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Gül M, Russo GI, Kandil H, Boitrelle F, Saleh R, Chung E, Kavoussi P, Mostafa T, Shah R, Agarwal A. Male Infertility: New Developments, Current Challenges, and Future Directions. World J Mens Health 2024; 42:502-517. [PMID: 38164030 PMCID: PMC11216957 DOI: 10.5534/wjmh.230232] [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: 08/16/2023] [Accepted: 08/27/2023] [Indexed: 01/03/2024] Open
Abstract
There have been many significant scientific advances in the diagnostics and treatment modalities in the field of male infertility in recent decades. Examples of these include assisted reproductive technologies, sperm selection techniques for intracytoplasmic sperm injection, surgical procedures for sperm retrieval, and novel tests of sperm function. However, there is certainly a need for new developments in this field. In this review, we discuss advances in the management of male infertility, such as seminal oxidative stress testing, sperm DNA fragmentation testing, genetic and epigenetic tests, genetic manipulations, artificial intelligence, personalized medicine, and telemedicine. The role of the reproductive urologist will continue to expand in future years to address different topzics related to diverse questions and controversies of pathophysiology, diagnosis, and therapy of male infertility, training researchers and physicians in medical and scientific research in reproductive urology/andrology, and further development of andrology as an independent specialty.
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Affiliation(s)
- Murat Gül
- Department of Urology, Selcuk University School of Medicine, Konya, Turkey
- Global Andrology Forum, Moreland Hills, OH, USA
| | - Giorgio Ivan Russo
- Urology Section, University of Catania, Catania, Italy
- Global Andrology Forum, Moreland Hills, OH, USA
| | - Hussein Kandil
- Fakih IVF Fertility Center, Abu Dhabi, UAE
- Global Andrology Forum, Moreland Hills, OH, USA
| | - Florence Boitrelle
- Reproductive Biology, Fertility Preservation, Andrology, CECOS, Poissy Hospital, Poissy, France
- Paris Saclay University, UVSQ, INRAE, BREED, Jouy-en-Josas, France
- Global Andrology Forum, Moreland Hills, OH, USA
| | - Ramadan Saleh
- Department of Dermatology, Venereology and Andrology, Faculty of Medicine, Sohag University, Sohag, Egypt
- Ajyal IVF Center, Ajyal Hospital, Sohag, Egypt
- Global Andrology Forum, Moreland Hills, OH, USA
| | - Eric Chung
- Department of Urology, Princess Alexandra Hospital, University of Queensland, Brisbane, QLD, Australia
- Global Andrology Forum, Moreland Hills, OH, USA
| | - Parviz Kavoussi
- Department of Reproductive Urology, Austin Fertility & Reproductive Medicine/Westlake IVF, Austin, TX, USA
- Global Andrology Forum, Moreland Hills, OH, USA
| | - Taymour Mostafa
- Department of Andrology, Sexology and STIs, Faculty of Medicine, Cairo University, Cairo, Egypt
- Global Andrology Forum, Moreland Hills, OH, USA
| | - Rupin Shah
- Department of Urology, Lilavati Hospital and Research Centre, Mumbai, India
- Well Women's Centre, Sir HN Reliance Foundation Hospital, Mumbai, India
- Global Andrology Forum, Moreland Hills, OH, USA
| | - Ashok Agarwal
- Global Andrology Forum, Moreland Hills, OH, USA
- Cleveland Clinic, Cleveland, OH, USA.
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Phua YL, D'Annibale OM, Karunanidhi A, Mohsen AW, Kirmse B, Dobrowolski SF, Vockley J. A multiomics approach reveals evidence for phenylbutyrate as a potential treatment for combined D,L-2- hydroxyglutaric aciduria. Mol Genet Metab 2024; 142:108495. [PMID: 38772223 DOI: 10.1016/j.ymgme.2024.108495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 03/30/2024] [Accepted: 05/13/2024] [Indexed: 05/23/2024]
Abstract
PURPOSE To identify therapies for combined D, L-2-hydroxyglutaric aciduria (C-2HGA), a rare genetic disorder caused by recessive variants in the SLC25A1 gene. METHODS Patients C-2HGA were identified and diagnosed by whole exome sequencing and biochemical genetic testing. Patient derived fibroblasts were then treated with phenylbutyrate and the functional effects assessed by metabolomics and RNA-sequencing. RESULTS In this study, we demonstrated that C-2HGA patient derived fibroblasts exhibited impaired cellular bioenergetics. Moreover, Fibroblasts form one patient exhibited worsened cellular bioenergetics when supplemented with citrate. We hypothesized that treating patient cells with phenylbutyrate (PB), an FDA approved pharmaceutical drug that conjugates glutamine for renal excretion, would reduce mitochondrial 2-ketoglutarate, thereby leading to improved cellular bioenergetics. Metabolomic and RNA-seq analyses of PB-treated fibroblasts demonstrated a significant decrease in intracellular 2-ketoglutarate, 2-hydroxyglutarate, and in levels of mRNA coding for citrate synthase and isocitrate dehydrogenase. Consistent with the known action of PB, an increased level of phenylacetylglutamine in patient cells was consistent with the drug acting as 2-ketoglutarate sink. CONCLUSION Our pre-clinical studies suggest that citrate supplementation has the possibility exacerbating energy metabolism in this condition. However, improvement in cellular bioenergetics suggests phenylbutyrate might have interventional utility for this rare disease.
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MESH Headings
- Humans
- Phenylbutyrates/pharmacology
- Phenylbutyrates/therapeutic use
- Fibroblasts/metabolism
- Fibroblasts/drug effects
- Glutarates/metabolism
- Ketoglutaric Acids/metabolism
- Energy Metabolism/drug effects
- Energy Metabolism/genetics
- Mitochondria/drug effects
- Mitochondria/metabolism
- Mitochondria/genetics
- Metabolomics
- Exome Sequencing
- Citrate (si)-Synthase/metabolism
- Citrate (si)-Synthase/genetics
- Brain Diseases, Metabolic, Inborn/drug therapy
- Brain Diseases, Metabolic, Inborn/genetics
- Brain Diseases, Metabolic, Inborn/metabolism
- Isocitrate Dehydrogenase/genetics
- Isocitrate Dehydrogenase/metabolism
- Brain Diseases, Metabolic/drug therapy
- Brain Diseases, Metabolic/genetics
- Brain Diseases, Metabolic/metabolism
- Brain Diseases, Metabolic/pathology
- Multiomics
- Mitochondrial Proteins
- Organic Anion Transporters
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Affiliation(s)
- Yu Leng Phua
- Department of Pediatrics, Division of Genetic and Genomic Medicine, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA; Department of Pathology, Clinical Biochemical Genetics Laboratory, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Olivia M D'Annibale
- Department of Pediatrics, Division of Genetic and Genomic Medicine, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA; Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, USA
| | - Anuradha Karunanidhi
- Department of Pediatrics, Division of Genetic and Genomic Medicine, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Al-Walid Mohsen
- Department of Pediatrics, Division of Genetic and Genomic Medicine, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA; Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, USA
| | - Brian Kirmse
- Department of Pediatrics, University of Mississippi Medical Center, Jackson, MS, USA
| | - Steven F Dobrowolski
- Department of Pathology, Clinical Biochemical Genetics Laboratory, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Jerry Vockley
- Department of Pediatrics, Division of Genetic and Genomic Medicine, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA; Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, USA.
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3
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Kwon S, Kim JW, Kim ES, Paik JH, Chung JH, Cho SW, Won TB, Rhee CS, Wee JH, Kim H. Assessment of TP53 and CDKN2A status as predictive markers of malignant transformation of sinonasal inverted papilloma. Sci Rep 2024; 14:14286. [PMID: 38902320 PMCID: PMC11190283 DOI: 10.1038/s41598-024-64901-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 06/13/2024] [Indexed: 06/22/2024] Open
Abstract
The mechanism and predictive biomarkers of sinonasal inverted papilloma (IP) transformation into squamous cell carcinoma (SCC) are still unclear. We investigated the genetic mutations involved and the predictive biomarkers. Fourteen patients with SCC arising from IP and six patients with IPs without malignant transformation (sIP) were included. DNA was extracted separately from areas of normal tissue, IP, dysplasia, and SCC. Whole exome sequencing and immunohistochemistry was performed. Major oncogenic mutations were observed in the progression from IP to SCC. The most frequently mutated genes were TP53 (39%) and CDKN2A (27%). Mutations in TP53 and/or CDKN2A were observed in three of six IPs with malignant transformation (cIP); none were observed in sIPs. Tumor mutational burden (TMB) increased from IP to SCC (0.64/Mb, 1.11/Mb, and 1.25 for IP, dysplasia, and SCC, respectively). TMB was higher in the cIPs than in the sIPs (0.64/Mb vs 0.3/Mb). Three cIPs showed a diffuse strong or null pattern in p53, and one showed a total loss of p16, a distinct pattern from sIPs. Our result suggests that TP53 and CDKN2A status can be predictive markers of malignant transformation of IP. Furthermore, immunohistochemistry of p53 and p16 expression can be surrogate markers for TP53 and CDKN2A status.
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MESH Headings
- Humans
- Papilloma, Inverted/genetics
- Papilloma, Inverted/pathology
- Papilloma, Inverted/metabolism
- Tumor Suppressor Protein p53/genetics
- Tumor Suppressor Protein p53/metabolism
- Cyclin-Dependent Kinase Inhibitor p16/genetics
- Cyclin-Dependent Kinase Inhibitor p16/metabolism
- Male
- Female
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/metabolism
- Middle Aged
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Aged
- Paranasal Sinus Neoplasms/genetics
- Paranasal Sinus Neoplasms/pathology
- Paranasal Sinus Neoplasms/metabolism
- Mutation
- Carcinoma, Squamous Cell/genetics
- Carcinoma, Squamous Cell/pathology
- Carcinoma, Squamous Cell/metabolism
- Adult
- Aged, 80 and over
- Exome Sequencing
- Immunohistochemistry
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Affiliation(s)
- Soohyeon Kwon
- Department of Pathology, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Republic of Korea
| | - Jeong-Whun Kim
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Republic of Korea
| | - Eun Sun Kim
- Department of Pathology, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Republic of Korea
| | - Jin Ho Paik
- Department of Pathology, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Republic of Korea
| | - Jin-Haeng Chung
- Department of Pathology, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Republic of Korea
| | - Sung-Woo Cho
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Republic of Korea
| | - Tae-Bin Won
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Republic of Korea
| | - Chae-Seo Rhee
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Republic of Korea
| | - Jee Hye Wee
- Department of Otorhinolaryngology-Head and Neck Surgery, Hallym University Sacred Heart Hospital, Hallym University College of Medicine, Anyang, Republic of Korea.
| | - Hyojin Kim
- Department of Pathology, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Republic of Korea.
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4
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Kernohan KD, Boycott KM. The expanding diagnostic toolbox for rare genetic diseases. Nat Rev Genet 2024; 25:401-415. [PMID: 38238519 DOI: 10.1038/s41576-023-00683-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/22/2023] [Indexed: 05/23/2024]
Abstract
Genomic technologies, such as targeted, exome and short-read genome sequencing approaches, have revolutionized the care of patients with rare genetic diseases. However, more than half of patients remain without a diagnosis. Emerging approaches from research-based settings such as long-read genome sequencing and optical genome mapping hold promise for improving the identification of disease-causal genetic variants. In addition, new omic technologies that measure the transcriptome, epigenome, proteome or metabolome are showing great potential for variant interpretation. As genetic testing options rapidly expand, the clinical community needs to be mindful of their individual strengths and limitations, as well as remaining challenges, to select the appropriate diagnostic test, correctly interpret results and drive innovation to address insufficiencies. If used effectively - through truly integrative multi-omics approaches and data sharing - the resulting large quantities of data from these established and emerging technologies will greatly improve the interpretative power of genetic and genomic diagnostics for rare diseases.
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Affiliation(s)
- Kristin D Kernohan
- CHEO Research Institute, University of Ottawa, Ottawa, ON, Canada
- Newborn Screening Ontario, CHEO, Ottawa, ON, Canada
| | - Kym M Boycott
- CHEO Research Institute, University of Ottawa, Ottawa, ON, Canada.
- Department of Genetics, CHEO, Ottawa, ON, Canada.
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5
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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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6
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Hramyka D, Sczakiel HL, Zhao MX, Stolpe O, Nieminen M, Adam R, Danyel M, Einicke L, Hägerling R, Knaus A, Mundlos S, Schwartzmann S, Seelow D, Ehmke N, Mensah MA, Boschann F, Beule D, Holtgrewe M. REEV: review, evaluate and explain variants. Nucleic Acids Res 2024:gkae366. [PMID: 38769069 DOI: 10.1093/nar/gkae366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 04/07/2024] [Accepted: 05/03/2024] [Indexed: 05/22/2024] Open
Abstract
In the era of high throughput sequencing, special software is required for the clinical evaluation of genetic variants. We developed REEV (Review, Evaluate and Explain Variants), a user-friendly platform for clinicians and researchers in the field of rare disease genetics. Supporting data was aggregated from public data sources. We compared REEV with seven other tools for clinical variant evaluation. REEV (semi-)automatically fills individual ACMG criteria facilitating variant interpretation. REEV can store disease and phenotype data related to a case to use these for phenotype similarity measures. Users can create public permanent links for individual variants that can be saved as browser bookmarks and shared. REEV may help in the fast diagnostic assessment of genetic variants in a clinical as well as in a research context. REEV (https://reev.bihealth.org/) is free and open to all users and there is no login requirement.
