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Tung JK, Devereaux KA, Erdmann AL, Schrijver I, Zehnder J, Suarez CJ. Potential pitfalls in multiplex PCR-based next-generation sequencing: a case-based report. J Clin Pathol 2023; 76:59-63. [PMID: 35145018 DOI: 10.1136/jclinpath-2021-208105] [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: 12/13/2021] [Accepted: 01/12/2022] [Indexed: 12/27/2022]
Abstract
Amplicon-based next-generation sequencing (NGS) assays employ highly sensitive, rapid, and cost-effective methods to detect clinically actionable mutations for the diagnosis, prognosis, and treatment of patients with cancer. However, recognition of certain limitations inherent to amplicon-based NGS assays is crucial for the correct interpretation and reporting of variants in the clinical setting. In this report, we illustrate three different potential pitfalls related to amplicon-based NGS assays based on our institutional experience and highlight how the risk of such events can be minimised.
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Affiliation(s)
- Jack K Tung
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Kelly A Devereaux
- Department of Pathology, NYU Grossman School of Medicine, New York City, New York, USA
| | | | - Iris Schrijver
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - James Zehnder
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Carlos J Suarez
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
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2
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Kondrashova O, Ho GY, Au-Yeung G, Leas L, Boughtwood T, Alsop K, Zapparoli G, Dobrovic A, Ko YA, Hsu AL, Love CJ, Lunke S, Wakefield MJ, McNally O, Quinn M, Ananda S, Neesham D, Hamilton A, Grossi M, Freimund A, Kanjanapan Y, Rischin D, Traficante N, Bowtell D, Scott CL, Christie M, Taylor GR, Mileshkin L, Waring PM. Clinical Utility of Real-Time Targeted Molecular Profiling in the Clinical Management of Ovarian Cancer: The ALLOCATE Study. JCO Precis Oncol 2019; 3:1-18. [DOI: 10.1200/po.19.00019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PURPOSE The ALLOCATE study was designed as a pilot to demonstrate the feasibility and clinical utility of real-time targeted molecular profiling of patients with recurrent or advanced ovarian cancer for identification of potential targeted therapies. PATIENTS AND METHODS A total of 113 patients with ovarian cancer of varying histologies were recruited from two tertiary hospitals, with 99 patient cases suitable for prospective analysis. Targeted molecular and methylation profiling of fresh biopsy and archived tumor samples were performed by screening for mutations or copy-number variations in 44 genes and for promoter methylation of BRCA1 and RAD51C. RESULTS Somatic genomic or methylation events were identified in 85% of all patient cases, with potentially actionable events with defined targeted therapies (including four resistance events) detected in 60% of all patient cases. On the basis of these findings, six patients received molecularly guided therapy, three patients had unsuspected germline cancer–associated BRCA1/ 2 mutations and were referred for genetic counseling, and two intermediate differentiated (grade 2) serous ovarian carcinomas were reclassified as low grade, leading to changes in clinical management. Additionally, secondary reversion mutations in BRCA1/ 2 were identified in fresh biopsy samples of two patients, consistent with clinical platinum/poly (ADP-ribose) polymerase inhibitor resistance. Timely reporting of results if molecular testing is done at disease recurrence, as well as early referral for patients with platinum-resistant cancers, were identified as factors that could improve the clinical utility of molecular profiling. CONCLUSION ALLOCATE molecular profiling identified known genomic and methylation alterations of the different ovarian cancer subtypes and was deemed feasible and useful in routine clinical practice. Better patient selection and access to a wider range of targeted therapies or clinical trials will further enhance the clinical utility of molecular profiling.
