Abstract

Introduction: Next-generation sequencing (NGS) has paved the way for precision oncology in oncology clinics today. With rapidly advancing therapeutics, it is becoming increasingly important to obtain information about the molecular milieu of a patient's tumor. However, reporting and interpreting of NGS is fraught with complexity and variability. To understand the questions surrounding NGS reporting in India, we conducted a survey.

Objectives: The aim of this study was to assess the gaps in NGS reporting and interpretation in Indian medical oncology clinics.

Materials and Methods: An anonymized 10-question survey-based study among Indian medical oncologists through Google forms was conducted between October 4 and 8, 2022.

Results: The sample size was n = 58. Seventy-one percent felt there was heterogeneity in NGS reporting, 72%-were unaware of NGS reporting guidelines, and 62%-did not feel the need for a molecular scientist assist in NGS interpretation. Almost all (98%) felt there was a need for uniform NGS reporting as well as an Indian NGS repository and data-sharing system (93%).

Conclusion: Our survey highlights the need for a uniform national guideline concerning NGS reporting.

Introduction

Precision medicine or personalized medicine uses molecular diagnostics to guide diagnosis and prognosis and to offer individualized therapy based on the presence of somatic and/or germline genetic alterations.[1] Next-generation sequencing (NGS) allows for multiple parallel sequencing of the whole genome, exome, or a targeted gene panel in a short time span. This has propelled the use of precision medicine in oncology clinics today with an unprecedented speed.[2] The relevance of NGS in the management of malignancy continues to grow with the advent of tissue-agnostic therapy.[3] However, there are multiple limitations to the purported benefits of utilizing NGS in clinical practice—difficulty in the interpretation of complex reports, lack of validation, sensitivity and specificity of reported results, relevance to variants detected, continuously evolving data, identifying fusions and indels, and the high cost of NGS. Tumor heterogeneity and adequate tissue material remain an added challenge. Once a proven targetable mutation is detected, access to costly drug and lack of clinical trials in India create an unnecessary, uncomfortable situation for the patients and their doctors.[4] [5]

To counteract these limitations, organizations have developed guidelines, from correct processing of the tissue samples to methods of validation and establishing controls to proper ways to compile an NGS report so that it is easier to apply in clinical settings.[6] [7] [8] [9] To understand the real-world challenges medical oncologists face in the country, we planned a short survey.

Materials and Methods

We conducted an anonymized survey-based study among Indian medical oncologists. Practicing medical oncologists were questioned regarding their views on NGS reporting and its applicability in day-to-day practice. The survey consisted of 10 questions, with yes/no ± maybe as options for 7 questions; 1 was on a Likert format of graded responses, and 2 were open-ended. Details of the survey are depicted in [Table 1].

| Fig 1 : Pie chart showing the distributions of answers to Questions 2 and 7.

While the majority (62%) did not feel the need for a molecular scientist to interpret an NGS report, overwhelmingly, 98%-felt an unfulfilled need for uniform NGS reporting. When asked if there was a “need for uniformity, accountability and quality assurance of NGS procedure and reporting in India,” 97%-responded in the affirmative. Similarly, almost all (93%) agreed that India should have an NGS repository and data-sharing system ([Fig. 2]).

| Figure 2: Bar diagram depicting answers to survey questions 3, 4, 6, 8, and 9.

About 40%-felt helpless when NGS reports suggest a therapy inaccessible to their patients ([Fig. 1]).

The final question asked the participants what parameters they would like to include in NGS reporting. The responses included suggestions such as a quality check, an explicit depiction of the method used, depth of reading, the number of reads, number of genes covered, tumor content, variant allele frequency and variants of unknown significance, allele frequency, actionable mutations and available drugs as well as incidence and available data of uncommon mutations, the tier of the mutations, fusions and whether RNA is used for checking them, tumor mutational burden with microsatellite instability, both RNA and DNA sequencing, mutations with prognostic implications, lab accreditation details, the platform used, haplotype map utilization for limits of detection, whether it is validated and compared to standard, and reporting in the context of the primary tumor diagnosis. Incorporation of the option of a certified genetic counsellor for both pre- and posttest counselling was also suggested.

Discussion

There is a pressing requirement for standardization of NGS reporting, validation of existing tests against a gold standard, and formalizing a set of recommendations per tumor site. Furthermore, the interpretation of a positive result, its applicability to a particular patient, and the ramifications of cost are essential concerns.