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Affiliation(s)
- Dzmitry Hramyka
- Berlin Institute of Health, Core Unit Bioinformatics, Berlin, Germany
| | - Henrike Lisa Sczakiel
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- BIH Biomedical Innovation Academy, Clinician Scientist Program, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
- RG Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Max Xiaohang Zhao
- Berlin Institute of Health, Core Unit Bioinformatics, Berlin, Germany
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Oliver Stolpe
- Berlin Institute of Health, Core Unit Bioinformatics, Berlin, Germany
| | - Mikko Nieminen
- Berlin Institute of Health, Core Unit Bioinformatics, Berlin, Germany
| | - Ronja Adam
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Magdalena Danyel
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- BIH Biomedical Innovation Academy, Clinician Scientist Program, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Lara Einicke
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - René Hägerling
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- BIH Biomedical Innovation Academy, Clinician Scientist Program, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
- RG Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Berlin Institute of Health , BIH Center for Regenerative Therapies, Berlin, Germany
| | - Alexej Knaus
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Germany
| | - Stefan Mundlos
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- RG Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Sarina Schwartzmann
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Dominik Seelow
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Nadja Ehmke
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Martin Atta Mensah
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- BIH Biomedical Innovation Academy, Digital Clinician Scientist Program, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Felix Boschann
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- BIH Biomedical Innovation Academy, Clinician Scientist Program, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Dieter Beule
- Berlin Institute of Health, Core Unit Bioinformatics, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Manuel Holtgrewe
- Berlin Institute of Health, Core Unit Bioinformatics, Berlin, Germany
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7
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Shalom S, Hanany M, Eilat A, Chowers I, Ben-Yosef T, Khateb S, Banin E, Sharon D. Simultaneous Detection of Common Founder Mutations Using a Cost-Effective Deep Sequencing Panel. Genes (Basel) 2024; 15:646. [PMID: 38790275 PMCID: PMC11120920 DOI: 10.3390/genes15050646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/13/2024] [Accepted: 05/16/2024] [Indexed: 05/26/2024] Open
Abstract
Inherited retinal diseases (IRDs) are a clinically and genetically heterogeneous group of diseases which cause visual loss due to Mendelian mutations in over 250 genes, making genetic diagnosis challenging and time-consuming. Here, we developed a new tool, CDIP (Cost-effective Deep-sequencing IRD Panel) in which a simultaneous sequencing of common mutations is performed. CDIP is based on simultaneous amplification of 47 amplicons harboring common mutations followed by next-generation sequencing (NGS). Following five rounds of calibration of NGS-based steps, CDIP was used in 740 IRD samples. The analysis revealed 151 mutations in 131 index cases. In 54 (7%) of these cases, CDIP identified the genetic cause of disease (the remaining were single-heterozygous recessive mutations). These include a patient that was clinically diagnosed with retinoschisis and found to be homozygous for NR2E3-c.932G>A (p.R311Q), and a patient with RP who is hemizygous for an RPGR variant, c.292C>A (p.H98N), which was not included in the analysis but is located in proximity to one of these mutations. CDIP is a cost-effective deep sequencing panel for simultaneous detection of common founder mutations. This protocol can be implemented for additional populations as well as additional inherited diseases, and mainly in populations with strong founder effects.
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Affiliation(s)
- Sapir Shalom
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel; (S.S.); (M.H.); (A.E.); (I.C.); (S.K.); (E.B.)
- Department of Military Medicine and “Tzameret”, Faculty of Medicine, Hebrew University of Jerusalem and Medical Corps, Israel Defense Forces, Jerusalem 91120, Israel
| | - Mor Hanany
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel; (S.S.); (M.H.); (A.E.); (I.C.); (S.K.); (E.B.)
| | - Avital Eilat
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel; (S.S.); (M.H.); (A.E.); (I.C.); (S.K.); (E.B.)
| | - Itay Chowers
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel; (S.S.); (M.H.); (A.E.); (I.C.); (S.K.); (E.B.)
| | - Tamar Ben-Yosef
- Rappaport Faculty of Medicine, Technion—Israel Institute of Technology, Haifa 3109601, Israel;
| | - Samer Khateb
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel; (S.S.); (M.H.); (A.E.); (I.C.); (S.K.); (E.B.)
| | - Eyal Banin
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel; (S.S.); (M.H.); (A.E.); (I.C.); (S.K.); (E.B.)
| | - Dror Sharon
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel; (S.S.); (M.H.); (A.E.); (I.C.); (S.K.); (E.B.)
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8
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Gwack J, Kim N, Park J. Improving the Yield of Genetic Diagnosis through Additional Genetic Panel Testing in Hereditary Ophthalmic Diseases. Curr Issues Mol Biol 2024; 46:5010-5022. [PMID: 38785568 PMCID: PMC11119902 DOI: 10.3390/cimb46050300] [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: 04/07/2024] [Revised: 05/17/2024] [Accepted: 05/18/2024] [Indexed: 05/25/2024] Open
Abstract
Numerous hereditary ophthalmic diseases display significant genetic diversity. Consequently, the utilization of gene panel sequencing allows a greater number of patients to receive a genetic diagnosis for their clinical manifestations. We investigated how to improve the yield of genetic diagnosis through additional gene panel sequencing in hereditary ophthalmic diseases. A gene panel sequencing consisting of a customized hereditary retinopathy panel or hereditary retinitis pigmentosa (RP) panel was prescribed and referred to a CAP-accredited clinical laboratory. If no significant mutations associated with hereditary retinopathy and RP were detected in either panel, additional gene panel sequencing was requested for research use, utilizing the remaining panel. After additional gene panel sequencing, a total of 16 heterozygous or homozygous variants were identified in 15 different genes associated with hereditary ophthalmic diseases. Of 15 patients carrying any candidate variants, the clinical symptoms could be tentatively accounted for by genetic mutations in seven patients. However, in the remaining eight patients, given the in silico mutation predictive analysis, variant allele frequency in gnomAD, inheritance pattern, and genotype-phenotype correlation, fully elucidating the clinical manifestations with the identified rare variant was challenging. Our study highlights the utility of gene panel sequencing in achieving accurate diagnoses for hereditary ophthalmic diseases and enhancing the diagnostic yield through additional gene panel sequencing. Thus, gene panel sequencing can serve as a primary tool for the genetic diagnosis of hereditary ophthalmic diseases, even in cases where a single genetic cause is suspected. With a deeper comprehension of the genetic mechanisms underlying these diseases, it becomes feasible.
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Affiliation(s)
- Jin Gwack
- Department of Preventive Medicine, Jeonbuk National University Medical School, Jeonju 54907, Republic of Korea;
| | - Namsu Kim
- Department of Laboratory Medicine, Jeonbuk National University Medical School and Hospital, Jeonju 54907, Republic of Korea;
- Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju 54907, Republic of Korea
| | - Joonhong Park
- Department of Laboratory Medicine, Jeonbuk National University Medical School and Hospital, Jeonju 54907, Republic of Korea;
- Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju 54907, Republic of Korea
- Department of Laboratory Medicine, Daejeon St. Mary’s Hospital, Daejeon 34943, Republic of Korea
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9
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Ge M, Ji C, Li H, Huang H. De Novo Mutation in KRT1 Leads to Epidermolytic Palmoplantar Keratoderma: from Chinese Traditional Treatment to Prenatal Diagnosis Using Whole-Exome Sequencing-Plus. DNA Cell Biol 2023; 42:645-652. [PMID: 37566479 DOI: 10.1089/dna.2023.0154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/13/2023] Open
Abstract
Congenital skin disorders are a class of complex genetic diseases that are difficult to diagnose and treat. We developed trio whole-exome sequencing-plus (WES-plus) for detecting de novo mutations and evaluated the use of traditional Chinese medicine (TCM) for treating congenital skin disorders. In this study, we successively performed panel-based next-generation sequencing (NGS) and Trio WES-plus in a child with frequent large blisters. Panel-based NGS revealed no pathogenic mutations. Trio WES-plus for resequencing based on cutaneous keratosis of the palms and feet detected a missense mutation (c.1436T>A, p.Ile479Asn) in the coding region of KRT1 in the child but not in his parents. Following prenatal diagnosis, a healthy second baby without the mutation was born. The disease symptoms of epidermolytic palmoplantar keratoderma (EPPK) application were improved by TCM and Western medicine. Our study revealed the pathogenicity of a de novo mutation in human KRT1, which expands the mutation spectrum of EPPK. Trio WES-plus is useful for diagnosing genetic diseases and providing genetic guidance from prenatal diagnosis to treatment.
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Affiliation(s)
- Mengdi Ge
- Department of Pediatrics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Chunmin Ji
- Department of Obstetrics and Gynecology, Air Force Hospital of Eastern Theater, Nanjing, China
| | - Huanzhen Li
- Department of Pediatrics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Huan Huang
- Department of Pediatrics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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10
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Chandy T. Intervention of next-generation sequencing in diagnosis of Alzheimer's disease: challenges and future prospects. Dement Neuropsychol 2023; 17:e20220025. [PMID: 37577182 PMCID: PMC10417152 DOI: 10.1590/1980-5764-dn-2022-0025] [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: 04/10/2022] [Revised: 04/10/2023] [Accepted: 05/17/2023] [Indexed: 08/15/2023] Open
Abstract
Clinical diagnosis of several neurodegenerative disorders based on clinical phenotype is challenging due to its heterogeneous nature and overlapping disease manifestations. Therefore, the identification of underlying genetic mechanisms is of paramount importance for better diagnosis and therapeutic regimens. With the emergence of next-generation sequencing, it becomes easier to identify all gene variants in the genome simultaneously, with a system-wide and unbiased approach. Presently various bioinformatics databases are maintained on discovered gene variants and phenotypic indications are available online. Since individuals are unique in their genome, evaluation based on their genetic makeup helps evolve the diagnosis, counselling, and treatment process at the personal level. This article aims to briefly summarize the utilization of next-generation sequencing in deciphering the genetic causes of Alzheimer's disease and address the limitations of whole genome and exome sequencing.
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Affiliation(s)
- Tijimol Chandy
- MedGenome Labs Pvt. Ltd., Bangalore-560100, Karnataka, India
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11
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Aspromonte MC, Conte AD, Zhu S, Tan W, Shen Y, Zhang Y, Li Q, Wang MH, Babbi G, Bovo S, Martelli PL, Casadio R, Althagafi A, Toonsi S, Kulmanov M, Hoehndorf R, Katsonis P, Williams A, Lichtarge O, Xian S, Surento W, Pejaver V, Mooney SD, Sunderam U, Srinivasan R, Murgia A, Piovesan D, Tosatto SCE, Leonardi E. CAGI6 ID-Challenge: Assessment of phenotype and variant predictions in 415 children with Neurodevelopmental Disorders (NDDs). RESEARCH SQUARE 2023:rs.3.rs-3209168. [PMID: 37577579 PMCID: PMC10418555 DOI: 10.21203/rs.3.rs-3209168/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
In the context of the Critical Assessment of the Genome Interpretation, 6th edition (CAGI6), the Genetics of Neurodevelopmental Disorders Lab in Padua proposed a new ID-challenge to give the opportunity of developing computational methods for predicting patient's phenotype and the causal variants. Eight research teams and 30 models had access to the phenotype details and real genetic data, based on the sequences of 74 genes (VCF format) in 415 pediatric patients affected by Neurodevelopmental Disorders (NDDs). NDDs are clinically and genetically heterogeneous conditions, with onset in infant age. In this study we evaluate the ability and accuracy of computational methods to predict comorbid phenotypes based on clinical features described in each patient and causal variants. Finally, we asked to develop a method to find new possible genetic causes for patients without a genetic diagnosis. As already done for the CAGI5, seven clinical features (ID, ASD, ataxia, epilepsy, microcephaly, macrocephaly, hypotonia), and variants (causative, putative pathogenic and contributing factors) were provided. Considering the overall clinical manifestation of our cohort, we give out the variant data and phenotypic traits of the 150 patients from CAGI5 ID-Challenge as training and validation for the prediction methods development.
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Affiliation(s)
| | | | - Shaowen Zhu
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843
| | - Wuwei Tan
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843
| | - Yang Shen
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843
| | | | - Qi Li
- CUHK Shenzhen Research Institute, Shenzhen
| | | | - Giulia Babbi
- Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna
| | - Samuele Bovo
- Department of Agricultural and Food Sciences, University of Bologna
| | - Pier Luigi Martelli
- Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna
| | - Rita Casadio
- Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna
| | - Azza Althagafi
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences & Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal 23
| | - Sumyyah Toonsi
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences & Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal 23
| | - Maxat Kulmanov
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences & Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal 23
| | - Robert Hoehndorf
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences & Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal 23
| | - Panagiotis Katsonis
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030
| | - Amanda Williams
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030
| | - Olivier Lichtarge
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030
| | - Su Xian
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA 98195
| | - Wesley Surento
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA 98195
| | - Vikas Pejaver
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Sean D Mooney
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA 98195
| | - Uma Sunderam
- Innovation Labs, Tata Consultancy Services, Hyderabad
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12
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Jaskiewicz K, Maleszka-Kurpiel M, Kabza M, Karolak JA, Gajecka M. Sequence variants contributing to dysregulated inflammatory responses across keratoconic cone surface in adolescent patients with keratoconus. Front Immunol 2023; 14:1197054. [PMID: 37483635 PMCID: PMC10359427 DOI: 10.3389/fimmu.2023.1197054] [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: 03/30/2023] [Accepted: 06/09/2023] [Indexed: 07/25/2023] Open
Abstract
Background Keratoconus (KTCN) is the most common corneal ectasia resulting in a conical shape of the cornea. Here, genomic variation in the corneal epithelium (CE) across the keratoconic cone surface in patients with KTCN and its relevance in the functioning of the immune system were assessed. Methods Samples from four unrelated adolescent patients with KTCN and two control individuals were obtained during the CXL and PRK procedures, respectively. Three topographic regions, central, middle, and peripheral, were separated towards the whole-genome sequencing (WGS) study embracing a total of 18 experimental samples. The coding and non-coding sequence variation, including structural variation, was assessed and then evaluated together with the previously reported transcriptomic outcomes for the same CE samples and full-thickness corneas. Results First, pathway enrichment analysis of genes with identified coding variants pointed to "Antigen presentation" and "Interferon alpha/beta signaling" as the most overrepresented pathways, indicating the involvement of inflammatory responses in KTCN. Both coding and non-coding sequence variants were found in genes (or in their close proximity) linked to the previously revealed KTCN-specific cellular components, namely, "Actin cytoskeleton", "Extracellular matrix", "Collagen-containing extracellular matrix", "Focal adhesion", "Hippo signaling pathway", and "Wnt signaling" pathways. No genomic heterogeneity across the corneal surface was found comparing the assessed topographic regions. Thirty-five chromosomal regions enriched in both coding and non-coding KTCN-specific sequence variants were revealed, with a most representative 5q locus previously recognized as involved in KTCN. Conclusion The identified genomic features indicate the involvement of innate and adaptive immune system responses in KTCN pathogenesis.
