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Kerkhof J, Rastin C, Schenkel L, Lin H, Sadikovic B. Clinical validation of a single NGS targeted panel pipeline using the KAPA HyperChoice system for detection of germline, somatic and mitochondrial sequence and copy number variants. Expert Rev Mol Diagn 2023; 23:827-841. [PMID: 37542410 DOI: 10.1080/14737159.2023.2245747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 07/19/2023] [Accepted: 08/04/2023] [Indexed: 08/06/2023]
Abstract
BACKGROUND Comprehensive molecular diagnostics are highly dependent on the technical performance of next-generation sequencing (NGS) pipelines, which are assessed by data quality, cost, turnaround time, and accuracy of detecting a range of sequence and copy number variants. METHODS A dataset of 285 clinically validated cases (205 retrospective and 80 prospective), carrying complex sequence and copy number variants and thousands of genetic polymorphisms underwent a clinical validation of the KAPA HyperChoice target enrichment system with parallel sample fidelity assessment across a number of NGS panels. The analysis included assessment of peripheral blood, urine, muscle and FFPE tissues. RESULTS High-quality and exceptionally uniform data with 100% coverage of all targeted panels were obtained, resulting in complete sensitivity and specificity for all variant types across nearly all panels and tissue types. Overall reduction in cost and turnaround times was obtained with the implementation of a parallel genotyping sample fidelity system. CONCLUSION Results of the laboratory quality improvement study focused on a single NGS pipeline that includes both nuclear and mitochondrial genomes demonstrated utility in the clinical setting to assess a range of referral reasons, necessary due to the complex molecular etiology of human genetic disorders, while reducing costs and turnaround times.
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Affiliation(s)
- Jennifer Kerkhof
- Molecular Genetics Laboratory, Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Cassandra Rastin
- Molecular Genetics Laboratory, Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Laila Schenkel
- Molecular Genetics Laboratory, Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Hanxin Lin
- Molecular Genetics Laboratory, Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Bekim Sadikovic
- Molecular Genetics Laboratory, Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
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2
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Ahmad E, Ali A, Nimisha, Kumar Sharma A, Ahmed F, Mehdi Dar G, Mohan Singh A, Apurva, Kumar A, Athar A, Parveen F, Mahajan B, Singh Saluja S. Molecular approaches in cancer. Clin Chim Acta 2022; 537:60-73. [DOI: https:/doi.org/10.1016/j.cca.2022.09.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2023]
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3
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Ahmad E, Ali A, Nimisha, Kumar Sharma A, Ahmed F, Mehdi Dar G, Mohan Singh A, Apurva, Kumar A, Athar A, Parveen F, Mahajan B, Singh Saluja S. Molecular approaches in cancer. Clin Chim Acta 2022; 537:60-73. [DOI: 10.1016/j.cca.2022.09.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 09/28/2022] [Accepted: 09/28/2022] [Indexed: 11/03/2022]
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Doculara L, Trahair TN, Bayat N, Lock RB. Circulating Tumor DNA in Pediatric Cancer. Front Mol Biosci 2022; 9:885597. [PMID: 35647029 PMCID: PMC9133724 DOI: 10.3389/fmolb.2022.885597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/25/2022] [Indexed: 11/13/2022] Open
Abstract
The measurement of circulating tumor DNA (ctDNA) has gained increasing prominence as a minimally invasive tool for the detection of cancer-specific markers in plasma. In adult cancers, ctDNA detection has shown value for disease-monitoring applications including tumor mutation profiling, risk stratification, relapse prediction, and treatment response evaluation. To date, there are ctDNA tests used as companion diagnostics for adult cancers and it is not understood why the same cannot be said about childhood cancer, despite the marked differences between adult and pediatric oncology. In this review, we discuss the current understanding of ctDNA as a disease monitoring biomarker in the context of pediatric malignancies, including the challenges associated with ctDNA detection in liquid biopsies. The data and conclusions from pediatric cancer studies of ctDNA are summarized, highlighting treatment response, disease monitoring and the detection of subclonal disease as applications of ctDNA. While the data from retrospective studies highlight the potential of ctDNA, large clinical trials are required for ctDNA analysis for routine clinical use in pediatric cancers. We outline the requirements for the standardization of ctDNA detection in pediatric cancers, including sample handling and reproducibility of results. With better understanding of the advantages and limitations of ctDNA and improved detection methods, ctDNA analysis may become the standard of care for patient monitoring in childhood cancers.
