim.2022.04.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 04/18/2022] [Accepted: 04/18/2022] [Indexed: 10/18/2022] Open
Abstract
PURPOSE The study aimed to determine the diagnostic yield, optimal timing, and methodology of next generation sequencing data reanalysis in suspected Mendelian disorders. METHODS We conducted a systematic review and meta-analysis of studies that conducted data reanalysis in patients with suspected Mendelian disorders. Random effects model was used to pool the estimated outcome with subgroup analysis stratified by timing, sequencing methodology, sample size, segregation, use of research validation, and artificial intelligence (AI) variant curation tools. RESULTS A search of PubMed, Embase, Scopus, and Web of Science between 2007 and 2021 yielded 9327 articles, of which 29 were selected. Significant heterogeneity was noted between studies. Reanalysis had an overall diagnostic yield of 0.10 (95% CI = 0.06-0.13). Literature updates accounted for most new diagnoses. Diagnostic yield was higher after 24 months, although this was not statistically significant. Increased diagnoses were obtained with research validation and data sharing. AI-based tools did not adversely affect reanalysis diagnostic rate. CONCLUSION Next generation sequencing data reanalysis can improve diagnostic yield. Owing to the heterogeneity of the studies, the optimal time to reanalysis and the impact of AI-based tools could not be determined with confidence. We propose standardized guidelines for future studies to reduce heterogeneity and improve the quality of the conclusions.
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Affiliation(s)
- Pei Dai
- Precision Immunology Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia; St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, New South Wales, Australia; Clinical Immunogenomics Research Consortium Australasia (CIRCA), Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Andrew Honda
- The Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Lisa Ewans
- Department of Clinical Genetics, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
| | - Julie McGaughran
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Leslie Burnett
- Precision Immunology Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia; St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, New South Wales, Australia; Clinical Immunogenomics Research Consortium Australasia (CIRCA), Garvan Institute of Medical Research, Sydney, New South Wales, Australia; The Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, New South Wales, Australia; Genetic Medicine Program, Northern Clinical School, Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia
| | - Matthew Law
- Biostatistics and Databases Program, The Kirby Institute, UNSW Sydney, Sydney, New South Wales, Australia
| | - Tri Giang Phan
- Precision Immunology Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia; St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, New South Wales, Australia; Clinical Immunogenomics Research Consortium Australasia (CIRCA), Garvan Institute of Medical Research, Sydney, New South Wales, Australia.
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Mighton C, Lerner‐Ellis J. Principles of molecular testing for hereditary cancer. Genes Chromosomes Cancer 2022; 61:356-381. [DOI: 10.1002/gcc.23048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 04/03/2022] [Accepted: 04/06/2022] [Indexed: 11/10/2022] Open
Affiliation(s)
- Chloe Mighton
- Laboratory Medicine and Pathology, Mount Sinai Hospital, Sinai Health Toronto ON Canada
- Lunenfeld Tanenbaum Research Institute, Sinai Health Toronto ON Canada
- Genomics Health Services Research Program Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto Toronto ON Canada
- Institute of Health Policy, Management and Evaluation, Dalla Lana School of Public Health University of Toronto Toronto ON Canada
| | - Jordan Lerner‐Ellis
- Laboratory Medicine and Pathology, Mount Sinai Hospital, Sinai Health Toronto ON Canada
- Lunenfeld Tanenbaum Research Institute, Sinai Health Toronto ON Canada
- Department of Laboratory Medicine and Pathobiology University of Toronto Toronto ON Canada