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Affiliation(s)
| | - Magdalena Maleszka-Kurpiel
- Optegra Eye Health Care Clinic in Poznan, Poznan, Poland
- Chair of Ophthalmology and Optometry, Poznan University of Medical Sciences, Poznan, Poland
| | - Michał Kabza
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland
| | - Justyna A. Karolak
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland
| | - Marzena Gajecka
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland
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13
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Mroczek M, Liu J, Sypniewski M, Pieńkowski T, Itrych B, Stojak J, Pronobis-Szczylik B, Stępień M, Kaja E, Dąbrowski M, Suchocki T, Wojtaszewska M, Zawadzki P, Mach A, Sztromwasser P, Król ZJ, Szyda J, Dobosz P. The cancer-risk variant frequency among Polish population reported by the first national whole-genome sequencing study. Front Oncol 2023; 13:1045817. [PMID: 36845707 PMCID: PMC9950741 DOI: 10.3389/fonc.2023.1045817] [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: 09/16/2022] [Accepted: 01/20/2023] [Indexed: 02/12/2023] Open
Abstract
Introduction Population-based cancer screening has raised many controversies in recent years, not only regarding the costs but also regarding the ethical nature and issues related to variant interpretation. Nowadays, genetic cancer screening standards are different in every country and usually encompass only individuals with a personal or family history of relevant cancer. Methods Here we performed a broad genetic screening for cancer-related rare germline variants on population data from the Thousand Polish Genomes database based on 1076 Polish unrelated individuals that underwent whole genome sequencing (WGS). Results We identified 19 551 rare variants in 806 genes related to oncological diseases, among them 89% have been located in non-coding regions. The combined BRCA1/BRCA2 pathogenic/likely pathogenic according to ClinVar allele frequency in the unselected population of 1076 Poles was 0.42%, corresponding to nine carriers. Discussion Altogether, on the population level, we found especially problematic the assessment of the pathogenicity of variants and the relation of ACMG guidelines to the population frequency. Some of the variants may be overinterpreted as disease-causing due to their rarity or lack of annotation in the databases. On the other hand, some relevant variants may have been overseen given that there is little pooled population whole genome data on oncology. Before population WGS screening will become a standard, further studies are needed to assess the frequency of the variants suspected to be pathogenic on the population level and with reporting of likely benign variants.
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Affiliation(s)
- Magdalena Mroczek
- Central Clinical Hospital of Ministry of the Interior and Administration in Warsaw, Warsaw, Poland,*Correspondence: Magdalena Mroczek,
| | - Jakub Liu
- Biostatistics Group, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Mateusz Sypniewski
- Central Clinical Hospital of Ministry of the Interior and Administration in Warsaw, Warsaw, Poland
| | - Tadeusz Pieńkowski
- Central Clinical Hospital of Ministry of the Interior and Administration in Warsaw, Warsaw, Poland,Postgraduate Medical Education Center, Warsaw, Poland
| | - Bartosz Itrych
- Central Clinical Hospital of Ministry of the Interior and Administration in Warsaw, Warsaw, Poland
| | - Joanna Stojak
- Central Clinical Hospital of Ministry of the Interior and Administration in Warsaw, Warsaw, Poland,Department of Experimental Embryology, Institute of Genetics and Animal Biotechnology, Polish Academy of Science, Jastrzębiec, Poland
| | | | - Maria Stępień
- Department of Sports Medicine, Doctoral School, Medical University of Lublin, Lublin, Poland
| | - Elżbieta Kaja
- Department of Medical Chemistry and Laboratory Medicine, Poznan University of Medical Sciences, Poznan, Poland
| | | | - Tomasz Suchocki
- Biostatistics Group, Wrocław University of Environmental and Life Sciences, Wrocław, Poland,National Research Institute of Animal Production, Balice, Poland
| | - Marzena Wojtaszewska
- Department of Haematology, Institute of Medical Sciences, College of Medical Sciences, University of Rzeszów, Rzeszów, Poland,Department of Haematology, Frederic Chopin Provincial Specialist Hospital, Rzeszów, Poland
| | | | - Anna Mach
- Department of Psychiatry, Medical University of Warsaw, Warsaw, Poland
| | | | - Zbigniew J. Król
- Central Clinical Hospital of Ministry of the Interior and Administration in Warsaw, Warsaw, Poland
| | - Joanna Szyda
- Biostatistics Group, Wrocław University of Environmental and Life Sciences, Wrocław, Poland,National Research Institute of Animal Production, Balice, Poland
| | - Paula Dobosz
- Central Clinical Hospital of Ministry of the Interior and Administration in Warsaw, Warsaw, Poland
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14
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Phua YL, D’Annibale OM, Karunanidhi A, Mohsen AW, Kirmse B, Dobrowolski SF, Vockley J. A multiomics approach to understanding pathology of Combined D,L-2- Hydroxyglutaric Aciduria and phenylbutyrate as potential treatment. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.02.526527. [PMID: 36778323 PMCID: PMC9915603 DOI: 10.1101/2023.02.02.526527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Combined D, L-2-Hydroxyglutaric Aciduria (D,L-2HGA) is a rare genetic disorder caused by recessive mutations in the SLC25A1 gene that encodes the mitochondrial citrate carrier protein (CIC). SLC25A1 deficiency leads to a secondary increase in mitochondrial 2-ketoglutarate that, in turn, is reduced to neurotoxic 2-hydroxyglutarate. Clinical symptoms of Combined D,L-2HGA include neonatal encephalopathy, respiratory insufficiency and often with death in infancy. No current therapies exist, although replenishing cytosolic stores by citrate supplementation to replenish cytosolic stores has been proposed. In this study, we demonstrated that patient derived fibroblasts exhibited impaired cellular bioenergetics that were worsened with citrate supplementation. We hypothesized treating patient cells with phenylbutyrate, an FDA approved pharmaceutical drug, would reduce mitochondrial 2-ketoglutarate, leading to improved cellular bioenergetics including oxygen consumption and fatty acid oxidation. Metabolomic and RNA-seq analyses demonstrated a significant decrease in intracellular 2-ketoglutarate, 2-hydroxyglutarate, and in levels of mRNA coding for citrate synthase and isocitrate dehydrogenase. Consistent with the known action of phenylbutyrate, detected levels of phenylacetylglutamine was consistent with the drug acting as 2-ketoglutarate sink in patient cells. Our pre-clinical studies suggest citrate supplementation is unlikely to be an effective treatment of the disorder. However, cellular bioenergetics suggests phenylbutyrate may have interventional utility for this rare disease.
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Affiliation(s)
- Yu Leng Phua
- Department of Pediatrics, Division of Genetic and Genomic Medicine, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA, USA
- Department of Pathology, Clinical Biochemical Genetics Laboratory, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Olivia M D’Annibale
- Department of Pediatrics, Division of Genetic and Genomic Medicine, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA, USA
- Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, USA
| | - Anuradha Karunanidhi
- Department of Pediatrics, Division of Genetic and Genomic Medicine, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Al-Walid Mohsen
- Department of Pediatrics, Division of Genetic and Genomic Medicine, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA, USA
- Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, USA
| | - Brian Kirmse
- Department of Pediatrics, University of Mississippi Medical Center, Jackson, MS, USA
| | - Steven F Dobrowolski
- Department of Pathology, Clinical Biochemical Genetics Laboratory, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Jerry Vockley
- Department of Pediatrics, Division of Genetic and Genomic Medicine, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA, USA
- Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, USA
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15
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The Genetics of Intellectual Disability. Brain Sci 2023; 13:brainsci13020231. [PMID: 36831774 PMCID: PMC9953898 DOI: 10.3390/brainsci13020231] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/23/2022] [Accepted: 01/16/2023] [Indexed: 02/03/2023] Open
Abstract
Intellectual disability (ID) has a prevalence of ~2-3% in the general population, having a large societal impact. The underlying cause of ID is largely of genetic origin; however, identifying this genetic cause has in the past often led to long diagnostic Odysseys. Over the past decades, improvements in genetic diagnostic technologies and strategies have led to these causes being more and more detectable: from cytogenetic analysis in 1959, we moved in the first decade of the 21st century from genomic microarrays with a diagnostic yield of ~20% to next-generation sequencing platforms with a yield of up to 60%. In this review, we discuss these various developments, as well as their associated challenges and implications for the field of ID, which highlight the revolutionizing shift in clinical practice from a phenotype-first into genotype-first approach.
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16
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The exploration of genetic aetiology and diagnostic strategy for 321 Chinese individuals with intellectual disability. Clin Chim Acta 2023; 538:94-103. [PMID: 36368352 DOI: 10.1016/j.cca.2022.10.023] [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: 08/31/2022] [Revised: 10/08/2022] [Accepted: 10/28/2022] [Indexed: 11/09/2022]
Abstract
BACKGROUND Intellectual disability is a heterogeneous neurodevelopmental disorder with complex genetic architectures. Different sequential methodologies are usually applied to identify the genetic aetiologies of ID patients. METHODS We collected 321 consecutive ID patients. All patients underwent karyotyping, while 293 and 164 cases further received copy number variation sequencing (CNV-seq) and whole-exome sequencing (WES). The updated WES technology can detect CNVs simultaneously. The diagnostic data from 137 patients who received WES and CNV-seq were used to define the approach that could be recommended as the first-tier test. RESULTS WES obtains the highest diagnostic yield of 50% (82/164), compared with karyotyping (7.79%, 25/321) and CNV-seq (19.80%, 58/293). Among the variants detected by WES, 66.67% (44/66) de novo and 57.58% (38/66) novel pathogenic/likely pathogenic (P/LP) variants were identified in patients with ID. Besides, 24 out of 25P/LP CNVs discovered by CNV-seq can also be accurately identified using WES in 137 patients who received WES and CNV-seq. Thus, genetic abnormalities found through karyotyping, CNV-seq, and WES can be completely detected by combined karyotyping and WES. CONCLUSIONS This study illustrates the genetic aberrations of a Chinese ID cohort and expands the mutation spectrum of ID-related genes. Compared with the conventional diagnostic strategy, a combination of karyotype analysis and WES could be recommended as the first-tier diagnostic strategy for ID patients.
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17
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Molecular Diagnosis of Hypertrophic Cardiomyopathy (HCM): In the Heart of Cardiac Disease. J Clin Med 2022; 12:jcm12010225. [PMID: 36615026 PMCID: PMC9821215 DOI: 10.3390/jcm12010225] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/21/2022] [Accepted: 12/23/2022] [Indexed: 12/29/2022] Open
Abstract
Hypertrophic cardiomyopathy (HCM) is an inherited myocardial disease with the presence of left ventricular hypertrophy (LVH). The disease is characterized by high locus, allelic and phenotypic heterogeneity, even among members of the same family. The list of confirmed and potentially relevant genes implicating the disease is constantly increasing, with novel genes frequently reported. Heterozygous alterations in the five main sarcomeric genes (MYBPC3, MYH7, TNNT2, TNNI3, and MYL2) are estimated to account for more than half of confirmed cases. The genetic discoveries of recent years have shed more light on the molecular pathogenic mechanisms of HCM, contributing to substantial advances in the diagnosis of the disease. Genetic testing applying next-generation sequencing (NGS) technologies and early diagnosis prior to the clinical manifestation of the disease among family members demonstrate an important improvement in the field.
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18
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Testard Q, Vanhoye X, Yauy K, Naud ME, Vieville G, Rousseau F, Dauriat B, Marquet V, Bourthoumieu S, Geneviève D, Gatinois V, Wells C, Willems M, Coubes C, Pinson L, Dard R, Tessier A, Hervé B, Vialard F, Harzallah I, Touraine R, Cogné B, Deb W, Besnard T, Pichon O, Laudier B, Mesnard L, Doreille A, Busa T, Missirian C, Satre V, Coutton C, Celse T, Harbuz R, Raymond L, Taly JF, Thevenon J. Exome sequencing as a first-tier test for copy number variant detection: retrospective evaluation and prospective screening in 2418 cases. J Med Genet 2022; 59:1234-1240. [PMID: 36137615 DOI: 10.1136/jmg-2022-108439] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 08/10/2022] [Indexed: 01/12/2023]
Abstract
BACKGROUND Despite the availability of whole exome (WES) and genome sequencing (WGS), chromosomal microarray (CMA) remains the first-line diagnostic test in most rare disorders diagnostic workup, looking for copy number variations (CNVs), with a diagnostic yield of 10%-20%. The question of the equivalence of CMA and WES in CNV calling is an organisational and economic question, especially when ordering a WGS after a negative CMA and/or WES. METHODS This study measures the equivalence between CMA and GATK4 exome sequencing depth of coverage method in detecting coding CNVs on a retrospective cohort of 615 unrelated individuals. A prospective detection of WES-CNV on a cohort of 2418 unrelated individuals, including the 615 individuals from the validation cohort, was performed. RESULTS On the retrospective validation cohort, every CNV detectable by the method (ie, a CNV with at least one exon not in a dark zone) was accurately called (64/64 events). In the prospective cohort, 32 diagnoses were performed among the 2418 individuals with CNVs ranging from 704 bp to aneuploidy. An incidental finding was reported. The overall increase in diagnostic yield was of 1.7%, varying from 1.2% in individuals with multiple congenital anomalies to 1.9% in individuals with chronic kidney failure. CONCLUSION Combining single-nucleotide variant (SNV) and CNV detection increases the suitability of exome sequencing as a first-tier diagnostic test for suspected rare Mendelian disorders. Before considering the prescription of a WGS after a negative WES, a careful reanalysis with updated CNV calling and SNV annotation should be considered.