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Affiliation(s)
- Louise Doculara
- Children’s Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Sydney, NSW, Australia
- School of Women’s and Children’s Health, UNSW Sydney, Sydney, NSW, Australia
- University of New South Wales Centre for Childhood Cancer Research, UNSW Sydney, Sydney, NSW, Australia
| | - Toby N. Trahair
- Children’s Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Sydney, NSW, Australia
- School of Women’s and Children’s Health, UNSW Sydney, Sydney, NSW, Australia
- Kids Cancer Centre, Sydney Children’s Hospital, Randwick, NSW, Australia
| | - Narges Bayat
- Children’s Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Sydney, NSW, Australia
- School of Women’s and Children’s Health, UNSW Sydney, Sydney, NSW, Australia
- University of New South Wales Centre for Childhood Cancer Research, UNSW Sydney, Sydney, NSW, Australia
| | - Richard B. Lock
- Children’s Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Sydney, NSW, Australia
- School of Women’s and Children’s Health, UNSW Sydney, Sydney, NSW, Australia
- University of New South Wales Centre for Childhood Cancer Research, UNSW Sydney, Sydney, NSW, Australia
- *Correspondence: Richard B. Lock,
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5
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Pfeifer JD, Loberg R, Lofton-Day C, Zehnbauer BA. Reference Samples to Compare Next-Generation Sequencing Test Performance for Oncology Therapeutics and Diagnostics. Am J Clin Pathol 2022; 157:628-638. [PMID: 34871357 DOI: 10.1093/ajcp/aqab164] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 08/24/2021] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVES Diversity of laboratory-developed tests (LDTs) using next-generation sequencing (NGS) raises concerns about their accuracy for selection of targeted therapies. A working group developed a pilot study of traceable reference samples to measure NGS LDT performance among a cohort of clinical laboratories. METHODS Human cell lines were engineered via CRISPR/Cas9 and prepared as formalin-fixed, paraffin-embedded cell pellets ("wet" samples) to assess the entire NGS test cycle. In silico mutagenized NGS sequence files ("dry" samples) were used to assess the bioinformatics component of the NGS test cycle. Single and multinucleotide variants (n = 36) of KRAS and NRAS were tested at 5% or 15% variant allele fraction to determine eligibility for therapy with the EGFR inhibitor panitumumab in the setting of metastatic colorectal cancer. RESULTS Twenty-one (21/21) laboratories tested wet samples; 19 of 21 analyzed dry samples. Of the laboratories that tested both the wet and dry samples, 7 (37%) of 19 laboratories correctly reported all variants, 3 (16%) of 19 had fewer than five errors, and 9 (47%) of 19 had five or more errors. Most errors were false negatives. CONCLUSIONS Genetically engineered cell lines and mutagenized sequence files are complementary reference samples for evaluating NGS test performance among clinical laboratories using LDTs. Variable accuracy in detection of genetic variants among some LDTs may identify different patient populations for targeted therapy.