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Affiliation(s)
- Olga Kondrashova
- University of Melbourne, Melbourne, Victoria, Australia
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- QIMR Berghofer Medical Research Institute, Queensland, Australia
| | - Gwo-Yaw Ho
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Royal Women’s Hospital, Parkville, Victoria, Australia
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - George Au-Yeung
- University of Melbourne, Melbourne, Victoria, Australia
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Leakhena Leas
- University of Melbourne, Melbourne, Victoria, Australia
| | | | - Kathryn Alsop
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Giada Zapparoli
- Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia
- La Trobe University, Bundoora, Victoria, Australia
| | - Alexander Dobrovic
- University of Melbourne, Melbourne, Victoria, Australia
- Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia
- La Trobe University, Bundoora, Victoria, Australia
| | - Yi-An Ko
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Arthur L. Hsu
- University of Melbourne, Melbourne, Victoria, Australia
| | - Clare J. Love
- University of Melbourne, Melbourne, Victoria, Australia
| | | | - Matthew J. Wakefield
- University of Melbourne, Melbourne, Victoria, Australia
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Orla McNally
- University of Melbourne, Melbourne, Victoria, Australia
- Royal Women’s Hospital, Parkville, Victoria, Australia
| | - Michael Quinn
- Royal Women’s Hospital, Parkville, Victoria, Australia
| | - Sumitra Ananda
- University of Melbourne, Melbourne, Victoria, Australia
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Royal Women’s Hospital, Parkville, Victoria, Australia
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | | | - Anne Hamilton
- University of Melbourne, Melbourne, Victoria, Australia
- Royal Women’s Hospital, Parkville, Victoria, Australia
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Marisa Grossi
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Alison Freimund
- University of Melbourne, Melbourne, Victoria, Australia
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Yada Kanjanapan
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Danny Rischin
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | | | - David Bowtell
- University of Melbourne, Melbourne, Victoria, Australia
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Clare L. Scott
- University of Melbourne, Melbourne, Victoria, Australia
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Royal Women’s Hospital, Parkville, Victoria, Australia
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Michael Christie
- University of Melbourne, Melbourne, Victoria, Australia
- Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Graham R. Taylor
- University of Melbourne, Melbourne, Victoria, Australia
- King’s College London, London, United Kingdom
| | - Linda Mileshkin
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
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Doig KD, Ellul J, Fellowes A, Thompson ER, Ryland G, Blombery P, Papenfuss AT, Fox SB. Canary: an atomic pipeline for clinical amplicon assays. BMC Bioinformatics 2017; 18:555. [PMID: 29246107 PMCID: PMC5732437 DOI: 10.1186/s12859-017-1950-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 11/22/2017] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND High throughput sequencing requires bioinformatics pipelines to process large volumes of data into meaningful variants that can be translated into a clinical report. These pipelines often suffer from a number of shortcomings: they lack robustness and have many components written in multiple languages, each with a variety of resource requirements. Pipeline components must be linked together with a workflow system to achieve the processing of FASTQ files through to a VCF file of variants. Crafting these pipelines requires considerable bioinformatics and IT skills beyond the reach of many clinical laboratories. RESULTS Here we present Canary, a single program that can be run on a laptop, which takes FASTQ files from amplicon assays through to an annotated VCF file ready for clinical analysis. Canary can be installed and run with a single command using Docker containerization or run as a single JAR file on a wide range of platforms. Although it is a single utility, Canary performs all the functions present in more complex and unwieldy pipelines. All variants identified by Canary are 3' shifted and represented in their most parsimonious form to provide a consistent nomenclature, irrespective of sequencing variation. Further, proximate in-phase variants are represented as a single HGVS 'delins' variant. This allows for correct nomenclature and consequences to be ascribed to complex multi-nucleotide polymorphisms (MNPs), which are otherwise difficult to represent and interpret. Variants can also be annotated with hundreds of attributes sourced from MyVariant.info to give up to date details on pathogenicity, population statistics and in-silico predictors. CONCLUSIONS Canary has been used at the Peter MacCallum Cancer Centre in Melbourne for the last 2 years for the processing of clinical sequencing data. By encapsulating clinical features in a single, easily installed executable, Canary makes sequencing more accessible to all pathology laboratories. Canary is available for download as source or a Docker image at https://github.com/PapenfussLab/Canary under a GPL-3.0 License.
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Affiliation(s)
- Kenneth D Doig
- Research Division, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia. .,Department of Pathology, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia. .,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia.
