Comprehensive genomic profiling reveals a unique genomic landscape in solid tumors in an Indian cancer cohort of 1000 patients: a single institutional experience
Abstract The use of Comprehensive Genomic Profiling (CGP) in clinical practice to detect broad-spectrum therapeutic, prognostic, and predictive biomarkers, including tumor mutational burden (TMB), microsatellite instability (MSI), somatic BRCA (sBRCA) and other homologous recombination repair genes...
Saved in:
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2025-04-01
|
| Series: | Scientific Reports |
| Subjects: | |
| Online Access: | https://doi.org/10.1038/s41598-025-94762-z |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1849737770018275328 |
|---|---|
| author | Mithua Ghosh Sheela Mysore Lingaraju Krishna C.R Gautam Balaram Ramya Kodandapani Vijay E Vijay K Suhas N Devika H Shekar Patil Satheesh Chiradoni Thungappa Somorat Bhattacharjee Sridhar P.S Roshni Dasgupta Mohammed Naseer Srinivas B.J Vishal Rao Veena Ramaswamy Radheshyam Naik Govind Babu Aarthi Ravichandran Urvashi Bahadur Krithika Murugan Mahesh B Lohith Reddy Ajaikumar Basavalinga S |
| author_facet | Mithua Ghosh Sheela Mysore Lingaraju Krishna C.R Gautam Balaram Ramya Kodandapani Vijay E Vijay K Suhas N Devika H Shekar Patil Satheesh Chiradoni Thungappa Somorat Bhattacharjee Sridhar P.S Roshni Dasgupta Mohammed Naseer Srinivas B.J Vishal Rao Veena Ramaswamy Radheshyam Naik Govind Babu Aarthi Ravichandran Urvashi Bahadur Krithika Murugan Mahesh B Lohith Reddy Ajaikumar Basavalinga S |
| author_sort | Mithua Ghosh |
| collection | DOAJ |
| description | Abstract The use of Comprehensive Genomic Profiling (CGP) in clinical practice to detect broad-spectrum therapeutic, prognostic, and predictive biomarkers, including tumor mutational burden (TMB), microsatellite instability (MSI), somatic BRCA (sBRCA) and other homologous recombination repair genes (HRRs) provides a more cost-efficient and tissue-preserving approach than serial single-biomarker analysis. A total of 1000 biopsy-proven cancer patients at the HCG cancer center were profiled in an IRB-approved prospective study. The findings were discussed in the multidisciplinary molecular tumor board (MTB), and recommendations were documented in electronic medical records (EMRs) for clinical management and follow-up. A total of 1747 genomic alterations were detected (mean 1.7 mutations/sample), with 80% of patients having genetic alterations with therapeutic and prognostic implications (Tier I-32%, Tier II-50%). CGP revealed a greater number of druggable genes (47%) than did small panels (14%). Tumor-agnostic markers for immunotherapy (IO) were observed in 16% of the current cohort, based on which IO was initiated. In 13.5% of the cohort, alterations in the HRR pathway including sBRCA (5.5%) were detected providing an option for treatment with platinum or PARP inhibitors. Other significant alterations included those in EGFR, KRAS/BRAF, PIK3CA, cKIT, PDGFRA, ARID1A, ARID2, and FGFR. RNA sequencing revealed 55 + RNA alterations, including those in TMPRSS-ERG, RPS6KB1-VMP1, EML4-ALK, NTRK, PDGFRA and EWSR. Clinical outcome data were available via EMR for 618 patients (62%), out of whom 419 patients had druggable mutations (67%; 95% CI 88.9–93.9%) and 39 patients had 1 or more mutations with prognostic implications. However, only 200 patients (44%; 95% CI 39.1–48.1%) were included in the MTB discussion. Based on genomics reports, the treatment regimen was changed for 137 and 61 patients with and without clinical inputs from the MTB, respectively. The overall change in therapy based on CGP in the clinical cohort was 43%, which was greater in patients enrolled for MTB than in patients who had not undergone MTB. At the interim analysis, with a median follow-up of 18 months (range 12–24 months) after the change in therapy as per genomics report, 97 patients (71%) were found to be alive thus establishing the importance of CGP and MTB in personalized genomics-driven treatment. |
| format | Article |
| id | doaj-art-c2571d7cfb484ca1aef66bdbaa9bbfd0 |
| institution | DOAJ |
| issn | 2045-2322 |
| language | English |
| publishDate | 2025-04-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj-art-c2571d7cfb484ca1aef66bdbaa9bbfd02025-08-20T03:06:49ZengNature PortfolioScientific Reports2045-23222025-04-0115111710.1038/s41598-025-94762-zComprehensive genomic profiling reveals a unique genomic landscape in solid tumors in an Indian cancer cohort of 1000 patients: a single institutional experienceMithua Ghosh0Sheela Mysore Lingaraju1Krishna C.R2Gautam Balaram3Ramya Kodandapani4Vijay E5Vijay K6Suhas N7Devika H8Shekar Patil9Satheesh Chiradoni Thungappa10Somorat Bhattacharjee11Sridhar P.S12Roshni Dasgupta13Mohammed Naseer14Srinivas B.J15Vishal Rao16Veena Ramaswamy17Radheshyam Naik18Govind Babu19Aarthi Ravichandran20Urvashi Bahadur21Krithika Murugan22Mahesh B23Lohith Reddy24Ajaikumar Basavalinga S25Triesta Sciences, A Unit of HeathCare Global Enterprises LimitedTriesta Sciences, A Unit of HeathCare Global Enterprises LimitedTriesta Sciences, A Unit of HeathCare Global Enterprises LimitedTriesta Sciences, A Unit of HeathCare Global Enterprises LimitedTriesta Sciences, A Unit of HeathCare Global Enterprises LimitedTriesta Sciences, A Unit