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Affiliation(s)
- John D Pfeifer
- Department of Pathology, Washington University School of Medicine, St Louis, MO, USA
| | - Robert Loberg
- Clinical Biomarkers and Diagnostics, Thousand Oaks, CA, USA
| | | | - Barbara A Zehnbauer
- Department of Pathology, Emory University School of Medicine, Atlanta, GA, USA
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Wang D, Zhang Y, li R, Li J, Zhang R. Consistency and reproducibility of large panel next-generation sequencing: Multi-laboratory assessment of somatic mutation detection on reference materials with mismatch repair and proofreading deficiency. J Adv Res 2022; 44:161-172. [PMID: 36725187 PMCID: PMC9937796 DOI: 10.1016/j.jare.2022.03.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 03/16/2022] [Accepted: 03/27/2022] [Indexed: 02/04/2023] Open
Abstract
INTRODUCTION Clinical precision oncology increasingly relies on accurate genome-wide profiling using large panel next generation sequencing; however, difficulties in accurate and consistent detection of somatic mutation from individual platforms and pipelines remain an open question. OBJECTIVES To obtain paired tumor-normal reference materials that can be effectively constructed and interchangeable with clinical samples, and evaluate the performance of 56 panels under routine testing conditions based on the reference samples. METHODS Genes involved in mismatch repair and DNA proofreading were knocked down using the CRISPR-Cas9 technology to accumulate somatic mutations in a defined GM12878 cell line. They were used as reference materials to comprehensively evaluate the reproducibility and accuracy of detection results of oncopanels and explore the potential influencing factors. RESULTS In total, 14 paired tumor-normal reference DNA samples from engineered cell lines were prepared, and a reference dataset comprising 168 somatic mutations in a high-confidence region of 1.8 Mb were generated. For mutations with an allele frequency (AF) of more than 5% in reference samples, 56 panels collectively reported 1306 errors, including 729 false negatives (FNs), 179 false positives (FPs) and 398 reproducibility errors. The performance metric varied among panels with precision and recall ranging from 0.773 to 1 and 0.683 to 1, respectively. Incorrect and inadequate filtering accounted for a large proportion of false discovery (including FNs and FPs), while low-quality detection, cross-contamination and other sequencing errors during the wet bench process were other sources of FNs and FPs. In addition, low AF (<5%) considerably influenced the reproducibility and comparability among panels. CONCLUSIONS This study provided an integrated practice for developing reference standard to assess oncopanels in detecting somatic mutations and quantitatively revealed the source of detection errors. It will promote optimization, validation, and quality control among laboratories with potential applicability in clinical use.
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Affiliation(s)
- Duo Wang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, P. R. China,Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P. R. China,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P. R. China
| | - Yuanfeng Zhang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, P. R. China,Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P. R. China,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P. R. China
| | - Rui li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, P. R. China,Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P. R. China,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P. R. China
| | - Jinming Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, P. R. China; Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P. R. China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P. R. China.
| | - Rui Zhang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, P. R. China; Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P. R. China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P. R. China.
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7
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Chappell K, Francou B, Habib C, Huby T, Leoni M, Cottin A, Nadal F, Adnet E, Paoli E, Oliveira C, Verstuyft C, Davit-Spraul A, Gaignard P, Lebigot E, Duclos-Vallee JC, Young J, Kamenicky P, Adams D, Echaniz-Laguna A, Gonzales E, Bouvattier C, Linglart A, Picard V, Bergoin E, Jacquemin E, Guiochon-Mantel A, Proust A, Bouligand J. Galaxy Is a Suitable Bioinformatics Platform for the Molecular Diagnosis of Human Genetic Disorders Using High-Throughput Sequencing Data Analysis. Five Years of Experience in a Clinical Laboratory. Clin Chem 2021; 68:313-321. [PMID: 34871369 DOI: 10.1093/clinchem/hvab220] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 09/13/2021] [Indexed: 12/12/2022]
Abstract
BACKGROUND To date, the usage of Galaxy, an open-source bioinformatics platform, has been reported primarily in research. We report 5 years' experience (2015 to 2020) with Galaxy in our hospital, as part of the "Assistance Publique-Hôpitaux de Paris" (AP-HP), to demonstrate its suitability for high-throughput sequencing (HTS) data analysis in a clinical laboratory setting. METHODS Our Galaxy instance has been running since July 2015 and is used daily to study inherited diseases, cancer, and microbiology. For the molecular diagnosis of hereditary diseases, 6970 patients were analyzed with Galaxy (corresponding to a total of 7029 analyses). RESULTS Using Galaxy, the time to process a batch of 23 samples-equivalent to a targeted DNA sequencing MiSeq run-from raw data to an annotated variant call file was generally less than 2 h for panels between 1 and 500 kb. Over 5 years, we only restarted the server twice for hardware maintenance and did not experience any significant troubles, demonstrating the robustness of our Galaxy installation in conjunction with HTCondor as a job scheduler and a PostgreSQL database. The quality of our targeted exome sequencing method was externally evaluated annually by the European Molecular Genetics Quality Network (EMQN). Sensitivity was mean (SD)% 99 (2)% for single nucleotide variants and 93 (9)% for small insertion-deletions. CONCLUSION Our experience with Galaxy demonstrates it to be a suitable platform for HTS data analysis with vast potential to benefit patient care in a clinical laboratory setting.