| | - Jason Ellul
- Research Division, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia
| | - Andrew Fellowes
- Department of Pathology, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia
| | - Ella R Thompson
- Department of Pathology, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
| | - Georgina Ryland
- Department of Pathology, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia
| | - Piers Blombery
- Department of Pathology, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia
| | - Anthony T Papenfuss
- Research Division, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, Australia.,Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Stephen B Fox
- Department of Pathology, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia.,Department of Pathology, University of Melbourne, Melbourne, Australia
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Zucca S, Villaraggia M, Gagliardi S, Grieco GS, Valente M, Cereda C, Magni P. Analysis of amplicon-based NGS data from neurological disease gene panels: a new method for allele drop-out management. BMC Bioinformatics 2016; 17:339. [PMID: 28185542 PMCID: PMC5123238 DOI: 10.1186/s12859-016-1189-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Amplicon-based targeted resequencing is a commonly adopted solution for next-generation sequencing applications focused on specific genomic regions. The reliability of such approaches rests on the high specificity and deep coverage, although sequencing artifacts attributable to PCR-like amplification can be encountered. Between these artifacts, allele drop-out, which is the preferential amplification of one allele, causes an artificial increase in homozygosity when heterozygous mutations fall on a primer pairing region. Here, a procedure to manage such artifacts, based on a pipeline composed of two steps of alignment and variant calling, is proposed. This methodology has been compared to the Illumina Custom Amplicon workflow, available on Illumina MiSeq, on the analysis of data obtained with four newly designed TruSeq Custom Amplicon gene panels. RESULTS Four gene panels, specific for Parkinson disease, for Intracerebral Hemorrhage Diseases (COL4A1 and COL4A2 genes) and for Familial Hemiplegic Migraine (CACNA1A and ATP1A2 genes) were designed. A total of 119 samples were re-sequenced with Illumina MiSeq sequencer and panel characterization in terms of coverage, number of variants found and allele drop-out potential impact has been carried out. Results show that 14 % of identified variants is potentially affected by allele drop-out artifacts and that both the Custom Amplicon workflow and the procedure proposed here could correctly identify them. Furthermore, a more complex configuration in presence of two mutations was simulated in silico. In this configuration, our proposed methodology outperforms Custom Amplicon workflow, being able to correctly identify two mutations in all the studied configurations. CONCLUSIONS Allele drop-out plays a crucial role in amplicon-based targeted re-sequencing and specific procedures in data analysis of amplicon data should be adopted. Although a consensus has been established in the elimination of primer sequences from aligned data (e.g., via primer sequence trimming or soft clipping), more complex configurations need to be managed in order to increase the retrieved information from available data. Our method shows how to manage one of these complex configurations, when two mutations occur.
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Affiliation(s)
- Susanna Zucca
- Department of Electrical, Computer and Biomedical engineering, University of Pavia, Pavia, 27100, Italy. .,Center of Genomics and post-Genomics, IRCCS National Institute of Neurology Foundation "C. Mondino", Pavia, 27100, Italy.
| | - Margherita Villaraggia
- Department of Electrical, Computer and Biomedical engineering, University of Pavia, Pavia, 27100, Italy
| | - Stella Gagliardi
- Center of Genomics and post-Genomics, IRCCS National Institute of Neurology Foundation "C. Mondino", Pavia, 27100, Italy
| | - Gaetano Salvatore Grieco
- Center of Genomics and post-Genomics, IRCCS National Institute of Neurology Foundation "C. Mondino", Pavia, 27100, Italy
| | - Marialuisa Valente
- Center of Genomics and post-Genomics, IRCCS National Institute of Neurology Foundation "C. Mondino", Pavia, 27100, Italy
| | - Cristina Cereda
- Center of Genomics and post-Genomics, IRCCS National Institute of Neurology Foundation "C. Mondino", Pavia, 27100, Italy
| | - Paolo Magni
- Department of Electrical, Computer and Biomedical engineering, University of Pavia, Pavia, 27100, Italy
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Park DJ, Li R, Lau E, Georgeson P, Nguyen-Dumont T, Pope BJ. UNDR ROVER - a fast and accurate variant caller for targeted DNA sequencing. BMC Bioinformatics 2016; 17:165. [PMID: 27083325 PMCID: PMC4833922 DOI: 10.1186/s12859-016-1014-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 04/06/2016] [Indexed: 11/24/2022] Open
Abstract
Background Previously, we described ROVER, a DNA variant caller which identifies genetic variants from PCR-targeted massively parallel sequencing (MPS) datasets generated by the Hi-Plex protocol. ROVER permits stringent filtering of sequencing chemistry-induced errors by requiring reported variants to appear in both reads of overlapping pairs above certain thresholds of occurrence. ROVER was developed in tandem with Hi-Plex and has been used successfully to screen for genetic mutations in the breast cancer predisposition gene PALB2. ROVER is applied to MPS data in BAM format and, therefore, relies on sequence reads being mapped to a reference genome. In this paper, we describe an improvement to ROVER, called UNDR ROVER (Unmapped primer-Directed ROVER), which accepts MPS data in FASTQ format, avoiding the need for a computationally expensive mapping stage. It does so by taking advantage of the location-specific nature of PCR-targeted MPS data. Results The UNDR ROVER algorithm achieves the same stringent variant calling as its predecessor with a significant runtime performance improvement. In one indicative sequencing experiment, UNDR ROVER (in its fastest mode) required 8-fold less sequential computation time than the ROVER pipeline and 13-fold less sequential computation time than a variant calling pipeline based on the popular GATK tool. UNDR ROVER is implemented in Python and runs on all popular POSIX-like operating systems (Linux, OS X). It requires as input a tab-delimited format file containing primer sequence information, a FASTA format file containing the reference genome sequence, and paired FASTQ files containing sequence reads. Primer sequences at the 5′ end of reads associate read-pairs with their targeted amplicon and, thus, their expected corresponding coordinates in the reference genome. The primer-intervening sequence of each read is compared against the reference sequence from the same location and variants are identified using the same algorithm as ROVER. Specifically, for a variant to be ‘called’ it must appear at the same location in both of the overlapping reads above user-defined thresholds of minimum number of reads and proportion of reads. Conclusions UNDR ROVER provides the same rapid and accurate genetic variant calling as its predecessor with greatly reduced computational costs.
