CC BY-NC-ND 4.0 · Indian J Med Paediatr Oncol 2021; 42(03): 221-228
DOI: 10.1055/s-0041-1732854
Mini-Review Article

Moving Next-Generation Sequencing into the Clinic

Omshree Shetty
1   Division of Molecular Pathology, Department of Pathology, Tata Memorial Centre, Homi Bhabha National Institute, Mumbai, Maharashtra, India
,
Mamta Gurav
1   Division of Molecular Pathology, Department of Pathology, Tata Memorial Centre, Homi Bhabha National Institute, Mumbai, Maharashtra, India
,
Prachi Bapat
1   Division of Molecular Pathology, Department of Pathology, Tata Memorial Centre, Homi Bhabha National Institute, Mumbai, Maharashtra, India
,
Nupur Karnik
2   Department of Pathology, Tata Memorial Centre, Homi Bhabha National Institute, Mumbai, Maharashtra, India
,
Gauri Wagh
2   Department of Pathology, Tata Memorial Centre, Homi Bhabha National Institute, Mumbai, Maharashtra, India
,
Trupti Pai
2   Department of Pathology, Tata Memorial Centre, Homi Bhabha National Institute, Mumbai, Maharashtra, India
,
Sridhar Epari
2   Department of Pathology, Tata Memorial Centre, Homi Bhabha National Institute, Mumbai, Maharashtra, India
,
Sangeeta Desai
2   Department of Pathology, Tata Memorial Centre, Homi Bhabha National Institute, Mumbai, Maharashtra, India
› Author Affiliations

Abstract

With an advancement in the field of molecular diagnostics, there has been a profound evolution in the testing modalities, especially in the field of oncology. In the past decade, sequencing technology has evolved drastically with the advent of high-throughput next-generation sequencing (NGS). Subsequently, the single-gene tests have been replaced by multigene panel-based assays, deep sequencing, massively parallel whole genome, whole-exome sequencing, and so on. NGS has provided molecular diagnostics professionals a wonderful tool to explore and unearth the genetic alterations, underpinning the pathophysiology of the disease. However, this development has posed new challenges which consist of the following; understanding the technology, types of platforms available, various sequencing strategies, bioinformatics and data analysis algorithm, reporting of various variants, and validation of assays and overall for developing NGS assay for clinical utility. The challenges involved sometimes impede development of these high-end assays in laboratories. The present article provides a broad overview of our journey in setting up the NGS assay in a molecular pathology laboratory at a tertiary care oncology center. We hereby describe various important points and steps to be followed while working on the NGS setup, right from its inception to final drafting of the reports, with inclusion of various validation steps. We aim at providing a beginner’s guide to set up NGS assays in the laboratory using recommended best practices and various international guidelines.



Publication History

Article published online:
21 September 2021

© 2021. Indian Society of Medical and Paediatric Oncology. This is an open access article published by Thieme under the terms of the Creative Commons Attribution-NonDerivative-NonCommercial-License, permitting copying and reproduction so long as the original work is given appropriate credit. Contents may not be used for commercial purposes, or adapted, remixed, transformed or built upon. (https://creativecommons.org/licenses/by-nc-nd/4.0/).

Thieme Medical and Scientific Publishers Private Ltd.
A-12, Second Floor, Sector -2, NOIDA -201301, India