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Affiliation(s)
- Kenneth Chappell
- Service de Génétique Moléculaire, Pharmacogénétique et Hormonologie, DMU15, AP-HP.Université Paris-Saclay, Hôpital Bicêtre, Le Kremlin Bicêtre, France.,MOODS Team, CESP, Inserm, Université Paris-Saclay, Faculté de Médecine Paris-Saclay, Le Kremlin Bicêtre, France.,Université Paris-Saclay, Faculté de Médecine, Inserm UMR_1185, Physiologie et Physiopathologie Endocriniennes, Le Kremlin Bicêtre, France
| | - Bruno Francou
- Service de Génétique Moléculaire, Pharmacogénétique et Hormonologie, DMU15, AP-HP.Université Paris-Saclay, Hôpital Bicêtre, Le Kremlin Bicêtre, France.,Université Paris-Saclay, Faculté de Médecine, Inserm UMR_1185, Physiologie et Physiopathologie Endocriniennes, Le Kremlin Bicêtre, France.,Plateforme d'Expertises Maladies Rares Paris-Saclay, APHP.Université Paris Saclay, Le Kremlin Bicêtre, France
| | - Christophe Habib
- Service de Génétique Moléculaire, Pharmacogénétique et Hormonologie, DMU15, AP-HP.Université Paris-Saclay, Hôpital Bicêtre, Le Kremlin Bicêtre, France.,Plateforme d'Expertises Maladies Rares Paris-Saclay, APHP.Université Paris Saclay, Le Kremlin Bicêtre, France
| | - Thomas Huby
- Service de Génétique Moléculaire, Pharmacogénétique et Hormonologie, DMU15, AP-HP.Université Paris-Saclay, Hôpital Bicêtre, Le Kremlin Bicêtre, France
| | - Marco Leoni
- Direction Informatique-Pôle Infrastructures Systèmes et Applications Critiques, Université Paris-Saclay, Orsay, France
| | - Aurélien Cottin
- Service de Génétique Moléculaire, Pharmacogénétique et Hormonologie, DMU15, AP-HP.Université Paris-Saclay, Hôpital Bicêtre, Le Kremlin Bicêtre, France.,Agroécologie, AgroSup Dijon, INRAE, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, France
| | - Florian Nadal
- Service de Génétique Moléculaire, Pharmacogénétique et Hormonologie, DMU15, AP-HP.Université Paris-Saclay, Hôpital Bicêtre, Le Kremlin Bicêtre, France
| | - Eric Adnet
- Direction Informatique, Assistance Publique Hôpitaux de Paris, AP-HP.Université Paris, Saclay, Le Kremlin Bicêtre, France
| | - Eric Paoli
- Direction Informatique, Assistance Publique Hôpitaux de Paris, AP-HP.Université Paris, Saclay, Le Kremlin Bicêtre, France
| | - Christophe Oliveira
- Service de Biochimie, AP-HP.Université Paris-Saclay, Hôpital Bicêtre, Le Kremlin Bicêtre, France
| | - Céline Verstuyft
- Service de Génétique Moléculaire, Pharmacogénétique et Hormonologie, DMU15, AP-HP.Université Paris-Saclay, Hôpital Bicêtre, Le Kremlin Bicêtre, France.,MOODS Team, CESP, Inserm, Université Paris-Saclay, Faculté de Médecine Paris-Saclay, Le Kremlin Bicêtre, France.,Plateforme d'Expertises Maladies Rares Paris-Saclay, APHP.Université Paris Saclay, Le Kremlin Bicêtre, France
| | - Anne Davit-Spraul
- Plateforme d'Expertises Maladies Rares Paris-Saclay, APHP.Université Paris Saclay, Le Kremlin Bicêtre, France.,Service de Biochimie, AP-HP.Université Paris-Saclay, Hôpital Bicêtre, Le Kremlin Bicêtre, France
| | - Pauline Gaignard
- Plateforme d'Expertises Maladies Rares Paris-Saclay, APHP.Université Paris Saclay, Le Kremlin Bicêtre, France.,Service de Biochimie, AP-HP.Université Paris-Saclay, Hôpital Bicêtre, Le Kremlin Bicêtre, France
| | - Elise Lebigot
- Plateforme d'Expertises Maladies Rares Paris-Saclay, APHP.Université Paris Saclay, Le Kremlin Bicêtre, France.,Service de Biochimie, AP-HP.Université Paris-Saclay, Hôpital Bicêtre, Le Kremlin Bicêtre, France
