Uniform Reporting of Next Generation Sequencing: Indian Society of Medical and Pediatric Oncology

Abstract

Introduction

Molecular oncology is the cornerstone for diagnosis, treatment, prognosis, and screening of individuals who present to an oncology clinic. The integration of molecular diagnostic techniques with therapeutic management of patients has resulted in unique biomarker development and improved clinical endpoints. Amongst all laboratory diagnostic techniques applied in oncology, next generation sequencing (NGS) of nucleic acids holds cardinal merit in the present day. Multi-omic biomarkers are the mainstay of selecting variation-specific targeted therapy and immunotherapy. Hence, it is essential to utilise the right diagnostic techniques and harmonize their reporting accurately against rigorous quality standards.

Objectives

We aimed to develop a consensus technical standard guideline on quality assurance and reporting of genetic tests that influence clinical decision making in oncology.

Materials and Methods

Under the initiative of Indian Society of Medical and Pediatric Oncology (ISMPO), a working group of national and international subject matter experts including clinicians, scientists, and bioinformaticians was formulated in 2022. Published scientific literature and laboratory technical standards were studied by this panel and a document for the Indian molecular oncology sector was drawn after obtaining consensus on every recommendation from all members of the working group.

Results

Guidelines for introducing uniformity in NGS reporting have been developed by a working group comprising of country's leading molecular oncologists, geneticists, and molecular pathologists alongside international experts, under the aegis of the Indian Society of Medical and Pediatric Oncology.

Conclusion

The proposed guidelines and recommendations are intended to be used as a framework to standardize NGS reporting across India, which in turn will enable clinicians and allied healthcare professionals to make informed decisions for unparalleled patient care.

Keywords

molecular oncology - next generation sequencing (NGS) - liquid biopsy - AMP-ASCO-CAP - ACMG - ESMO - ESCAT

Note

This document has been prepared with contributions from the members of the working committee and in accordance with a consensus on the guidelines presented herewith.

Authors' Contributions

A.R.I.: Conceptualization, manuscript writing, and editing.

A.P.: Conceptualization, Manuscript editing.

A.C.: Manuscript writing.

H.S.: Manuscript writing.

V.V.: Manuscript writing.

M.S.: Manuscript writing.

N.P.: Manuscript writing.

A.D.: Manuscript writing and editing.

A.S.: Manuscript writing and editing.

Others: Manuscript editing.

Patient's Consent

Patient consent is not required for the article as patient data was not used or patients recruited for this technical standards document.

^* Co-first authors.

^# Co-corresponding authors.