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Affiliation(s)
- Quentin Testard
- Service de Génétique, Eurofins Biomnis, Lyon, France.,Service de Génétique et Procréation, CHU Grenoble Alpes, Grenoble, France.,CNRS UMR 5309, INSERM, U1209, Université Grenoble Alpes, Institute for Advanced Bioscience, Grenoble, France
| | | | - Kevin Yauy
- CNRS UMR 5309, INSERM, U1209, Université Grenoble Alpes, Institute for Advanced Bioscience, Grenoble, France.,SeqOne Genomics, Montpellier, France
| | | | - Gaelle Vieville
- Service de Génétique et Procréation, CHU Grenoble Alpes, Grenoble, France
| | | | - Benjamin Dauriat
- Service de Cytogénétique, Génétique Médicale et Biologie de la Reproduction, CHU Limoges, Limoges, France
| | - Valentine Marquet
- Service de Cytogénétique, Génétique Médicale et Biologie de la Reproduction, CHU Limoges, Limoges, France
| | - Sylvie Bourthoumieu
- Service de Cytogénétique, Génétique Médicale et Biologie de la Reproduction, CHU Limoges, Limoges, France
| | - David Geneviève
- Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, CHU Montpellier, Montpellier, France.,Unité INSERM U1183, University Montpellier 1, Montpellier, France
| | - Vincent Gatinois
- Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, CHU Montpellier, Montpellier, France
| | - Constance Wells
- Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, CHU Montpellier, Montpellier, France
| | - Marjolaine Willems
- Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, CHU Montpellier, Montpellier, France
| | - Christine Coubes
- Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, CHU Montpellier, Montpellier, France
| | - Lucile Pinson
- Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, CHU Montpellier, Montpellier, France
| | - Rodolphe Dard
- Département de Génétique, CHI Poissy-Saint-Germain-en-Laye, Saint-Germain-en-Laye, France
| | - Aude Tessier
- Département de Génétique, CHI Poissy-Saint-Germain-en-Laye, Saint-Germain-en-Laye, France
| | - Bérénice Hervé
- Département de Génétique, CHI Poissy-Saint-Germain-en-Laye, Saint-Germain-en-Laye, France
| | - François Vialard
- Département de Génétique, CHI Poissy-Saint-Germain-en-Laye, Saint-Germain-en-Laye, France
| | - Ines Harzallah
- Service de génétique clinique, chromosomique et moléculaire, CHU Saint-Étienne, Saint-Etienne, France
| | - Renaud Touraine
- Service de génétique clinique, chromosomique et moléculaire, CHU Saint-Étienne, Saint-Etienne, France
| | - Benjamin Cogné
- Service de Génétique Médicale, CHU Nantes, Nantes, France
| | - Wallid Deb
- Service de Génétique Médicale, CHU Nantes, Nantes, France
| | - Thomas Besnard
- Service de Génétique Médicale, CHU Nantes, Nantes, France
| | - Olivier Pichon
- Service de Génétique Médicale, CHU Nantes, Nantes, France
| | - Béatrice Laudier
- Laboratoire d'Immunologie et Neurogénétique Expérimentales et Moléculaires INEM UMR7355, CHR d'Orléans, Orléans, France
| | - Laurent Mesnard
- Sorbonne Université, Urgences Néphrologiques et Transplantation Rénale, APHP, Hôpital Tenon, Paris, France
| | - Alice Doreille
- Sorbonne Université, Urgences Néphrologiques et Transplantation Rénale, APHP, Hôpital Tenon, Paris, France
| | - Tiffany Busa
- Département de génétique médicale, AP HM, Hôpital de la Timone Enfant, Marseille, France
| | - Chantal Missirian
- Département de génétique médicale, AP HM, Hôpital de la Timone Enfant, Marseille, France
| | - Véronique Satre
- Service de Génétique et Procréation, CHU Grenoble Alpes, Grenoble, France.,CNRS UMR 5309, INSERM, U1209, Université Grenoble Alpes, Institute for Advanced Bioscience, Grenoble, France
| | - Charles Coutton
- Service de Génétique et Procréation, CHU Grenoble Alpes, Grenoble, France.,CNRS UMR 5309, INSERM, U1209, Université Grenoble Alpes, Institute for Advanced Bioscience, Grenoble, France
| | - Tristan Celse
- Service de Génétique et Procréation, CHU Grenoble Alpes, Grenoble, France
| | - Radu Harbuz
- Service de Génétique et Procréation, CHU Grenoble Alpes, Grenoble, France
| | - Laure Raymond
- Service de Génétique, Eurofins Biomnis, Lyon, France
| | | | - Julien Thevenon
- Service de Génétique et Procréation, CHU Grenoble Alpes, Grenoble, France .,CNRS UMR 5309, INSERM, U1209, Université Grenoble Alpes, Institute for Advanced Bioscience, Grenoble, France
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Avram CM, Caughey AB, Norton ME, Sparks TN. Cost-Effectiveness of Exome Sequencing versus Targeted Gene Panels for Prenatal Diagnosis of Fetal Effusions and Non-Immune Hydrops Fetalis. Am J Obstet Gynecol MFM 2022; 4:100724. [PMID: 35995366 PMCID: PMC9938838 DOI: 10.1016/j.ajogmf.2022.100724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 08/04/2022] [Accepted: 08/15/2022] [Indexed: 10/31/2022]
Abstract
BACKGROUND Although exome sequencing has a greater overall diagnostic yield than targeted gene panels in the evaluation of nonimmune hydrops fetalis and fetal effusions, the cost-effectiveness of this approach is not known. OBJECTIVE This study aimed to evaluate the costs and outcomes of targeted gene panels vs exome sequencing for prenatally diagnosed nonimmune hydrops fetalis and fetal effusions when next-generation sequencing is pursued following nondiagnostic standard nonimmune hydrops fetalis evaluations, including karyotype or chromosomal microarray. STUDY DESIGN A decision-analytical model was designed using TreeAge Pro to compare 10 genetic testing strategies, including a single test only (RASopathy, metabolic, or nonimmune hydrops fetalis-targeted gene panel or exome sequencing), sequential testing (RASopathy panel followed by nonimmune hydrops fetalis panel, metabolic panel followed by nonimmune hydrops fetalis panel, RASopathy panel followed by exome sequencing, metabolic panel followed by exome sequencing, and nonimmune hydrops fetalis panel followed by exome sequencing), and no additional genetic testing. Our theoretical cohort included cases with normal karyotype and/or microarray and excluded cases of alloimmunization and congenital viral infections. As nonimmune hydrops fetalis and fetal effusions can present throughout gestation, whereas pregnancy management options vary depending on gestational age, outcomes were calculated for 3 time intervals: 10 to 18, 18 to 22, and >22 weeks of gestation. The primary outcome was incremental cost per quality-adjusted life year. Additional outcomes included termination of pregnancy, stillbirth, neonatal death, and neonates born with mild, moderate, and severe or profound disease phenotypes. The cost-effectiveness threshold was $100,000 per quality-adjusted life year. RESULTS Among women <18 weeks of gestation, exome sequencing alone was the dominant strategy associated with the lowest costs ($221 million) and the highest quality-adjusted life years (10,288). Strategies with exome sequencing alone or as a sequential test resulted in more terminations but fewer stillbirths, neonatal deaths (NNDs), and affected infants than strategies without exome sequencing. Among women between 18 and 22 weeks of gestation, exome sequencing alone was also associated with the lowest costs ($188 million) and the highest quality-adjusted life years (8734), and similar trends were observed in pregnancy outcomes. Among patients >22 weeks of gestations, when termination was not available, exome sequencing was associated with lower costs ($300 million) and the highest quality-adjusted life years (8492). Exome sequencing was cost-effective up to a cost per test of $50,451 at <18 weeks of gestation, $50,423 at 18 to 22 weeks of gestation, and $9530 at >22 weeks of gestation. Targeted genetic panels and exome sequencing were cost-effective strategies compared with no additional genetic testing. CONCLUSION For cases of nonimmune hydrops fetalis and fetal effusions with nondiagnostic karyotype or microarray, next-generation sequencing was cost-effective compared with a strategy without additional genetic testing. For those that undergo next-generation sequencing, exome sequencing was the cost-effective strategy compared with all other testing strategies using targeted gene panels, leading to lower costs and fewer adverse perinatal outcomes. Exome sequencing was cost-effective in a setting without the option for pregnancy termination. These data supported the routine use of exome sequencing when next-generation sequencing is pursued for establishing a genetic diagnosis underlying otherwise unexplained nonimmune hydrops fetalis and fetal effusions.
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Affiliation(s)
- Carmen M Avram
- Duke University Medical Center, Durham, NC (Carmen M. Avram, MD).
| | - Aaron B Caughey
- Oregon Health & Science University, Portland, OR (Aaron B. Caughey, MD, PhD)
| | - Mary E Norton
- University of California, San Francisco, San Francisco, CA (Mary E. Norton, MD, Teresa N. Sparks, MD, MAS)
| | - Teresa N Sparks
- University of California, San Francisco, San Francisco, CA (Mary E. Norton, MD, Teresa N. Sparks, MD, MAS)
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Chueh HW, Hwang SM, Shim YJ, Lee JM, Park HS, Lee JH, Nam Y, Kim N, Jung HL, Choi HS. Korean clinical practice guidelines for the diagnosis of hereditary hemolytic anemia. Blood Res 2022; 57:86-94. [PMID: 35593002 PMCID: PMC9242826 DOI: 10.5045/br.2022.2021224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/03/2022] [Accepted: 02/28/2022] [Indexed: 01/19/2023] Open
Abstract
Although the prevalence of hereditary hemolytic anemia (HHA) is relatively low in Korea, it has been gradually increasing in recent decades due to increment in the proportions of hemoglobinopathies from immigrants of South East Asia, raising awareness of the disease among clinicians, and advances in diagnostic technology. As such, the red blood cell (RBC) Disorder Working Party (WP), previously called HHA WP, of the Korean Society of Hematology (KSH) developed the Korean Standard Operating Procedures (SOPs) for the diagnosis of HHA in 2007. These SOPs have been continuously revised and updated following advances in diagnostic technology [e.g., flow cytometric osmotic fragility test (FOFT) and eosin-5-maleimide (EMA) binding test], current methods for membrane protein or enzyme analysis [e.g., liquid chromatography-tandem mass spectrometry (LC-MS/MS), ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS), high-performance liquid chromatography (HPLC)], and molecular genetic tests using next-generation sequencing (NGS). However, the diagnosis and treatment of HHA remain challenging as they require considerable experience and understanding of the disease. Therefore, in this new Korean Clinical Practice Guidelines for the Diagnosis of HHA, on behalf of the RBC Disorder WP of KSH, updated guidelines to approach patients suspected of HHA are summarized. NGS is proposed to perform prior to membrane protein or enzyme analysis by LC-MS/MS, UPLC-MS/MS or HPLC techniques due to the availability of gene testing in more laboratories in Korea. We hope that this guideline will be helpful for clinicians in making diagnostic decisions for patients with HHA in Korea.
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Affiliation(s)
- Hee Won Chueh
- Department of Pediatrics, Dong-A University, College of Medicine, Busan, Korea
| | - Sang Mee Hwang
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam, Department of Pediatrics, Cheongju, Korea
| | - Ye Jee Shim
- Keimyung University School of Medicine, Keimyung University Dongsan Hospital, Cheongju, Korea
| | - Jae Min Lee
- Yeungnam University Medical Center, Daegu, Department of Laboratory Medicine, Cheongju, Korea
| | - Hee Sue Park
- Chungbuk National University Hospital, Cheongju, Korea
| | - Joon Hee Lee
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam, Department of Pediatrics, Cheongju, Korea
| | - Youngwon Nam
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam, Department of Pediatrics, Cheongju, Korea
| | - Namhee Kim
- Dong-A University, College of Medicine, Busan, Department of Pediatrics, Seoul, Korea
| | - Hye Lim Jung
- Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hyoung Soo Choi
- Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
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Mastromoro G, Guadagnolo D, Khaleghi Hashemian N, Marchionni E, Traversa A, Pizzuti A. Molecular Approaches in Fetal Malformations, Dynamic Anomalies and Soft Markers: Diagnostic Rates and Challenges-Systematic Review of the Literature and Meta-Analysis. Diagnostics (Basel) 2022; 12:575. [PMID: 35328129 PMCID: PMC8947110 DOI: 10.3390/diagnostics12030575] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/11/2022] [Accepted: 02/21/2022] [Indexed: 02/06/2023] Open
Abstract
Fetal malformations occur in 2-3% of pregnancies. They require invasive procedures for cytogenetics and molecular testing. "Structural anomalies" include non-transient anatomic alterations. "Soft markers" are often transient minor ultrasound findings. Anomalies not fitting these definitions are categorized as "dynamic". This meta-analysis aims to evaluate the diagnostic yield and the rates of variants of uncertain significance (VUSs) in fetuses undergoing molecular testing (chromosomal microarray (CMA), exome sequencing (ES), genome sequencing (WGS)) due to ultrasound findings. The CMA diagnostic yield was 2.15% in single soft markers (vs. 0.79% baseline risk), 3.44% in multiple soft markers, 3.66% in single structural anomalies and 8.57% in multiple structural anomalies. Rates for specific subcategories vary significantly. ES showed a diagnostic rate of 19.47%, reaching 27.47% in multiple structural anomalies. WGS data did not allow meta-analysis. In fetal structural anomalies, CMA is a first-tier test, but should be integrated with karyotype and parental segregations. In this class of fetuses, ES presents a very high incremental yield, with a significant VUSs burden, so we encourage its use in selected cases. Soft markers present heterogeneous CMA results from each other, some of them with risks comparable to structural anomalies, and would benefit from molecular analysis. The diagnostic rate of multiple soft markers poses a solid indication to CMA.
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Affiliation(s)
- Gioia Mastromoro
- Department of Experimental Medicine, Policlinico Umberto I Hospital, Sapienza University of Rome, 00161 Rome, Italy; (D.G.); (N.K.H.); (E.M.); (A.T.); (A.P.)