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Collen LV, Kim DY, Field M, Okoroafor I, Saccocia G, Whitcomb SD, Green J, Dong MD, Barends J, Carey B, Weatherly ME, Rockowitz S, Sliz P, Liu E, Eran A, Grushkin-Lerner L, Bousvaros A, Muise AM, Klein C, Mitsialis V, Ouahed J, Snapper SB. Clinical Phenotypes and Outcomes in Monogenic Versus Non-monogenic Very Early Onset Inflammatory Bowel Disease. J Crohns Colitis 2022; 16:1380-1396. [PMID: 35366317 PMCID: PMC9455789 DOI: 10.1093/ecco-jcc/jjac045] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 01/31/2022] [Accepted: 03/31/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND AND AIMS Over 80 monogenic causes of very early onset inflammatory bowel disease [VEOIBD] have been identified. Prior reports of the natural history of VEOIBD have not considered monogenic disease status. The objective of this study is to describe clinical phenotypes and outcomes in a large single-centre cohort of patients with VEOIBD and universal access to whole exome sequencing [WES]. METHODS Patients receiving IBD care at a single centre were prospectively enrolled in a longitudinal data repository starting in 2012. WES was offered with enrollment. Enrolled patients were filtered by age of diagnosis <6 years to comprise a VEOIBD cohort. Monogenic disease was identified by filtering proband variants for rare, loss-of-function, or missense variants in known VEOIBD genes inherited according to standard Mendelian inheritance patterns. RESULTS This analysis included 216 VEOIBD patients, followed for a median of 5.8 years. Seventeen patients [7.9%] had monogenic disease. Patients with monogenic IBD were younger at diagnosis and were more likely to have Crohn's disease phenotype with higher rates of stricturing and penetrating disease and extraintestinal manifestations. Patients with monogenic disease were also more likely to experience outcomes of intensive care unit [ICU] hospitalisation, gastrostomy tube, total parenteral nutrition use, stunting at 3-year follow-up, haematopoietic stem cell transplant, and death. A total of 41 patients [19.0%] had infantile-onset disease. After controlling for monogenic disease, patients with infantile-onset IBD did not have increased risk for most severity outcomes. CONCLUSIONS Monogenic disease is an important driver of disease severity in VEOIBD. WES is a valuable tool in prognostication and management of VEOIBD.
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Affiliation(s)
- Lauren V Collen
- Corresponding authors: Lauren V. Collen, 300 Longwood Avenue, Enders 670, Boston, MA 02115, USA. Tel.: 617-919-4973; fax: 617-730-0498;
| | - David Y Kim
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Boston Children’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Michael Field
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Boston Children’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Ibeawuchi Okoroafor
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Boston Children’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Gwen Saccocia
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Boston Children’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Sydney Driscoll Whitcomb
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Boston Children’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Julia Green
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Boston Children’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Michelle Dao Dong
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Boston Children’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Jared Barends
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Boston Children’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Bridget Carey
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Boston Children’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Madison E Weatherly
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Boston Children’s Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Shira Rockowitz
- Manton centre for Orphan Disease Research, Boston Children’s Hospital, Boston, MA, USA
| | - Piotr Sliz
- Manton centre for Orphan Disease Research, Boston Children’s Hospital, Boston, MA, USA,Division of Molecular Medicine, Boston Children’s Hospital, Boston, MA, USA
| | - Enju Liu
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Boston Children’s Hospital and Harvard Medical School, Boston, MA, USA,Institutional centres for Clinical and Translational Research, Boston Children’s Hospital, Boston, MA, USA
| | - Alal Eran
- Computational Health Informatics Program, Boston Children’s Hospital, Boston, MA, USA,Harvard Medical School, Department of Biomedical Informatics, Boston, MA, USA,Department of Life Sciences and Zlotowski centre for Neuroscience, Ben Gurion University of the Negev, Beer-Sheva, Israel
| | - Leslie Grushkin-Lerner
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Boston Children’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Athos Bousvaros
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Boston Children’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Aleixo M Muise