The promise of precision medicine comes from specific therapies tailored to the genomic landscape of a patient's tumor, the growing successful avenues of tumor-agnostic therapy,[3] [10] the favorable toxicity and better outcome profile of targeted therapy that act on oncogenic drivers,[11] and the indubitable success of immunotherapy.[12] However, this arena is clouded with uncertainty and limitations.[13] Even among oncologists using NGS routinely, the confidence to correctly interpret reports is low to moderate.[14] This partly stems from the continuously evolving body of literature surrounding genetic alterations—what is a “variant of unknown significance” today may be a targetable mutation tomorrow. In addition, many abnormalities identified in tumor DNA are often also seen in normal cells, which do not progress to a malignant state.[15] Furthermore, the detection of fusions and genetic aberrations affecting introns are complex and, many times, require additional RNA-based NGS.

A sizeable self-reported survey in 2018 by Freedman et al revealed that 75%-of oncologists use NGS in routine clinical practice, with younger age of the physician, setting of an academic center, access to genomic training, and molecular-based tumor boards predicting greater usage. Compared with our study, in which 62%-did not feel the need for a molecular scientist to interpret the NGS report, 49%-in the study by Freedman et al had no difficulty in comprehending NGS reports.[13]

An important aspect of the applicability of NGS reporting is the financial burden of testing and the action that can be taken if a positive result is obtained. The ESMO/ESCAT guidelines address this issue. They have recommended NGS testing in only certain malignancies, such as lung adenocarcinoma, cholangiocarcinoma, and prostate cancer, where testing by NGS is more financially sound than other methods of molecular testing. On the other hand, for colon cancer, NGS is suggested as an alternative to polymerase chain reaction testing. The ESMO guidelines further have divided the possible genetic alterations into priority levels, labelled as tiers, which help guide management.[9] [16]

In contrast to most developing countries, India is one of the few nations contributing to genomic research and development significantly.[17] The unique health care model of India with the availability of approved generic drugs,[18] both government and privatized health care, emerging indigenous techniques of NGS, and the rapidly developing science of precision medicine all culminate in a strong message for the need for standardized NGS reporting guidelines, a sentiment shared by 98%-of our responders. Most of our participants felt the need for an Indian repository (93%). There is a need for a repository consisting of Indian variants of known and unknown targets to identify and address ethnic differences, as large international databases such as The Cancer Genome Atlas (TCGA) have largely underrepresented the Asian and African populations.[19] [20]

Our study has certain limitations of small sample size and lack of demographic data and predictive factors impacting results, being an anonymized questionnaire. However, it is the first survey of its kind to be conducted in our country that have taken the questions of importance to the community and academic oncologist alike.

Conclusion

To conclude, our study has highlighted the imminent need of a national-level protocol to be established for the clinical application of genomic data to optimize patient care.

Conflict of Interest

None declared.

Acknowledgment

We thank all medical oncologists who participated in the survey.

Author Contribution:

Neha Pathak: intellectual content, literature search, manuscript preparation, manuscript writing, and manuscript review.

Anu R. I.: concept, design, intellectual content, data acquisition, data analysis, and statistical analysis.

Padmaj Kulkarni: design, manuscript editing, and manuscript review.

Amol Patel: concept, design, intellectual content, data acquisition, data analysis, statistical analysis, literature search, and manuscript review.