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22
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Devarajan P, Chertow GM, Susztak K, Levin A, Agarwal R, Stenvinkel P, Chapman AB, Warady BA. Emerging Role of Clinical Genetics in CKD. Kidney Med 2022; 4:100435. [PMID: 35372818 PMCID: PMC8971313 DOI: 10.1016/j.xkme.2022.100435] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Chronic kidney disease (CKD) afflicts 15% of adults in the United States, of whom 25% have a family history. Genetic testing is supportive in identifying and possibly confirming diagnoses of CKD, thereby guiding care. Advances in the clinical genetic evaluation include next-generation sequencing with targeted gene panels, whole exome sequencing, and whole genome sequencing. These platforms provide DNA sequence reads with excellent coverage throughout the genome and have identified novel genetic causes of CKD. New pathologic genetic variants identified in previously unrecognized biological pathways have elucidated disease mechanisms underlying CKD etiologies, potentially establishing prognosis and guiding treatment selection. Molecular diagnoses using genetic sequencing can detect rare, potentially treatable mutations, avoid misdiagnoses, guide selection of optimal therapy, and decrease the risk of unnecessary and potentially harmful interventions. Genetic testing has been widely adopted in pediatric nephrology; however, it is less frequently used to date in adult nephrology. Extension of clinical genetic approaches to adult patients may achieve similar benefits in diagnostic refinement and treatment selection. This review aimed to identify clinical CKD phenotypes that may benefit the most from genetic testing, outline the commonly available platforms, and provide examples of successful deployment of these approaches in CKD.
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23
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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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24
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Suhaimi SA, Zulkipli IN, Ghani H, Abdul-Hamid MRW. Applications of next generation sequencing in the screening and diagnosis of thalassemia: A mini-review. Front Pediatr 2022; 10:1015769. [PMID: 36245713 PMCID: PMC9557073 DOI: 10.3389/fped.2022.1015769] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 09/07/2022] [Indexed: 11/13/2022] Open
Abstract
Thalassemias are a group of inherited blood disorders that affects 5-7% of the world population. Comprehensive screening strategies are essential for the management and prevention of this disorder. Today, many clinical and research laboratories have widely utilized next-generation sequencing (NGS) technologies to identify diseases, from germline and somatic disorders to infectious diseases. Yet, NGS application in thalassemia is limited and has just recently surfaced due to current demands in seeking alternative DNA screening tools that are more efficient, versatile, and cost-effective. This review aims to understand the several aspects of NGS technology, including its most current and expanding uses, advantages, and limitations, along with the issues and solutions related to its integration into routine screening and diagnosis of thalassemias. Hitherto, NGS has been a groundbreaking technology that offers tremendous improvements as a diagnostic tool for thalassemia in terms of its higher throughput, accuracy, and adaptability. The superiority of NGS in detecting rare variants, solving complex hematological problems, and providing non-invasive alternatives to neonatal diagnosis cannot be overlooked. However, several pitfalls still preclude its use as a stand-alone technique over conventional methods.
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Affiliation(s)
| | | | - Hazim Ghani
- PAPRSB Institute of Health Sciences, Universiti Brunei Darussalam, Gadong, Brunei
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Albobali Y, Shahwan MY, Madi MY, Al-Nuaimi S. Two Sisters From Qatar With TUSC3 Genetic Mutation: Psychiatric Considerations. Cureus 2021; 13:e17616. [PMID: 34646667 PMCID: PMC8483409 DOI: 10.7759/cureus.17616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/31/2021] [Indexed: 11/29/2022] Open
Abstract
Defects in the tumor suppressor candidate 3 (TUSC3) gene have been identified in individuals with autosomal recessive intellectual disability (ARID). Our report on two sisters from Qatar with a mutation in the TUSC3 gene focuses on the behavioral manifestations and management provided to them. The sisters, daughters of consanguineous parents, exhibited aggressive and impulsive behavior, along with hyperactivity and emotional dysregulation. They also exhibited abnormal sleep and eating patterns. Behavioral therapy and psychotropic medications including aripiprazole 3.75mg, clonidine 0.025mg, and guanfacine 1mg were used for the management of aggressive and agitated behavior. The two girls showed a reduction in aggressive behavior, hyperactivity, impulsivity, and insomnia in response to 2mg daily of guanfacine. Few families around the world were reported to have mutations in the TUSC3 gene resulting in intellectual disability. We describe the first two reported cases of TUSC3 gene mutation in Qatar. We encourage further research to study the effects of TUSC3 gene mutation, its manifestations, and treatment.
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Affiliation(s)
| | | | - Mahmoud Y Madi
- Internal Medicine, University of Kansas Medical Center (KUMC), Kansas City, USA
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26
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Liu Y, Teng Y, Li Z, Cui J, Liang D, Wu L. Increase in diagnostic yield achieved for 174 whole-exome sequencing cases reanalyzed 1-2 years after initial analysis. Clin Chim Acta 2021; 523:163-168. [PMID: 34560057 DOI: 10.1016/j.cca.2021.09.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/09/2021] [Accepted: 09/16/2021] [Indexed: 11/19/2022]
Abstract
BACKGROUND Some missed diagnoses have been presented in whole-exome sequencing (WES) analysis for cases with possible Mendelian diseases. To assess how much contributions of WES reanalysis might improve diagnostic yield, we reviewed the WES data of 174 undiagnosed cases. METHODS We performed reanalysis with an updated bioinformatics pipeline involving better algorithms and updated databases so that CNVs and SNVs in intron regions and InDels within 10-50 bp can be detected. Upgraded variant interpretation processes, including updated software packages, databases and literature, expanded knowledge of genes and diseases, extended filtering conditions and phenotype reevaluation, were also implemented for reanalysis. Candidate variants were classified by ACMG guidelines and certified by Sanger sequencing, qPCR or MLPA. RESULTS Fourteen additional cases received new diagnosis in the reanalysis. The results which became positive were sorted according to the following aspects: detection of CNVs; diagnosis by SNVs in intron regions or InDels within 10-50 bp; reclassification due to new reports of variants or gene-disease relationships; digenic inheritance leading to disease; disease caused by frequent variations in the general population; and accurate phenotype assessment enabling the establishment of the molecular diagnosis. CONCLUSION Our study improved diagnosis yield through an optimized bioinformatics pipeline and variant interpretation strategy of WES and provided analysis experience learned from the WES reanalysis to reduce missed diagnoses.
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Affiliation(s)
- Yingdi Liu
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410078, China
| | - Yanling Teng
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410078, China
| | - Zhuo Li
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410078, China
| | - Jingyi Cui
- Department of Medical Genetics, Hunan Jiahui Genetics Hospital, Changsha, Hunan 410078, China
| | - Desheng Liang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410078, China; Department of Medical Genetics, Hunan Jiahui Genetics Hospital, Changsha, Hunan 410078, China.
| | - Lingqian Wu
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410078, China; Department of Medical Genetics, Hunan Jiahui Genetics Hospital, Changsha, Hunan 410078, China.
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Applying Bioinformatic Platforms, In Vitro, and In Vivo Functional Assays in the Characterization of Genetic Variants in the GH/IGF Pathway Affecting Growth and Development. Cells 2021; 10:cells10082063. [PMID: 34440832 PMCID: PMC8392544 DOI: 10.3390/cells10082063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 08/06/2021] [Accepted: 08/09/2021] [Indexed: 02/07/2023] Open
Abstract
Heritability accounts for over 80% of adult human height, indicating that genetic variability is the main determinant of stature. The rapid technological development of Next-Generation Sequencing (NGS), particularly Whole Exome Sequencing (WES), has resulted in the characterization of several genetic conditions affecting growth and development. The greatest challenge of NGS remains the high number of candidate variants identified. In silico bioinformatic tools represent the first approach for classifying these variants. However, solving the complicated problem of variant interpretation requires the use of experimental approaches such as in vitro and, when needed, in vivo functional assays. In this review, we will discuss a rational approach to apply to the gene variants identified in children with growth and developmental defects including: (i) bioinformatic tools; (ii) in silico modeling tools; (iii) in vitro functional assays; and (iv) the development of in vivo models. While bioinformatic tools are useful for a preliminary selection of potentially pathogenic variants, in vitro—and sometimes also in vivo—functional assays are further required to unequivocally determine the pathogenicity of a novel genetic variant. This long, time-consuming, and expensive process is the only scientifically proven method to determine causality between a genetic variant and a human genetic disease.
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28
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Bayle A, Droin N, Besse B, Zou Z, Boursin Y, Rissel S, Solary E, Lacroix L, Rouleau E, Borget I, Bonastre J. Whole exome sequencing in molecular diagnostics of cancer decreases over time: evidence from a cost analysis in the French setting. THE EUROPEAN JOURNAL OF HEALTH ECONOMICS : HEPAC : HEALTH ECONOMICS IN PREVENTION AND CARE 2021; 22:855-864. [PMID: 33765190 DOI: 10.1007/s10198-021-01293-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 03/16/2021] [Indexed: 05/06/2023]
Abstract
OBJECTIVES Although high-throughput sequencing is revolutionising medicine, data on the actual cost of whole exome sequencing (WES) applications are needed. We aimed at assessing the cost of WES at a French cancer institute in 2015 and 2018. METHODS Actual costs of WES application in oncology research were determined using both micro-costing and gross-costing for the years 2015 and 2018, before and after the acquisition of a new sequencer. The entire workflow process of a WES test was tracked, and the number and unit price of each resource were identified at the most detailed level, from library preparation to bioinformatics analyses. In addition, we conducted an ad hoc analysis of the bioinformatics storage costs of data issued from WES analyses. RESULTS The cost of WES has decreased substantially, from €1921 per sample (i.e. cost of €3842 per patient) in 2015 to €804 per sample (i.e. cost of €1,608 per patient) in 2018, representing a decrease of 58%. In the meantime, the cost of bioinformatics storage has increased from €19,836 to €200,711. CONCLUSION This study suggests that WES cost has decreased significantly in recent years. WES has become affordable, even though clinical utility and efficiency still need to be confirmed.
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Affiliation(s)
- Arnaud Bayle
- Biostatistics and Epidemiology Unit, Gustave Roussy Cancer Centre, 114 rue Edouard Vaillant, 94805, Villejuif Cedex, France.
- Centre for Research in Epidemiology and Population Health, INSERM U1018, Villejuif, France.
- Université Paris-Sud, Orsay, France.
| | - N Droin
- Biostatistics and Epidemiology Unit, Gustave Roussy Cancer Centre, 114 rue Edouard Vaillant, 94805, Villejuif Cedex, France
- UMS CNRS 3655 and INSERM US23, AMMICa, Gustave Roussy, Villejuif, France
| | - B Besse
- Biostatistics and Epidemiology Unit, Gustave Roussy Cancer Centre, 114 rue Edouard Vaillant, 94805, Villejuif Cedex, France
| | - Z Zou
- Biostatistics and Epidemiology Unit, Gustave Roussy Cancer Centre, 114 rue Edouard Vaillant, 94805, Villejuif Cedex, France
- Centre for Research in Epidemiology and Population Health, INSERM U1018, Villejuif, France
| | - Y Boursin
- Digital Transformation and IT System Department, Gustave Roussy Cancer Centre, 94805, Villejuif, France
| | - S Rissel
- Biostatistics and Epidemiology Unit, Gustave Roussy Cancer Centre, 114 rue Edouard Vaillant, 94805, Villejuif Cedex, France
| | - E Solary
- Biostatistics and Epidemiology Unit, Gustave Roussy Cancer Centre, 114 rue Edouard Vaillant, 94805, Villejuif Cedex, France
- Université Paris-Sud, Orsay, France
| | - L Lacroix
- Biostatistics and Epidemiology Unit, Gustave Roussy Cancer Centre, 114 rue Edouard Vaillant, 94805, Villejuif Cedex, France
- UMS CNRS 3655 and INSERM US23, AMMICa, Gustave Roussy, Villejuif, France
- Université Paris-Sud, Orsay, France
| | - E Rouleau
- Biostatistics and Epidemiology Unit, Gustave Roussy Cancer Centre, 114 rue Edouard Vaillant, 94805, Villejuif Cedex, France
| | - I Borget
- Biostatistics and Epidemiology Unit, Gustave Roussy Cancer Centre, 114 rue Edouard Vaillant, 94805, Villejuif Cedex, France
- Centre for Research in Epidemiology and Population Health, INSERM U1018, Villejuif, France
- Université Paris-Sud, Orsay, France
| | - J Bonastre
- Biostatistics and Epidemiology Unit, Gustave Roussy Cancer Centre, 114 rue Edouard Vaillant, 94805, Villejuif Cedex, France
- Centre for Research in Epidemiology and Population Health, INSERM U1018, Villejuif, France
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Bayes-Genis A, Liu PP, Lanfear DE, de Boer RA, González A, Thum T, Emdin M, Januzzi JL. Omics phenotyping in heart failure: the next frontier. Eur Heart J 2021; 41:3477-3484. [PMID: 32337540 DOI: 10.1093/eurheartj/ehaa270] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 02/23/2020] [Accepted: 03/30/2020] [Indexed: 12/16/2022] Open
Abstract
This state-of-the-art review aims to provide an up-to-date look at breakthrough omic technologies that are helping to unravel heart failure (HF) disease mechanisms and heterogeneity. Genomics, transcriptomics, proteomics, and metabolomics in HF are reviewed in depth. In addition, there is a thorough, expert discussion regarding the value of omics in identifying novel disease pathways, advancing understanding of disease mechanisms, differentiating HF phenotypes, yielding biomarkers for diagnosis or prognosis, or identifying new therapeutic targets in HF. The combination of multiple omics technologies may create a more comprehensive picture of the factors and physiology involved in HF than achieved by either one alone and provides a rich resource for predictive phenotype modelling. However, the successful translation of omics tools as solutions to clinical HF requires that the observations are robust and reproducible and can be validated across multiple independent populations to ensure confidence in clinical decision-making.