- SickKids Inflammatory Bowel Disease centre, Research Institute, Hospital for Sick Children, Toronto, ON, Canada,Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, University of Toronto, Toronto, ON, Canada,Institute of Medical Science, University of Toronto, Toronto, ON, Canada
| | - Christoph Klein
- Department of Pediatrics, Dr. von Hauner Children’s Hospital, LMU Klinikum, and Gene centre, Ludwig Maximilians Universität München, München,Germany
| | - Vanessa Mitsialis
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Boston Children’s Hospital and Harvard Medical School, Boston, MA, USA,Division of Gastroenterology, Department of Medicine, Brigham & Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Scott B Snapper
- Scott B. Snapper, 300 Longwood Avenue, Enders 670, Boston, MA 02115, USA. Tel: 617-919-4973; fax: 617-730-0498;
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Mustafi D, Hisama FM, Huey J, Chao JR. The current state of genetic testing platforms for inherited retinal diseases. Ophthalmol Retina 2022; 6:702-710. [PMID: 35307606 PMCID: PMC9356993 DOI: 10.1016/j.oret.2022.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 03/08/2022] [Accepted: 03/14/2022] [Indexed: 11/30/2022]
Abstract
PURPOSE To evaluate genetic testing platforms used to aid in the diagnosis of inherited retinal degenerations (IRDs). DESIGN Evaluation of diagnostic test or technology SUBJECTS: Targeted genetic panel testing for IRDs METHODS, INTERVENTION, OR TESTING: Data collected regarding targeted genetic panel testing for IRDs offered by different labs were investigated for inclusion of coding and non-coding variants in disease genes. Both large IRD panels and smaller, more focused disease specific panels were included in the analysis. MAIN OUTCOME MEASURES Number of disease genes tested as well as the commonality and uniqueness across testing platforms in both coding and non-coding variants of disease. RESULTS Across the three IRD panel tests investigated, 409 unique genes are represented, of which 269 genes are tested by all three panels. The top 20 genes known to cause over 70% of all IRDs are represented in the 269 common genes tested by all three panels. In addition, 138 non-coding variants are assayed across the three platforms in 50 unique genes. Focused disease specific panels exhibited significant variability across 5 testing platforms that were studied. CONCLUSIONS Ordering genetic testing for IRDs is not straightforward, as evidenced by the multitude of panels available to providers. It is important that there is coverage of both coding and non-coding regions in IRD genes to offer a diagnosis in these patients. This paper details the diversity of testing platforms currently available to clinicians and provides a thorough explanation of genes tested in the different IRD panels. In a time of increased importance for clinical genetic testing of IRD patients, knowledge of the proper test to order is paramount.
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Affiliation(s)
- Debarshi Mustafi
- Department of Ophthalmology, University of Washington, Seattle, Washington; Department of Ophthalmology, Seattle Children's Hospital, Seattle, Washington.
| | - Fuki M Hisama
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington
| | - Jennifer Huey
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington
| | - Jennifer R Chao
- Department of Ophthalmology, University of Washington, Seattle, Washington
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Exome sequencing vs targeted gene panels for the evaluation of nonimmune hydrops fetalis. Am J Obstet Gynecol 2022; 226:128.e1-128.e11. [PMID: 34331894 PMCID: PMC8748274 DOI: 10.1016/j.ajog.2021.07.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 06/28/2021] [Accepted: 07/22/2021] [Indexed: 01/03/2023]
Abstract
BACKGROUND Next-generation sequencing is increasingly used in prenatal diagnosis. Targeted gene panels and exome sequencing are both available, but the comparative diagnostic yields of these approaches are not known. OBJECTIVE We compared the diagnostic yield of exome sequencing with the simulated application of commercial targeted gene panels in a large cohort of fetuses with nonimmune hydrops fetalis. STUDY DESIGN This was a secondary analysis of a cohort study of exome sequencing for nonimmune hydrops fetalis, in which recruitment, exome sequencing, and phenotype-driven variant analysis were completed in 127 pregnancies with features of nonimmune hydrops fetalis. An Internet search was performed to identify commercial laboratories that offer targeted gene panels for the prenatal evaluation of nonimmune hydrops fetalis or for specific disorders associated with nonimmune hydrops fetalis using the terms "non-immune