References

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1. Conway JR, Warner JL, Rubinstein WS, Miller RS. Next-generation sequencing and the clinical oncology workflow: data challenges, proposed solutions, and a call to action. JCO Precis Oncol 2019; 3 (03) 1-10
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2. Seligson ND, Knepper TC, Ragg S, Walko CM. Developing drugs for tissue-agnostic indications: a paradigm shift in leveraging cancer biology for precision medicine. Clin Pharmacol Ther 2021; 109 (02) 334-342
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3. Morganti S, Tarantino P, Ferraro E. et al. Complexity of genome sequencing and reporting: next generation sequencing (NGS) technologies and implementation of precision medicine in real life. Crit Rev Oncol Hematol 2019; 133: 171-182
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4. Xuan J, Yu Y, Qing T, Guo L, Shi L. Next-generation sequencing in the clinic: promises and challenges. Cancer Lett 2013; 340 (02) 284-295
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5. Weiss MM, Van der Zwaag B, Jongbloed JDH. et al. Best practice guidelines for the use of next-generation sequencing applications in genome diagnostics: a national collaborative study of Dutch genome diagnostic laboratories. Hum Mutat 2013; 34 (10) 1313-1321
   CrossrefPubMedGoogle Scholar
6. Hatanaka Y, Kuwata T, Morii E. et al. The Japanese Society of Pathology Practical Guidelines on the handling of pathological tissue samples for cancer genomic medicine. Pathol Int 2021; 71 (11) 725-740
   CrossrefPubMedGoogle Scholar
7. 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
   CrossrefPubMedGoogle Scholar
8. Mosele F, Remon J, Mateo J. et al. Recommendations for the use of next-generation sequencing (NGS) for patients with metastatic cancers: a report from the ESMO Precision Medicine Working Group. Ann Oncol 2020; 31 (11) 1491-1505
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9. Subbiah V, Wolf J, Konda B. et al. Tumour-agnostic efficacy and safety of selpercatinib in patients with RET fusion-positive solid tumours other than lung or thyroid tumours (LIBRETTO-001): a phase 1/2, open-label, basket trial. Lancet Oncol 2022; 23 (10) 1261-1273
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11. Esfahani K, Roudaia L, Buhlaiga N, Del Rincon SV, Papneja N, Miller Jr WH. A review of cancer immunotherapy: from the past, to the present, to the future. Curr Oncol 2020; 27 (Suppl. 02) S87-S97
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12. Freedman AN, Klabunde CN, Wiant K. et al. Use of next-generation sequencing tests to guide cancer treatment: results from a nationally representative survey of oncologists in the United States. JCO Precis Oncol 2018; 2 (02) 1-13
    CrossrefPubMedGoogle Scholar
13. Gray SW, Park ER, Najita J. et al. Oncologists' and cancer patients' views on whole-exome sequencing and incidental findings: results from the CanSeq study. Genet Med 2016; 18 (10) 1011-1019
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14. Kennedy SR, Zhang Y, Risques RA. Cancer-associated mutations but no cancer: insights into the early steps of carcinogenesis and implications for early cancer detection. Trends Cancer 2019; 5 (09) 531-540
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15. Mateo J, Chakravarty D, Dienstmann R. et al. A framework to rank genomic alterations as targets for cancer precision medicine: the ESMO Scale for Clinical Actionability of molecular Targets (ESCAT). Ann Oncol 2018; 29 (09) 1895-1902
    CrossrefPubMedGoogle Scholar
16. Helmy M, Awad M, Mosa KA. Limited resources of genome sequencing in developing countries: challenges and solutions. Appl Transl Genomics 2016; 9: 15-19
    CrossrefPubMedGoogle Scholar
17. George T, Baliga MS. Generic anticancer drugs of the Jan Aushadhi scheme in India and their branded counterparts: the first cost comparison study. Cureus 2021; 13 (11) e19231
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18. Bentley AR, Callier S, Rotimi CN. Diversity and inclusion in genomic research: why the uneven progress?. J Community Genet 2017; 8 (04) 255-266
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19. Pemmasani SK, Raman R, Mohapatra R, Vidyasagar M, Acharya A. A review on the challenges in Indian genomics research for variant identification and interpretation. Front Genet 2020; 11: 753

| Fig 1 : Pie chart showing the distributions of answers to Questions 2 and 7.

| Figure 2: Bar diagram depicting answers to survey questions 3, 4, 6, 8, and 9.