 
  • References

  • 1 Shen T, Pajaro-Van de Stadt SH, Yeat NC, Lin JC-H. Clinical applications of next generation sequencing in cancer: from panels, to exomes, to genomes. Front Genet 2015; 6: 215
  • 2 Richards S, Aziz N, Bale S. et al ACMG Laboratory Quality Assurance Committee. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med 2015; 17 (05) 405-424
  • 3 Xu J, Gong B, Wu L, Thakkar S, Hong H, Tong W. Comprehensive assessments of RNA-seq by the SEQC consortium: FDA-led efforts advance precision medicine. Pharmaceutics 2016; 8 (01) E8
  • 4 Zhang X, Liang Z, Wang S. et al Application of next-generation sequencing technology to precision medicine in cancer: joint consensus of the Tumor Biomarker Committee of the Chinese Society of Clinical Oncology. Cancer Biol Med 2019; 16 (01) 189-204
  • 5 Cheng DT, Mitchell TN, Zehir A. et al Memorial sloan kettering- integrated mutation profiling of actionable cancer targets (MSK-IMPACT): A hybridization capture-based next-generation sequencing clinical assay for solid tumor molecular oncology. J Mol Diagn 2015; 17 (03) 251-264
  • 6 Jennings LJ, Arcila ME, Corless C. et al Guidelines for validation of next-generation sequencing-based oncology panels: a joint consensus recommendation of the Association for Molecular Pathology and College of American Pathologists. J Mol Diagn 2017; 19 (03) 341-365
  • 7 Richards S, Aziz N, Bale S. et al Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med 2015; 17 (05) 405-424
  • 8 Li MM, Datto M, Duncavage EJ. et al Standards and guidelines for the interpretation and reporting of sequence variants in cancer: a joint consensus recommendation of the Association for Molecular Pathology, American Society of Clinical Oncology, and College of American Pathologists. J Mol Diagn 2017; 19 (01) 4-23
  • 9 Aziz N, Zhao Q, Bry L. et al College of American Pathologists’ laboratory standards for next-generation sequencing clinical tests. Arch Pathol Lab Med 2015; 139 (04) 481-493
  • 10 El-Deiry WS, Goldberg RM, Lenz HJ. et al The current state of molecular testing in the treatment of patients with solid tumors, 2019. CA Cancer J Clin 2019; 69 (04) 305-343
  • 11 Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 2010; 26 (05) 589-595
  • 12 Roy S, Coldren C, Karunamurthy A. et al Standards and guidelines for validating next-generation sequencing bioinformatics pipelines: a joint recommendation of the Association for Molecular Pathology and the College of American Pathologists. J Mol Diagn 2018; 20 (01) 4-27
  • 13 Larson DE, Harris CC, Chen K. et al SomaticSniper: identification of somatic point mutations in whole genome sequencing data. Bioinformatics 2012; 28 (03) 311-317
  • Garrison E, Marth G. Haplotype-based variant detection from short-read sequencing. Available at: https://arxiv.org/pdf/1207.3907.pdf. Accessed June 29, 2021
  • 15 Schrijver I, Farkas DH, Gibson JS, Lyon E. AMP Executive Committee. The evolving role of the laboratory professional in the age of genome sequencing: a vision of the association for molecular pathology. J Mol Diagn 2015; 17 (04) 335-338
  • 16 Eijkelenboom A, Tops BB, van den Berg A. et al Recommendations for the clinical interpretation and reporting of copy number gains using gene panel NGS analysis in routine diagnostics. Virchows Arch 2019; 474 (06) 673-680
  • 17 Gulley LM, Braziel RM, Halling KC. et al Molecular Pathology Resource Committee, College of American Pathologists. Clinical laboratory reports in molecular pathology. Arch Pathol Lab Med 2007; 131 (06) 852-863
  • 18 Meldrum C, Doyle MA, Tothill RW. Next-generation sequencing for cancer diagnostics: a practical perspective. Clin Biochem Rev 2011; 32 (04) 177-195
  • 19 Luthra R, Chen H, Roy-Chowdhuri S, Singh RR. Next-generation sequencing in clinical molecular diagnostics of cancer: advantages and challenges 2015; 32 (04) 177-195
  • 20 Feldman GL, Schrijver I, Lyon E, Palomaki GE. CAP/ACMG Biochemical and Molecular Genetics Resource Committee. Results of the College of American Pathology/American College of Medical Genetics and Genomics external proficiency testing from 2006 to 2013 for three conditions prevalent in the Ashkenazi Jewish population. Genet Med 2014; 16 (09) 695-702
  • 21 Perera-Bel J, Hutter B, Heining C. et al From somatic variants towards precision oncology: Evidence-driven reporting of treatment options in molecular tumor boards. Genome Med 2018; 10 (01) 18
  • 22 Luchini C, Lawlor RT, Milella M, Scarpa A. Molecular tumor boards in clinical practice. Trends Cancer 2020; 6 (09) 738-744