hydrops fetalis," "fetal non-immune hydrops," "hydrops," "cystic hygroma," "lysosomal storage disease," "metabolic disorder," "inborn error of metabolism," "RASopathy," and "Noonan." Our primary outcome was the proportion of all genetic variants identified through exome sequencing that would have been identified if a targeted gene panel had instead been used. The secondary outcomes were the proportion of genetic variants that would have been identified by type of targeted gene panel (general nonimmune hydrops fetalis, RASopathy, or metabolic) and the percent of variants of uncertain significance that would have been identified on the panels, assuming 100% analytical sensitivity and specificity of panels for variants in the included genes. RESULTS Exome sequencing identified a pathogenic or likely pathogenic variant in 37 of 127 cases (29%) in a total of 29 genes. A variant of uncertain significance, strongly suspected to be associated with the phenotype, was identified in another 12 cases (9%). We identified 7 laboratories that offer 10 relevant targeted gene panels; 6 are described as RASopathy panels, 3 as nonimmune hydrops fetalis panels, and 1 as a metabolic panel. The median number of genes included on each of these panels is 22, ranging from 11 to 148. Had a nonimmune hydrops fetalis targeted gene panel been used instead of exome sequencing, 13 to 15 of the 29 genes (45%-52%) identified in our nonimmune hydrops fetalis cohort would have been sequenced, and 19 to 24 of the pathogenic variants (51%-62%) would have been detected. The yield was predicted to be the lowest with the metabolic panel (11%) and the highest with the largest nonimmune hydrops fetalis panel (62%). The largest nonimmune hydrops fetalis targeted gene panel would have had a diagnostic yield of 18% compared with 29% with exome sequencing. The exome sequencing platform used provided 30× or more coverage for all of the exons on the commercial targeted gene panels, supporting our assumption of 100% analytical sensitivity for exome sequencing. CONCLUSION The broader coverage of exome sequencing for genetically heterogeneous disorders, such as nonimmune hydrops fetalis, made it a superior alternative to targeted gene panel testing.
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Buja LM, Zhao B, Segura A, Lelenwa L, McDonald M, Michaud K. Cardiovascular pathology: guide to practice and training. Cardiovasc Pathol 2022. [DOI: 10.1016/b978-0-12-822224-9.00001-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
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Lee S, Jang SS, Park S, Yoon JG, Kim SY, Lim BC, Chae JH. The extended clinical and genetic spectrum of CTNNB1-related neurodevelopmental disorder. Front Pediatr 2022; 10:960450. [PMID: 35935366 PMCID: PMC9353113 DOI: 10.3389/fped.2022.960450] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 06/28/2022] [Indexed: 11/19/2022] Open
Abstract
PURPOSE Loss-of-function mutations of CTNNB1 have been established as the cause of neurodevelopmental disorder with spastic diplegia and visual defects. Although most patients share key phenotypes such as global developmental delay and intellectual disability, patients with CTNNB1-related neurodevelopmental disorder show a broad spectrum of clinical features. METHODS We enrolled 13 Korean patients with CTNNB1-related neurodevelopmental disorder who visited Seoul National University Children's Hospital (5 female and 8 male patients with ages ranging from 4 to 22 years). They were all genetically confirmed as having pathogenic loss-of-function variants in CTNNB1 using trio or singleton whole exome sequencing. Variants called from singleton analyses were confirmed to be de novo through parental Sanger sequencing. RESULTS We identified 11 de novo truncating variants in CTNNB1 in 13 patients, and two pathogenic variants, c.1867C > T (p.Gln623Ter) and c.1420C > T (p.Arg474Ter), found in two unrelated patients, respectively. Five of them were novel pathogenic variants not listed in the ClinVar database. While all patients showed varying degrees of intellectual disability, impaired motor performance, and ophthalmologic problems, none of them had structural brain abnormalities or seizure. In addition, there were three female patients who showed autistic features, such as hand stereotypy, bruxism, and abnormal breathing. A literature review revealed a female predominance of autistic features in CTNNB1-related neurodevelopmental disorder. CONCLUSION This is one of the largest single-center cohorts of CTNNB1-related neurodevelopmental disorder. This study investigated variable clinical features of patients and has expanded the clinical and genetic spectrum of the disease.