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Affiliation(s)
- Daniel J Park
- Genetic Epidemiology Laboratory, School of Biomedical Sciences, Medical Building, The University of Melbourne, Melbourne, Victoria, 3010, Australia.,Victorian Life Sciences Computation Initiative, The University of Melbourne, Melbourne, Victoria, 3053, Australia
| | - Roger Li
- Department of Computing and Information Systems, The University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Edmund Lau
- Victorian Life Sciences Computation Initiative, The University of Melbourne, Melbourne, Victoria, 3053, Australia
| | - Peter Georgeson
- Victorian Life Sciences Computation Initiative, The University of Melbourne, Melbourne, Victoria, 3053, Australia
| | - Tú Nguyen-Dumont
- Genetic Epidemiology Laboratory, School of Biomedical Sciences, Medical Building, The University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Bernard J Pope
- Department of Computing and Information Systems, The University of Melbourne, Melbourne, Victoria, 3010, Australia. .,Victorian Life Sciences Computation Initiative, The University of Melbourne, Melbourne, Victoria, 3053, Australia.
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Kondrashova O, Love CJ, Lunke S, Hsu AL, Waring PM, Taylor GR. High-Throughput Amplicon-Based Copy Number Detection of 11 Genes in Formalin-Fixed Paraffin-Embedded Ovarian Tumour Samples by MLPA-Seq. PLoS One 2015; 10:e0143006. [PMID: 26569395 PMCID: PMC4646639 DOI: 10.1371/journal.pone.0143006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 10/29/2015] [Indexed: 11/19/2022] Open
Abstract
Whilst next generation sequencing can report point mutations in fixed tissue tumour samples reliably, the accurate determination of copy number is more challenging. The conventional Multiplex Ligation-dependent Probe Amplification (MLPA) assay is an effective tool for measurement of gene dosage, but is restricted to around 50 targets due to size resolution of the MLPA probes. By switching from a size-resolved format, to a sequence-resolved format we developed a scalable, high-throughput, quantitative assay. MLPA-seq is capable of detecting deletions, duplications, and amplifications in as little as 5ng of genomic DNA, including from formalin-fixed paraffin-embedded (FFPE) tumour samples. We show that this method can detect BRCA1, BRCA2, ERBB2 and CCNE1 copy number changes in DNA extracted from snap-frozen and FFPE tumour tissue, with 100% sensitivity and >99.5% specificity.
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Affiliation(s)
- Olga Kondrashova
- Department of Pathology, University of Melbourne, Melbourne, VIC, Australia
| | - Clare J. Love
- Department of Pathology, University of Melbourne, Melbourne, VIC, Australia
| | - Sebastian Lunke
- Department of Pathology, University of Melbourne, Melbourne, VIC, Australia
| | - Arthur L. Hsu
- Department of Pathology, University of Melbourne, Melbourne, VIC, Australia
| | - Australian Ovarian Cancer Study (AOCS) Group
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Centre for Cancer Research, University of Sydney at Westmead Millennium Institute, and Departments of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales, Australia
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Paul M. Waring
- Department of Pathology, University of Melbourne, Melbourne, VIC, Australia
| | - Graham R. Taylor
- Department of Pathology, University of Melbourne, Melbourne, VIC, Australia
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