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Affiliation(s)
- Antoni Bayes-Genis
- Heart Institute (iCor), University Hospital Germans Trias i Pujol, Badalona, Spain.,CIBERCV, Instituto de Salud Carlos III, Madrid, Spain.,Department of Medicine, Universitat Autònoma Barcelona
| | - Peter P Liu
- University of Ottawa Heart Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - David E Lanfear
- Henry Ford Heart and Vascular Institute, Center for Individualized and Genomic Medicine Research, Henry Ford Hospital, Detroit, MI, USA
| | - Rudolf A de Boer
- Department of Cardiology, University of Groningen, University Medical Center, Groningen, The Netherlands
| | - Arantxa González
- CIBERCV, Instituto de Salud Carlos III, Madrid, Spain.,Program of Cardiovascular Diseases, CIMA Universidad de Navarra and IdiSNA, Pamplona, Spain
| | - Thomas Thum
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Hannover, Germany
| | - Michele Emdin
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy.,Fondazione Toscana G. Monasterio, Pisa, Italy
| | - James L Januzzi
- Cardiology Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
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Abstract
PURPOSE OF REVIEW Perinatal disorders include stillbirth, congenital structural anomalies, and critical illnesses in neonates. The cause of these is often unknown despite a thorough clinical workup. Genetic diseases cause a significant portion of perinatal disorders. The purpose of this review is to describe recent advances in genetic testing of perinatal disorders of unknown cause and to provide a potential diagnostic strategy. RECENT FINDINGS Exome and genome sequencing (ES and GS) have demonstrated that significant portions of perinatal disorders are caused by genetic disease. However, estimates of the exact proportion have varied widely across fetal and neonatal cohorts and most of the genetic diagnoses found in recent studies have been unique to individual cases. Having a specific genetic diagnosis provides significant clinical utility, including improved prognostication of the outcome, tailored therapy, directed testing for associated syndromic manifestations, referral to appropriate subspecialists, family planning, and redirection of care. SUMMARY Perinatal disorders of unknown cause, with nonspecific presentations, are often caused by genetic diseases best diagnosed by ES or GS. Prompt diagnosis facilitates improved clinical care. Improvements in noninvasive sampling, variant interpretation, and population-level research will further enhance the clinical utility of genetic testing. VIDEO ABSTRACT http://links.lww.com/MOP/A61.
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Affiliation(s)
- Thomas Hays
- Division of Neonatology, Department of Pediatrics, Columbia University Irving Medical Center, New York, New York, USA
| | - Ronald J. Wapner
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, New York, USA
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, New York, USA
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31
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Vrijenhoek T, Tonisson N, Kääriäinen H, Leitsalu L, Rigter T. Clinical genetics in transition-a comparison of genetic services in Estonia, Finland, and the Netherlands. J Community Genet 2021; 12:277-290. [PMID: 33704686 PMCID: PMC7948164 DOI: 10.1007/s12687-021-00514-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 02/18/2021] [Indexed: 11/25/2022] Open
Abstract
Genetics has traditionally enabled the reliable diagnosis of patients with rare genetic disorders, thus empowering the key role of today's clinical geneticists in providing healthcare. With the many novel technologies that have expanded the genetic toolkit, genetics is increasingly evolving beyond rare disease diagnostics. When placed in a transition context-like we do here-clinical genetics is likely to become a fully integral part of future healthcare and clinical genetic expertise will be required increasingly outside traditional clinical genetic settings. We explore transition effects on the thinking (culture), organizing (structure), and performing (practice) in clinical genetics, taking genetic healthcare in Estonia, Finland, and the Netherlands as examples. Despite clearly distinct healthcare histories, all three countries have initially implemented genetic healthcare in a rather similar fashion: as a diagnostic tool for predominantly rare congenital diseases, with clinical geneticists as the main providers. Dynamics at different levels, such as emerging technologies, biobanks and data infrastructure, and legislative frameworks, may require development of a new system attuned with the demands and (historic) context of specific countries. Here, we provide an overview of genetic service provisions in Estonia, Finland, and the Netherlands to consider the impact of historic and recent events on prospective developments in genetic healthcare.
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Affiliation(s)
- T Vrijenhoek
- Department of Genetics, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - N Tonisson
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
- Dept. of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
| | - H Kääriäinen
- Finnish Institute for Health and Welfare, Helsinki, Finland
| | - L Leitsalu
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - T Rigter
- Department of Clinical Genetics, Section Community Genetics & Amsterdam Public Health Research Institute, Amsterdam University Medical Centre, Location VUmc, Amsterdam, The Netherlands.
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32
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Torra R, Furlano M, Ortiz A, Ars E. Genetic kidney diseases as an underrecognized cause of chronic kidney disease: the key role of international registry reports. Clin Kidney J 2021; 14:1879-1885. [PMID: 34345410 PMCID: PMC8323147 DOI: 10.1093/ckj/sfab056] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Indexed: 01/01/2023] Open
Abstract
Inherited kidney diseases (IKDs) are among the leading causes of early-onset chronic kidney disease (CKD) and are responsible for at least 10-15% of cases of kidney replacement therapy (KRT) in adults. Paediatric nephrologists are very aware of the high prevalence of IKDs among their patients, but this is not the case for adult nephrologists. Recent publications have demonstrated that monogenic diseases account for a significant percentage of adult cases of CKD. A substantial number of these patients have received a non-specific/incorrect diagnosis or a diagnosis of CKD of unknown aetiology, which precludes correct treatment, follow-up and genetic counselling. There are a number of reasons why genetic kidney diseases are difficult to diagnose in adulthood: (i) adult nephrologists, in general, are not knowledgeable about IKDs; (ii) existence of atypical phenotypes; (iii) genetic testing is not universally available; (iv) family history is not always available or may be negative; (v) lack of knowledge of various genotype-phenotype relationships and (vi) conflicting interpretation of the pathogenicity of many sequence variants. Registries can contribute to visualize the burden of IKDs by regularly grouping all IKDs in their annual reports, as is done for glomerulonephritis or interstitial diseases, rather than reporting only cystic disease and hiding other IKDs under labels such as 'miscellaneous' or 'other'. Any effort to reduce the percentage of patients needing KRT with a diagnosis of 'nephropathy of unknown etiology' or an unspecific/incorrect diagnosis should be encouraged as a step towards precision nephrology. Genetic testing may be of value in this context but should not be used indiscriminately, but rather on the basis of a deep knowledge of IKDs.
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Affiliation(s)
- Roser Torra
- Department of Nephrology, Inherited Kidney Diseases, Fundació Puigvert, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Medicine Department-Universitat Autónoma de Barcelona, REDinREN, Instituto de Investigación Carlos III, Barcelona, Spain
| | - Mónica Furlano
- Department of Nephrology, Inherited Kidney Diseases, Fundació Puigvert, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Medicine Department-Universitat Autónoma de Barcelona, REDinREN, Instituto de Investigación Carlos III, Barcelona, Spain
| | - Alberto Ortiz
- IIS-Fundación Jimenez Diaz, School of Medicine, Universidad Autónoma de Madrid, Fundación Renal Iñigo Alvarez de Toledo-IRSIN, REDinREN, Instituto de Investigación Carlos III, Madrid, Spain
| | - Elisabet Ars
- Molecular Biology Laboratory, Fundació Puigvert, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Universitat Autónoma de Barcelona, REDinREN, Instituto de Investigación Carlos III, Barcelona, Spain
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Butz H, Blair J, Patócs A. Molecular genetic testing strategies used in diagnostic flow for hereditary endocrine tumour syndromes. Endocrine 2021; 71:641-652. [PMID: 33570725 PMCID: PMC8016766 DOI: 10.1007/s12020-021-02636-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 01/18/2021] [Indexed: 12/27/2022]
Abstract
INTRODUCTION Although current guidelines prefer the use of targeted testing or small-scale gene panels for identification of genetic susceptibility of hereditary endocrine tumour syndromes, next generation sequencing based strategies have been widely introduced into every day clinical practice. The application of next generation sequencing allows rapid testing of multiple genes in a cost effective manner. Increasing knowledge about these techniques and the demand from health care providers and society, shift the molecular genetic testing towards using high-throughput approaches. PURPOSE In this expert opinion, the authors consider the molecular diagnostic workflow step by step, evaluating options and challenges of gathering family information, pre- and post-test genetic counselling, technical and bioinformatical analysis related issues and difficulties in clinical interpretation focusing on molecular genetic testing of hereditary endocrine tumour syndromes. RESULT AND CONCLUSION Considering all these factors, a diagnostic genetic workflow is also proposed for selection of the best approach for testing of patients with hereditary genetic tumour syndromes in order to minimalize difficult interpretation, unwanted patient anxiety, unnecessary medical interventions and cost. There are potential benefits of utilizing high throughput approaches however, important limitations have to be considered and should discussed towards the clinicians and patients.
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Affiliation(s)
- Henriett Butz
- Department of Molecular Genetics, National Institute of Oncology, Budapest, Hungary
- Hereditary Cancers Research Group, Hungarian Academy of Sciences-Semmelweis University, Budapest, Hungary
- Department of Laboratory Medicine, Semmelweis University, Budapest, Hungary
| | - Jo Blair
- Alder Hey Children's Hospital-NHS Foundation Trust, Liverpool, United Kingdom
| | - Attila Patócs
- Department of Molecular Genetics, National Institute of Oncology, Budapest, Hungary.
- Hereditary Cancers Research Group, Hungarian Academy of Sciences-Semmelweis University, Budapest, Hungary.
- Department of Laboratory Medicine, Semmelweis University, Budapest, Hungary.
- Semmelweis University, Budapest, Hungary.
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Abstract
Neurodevelopmental disorders are the most prevalent chronic medical conditions encountered in pediatric primary care. In addition to identifying appropriate descriptive diagnoses and guiding families to evidence-based treatments and supports, comprehensive care for individuals with neurodevelopmental disorders includes a search for an underlying etiologic diagnosis, primarily through a genetic evaluation. Identification of an underlying genetic etiology can inform prognosis, clarify recurrence risk, shape clinical management, and direct patients and families to condition-specific resources and supports. Here we review the utility of genetic testing in patients with neurodevelopmental disorders and describe the three major testing modalities and their yields - chromosomal microarray, exome sequencing (with/without copy number variant calling), and FMR1 CGG repeat analysis for fragile X syndrome. Given the diagnostic yield of genetic testing and the potential for clinical and personal utility, there is consensus that genetic testing should be offered to all patients with global developmental delay, intellectual disability, and/or autism spectrum disorder. Despite this recommendation, data suggest that a minority of children with autism spectrum disorder and intellectual disability have undergone genetic testing. To address this gap in care, we describe a structured but flexible approach to facilitate integration of genetic testing into clinical practice across pediatric specialties and discuss future considerations for genetic testing in neurodevelopmental disorders to prepare pediatric providers to care for patients with such diagnoses today and tomorrow.
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Affiliation(s)
- Juliann M. Savatt
- Autism & Developmental Medicine Institute, Geisinger, Danville, PA, United States
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35
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Guadagnolo D, Mastromoro G, Di Palma F, Pizzuti A, Marchionni E. Prenatal Exome Sequencing: Background, Current Practice and Future Perspectives-A Systematic Review. Diagnostics (Basel) 2021; 11:diagnostics11020224. [PMID: 33540854 PMCID: PMC7913004 DOI: 10.3390/diagnostics11020224] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/29/2021] [Accepted: 01/31/2021] [Indexed: 12/16/2022] Open
Abstract
The introduction of Next Generation Sequencing (NGS) technologies has exerted a significant impact on prenatal diagnosis. Prenatal Exome Sequencing (pES) is performed with increasing frequency in fetuses with structural anomalies and negative chromosomal analysis. The actual diagnostic value varies extensively, and the role of incidental/secondary or inconclusive findings and negative results has not been fully ascertained. We performed a systematic literature review to evaluate the diagnostic yield, as well as inconclusive and negative-result rates of pES. Papers were divided in two groups. The former includes fetuses presenting structural anomalies, regardless the involved organ; the latter focuses on specific class anomalies. Available findings on non-informative or negative results were gathered as well. In the first group, the weighted average diagnostic yield resulted 19%, and inconclusive finding rate 12%. In the second group, the percentages were extremely variable due to differences in sample sizes and inclusion criteria, which constitute major determinants of pES efficiency. Diagnostic pES availability and its application have a pivotal role in prenatal diagnosis, though more homogeneity in access criteria and a consensus on clinical management of controversial information management is envisageable to reach widespread use in the near future.
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Affiliation(s)
- Daniele Guadagnolo
- Department of Experimental Medicine, Policlinico Umberto I Hospital, Sapienza University of Rome, 00161 Rome, Italy; (D.G.); (G.M.); (F.D.P.); (A.P.)
| | - Gioia Mastromoro
- Department of Experimental Medicine, Policlinico Umberto I Hospital, Sapienza University of Rome, 00161 Rome, Italy; (D.G.); (G.M.); (F.D.P.); (A.P.)
| | - Francesca Di Palma
- Department of Experimental Medicine, Policlinico Umberto I Hospital, Sapienza University of Rome, 00161 Rome, Italy; (D.G.); (G.M.); (F.D.P.); (A.P.)
| | - Antonio Pizzuti
- Department of Experimental Medicine, Policlinico Umberto I Hospital, Sapienza University of Rome, 00161 Rome, Italy; (D.G.); (G.M.); (F.D.P.); (A.P.)
- Clinical Genomics Unit, IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo (FG), Italy
| | - Enrica Marchionni
- Department of Experimental Medicine, Policlinico Umberto I Hospital, Sapienza University of Rome, 00161 Rome, Italy; (D.G.); (G.M.); (F.D.P.); (A.P.)
- Correspondence:
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36
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Detection of aberrant splicing events in RNA-seq data using FRASER. Nat Commun 2021; 12:529. [PMID: 33483494 PMCID: PMC7822922 DOI: 10.1038/s41467-020-20573-7] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 12/07/2020] [Indexed: 12/28/2022] Open
Abstract
Aberrant splicing is a major cause of rare diseases. However, its prediction from genome sequence alone remains in most cases inconclusive. Recently, RNA sequencing has proven to be an effective complementary avenue to detect aberrant splicing. Here, we develop FRASER, an algorithm to detect aberrant splicing from RNA sequencing data. Unlike existing methods, FRASER captures not only alternative splicing but also intron retention events. This typically doubles the number of detected aberrant events and identified a pathogenic intron retention in MCOLN1 causing mucolipidosis. FRASER automatically controls for latent confounders, which are widespread and affect sensitivity substantially. Moreover, FRASER is based on a count distribution and multiple testing correction, thus reducing the number of calls by two orders of magnitude over commonly applied z score cutoffs, with a minor loss of sensitivity. Applying FRASER to rare disease diagnostics is demonstrated by reprioritizing a pathogenic aberrant exon truncation in TAZ from a published dataset. FRASER is easy to use and freely available.