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Affiliation(s)
- Seungbok Lee
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, South Korea.,Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Children's Hospital, Seoul, South Korea
| | - Se Song Jang
- Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Children's Hospital, Seoul, South Korea
| | - Soojin Park
- Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Children's Hospital, Seoul, South Korea
| | - Jihoon G Yoon
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, South Korea
| | - Soo Yeon Kim
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, South Korea.,Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Children's Hospital, Seoul, South Korea
| | - Byung Chan Lim
- Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Children's Hospital, Seoul, South Korea
| | - Jong Hee Chae
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, South Korea.,Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Children's Hospital, Seoul, South Korea
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Gabriel H, Korinth D, Ritthaler M, Schulte B, Battke F, von Kaisenberg C, Wüstemann M, Schulze B, Friedrich-Freksa A, Pfeiffer L, Entezami M, Schröer A, Bürger J, Schwaibold EMC, Lebek H, Biskup S. Trio exome sequencing is highly relevant in prenatal diagnostics. Prenat Diagn 2021; 42:845-851. [PMID: 34958143 PMCID: PMC9305182 DOI: 10.1002/pd.6081] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 12/26/2022]
Abstract
Objective About 3% of newborns show malformations, with about 20% of the affected having genetic causes. Clarification of genetic diseases in postnatal diagnostics was significantly improved with high‐throughput sequencing, in particular through whole exome sequencing covering all protein‐coding regions. Here, we aim to extend the use of this technology to prenatal diagnostics. Method Between 07/2018 and 10/2020, 500 pregnancies with fetal ultrasound abnormalities were analyzed after genetic counseling as part of prenatal diagnostics using WES of the fetus and parents. Results Molecular genetic findings could explain ultrasound abnormalities in 38% of affected fetuses. In 47% of these, disease‐causing de novo variants were found. Pathogenic variants in genes with autosomal recessive or X‐linked inheritance were detected in more than one‐third (70/189 = 37%). The latter are associated with increased probability of recurrence, making their detection important for further pregnancies. Average time from sample receipt to report was 12 days in the recent cases. Conclusion Trio exome sequencing is a useful addition to prenatal diagnostics due to its high diagnostic yield and short processing time (comparable to chromosome analysis). It covers a wide spectrum of genetic changes. Comprehensive interdisciplinary counseling before and after diagnostics is indispensable.
What's already known about this topic?
It is known that about 20% of malformations in newborns can be associated with genetic causes. Whole‐exome sequencing, and especially trio exome sequencing, is an established and successful method in postnatal genetic diagnostics. Diagnostic yield for trio exome sequencing is around 37%.
What does this study add?
We show that trio exome sequencing is a fast and comprehensive method in prenatal diagnostics with diagnostic yield similar to that of postnatal trio exome sequencing. We provide case solution rates for different phenotypic observations from 19% for abnormalities of internal organs up to 52% for skeletal malformations.
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Affiliation(s)
| | - Dirk Korinth
- Praxis für Humangenetik Tübingen, Tübingen, Germany
| | | | | | | | | | - Max Wüstemann
- Zentrum für Pränatalmedizin Hannover, Hannover, Germany
| | | | | | - Lutz Pfeiffer
- Medicover Humangenetik Berlin-Lichtenberg, Berlin, Germany
| | | | | | | | | | - Holger Lebek
- Pränatale Diagnostik Berlin-Lichtenberg, Berlin, Germany
| | - Saskia Biskup
- Praxis für Humangenetik Tübingen, Tübingen, Germany.,CeGaT GmbH, Tübingen, Germany
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