| | - Jean-Charles Duclos-Vallee
- Plateforme d'Expertises Maladies Rares Paris-Saclay, APHP.Université Paris Saclay, Le Kremlin Bicêtre, France.,Centre Hépatobiliaire, FHU Hepatinov, AP-HP.Université Paris-Saclay and Inserm Unit UMR 1193 Hôpital Paul Brousse, Villejuif, France
| | - Jacques Young
- Université Paris-Saclay, Faculté de Médecine, Inserm UMR_1185, Physiologie et Physiopathologie Endocriniennes, Le Kremlin Bicêtre, France.,Plateforme d'Expertises Maladies Rares Paris-Saclay, APHP.Université Paris Saclay, Le Kremlin Bicêtre, France.,Service d'Endocrinologie et des Maladies de la Reproduction, AP-HP.Université Paris-Saclay, Hôpital Bicêtre, Le Kremlin Bicêtre, France
| | - Peter Kamenicky
- Université Paris-Saclay, Faculté de Médecine, Inserm UMR_1185, Physiologie et Physiopathologie Endocriniennes, Le Kremlin Bicêtre, France.,Plateforme d'Expertises Maladies Rares Paris-Saclay, APHP.Université Paris Saclay, Le Kremlin Bicêtre, France.,Service d'Endocrinologie et des Maladies de la Reproduction, AP-HP.Université Paris-Saclay, Hôpital Bicêtre, Le Kremlin Bicêtre, France
| | - David Adams
- Plateforme d'Expertises Maladies Rares Paris-Saclay, APHP.Université Paris Saclay, Le Kremlin Bicêtre, France.,Service de Neurologie, AP-HP.Université Paris-Saclay, Hôpital Bicêtre, Le Kremlin Bicêtre, France
| | - Andoni Echaniz-Laguna
- Plateforme d'Expertises Maladies Rares Paris-Saclay, APHP.Université Paris Saclay, Le Kremlin Bicêtre, France.,Service de Neurologie, AP-HP.Université Paris-Saclay, Hôpital Bicêtre, Le Kremlin Bicêtre, France
| | - Emmanuel Gonzales
- Plateforme d'Expertises Maladies Rares Paris-Saclay, APHP.Université Paris Saclay, Le Kremlin Bicêtre, France.,Service d'Hépatologie et de Transplantation Hépatique Pédiatriques, Centre de Référence National de Maladies Rares du Foie, FILFOIE, ERN RARE LIVER, AP-HP.Université Paris-Saclay, Hôpital Bicêtre, Le Kremlin Bicêtre and UMR_S 1193, Université Paris-Saclay, Hepatinov, Orsay, France
| | - Claire Bouvattier
- Université Paris-Saclay, Faculté de Médecine, Inserm UMR_1185, Physiologie et Physiopathologie Endocriniennes, Le Kremlin Bicêtre, France.,Plateforme d'Expertises Maladies Rares Paris-Saclay, APHP.Université Paris Saclay, Le Kremlin Bicêtre, France.,Service d'Endocrinologie et Diabéte de l'enfant, DMU SEA, AP-HP.Université Paris-Saclay, Hôpital Bicêtre, Le Kremlin Bicêtre, France
| | - Agnes Linglart
- Université Paris-Saclay, Faculté de Médecine, Inserm UMR_1185, Physiologie et Physiopathologie Endocriniennes, Le Kremlin Bicêtre, France.,Plateforme d'Expertises Maladies Rares Paris-Saclay, APHP.Université Paris Saclay, Le Kremlin Bicêtre, France.,Service d'Endocrinologie et Diabéte de l'enfant, DMU SEA, AP-HP.Université Paris-Saclay, Hôpital Bicêtre, Le Kremlin Bicêtre, France
| | - Véronique Picard
- Plateforme d'Expertises Maladies Rares Paris-Saclay, APHP.Université Paris Saclay, Le Kremlin Bicêtre, France.,Service d'Hématologie, AP-HP.Université Paris-Saclay, Hôpital Bicêtre, Le Kremlin Bicêtre, France
| | - Emilie Bergoin
- Service d'Assurance Qualité, DMU15, AP-HP.Université Paris-Saclay, Hôpital Bicêtre, Le Kremlin Bicêtre, France
| | - Emmanuel Jacquemin