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37
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Lambert MP. Improving interpretation of genetic testing for hereditary hemorrhagic, thrombotic, and platelet disorders. HEMATOLOGY. AMERICAN SOCIETY OF HEMATOLOGY. EDUCATION PROGRAM 2020; 2020:76-81. [PMID: 33275718 PMCID: PMC7727548 DOI: 10.1182/hematology.2020000091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The last 10 years have seen an explosion in the amount of data available through next-generation sequencing. These data are advancing quickly, and this pace makes it difficult for most practitioners to easily keep up with all of the new information. Complicating this understanding is sometimes conflicting information about variant pathogenicity or even about the role of some genes in the pathogenesis of disease. The more widespread clinical use of sequencing has expanded phenotypes, including the identification of mild phenotypes associated with previously serious disease, such as with some variants in RUNX1, MYH9, ITG2A, and others. Several organizations have taken up the task of cataloging and systematically evaluating genes and variants using a standardized approach and making the data publicly available so that others can benefit from their gene/variant curation. The efforts in testing for hereditary hemorrhagic, thrombotic, and platelet disorders have been led by the International Society on Thrombosis and Haemostasis Scientific Standardization Committee on Genomics in Thrombosis and Hemostasis, the American Society of Hematology, and the National Institutes of Health National Human Genome Research Institute Clinical Genome Resource. This article outlines current efforts to improve the interpretation of genetic testing and the role of standardizing and disseminating information. By assessing the strength of gene-disease associations, standardizing variant curation guidelines, sharing genomic data among expert members, and incorporating data from existing disease databases, the number of variants of uncertain significance will decrease, thereby improving the value of genetic testing as a diagnostic tool.
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Affiliation(s)
- Michele P Lambert
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA; and Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
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38
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Zhu T, Gong X, Bei F, Ma L, Chen Y, Zhang Y, Wang X, Sun J, Wang J, Qiu G, Sun J, Sun Y, Zhang Y. Application of Next-Generation Sequencing for Genetic Diagnosis in Neonatal Intensive Care Units: Results of a Multicenter Study in China. Front Genet 2020; 11:565078. [PMID: 33240318 PMCID: PMC7677510 DOI: 10.3389/fgene.2020.565078] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 09/29/2020] [Indexed: 12/01/2022] Open
Abstract
To identify next-generation-sequencing (NGS) clinical usability and to propose a standard diagnostic routine for critically ill infants, aged less than 100 days and suspected of having a genetically heterogeneous condition, a retrospective study was conducted between January 2016 and December 2018 at neonatal intensive care units (NICUs) of three tertiary hospitals in Shanghai, China. Whole-exome sequencing (WES) or panel sequencing was performed on 307 patients. Trio-WES, trio-panel, proband-WES, and proband-panel diagnostic yields were 39.71% (83/209), 68.75% (22/32), 59.09% (26/44), and 33.33% (4/12), respectively. Definitive molecular diagnoses of 142 infants (46.25%) uncovered 99 disorders; 21 disorders displayed on 44.37% of the diagnosed patients. Genetic etiologies were identified for 61.73% (50/81) of the deceased infants. One in three (29.58%) diagnosed infants exhibited one of the following four clinical traits which had a higher odds of diagnostic rate: integument abnormality (adjusted odds ratio [aOR], 19.7; 95% confidence interval [CI], 2.5–156.3), complex immune-related phenotypes (aOR, 9.2; 95% CI, 1.4–83.5), mixed nervous system phenotypes and congenital anomalies (aOR, 5.0; 95% CI, 1.3–19.1), or mixed metabolism and nervous system phenotypes (aOR, 4.5; 95% CI, 1.0–21.5). Our results demonstrated that NGS was an effective diagnostic tool. Infants exhibiting integument, complex immune-related conditions, metabolism, and nervous signs have higher chances of carrying variants in known disease-causing genes. The number of specific phenotypes could be used as an independent predictor of a positive molecular diagnosis, rather than an isolated abnormality. We developed a molecular diagnostic procedure for the use of NGS for diagnosis in Chinese NICU population based on individual characteristics.
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Affiliation(s)
- Tianwen Zhu
- Department of Neonatology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaohui Gong
- Department of Neonatology, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Fei Bei
- Department of Neonatology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Li Ma
- Department of Neonatology, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yan Chen
- Department of Neonatology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yonghong Zhang
- Department of Neonatology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xia Wang
- Department of Neonatology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jingjing Sun
- Department of Neonatology, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jian Wang
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Gang Qiu
- Department of Neonatology, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jianhua Sun
- Department of Neonatology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yu Sun
- Department of Pediatric Endocrinology/Genetics, Xinhua Hospital, Shanghai Institute for Pediatric Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yongjun Zhang
- Department of Neonatology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Lewis C, Hammond J, Hill M, Searle B, Hunter A, Patch C, Chitty LS, Sanderson SC. Young people's understanding, attitudes and involvement in decision-making about genome sequencing for rare diseases: A qualitative study with participants in the UK 100, 000 Genomes Project. Eur J Med Genet 2020; 63:104043. [DOI: 10.1016/j.ejmg.2020.104043] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 08/18/2020] [Accepted: 08/18/2020] [Indexed: 12/12/2022]
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40
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Wang M, Zhang R, Li J. CRISPR/cas systems redefine nucleic acid detection: Principles and methods. Biosens Bioelectron 2020; 165:112430. [PMID: 32729545 PMCID: PMC7341063 DOI: 10.1016/j.bios.2020.112430] [Citation(s) in RCA: 105] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 06/24/2020] [Accepted: 07/06/2020] [Indexed: 12/15/2022]
Abstract
Methods that enable rapid, sensitive and specific analyses of nucleic acid sequences have positive effects on precise disease diagnostics and effective clinical treatments by providing direct insight into clinically relevant genetic information. Thus far, many CRISPR/Cas systems have been repurposed for diagnostic functions and are revolutionizing the accessibility of robust diagnostic tools due to their high flexibility, sensitivity and specificity. As RNA-guided targeted recognition effectors, Cas9 variants have been utilized for a variety of diagnostic applications, including biosensing assays, imaging assays and target enrichment for next-generation sequencing (NGS), thereby enabling the development of flexible and cost-effective tests. In addition, the ensuing discovery of Cas proteins (Cas12 and Cas13) with collateral cleavage activities has facilitated the development of numerous diagnostic tools for rapid and portable detection, and these tools have great potential for point-of-care settings. However, representative reviews proposed on this topic are mainly confined to classical biosensing applications; thus, a comprehensive and systematic description of this fast-developing field is required. In this review, based on the detection principle, we provide a detailed classification and comprehensive discussion of recent works that harness these CRISPR-based diagnostic tools from a new perspective. Furthermore, current challenges and future perspectives of CRISPR-based diagnostics are outlined.
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Affiliation(s)
- Meng Wang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China; Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, PR China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China
| | - Rui Zhang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China; Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, PR China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China
| | - Jinming Li
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China; Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, PR China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China.
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41
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Holtgrewe M, Stolpe O, Nieminen M, Mundlos S, Knaus A, Kornak U, Seelow D, Segebrecht L, Spielmann M, Fischer-Zirnsak B, Boschann F, Scholl U, Ehmke N, Beule D. VarFish: comprehensive DNA variant analysis for diagnostics and research. Nucleic Acids Res 2020; 48:W162-W169. [PMID: 32338743 PMCID: PMC7319464 DOI: 10.1093/nar/gkaa241] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 03/27/2020] [Accepted: 04/16/2020] [Indexed: 12/18/2022] Open
Abstract
VarFish is a user-friendly web application for the quality control, filtering, prioritization, analysis, and user-based annotation of DNA variant data with a focus on rare disease genetics. It is capable of processing variant call files with single or multiple samples. The variants are automatically annotated with population frequencies, molecular impact, and presence in databases such as ClinVar. Further, it provides support for pathogenicity scores including CADD, MutationTaster, and phenotypic similarity scores. Users can filter variants based on these annotations and presumed inheritance pattern and sort the results by these scores. Variants passing the filter are listed with their annotations and many useful link-outs to genome browsers, other gene/variant data portals, and external tools for variant assessment. VarFish allows users to create their own annotations including support for variant assessment following ACMG-AMP guidelines. In close collaboration with medical practitioners, VarFish was designed for variant analysis and prioritization in diagnostic and research settings as described in the software's extensive manual. The user interface has been optimized for supporting these protocols. Users can install VarFish on their own in-house servers where it provides additional lab notebook features for collaborative analysis and allows re-analysis of cases, e.g. after update of genotype or phenotype databases.
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Affiliation(s)
- Manuel Holtgrewe
- CUBI - Core Unit Bioinformatics, Berlin Institute of Health, Berlin 10117, Germany.,Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 10117, Germany
| | - Oliver Stolpe
- CUBI - Core Unit Bioinformatics, Berlin Institute of Health, Berlin 10117, Germany.,Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 10117, Germany
| | - Mikko Nieminen
- CUBI - Core Unit Bioinformatics, Berlin Institute of Health, Berlin 10117, Germany.,Max Delbrück Center for Molecular Medicine, Berlin 13125, Germany
| | - Stefan Mundlos
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 13353, Germany.,Development and Disease Group, Max Planck Institute for Medical Genetics, Berlin 14195, Germany
| | - Alexej Knaus
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Bonn 53127, Germany
| | - Uwe Kornak
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 13353, Germany.,Development and Disease Group, Max Planck Institute for Medical Genetics, Berlin 14195, Germany
| | - Dominik Seelow
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 13353, Germany.,Berlin Institute of Health (BIH), Anna-Louisa-Karsch-Str. 2, 10178 Berlin, Germany
| | - Lara Segebrecht
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 13353, Germany
| | - Malte Spielmann
- Development and Disease Group, Max Planck Institute for Medical Genetics, Berlin 14195, Germany.,Institut für Humangenetik Lübeck, Universität zu Lübeck, 23538 Lübeck, Germany
| | - Björn Fischer-Zirnsak
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 13353, Germany.,Development and Disease Group, Max Planck Institute for Medical Genetics, Berlin 14195, Germany
| | - Felix Boschann
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 13353, Germany
| | - Ute Scholl
- Berlin Institute of Health (BIH), Anna-Louisa-Karsch-Str. 2, 10178 Berlin, Germany.,Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Nephrology and Medical Intensive Care, BCRT - Berlin Institute of Health Center for Regenerative Therapies, 13353 Berlin, Germany
| | - Nadja Ehmke
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 13353, Germany
| | - Dieter Beule
- CUBI - Core Unit Bioinformatics, Berlin Institute of Health, Berlin 10117, Germany.,Max Delbrück Center for Molecular Medicine, Berlin 13125, Germany
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42
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Yang XR, Benson MD, MacDonald IM, Innes AM. A diagnostic approach to syndromic retinal dystrophies with intellectual disability. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2020; 184:538-570. [PMID: 32918368 DOI: 10.1002/ajmg.c.31834] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/30/2020] [Accepted: 08/05/2020] [Indexed: 12/20/2022]
Abstract
Inherited retinal dystrophies are a group of monogenic disorders that, as a whole, contribute significantly to the burden of ocular disease in both pediatric and adult patients. In their syndromic forms, retinal dystrophies can be observed in association with intellectual disability, frequently alongside other systemic manifestations. There are now over 80 genes implicated in syndromic retinal dystrophies with intellectual disability. Identifying and accurately characterizing these disorders allows the clinician to narrow the differential diagnosis, evaluate for relevant associated features, arrive at a timely and accurate diagnosis, and address both sight-threatening ocular manifestations and morbidity-causing systemic manifestations. The co-occurrence of retinal dystrophy and intellectual disability in an individual can be challenging to investigate, diagnose, and counsel given the considerable phenotypic and genotypic heterogeneity that exists within this broad group of disorders. We performed a review of the current literature and propose an algorithm to facilitate the evaluation, and clinical and mechanistic classification, of these individuals.
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Affiliation(s)
- Xiao-Ru Yang
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Matthew D Benson
- Department of Ophthalmology, University of Alberta, Edmonton, Alberta, Canada
| | - Ian M MacDonald
- Department of Ophthalmology, University of Alberta, Edmonton, Alberta, Canada.,Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
| | - A Micheil Innes
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.,Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
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43
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Hays T, Groopman EE, Gharavi AG. Genetic testing for kidney disease of unknown etiology. Kidney Int 2020; 98:590-600. [PMID: 32739203 PMCID: PMC7784921 DOI: 10.1016/j.kint.2020.03.031] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 03/09/2020] [Accepted: 03/25/2020] [Indexed: 01/01/2023]
Abstract
In many cases of chronic kidney disease, the cause of disease remains unknown despite a thorough nephrologic workup. Genetic testing has revolutionized many areas of medicine and promises to empower diagnosis and targeted management of such cases of kidney disease of unknown etiology. Recent studies using genetic testing have demonstrated that Mendelian etiologies account for approximately 20% of cases of kidney disease of unknown etiology. Although genetic testing has significant benefits, including tailoring of therapy, informing targeted workup, detecting extrarenal disease, counseling patients and families, and redirecting care, it also has important limitations and risks that must be considered.
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Affiliation(s)
- Thomas Hays
- Department of Pediatrics, Division of Neonatology and Perinatology, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - Emily E Groopman
- Department of Medicine, Division of Nephrology, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - Ali G Gharavi
- Department of Medicine, Division of Nephrology, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA; Institute for Genomic Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA; Center for Precision Medicine and Genomics, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA.