Publication History

Article published online:
21 March 2025

• Bibliography

• 1 ACMG Technical Standards for Clinical Genetics Laboratories (2021 Revision) [Internet]. [cited 2025 Mar 3]. Available from: https://www.acmg.net/ACMG/Medical-Genetics-Practice-Resources/Genetics_Lab_Standards/ACMG/Medical-Genetics-Practice-Resources/Genetics_Lab_Standards.aspx?hkey=0e473683-3910-420c-9efb-958707c59589
• 2 den Dunnen JT, Dalgleish R, Maglott DR. et al. HGVS recommendations for the description of sequence variants: 2016 update. Hum Mutat 2016; 37 (06) 564-569
• 3 Bruford EA, Braschi B, Denny P, Jones TEM, Seal RL, Tweedie S. Guidelines for human gene nomenclature. Nat Genet 2020; 52 (08) 754-758
• 4 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
• 5 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
• 6 Sanchez-Vega F, Mina M, Armenia J. et al; Cancer Genome Atlas Research Network. Oncogenic signaling pathways in the cancer genome atlas. Cell 2018; 173 (02) 321-337.e10
• 7 Clinical laboratory improvement amendments (CLIA). Cdc.gov. 2023. Accessed June 19, 2022 at: https://www.cdc.gov/clia/index.html
• 8 Chougule A, Jagtap V, Nikam A. et al. Comprehensive development and implementation of good laboratory practice for NGS based targeted panel on solid tumor FFPE tissues in diagnostics. Diagnostics (Basel) 2022; 12 (05) 1291
• 9 Jäger N. Bioinformatics workflows for clinical applications in precision oncology. Semin Cancer Biol 2022; 84: 103-112
• 10 Siegmund SE, Manning DK, Davineni PK, Dong F. Deriving tumor purity from cancer next generation sequencing data: applications for quantitative ERBB2 (HER2) copy number analysis and germline inference of BRCA1 and BRCA2 mutations. Mod Pathol 2022; 35 (10) 1458-1467
• 11 Devereaux KA, Souers RJ, Graham RP. et al. Neoplastic cellularity assessment in molecular testing. Arch Pathol Lab Med 2022; 146 (09) 1062-1071
• 12 Kofanova O, Bellora C, Garcia Frasquilho S. et al. Standardization of the preanalytical phase of DNA extraction from fixed tissue for next-generation sequencing analyses. N Biotechnol 2020; 54: 52-61
• 13 Lone SN, Nisar S, Masoodi T. et al. Liquid biopsy: a step closer to transform diagnosis, prognosis and future of cancer treatments. Mol Cancer 2022; 21 (01) 79
• 14 Illumina.pvt Tech notes.Quality Scores for Next-Generation Sequencing Assessing sequencing accuracy using Phred quality scoring. Available at: https://www.illumina.com/documents/products/technotes/technote_Q-Scores.pdf
• 15 NCI dictionary of Cancer Terms [Internet]. National Cancer Institute. 2011. Accessed June 19, 2023 at: https://www.cancer.gov/publications/dictionaries/cancer-terms/def/tumor-mutational-burden
• 16 Lawlor RT, Mattiolo P, Mafficini A. et al. Tumor mutational burden as a potential biomarker for immunotherapy in pancreatic cancer: systematic review and still-open questions. Cancers (Basel) 2021; 13 (13) 3119
• 17 NCI dictionary of Cancer Terms. National Cancer Institute. 2011. Accessed June 19, 2023 at: https://www.cancer.gov/publications/dictionaries/cancer-terms/def/msi
• 18 Li K, Luo H, Huang L, Luo H, Zhu X. Microsatellite instability: a review of what the oncologist should know. Cancer Cell Int 2020; 20: 16
• 19 Stewart MD, Merino Vega D, Arend RC. et al. Homologous recombination deficiency: concepts, definitions, and assays. Oncologist 2022; 27 (03) 167-174
• 20 NCI dictionary of Cancer Terms. National Cancer Institute. 2011. Accessed June 19, 2023 at: https://www.cancer.gov/publications/dictionaries/cancer-terms/def/variant-of-uncertain-significance
• 21 Education MCL. Selecting pathology specimens for solid tumors next-generation sequencing. Insights. 2020. Accessed June 19, 2023 at: https://news.mayocliniclabs.com/2020/02/03/selecting-pathology-specimens-for-solid-tumors-next-generation-sequencing/
• 22 Viray H, Li K, Long TA. et al. A prospective, multi-institutional diagnostic trial to determine pathologist accuracy in estimation of percentage of malignant cells. Arch Pathol Lab Med 2013; 137 (11) 1545-1549
• 23 Portier BP, Wang Z, Downs-Kelly E. et al. Delay to formalin fixation ‘cold ischemia time’: effect on ERBB2 detection by in-situ hybridization and immunohistochemistry. Mod Pathol 2013; 26 (01) 1-9
• 24 Hunt JL. Molecular pathology in anatomic pathology practice: a review of basic principles. Arch Pathol Lab Med 2008; 132 (02) 248-260
• 25 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
• 26 Scheuner MT, Hilborne L, Brown J, Lubin IM. members of the RAND Molecular Genetic Test Report Advisory Board. A report template for molecular genetic tests designed to improve communication between the clinician and laboratory. Genet Test Mol Biomarkers 2012; 16 (07) 761-769
• 27 Lubin IM, McGovern MM, Gibson Z. et al. Clinician perspectives about molecular genetic testing for heritable conditions and development of a clinician-friendly laboratory report. J Mol Diagn 2009; 11 (02) 162-171
• 28 Lubin IM, Caggana M, Constantin C. et al. Ordering molecular genetic tests and reporting results: practices in laboratory and clinical settings. J Mol Diagn 2008; 10 (05) 459-468
• 29 Rehm HL, Bale SJ, Bayrak-Toydemir P. et al; Working Group of the American College of Medical Genetics and Genomics Laboratory Quality Assurance Commitee. ACMG clinical laboratory standards for next-generation sequencing. Genet Med 2013; 15 (09) 733-747
• 30 Sorber L, Zwaenepoel K, Jacobs J. et al. Specialized blood collection tubes for liquid biopsy: improving the pre-analytical conditions. Mol Diagn Ther 2020; 24 (01) 113-124
• 31 Ascierto PA, Bifulco C, Palmieri G, Peters S, Sidiropoulos N. Preanalytic variables and tissue stewardship for reliable next-generation sequencing (NGS) clinical analysis. J Mol Diagn 2019; 21 (05) 756-767
• 32 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
• 33 McKenna A, Hanna M, Banks E. et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 2010; 20 (09) 1297-1303
• 34 DePristo MA, Banks E, Poplin R. et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 2011; 43 (05) 491-498
• 35 Van der Auwera GA, Carneiro MO, Hartl C. et al. From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline. Curr Protoc Bioinformatics 2013;43(1110):10.1, 33
• 36 Poplin R, Ruano-Rubio V, DePristo MA. et al. Scaling accurate genetic variant discovery to tens of thousands of samples. bioRxiv. 2017. Available from: http://dx.doi.org/10.1101/201178
• 37 Van Der Auwera GO, Connor BD. Genomics in the Cloud: Using Docker, GATK, and WDL in Terra. Sebastopol, CA: O'Reilly Media; 2020
• 38 Einaga N, Yoshida A, Noda H. et al. Assessment of the quality of DNA from various formalin-fixed paraffin-embedded (FFPE) tissues and the use of this DNA for next-generation sequencing (NGS) with no artifactual mutation. PLoS One 2017; 12 (05) e0176280
• 39 Department of Biotechnology Ministry of Science & Technology. 2019. Biological data storage, access and sharing policy of India, Government of India. Accessed June 19, 2023 at: https://dbtindia.gov.in/sites/default/files/Draft1-Biological_Data_Policy.pdf
• 40 Siu LL, Lawler M, Haussler D. et al. Facilitating a culture of responsible and effective sharing of cancer genome data. Nat Med 2016; 22 (05) 464-471
• 41 van der Velde KJ, Singh G, Kaliyaperumal R. et al. FAIR Genomes metadata schema promoting Next Generation Sequencing data reuse in Dutch healthcare and research. Sci Data 2022; 9 (01) 169
• 42 Cdc.gov. Accessed June 19, 2023 at: https://www.cdc.gov/lab-quality/php/ngs-quality-initiative/ and https://www.cdc.gov/cliac/docs/november-2021/8a_cdc-ngs-rfi_comment-analysis-report.pdf
• 43 Kinjo S, Monma N, Misu S. et al. Maser: one-stop platform for NGS big data from analysis to visualization. Database (Oxford) 2018; 2018 (01) bay027