- Plateforme d'Expertises Maladies Rares Paris-Saclay, APHP.Université Paris Saclay, Le Kremlin Bicêtre, France.,Service d'Hépatologie et de Transplantation Hépatique Pédiatriques, Centre de Référence National de Maladies Rares du Foie, FILFOIE, ERN RARE LIVER, AP-HP.Université Paris-Saclay, Hôpital Bicêtre, Le Kremlin Bicêtre and UMR_S 1193, Université Paris-Saclay, Hepatinov, Orsay, France
| | - Anne Guiochon-Mantel
- Service de Génétique Moléculaire, Pharmacogénétique et Hormonologie, DMU15, AP-HP.Université Paris-Saclay, Hôpital Bicêtre, Le Kremlin Bicêtre, France.,Université Paris-Saclay, Faculté de Médecine, Inserm UMR_1185, Physiologie et Physiopathologie Endocriniennes, Le Kremlin Bicêtre, France.,Plateforme d'Expertises Maladies Rares Paris-Saclay, APHP.Université Paris Saclay, Le Kremlin Bicêtre, France
| | - Alexis Proust
- Service de Génétique Moléculaire, Pharmacogénétique et Hormonologie, DMU15, AP-HP.Université Paris-Saclay, Hôpital Bicêtre, Le Kremlin Bicêtre, France
| | - Jérôme Bouligand
- Service de Génétique Moléculaire, Pharmacogénétique et Hormonologie, DMU15, AP-HP.Université Paris-Saclay, Hôpital Bicêtre, Le Kremlin Bicêtre, France.,Université Paris-Saclay, Faculté de Médecine, Inserm UMR_1185, Physiologie et Physiopathologie Endocriniennes, Le Kremlin Bicêtre, France.,Plateforme d'Expertises Maladies Rares Paris-Saclay, APHP.Université Paris Saclay, Le Kremlin Bicêtre, France
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8
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Ménard T, Barros A, Ganter C. Clinical Quality Considerations when Using Next-Generation Sequencing (NGS) in Clinical Drug Development. Ther Innov Regul Sci 2021; 55:1066-1074. [PMID: 34046876 PMCID: PMC8332578 DOI: 10.1007/s43441-021-00308-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 05/19/2021] [Indexed: 11/30/2022]
Abstract
Next-generation sequencing (NGS) and decreased costs of genomic testing are changing the paradigm in precision medicine and continue to fuel innovation. Integration of NGS into clinical drug development has the potential to accelerate clinical trial conduct and ultimately will shape the landscape of clinical care by making it easier to identify patients who would benefit from particular therapy(ies) and to monitor treatment outcomes with less invasive tests. This has led to an increased use of NGS service providers by pharmaceutical sponsors: to screen patients for clinical trials eligibility and for patient stratification, expanded Companion Diagnostic (CDx) development for treatment recommendations and Comprehensive Genomic profiling (CGP). These changes are reshaping the face of clinical quality considerations for precision medicine. Although some clinical quality considerations do exist in Health Authorities (HA) guidances and regulations (e.g., International Conference of Harmonization Good Clinical Practices-GCP), there is currently no holistic GxP-like detailed framework for pharmaceutical sponsors using NGS service providers in clinical trials, or for the development of CDx and CGP. In this research, we identified existing and applicable regulations, guidelines and recommendations that could be translated into clinical quality considerations related to technology, data quality, patients and oversight. We propose these considerations as a basis for pharmaceutical sponsors using NGS service providers in clinical drug development to develop a set of guidelines for NGS clinical quality.