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44
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Shedding light on dark genes: enhanced targeted resequencing by optimizing the combination of enrichment technology and DNA fragment length. Sci Rep 2020; 10:9424. [PMID: 32523024 PMCID: PMC7287100 DOI: 10.1038/s41598-020-66331-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 04/23/2020] [Indexed: 12/16/2022] Open
Abstract
The exome contains many obscure regions difficult to explore with current short-read sequencing methods. Repetitious genomic regions prevent the unique alignment of reads, which is essential for the identification of clinically-relevant genetic variants. Long-read technologies attempt to resolve multiple-mapping regions, but they still produce many sequencing errors. Thus, a new approach is required to enlighten the obscure regions of the genome and rescue variants that would be otherwise neglected. This work aims to improve the alignment of multiple-mapping reads through the extension of the standard DNA fragment size. As Illumina can sequence fragments up to 550 bp, we tested different DNA fragment lengths using four major commercial WES platforms and found that longer DNA fragments achieved a higher genotypability. This metric, which indicates base calling calculated by combining depth of coverage with the confidence of read alignment, increased from hundreds to thousands of genes, including several associated with clinical phenotypes. While depth of coverage has been considered crucial for the assessment of WES performance, we demonstrated that genotypability has a greater impact in revealing obscure regions, with ~1% increase in variant calling in respect to shorter DNA fragments. Results confirmed that this approach enlightened many regions previously not explored.
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45
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Kosukcu C, Taskiran EZ, Batu ED, Sag E, Bilginer Y, Alikasifoglu M, Ozen S. Whole exome sequencing in unclassified autoinflammatory diseases: more monogenic diseases in the pipeline? Rheumatology (Oxford) 2020; 60:607-616. [DOI: 10.1093/rheumatology/keaa165] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 03/10/2020] [Indexed: 12/30/2022] Open
Abstract
Abstract
Objective
Autoinflammatory diseases (AIDs) are characterized by recurrent sterile systemic inflammation attacks. More than half of the patients remain genetically undiagnosed with next-generation sequencing panels for common AIDs. In this study, we aimed to define phenotype-genotype correlations in a cohort of unclassified AID patients via whole exome sequencing (WES).
Methods
Patients with features of AIDs were included in this study followed in the Department of Pediatric Rheumatology at Hacettepe University. They were first screened for MEFV with Sanger sequencing and then WES performed for the patients with clinically insignificant results. Pre-analysis of WES data was done by considering the 13 most common AID-related genes. Further bioinformatic analysis was performed if the patient remained genetically undiagnosed.
Results
The median age at disease onset was 1.2 years (range 0.2–16) and at the time of study recruitment was 14 years (range 3.5–17). In our cohort, WES provided a definite or probable disease-causing variant in 4 of 11 patients (36%). Heterozygous mutations for two of these genes were previously associated with neurological defects (ADAM17, TBK1), also homozygous ADAM17 mutations were observed in one family with neonatal inflammatory skin and bowel disease. Besides, two genes (LIG4, RAG1) were associated with immunodeficiency although the patients had presented with inflammatory features. Finally, for one patient, we associated a strong candidate gene (NLRC3) with autoinflammatory features.
Conclusion
WES strategy is cost-effective and provides substantial results for a selected group of undefined AID patients. Our results will contribute to the spectrum of unclassified AIDs.
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Affiliation(s)
- Can Kosukcu
- Department of Bioinformatics, Institute of Health Sciences, Ankara, Turkey
| | - Ekim Z Taskiran
- Faculty of Medicine, Department of Medical Genetics, Ankara, Turkey
| | - Ezgi Deniz Batu
- Department of Pediatric Rheumatology, Hacettepe University, Ankara, Turkey
| | - Erdal Sag
- Department of Pediatric Rheumatology, Hacettepe University, Ankara, Turkey
| | - Yelda Bilginer
- Department of Pediatric Rheumatology, Hacettepe University, Ankara, Turkey
| | | | - Seza Ozen
- Department of Pediatric Rheumatology, Hacettepe University, Ankara, Turkey
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46
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Hombach D, Schuelke M, Knierim E, Ehmke N, Schwarz JM, Fischer-Zirnsak B, Seelow D. MutationDistiller: user-driven identification of pathogenic DNA variants. Nucleic Acids Res 2020; 47:W114-W120. [PMID: 31106342 PMCID: PMC6602447 DOI: 10.1093/nar/gkz330] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 04/12/2019] [Accepted: 05/10/2019] [Indexed: 01/10/2023] Open
Abstract
MutationDistiller is a freely available online tool for user-driven analyses of Whole Exome Sequencing data. It offers a user-friendly interface aimed at clinicians and researchers, who are not necessarily bioinformaticians. MutationDistiller combines MutationTaster's pathogenicity predictions with a phenotype-based approach. Phenotypic information is not limited to symptoms included in the Human Phenotype Ontology (HPO), but may also comprise clinical diagnoses and the suspected mode of inheritance. The search can be restricted to lists of candidate genes (e.g. virtual gene panels) and by tissue-specific gene expression. The inclusion of GeneOntology (GO) and metabolic pathways facilitates the discovery of hitherto unknown disease genes. In a novel approach, we trained MutationDistiller's HPO-based prioritization on authentic genotype-phenotype sets obtained from ClinVar and found it to match or outcompete current prioritization tools in terms of accuracy. In the output, the program provides a list of potential disease mutations ordered by the likelihood of the affected genes to cause the phenotype. MutationDistiller provides links to gene-related information from various resources. It has been extensively tested by clinicians and their suggestions have been valued in many iterative cycles of revisions. The tool, a comprehensive documentation and examples are freely available at https://www.mutationdistiller.org/.
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Affiliation(s)
- Daniela Hombach
- Berliner Institut für Gesundheitsforschung (BIH), Berlin, Germany Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität Berlin, and Berlin Institute of Health, Berlin, Germany.,Charité-Universitätsmedizin Berlin, Charité-BIH Centrum for Therapy and Research, Berlin, Germany.,NeuroCure Cluster of Excellence, Berlin, Germany
| | - Markus Schuelke
- NeuroCure Cluster of Excellence, Berlin, Germany.,Department of Neuropaediatrics, Berlin, Germany
| | - Ellen Knierim
- NeuroCure Cluster of Excellence, Berlin, Germany.,Department of Neuropaediatrics, Berlin, Germany
| | - Nadja Ehmke
- Institute of Medical Genetics and Human Genetics, Berlin, Germany
| | - Jana Marie Schwarz
- Charité-Universitätsmedizin Berlin, Charité-BIH Centrum for Therapy and Research, Berlin, Germany.,NeuroCure Cluster of Excellence, Berlin, Germany.,Department of Neuropaediatrics, Berlin, Germany
| | - Björn Fischer-Zirnsak
- Institute of Medical Genetics and Human Genetics, Berlin, Germany.,Max-Planck-Institute for Molecular Genetics, RG Development & Disease, Berlin, Germany
| | - Dominik Seelow
- Berliner Institut für Gesundheitsforschung (BIH), Berlin, Germany Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität Berlin, and Berlin Institute of Health, Berlin, Germany.,Charité-Universitätsmedizin Berlin, Charité-BIH Centrum for Therapy and Research, Berlin, Germany
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47
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Ramos-Fuentes F, González-Meneses A, Ars E, Hernández-Jaras J. Genetic Diagnosis of Rare Diseases: Past and Present. Adv Ther 2020; 37:29-37. [PMID: 32236876 DOI: 10.1007/s12325-019-01176-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Indexed: 12/18/2022]
Abstract
Rare diseases are heterogeneous life-threatening or seriously debilitating conditions that affect < 1 in 2000 individuals, and most have a genetic component. The diagnostic process is usually based on classic clinical practices, such as physical examination, personal and family history (inheritance pattern), laboratory tests and image studies, but diagnosis can be delayed several years after the initiation of symptoms. The advances in molecular genetics that have taken place in recent years have led to an important shift in medical practice and in its approach to the diagnosis and treatment of many rare diseases. The objective of this review is to promote a better understanding of the mechanisms underlying genetic diseases in humans and the tools available for their diagnosis. A practical example of X-linked hypophosphataemic rickets is described.
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48
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Dunn PJ, Maher BH, Albury CL, Stuart S, Sutherland HG, Maksemous N, Benton MC, Smith RA, Haupt LM, Griffiths LR. Tiered analysis of whole-exome sequencing for epilepsy diagnosis. Mol Genet Genomics 2020; 295:751-763. [DOI: 10.1007/s00438-020-01657-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 02/19/2020] [Indexed: 12/11/2022]
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49
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Seale K, Burger M, Posthumus M, Häger CK, Stattin E, Nilsson KG, Collins M, September AV. The Apoptosis Pathway and CASP8 Variants Conferring Risk for Acute and Overuse Musculoskeletal Injuries. J Orthop Res 2020; 38:680-688. [PMID: 31692049 DOI: 10.1002/jor.24504] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 10/14/2019] [Indexed: 02/04/2023]
Abstract
Rotator cuff tendinopathy (RCT), anterior cruciate ligament (ACL) ruptures, and carpal tunnel syndrome (CTS), are examples of chronic (RCT and CTS) and acute (ACL ruptures) musculoskeletal soft tissue injuries. These injuries are multifactorial in nature, with several identified intrinsic and extrinsic risk factors. Previous studies have implicated specific sequence variants within genes encoding structural and regulatory components of the extracellular matrix of tendons and/ligaments to predispose individuals to these injuries. An example, includes the association of sequence variants within the apoptotic regulatory gene, caspase-8 (CASP8) with other musculoskeletal injury phenotypes, such as Achilles tendinopathy. The primary aim of this study was, therefore, to investigate previously implicated DNA sequence variants within CASP8: rs3834129 (ins/del) and rs1045485 (G/C), and the rs13113 (T/A) identified using a whole exome sequencing approach, with risk of musculoskeletal injury phenotypes (RCT, ACL ruptures, and CTS) in three independent studies. In addition, the aim was to implicate a CASP8 genomic interval in the modulation of risk of RCT, ACL ruptures, or CTS. It was found that the AA genotype of CASP8 rs13113 (T/A) was independently associated with increased risk for CTS. In addition, it was found that the del-C haplotype (rs3834129-rs1045485) was significantly associated with non-contact ACL ruptures, which is in alignment with previous research findings. Collectively, the results of this study implicate the apoptosis pathway as biologically significant in the underlying pathogenesis of musculoskeletal injury phenotypes. These findings should be repeated in larger sample cohorts and across different populations. © 2019 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 38:680-688, 2020.
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Affiliation(s)
- Kirsten Seale
- Department of Human Biology, Division of Exercise Science and Sports Medicine, Faculty of Health Sciences, University of Cape Town, Postal: No 1 Boundary Road, ESSM Level 3, SISSA Building Newlands, Cape Town, 7700, South Africa
| | - Marilize Burger
- Department of Human Biology, Division of Exercise Science and Sports Medicine, Faculty of Health Sciences, University of Cape Town, Postal: No 1 Boundary Road, ESSM Level 3, SISSA Building Newlands, Cape Town, 7700, South Africa.,Department of Surgical Sciences, Division of Orthopaedic Surgery, Faculty of Medicine and Health Sciences, Stellenbosch University, Stellenbosch, South Africa
| | - Michael Posthumus
- Department of Human Biology, Division of Exercise Science and Sports Medicine, Faculty of Health Sciences, University of Cape Town, Postal: No 1 Boundary Road, ESSM Level 3, SISSA Building Newlands, Cape Town, 7700, South Africa
| | - Charlotte K Häger
- Department of Community Medicine and Rehabilitation, Umeå University, Umeå, Sweden
| | - Evalena Stattin
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Kjell G Nilsson
- Department of Surgical and Perioperative Sciences, Umeå University, Umeå, Sweden
| | - Malcolm Collins
- Department of Human Biology, Division of Exercise Science and Sports Medicine, Faculty of Health Sciences, University of Cape Town, Postal: No 1 Boundary Road, ESSM Level 3, SISSA Building Newlands, Cape Town, 7700, South Africa
| | - Alison V September
- Department of Human Biology, Division of Exercise Science and Sports Medicine, Faculty of Health Sciences, University of Cape Town, Postal: No 1 Boundary Road, ESSM Level 3, SISSA Building Newlands, Cape Town, 7700, South Africa.,Division of Exercise Science and Sports Medicine, International Federation of Sports Medicine (FIMS) Collaborative Centre of Sports Medicine, Cape Town, South Africa.,UCT Research Centre for Health through Physical Activity, Lifestyle and Sport (HPALS), Division of Exercise Science and Sports Medicine, University of Cape Town, Cape Town, South Africa
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50
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Validating a targeted next-generation sequencing assay and profiling somatic variants in Chinese non-small cell lung cancer patients. Sci Rep 2020; 10:2070. [PMID: 32034196 PMCID: PMC7005734 DOI: 10.1038/s41598-020-58819-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 11/29/2019] [Indexed: 02/05/2023] Open
Abstract
Non-small cell lung cancer (NSCLC) is featured with complex genomic alterations. Molecular profiling of large cohort of NSCLC patients is thus a prerequisite for precision medicine. We first validated the detection performance of a next-generation sequencing (NGS) cancer hotspot panel, OncoAim, on formalin-fixed paraffin-embedded (FFPE) samples. We then utilized OncoAim to delineate the genomic aberrations in Chinese NSCLC patients. Overall detection performance was powerful for mutations with allele frequency (MAF) ≥ 5% at >500 × coverage depth, with >99% sensitivity, high specificity (positive predictive value > 99%), 94% accuracy and 96% repeatability. Profiling 422 NSCLC FFPE samples revealed that patient characteristics, including gender, age, lymphatic spread, histologic grade and histologic subtype were significantly associated with the mutation incidence of EGFR and TP53. Moreover, RTK signaling pathway activation was enriched in adenocarcinoma, while PI(3)K pathway activation, oxidative stress pathway activation, and TP53 pathway inhibition were more prevalent in squamous cell carcinoma. Additionally, novel co-existence (e.g., variants in BRAF and PTEN) and mutual-exclusiveness (e.g., alterations in EGFR and NFE2L2) were found. Finally, we revealed distinct mutation spectrum in TP53, as well as a previously undervalued PTEN aberration. Our findings could aid in improving diagnosis, prognosis and personalized therapeutic decisions of Chinese NSCLC patients.
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