References

Ginsburg GS, Phillips KA. Precision medicine: from science to value. Health Aff (Millwood) 2018; 37 (05) 694-701
CrossrefPubMedGoogle Scholar
1. Conway JR, Warner JL, Rubinstein WS, Miller RS. Next-generation sequencing and the clinical oncology workflow: data challenges, proposed solutions, and a call to action. JCO Precis Oncol 2019; 3 (03) 1-10
   CrossrefPubMedGoogle Scholar
2. Seligson ND, Knepper TC, Ragg S, Walko CM. Developing drugs for tissue-agnostic indications: a paradigm shift in leveraging cancer biology for precision medicine. Clin Pharmacol Ther 2021; 109 (02) 334-342
   CrossrefPubMedGoogle Scholar
3. Morganti S, Tarantino P, Ferraro E. et al. Complexity of genome sequencing and reporting: next generation sequencing (NGS) technologies and implementation of precision medicine in real life. Crit Rev Oncol Hematol 2019; 133: 171-182
   CrossrefPubMedGoogle Scholar
4. Xuan J, Yu Y, Qing T, Guo L, Shi L. Next-generation sequencing in the clinic: promises and challenges. Cancer Lett 2013; 340 (02) 284-295
   CrossrefPubMedGoogle Scholar
5. Weiss MM, Van der Zwaag B, Jongbloed JDH. et al. Best practice guidelines for the use of next-generation sequencing applications in genome diagnostics: a national collaborative study of Dutch genome diagnostic laboratories. Hum Mutat 2013; 34 (10) 1313-1321
   CrossrefPubMedGoogle Scholar
6. Hatanaka Y, Kuwata T, Morii E. et al. The Japanese Society of Pathology Practical Guidelines on the handling of pathological tissue samples for cancer genomic medicine. Pathol Int 2021; 71 (11) 725-740
   CrossrefPubMedGoogle Scholar
7. 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
   CrossrefPubMedGoogle Scholar
8. Mosele F, Remon J, Mateo J. et al. Recommendations for the use of next-generation sequencing (NGS) for patients with metastatic cancers: a report from the ESMO Precision Medicine Working Group. Ann Oncol 2020; 31 (11) 1491-1505
   CrossrefPubMedGoogle Scholar
9. Subbiah V, Wolf J, Konda B. et al. Tumour-agnostic efficacy and safety of selpercatinib in patients with RET fusion-positive solid tumours other than lung or thyroid tumours (LIBRETTO-001): a phase 1/2, open-label, basket trial. Lancet Oncol 2022; 23 (10) 1261-1273
   CrossrefPubMedGoogle Scholar
10. Hendriks LE, Kerr KM, Menis J. et al; ESMO Guidelines Committee. Electronic address: clinicalguidelines@esmo.org. Oncogene-addicted metastatic non-small-cell lung cancer: ESMO Clinical Practice Guideline for diagnosis, treatment and follow-up. Ann Oncol 2023; 34 (04) 339-357
    CrossrefPubMedGoogle Scholar
11. Esfahani K, Roudaia L, Buhlaiga N, Del Rincon SV, Papneja N, Miller Jr WH. A review of cancer immunotherapy: from the past, to the present, to the future. Curr Oncol 2020; 27 (Suppl. 02) S87-S97
    CrossrefPubMedGoogle Scholar
12. Freedman AN, Klabunde CN, Wiant K. et al. Use of next-generation sequencing tests to guide cancer treatment: results from a nationally representative survey of oncologists in the United States. JCO Precis Oncol 2018; 2 (02) 1-13
    CrossrefPubMedGoogle Scholar
13. Gray SW, Park ER, Najita J. et al. Oncologists' and cancer patients' views on whole-exome sequencing and incidental findings: results from the CanSeq study. Genet Med 2016; 18 (10) 1011-1019
    CrossrefPubMedGoogle Scholar
14. Kennedy SR, Zhang Y, Risques RA. Cancer-associated mutations but no cancer: insights into the early steps of carcinogenesis and implications for early cancer detection. Trends Cancer 2019; 5 (09) 531-540
    CrossrefPubMedGoogle Scholar
15. Mateo J, Chakravarty D, Dienstmann R. et al. A framework to rank genomic alterations as targets for cancer precision medicine: the ESMO Scale for Clinical Actionability of molecular Targets (ESCAT). Ann Oncol 2018; 29 (09) 1895-1902
    CrossrefPubMedGoogle Scholar
16. Helmy M, Awad M, Mosa KA. Limited resources of genome sequencing in developing countries: challenges and solutions. Appl Transl Genomics 2016; 9: 15-19
    CrossrefPubMedGoogle Scholar
17. George T, Baliga MS. Generic anticancer drugs of the Jan Aushadhi scheme in India and their branded counterparts: the first cost comparison study. Cureus 2021; 13 (11) e19231
    PubMedGoogle Scholar
18. Bentley AR, Callier S, Rotimi CN. Diversity and inclusion in genomic research: why the uneven progress?. J Community Genet 2017; 8 (04) 255-266
    CrossrefPubMedGoogle Scholar
19. Pemmasani SK, Raman R, Mohapatra R, Vidyasagar M, Acharya A. A review on the challenges in Indian genomics research for variant identification and interpretation. Front Genet 2020; 11: 753