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Affiliation(s)
| | - Alaina Barros
- Genentech Inc. - A Member of the Roche Group, South San Francisco, USA
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9
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Savarese M, Välipakka S, Johari M, Hackman P, Udd B. Is Gene-Size an Issue for the Diagnosis of Skeletal Muscle Disorders? J Neuromuscul Dis 2021; 7:203-216. [PMID: 32176652 PMCID: PMC7369045 DOI: 10.3233/jnd-190459] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Human genes have a variable length. Those having a coding sequence of extraordinary length and a high number of exons were almost impossible to sequence using the traditional Sanger-based gene-by-gene approach. High-throughput sequencing has partly overcome the size-related technical issues, enabling a straightforward, rapid and relatively inexpensive analysis of large genes. Several large genes (e.g. TTN, NEB, RYR1, DMD) are recognized as disease-causing in patients with skeletal muscle diseases. However, because of their sheer size, the clinical interpretation of variants in these genes is probably the most challenging aspect of the high-throughput genetic investigation in the field of skeletal muscle diseases. The main aim of this review is to discuss the technical and interpretative issues related to the diagnostic investigation of large genes and to reflect upon the current state of the art and the future advancements in the field.
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Affiliation(s)
- Marco Savarese
- Folkhälsan Research Center, Helsinki, Finland.,Department of Medical Genetics, Medicum, University of Helsinki, Helsinki, Finland
| | - Salla Välipakka
- Folkhälsan Research Center, Helsinki, Finland.,Department of Medical Genetics, Medicum, University of Helsinki, Helsinki, Finland
| | - Mridul Johari
- Folkhälsan Research Center, Helsinki, Finland.,Department of Medical Genetics, Medicum, University of Helsinki, Helsinki, Finland
| | - Peter Hackman
- Folkhälsan Research Center, Helsinki, Finland.,Department of Medical Genetics, Medicum, University of Helsinki, Helsinki, Finland
| | - Bjarne Udd
- Folkhälsan Research Center, Helsinki, Finland.,Department of Medical Genetics, Medicum, University of Helsinki, Helsinki, Finland.,Neuromuscular Research Center, Tampere University and University Hospital, Tampere, Finland.,Department of Neurology, Vaasa Central Hospital, Vaasa, Finland
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10
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Zhong Y, Xu F, Wu J, Schubert J, Li MM. Application of Next Generation Sequencing in Laboratory Medicine. Ann Lab Med 2021; 41:25-43. [PMID: 32829577 PMCID: PMC7443516 DOI: 10.3343/alm.2021.41.1.25] [Citation(s) in RCA: 102] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 03/24/2020] [Accepted: 08/07/2020] [Indexed: 12/12/2022] Open
Abstract
The rapid development of next-generation sequencing (NGS) technology, including advances in sequencing chemistry, sequencing technologies, bioinformatics, and data interpretation, has facilitated its wide clinical application in precision medicine. This review describes current sequencing technologies, including short- and long-read sequencing technologies, and highlights the clinical application of NGS in inherited diseases, oncology, and infectious diseases. We review NGS approaches and clinical diagnosis for constitutional disorders; summarize the application of U.S. Food and Drug Administration-approved NGS panels, cancer biomarkers, minimal residual disease, and liquid biopsy in clinical oncology; and consider epidemiological surveillance, identification of pathogens, and the importance of host microbiome in infectious diseases. Finally, we discuss the challenges and future perspectives of clinical NGS tests.
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Affiliation(s)
- Yiming Zhong
- Department of Pathology & Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA,
USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA,
USA
| | - Feng Xu
- Department of Pathology & Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA,
USA
| | - Jinhua Wu
- Department of Pathology & Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA,
USA
| | - Jeffrey Schubert
- Department of Pathology & Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA,
USA
| | - Marilyn M. Li
- Department of Pathology & Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA,
USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA,
USA
- Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA,
USA
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Delcourt T, Vanneste K, Soumali MR, Coucke W, Ghislain V, Hebrant A, Van Valckenborgh E, De Keersmaecker SCJ, Roosens NH, Van De Walle P, Van Den Bulcke M, Antoniou A. NGS for (Hemato-) Oncology in Belgium: Evaluation of Laboratory Performance and Feasibility of a National External Quality Assessment Program. Cancers (Basel) 2020; 12:E3180. [PMID: 33138022 PMCID: PMC7692129 DOI: 10.3390/cancers12113180] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 10/23/2020] [Accepted: 10/26/2020] [Indexed: 01/08/2023] Open
Abstract
Next-generation sequencing (NGS) is being integrated into routine clinical practice in the field of (hemato-) oncology to search for variants with diagnostic, prognostic, or therapeutic value at potentially low allelic frequencies. The complex sequencing workflows used require careful validation and continuous quality control. Participation in external quality assessments (EQA) helps laboratories evaluate their performance and guarantee the validity of tests results with the ultimate goal of ensuring high-quality patient care. Here, we describe three benchmarking trials performed during the period 2017-2018 aiming firstly at establishing the state-of-the-art and secondly setting up a NGS-specific EQA program at the national level in the field of clinical (hemato-) oncology in Belgium. DNA samples derived from cell line mixes and artificially mutated cell lines, designed to carry variants of clinical relevance occurring in solid tumors, hematological malignancies, and BRCA1/BRCA2 genes, were sent to Belgian human genetics, anatomic pathology, and clinical biology laboratories, to be processed following routine practices, together with surveys covering technical aspects of the NGS workflows. Despite the wide variety of platforms and workflows currently applied in routine clinical practice, performance was satisfactory, since participating laboratories identified the targeted variants with success rates ranging between 93.06% and 97.63% depending on the benchmark, and few false negative or repeatability issues were identified. However, variant reporting and interpretation varied, underlining the need for further standardization. Our approach showcases the feasibility of developing and implementing EQA for routine clinical practice in the field of (hemato-) oncology, while highlighting the challenges faced.
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Affiliation(s)
- Thomas Delcourt
- Transversal activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium; (T.D.); (K.V.); (S.C.J.D.K.); (N.H.R.)
| | - Kevin Vanneste
- Transversal activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium; (T.D.); (K.V.); (S.C.J.D.K.); (N.H.R.)
| | - Mohamed Rida Soumali
- Quality of Laboratories, Sciensano, 1050 Brussels, Belgium; (M.R.S.); (W.C.); (V.G.); (P.V.D.W.)
| | - Wim Coucke
- Quality of Laboratories, Sciensano, 1050 Brussels, Belgium; (M.R.S.); (W.C.); (V.G.); (P.V.D.W.)
| | - Vanessa Ghislain
- Quality of Laboratories, Sciensano, 1050 Brussels, Belgium; (M.R.S.); (W.C.); (V.G.); (P.V.D.W.)
| | - Aline Hebrant
- Cancer Centre, Sciensano, 1050 Brussels, Belgium; (A.H.); (E.V.V.); (M.V.D.B.)
| | | | - Sigrid C. J. De Keersmaecker
- Transversal activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium; (T.D.); (K.V.); (S.C.J.D.K.); (N.H.R.)
| | - Nancy H. Roosens
- Transversal activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium; (T.D.); (K.V.); (S.C.J.D.K.); (N.H.R.)
| | - Philippe Van De Walle
- Quality of Laboratories, Sciensano, 1050 Brussels, Belgium; (M.R.S.); (W.C.); (V.G.); (P.V.D.W.)
| | - Marc Van Den Bulcke
- Cancer Centre, Sciensano, 1050 Brussels, Belgium; (A.H.); (E.V.V.); (M.V.D.B.)
| | - Aline Antoniou
- Quality of Laboratories, Sciensano, 1050 Brussels, Belgium; (M.R.S.); (W.C.); (V.G.); (P.V.D.W.)
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Abstract
Cancer researchers require accurate diagnoses for the samples, cell lines, patients or populations that they study. These diagnoses are underpinned by an internationally accepted taxonomy - the World Health Organization Classification of Tumours. This is still largely based on the histopathological examination of biopsy specimens, but increasingly also molecular methods and radiological examination of patients. Classifications evolve as new evidence arises, and for tumours that evidence is available in a quantity that is both remarkable and daunting. Evaluating this deluge of new information and incorporating it into the World Health Organization Classification of Tumours is now the responsibility of an editorial board, and up to 200 editors and authors work on each system to update it within the new 5th edition. Just as cancer researchers depend on the classification for diagnoses, so too the classification depends on the generation of high-quality, trustworthy data by cancer researchers. It is not just a case of quantity but quality too. Scientific fraud is thankfully rare, but high-profile cases are damaging and standards need to improve, not least to ensure that accurate information enters the classification.
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Affiliation(s)
- Ian A Cree
- International Agency for Research on Cancer (IARC), World Health Organization, Lyon, France
| | - B Iciar Indave
- International Agency for Research on Cancer (IARC), World Health Organization, Lyon, France
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