of HeathCare Global Enterprises LimitedTriesta Sciences, A Unit of HeathCare Global Enterprises LimitedTriesta Sciences, A Unit of HeathCare Global Enterprises LimitedTriesta Sciences, A Unit of HeathCare Global Enterprises LimitedHealthCare Global Enterprises LimitedHealthCare Global Enterprises LimitedHealthCare Global Enterprises LimitedHealthCare Global Enterprises LimitedHealthCare Global Enterprises LimitedHealthCare Global Enterprises LimitedHealthCare Global Enterprises LimitedHealthCare Global Enterprises LimitedTriesta Sciences, A Unit of HeathCare Global Enterprises LimitedHealthCare Global Enterprises LimitedHealthCare Global Enterprises LimitedStrand Life SciencesStrand Life SciencesHealthCare Global Enterprises LimitedHealthCare Global Enterprises LimitedHealthCare Global Enterprises LimitedHealthCare Global Enterprises LimitedAbstract The use of Comprehensive Genomic Profiling (CGP) in clinical practice to detect broad-spectrum therapeutic, prognostic, and predictive biomarkers, including tumor mutational burden (TMB), microsatellite instability (MSI), somatic BRCA (sBRCA) and other homologous recombination repair genes (HRRs) provides a more cost-efficient and tissue-preserving approach than serial single-biomarker analysis. A total of 1000 biopsy-proven cancer patients at the HCG cancer center were profiled in an IRB-approved prospective study. The findings were discussed in the multidisciplinary molecular tumor board (MTB), and recommendations were documented in electronic medical records (EMRs) for clinical management and follow-up. A total of 1747 genomic alterations were detected (mean 1.7 mutations/sample), with 80% of patients having genetic alterations with therapeutic and prognostic implications (Tier I-32%, Tier II-50%). CGP revealed a greater number of druggable genes (47%) than did small panels (14%). Tumor-agnostic markers for immunotherapy (IO) were observed in 16% of the current cohort, based on which IO was initiated. In 13.5% of the cohort, alterations in the HRR pathway including sBRCA (5.5%) were detected providing an option for treatment with platinum or PARP inhibitors. Other significant alterations included those in EGFR, KRAS/BRAF, PIK3CA, cKIT, PDGFRA, ARID1A, ARID2, and FGFR. RNA sequencing revealed 55 + RNA alterations, including those in TMPRSS-ERG, RPS6KB1-VMP1, EML4-ALK, NTRK, PDGFRA and EWSR. Clinical outcome data were available via EMR for 618 patients (62%), out of whom 419 patients had druggable mutations (67%; 95% CI 88.9–93.9%) and 39 patients had 1 or more mutations with prognostic implications. However, only 200 patients (44%; 95% CI 39.1–48.1%) were included in the MTB discussion. Based on genomics reports, the treatment regimen was changed for 137 and 61 patients with and without clinical inputs from the MTB, respectively. The overall change in therapy based on CGP in the clinical cohort was 43%, which was greater in patients enrolled for MTB than in patients who had not undergone MTB. At the interim analysis, with a median follow-up of 18 months (range 12–24 months) after the change in therapy as per genomics report, 97 patients (71%) were found to be alive thus establishing the importance of CGP and MTB in personalized genomics-driven treatment.https://doi.org/10.1038/s41598-025-94762-zComprehensive genomic profilingNext-generation sequencingPrecision oncologyTargeted therapyImmunotherapyMultidisciplinary molecular tumor board |
| spellingShingle | Mithua Ghosh Sheela Mysore Lingaraju Krishna C.R Gautam Balaram Ramya Kodandapani Vijay E Vijay K Suhas N Devika H Shekar Patil Satheesh Chiradoni Thungappa Somorat Bhattacharjee Sridhar P.S Roshni Dasgupta Mohammed Naseer Srinivas B.J Vishal Rao Veena Ramaswamy Radheshyam Naik Govind Babu Aarthi Ravichandran Urvashi Bahadur Krithika Murugan Mahesh B Lohith Reddy Ajaikumar Basavalinga S Comprehensive genomic profiling reveals a unique genomic landscape in solid tumors in an Indian cancer cohort of 1000 patients: a single institutional experience Scientific Reports Comprehensive genomic profiling Next-generation sequencing Precision oncology Targeted therapy Immunotherapy Multidisciplinary molecular tumor board |
| title | Comprehensive genomic profiling reveals a unique genomic landscape in solid tumors in an Indian cancer cohort of 1000 patients: a single institutional experience |
| title_full | Comprehensive genomic profiling reveals a unique genomic landscape in solid tumors in an Indian cancer cohort of 1000 patients: a single institutional experience |
| title_fullStr | Comprehensive genomic profiling reveals a unique genomic landscape in solid tumors in an Indian cancer cohort of 1000 patients: a single institutional experience |
| title_full_unstemmed | Comprehensive genomic profiling reveals a unique genomic landscape in solid tumors in an Indian cancer cohort of 1000 patients: a single institutional experience |
| title_short | Comprehensive genomic profiling reveals a unique genomic landscape in solid tumors in an Indian cancer cohort of 1000 patients: a single institutional experience |
| title_sort | comprehensive genomic profiling reveals a unique genomic landscape in solid tumors in an indian cancer cohort of 1000 patients a single institutional experience |
| topic | Comprehensive genomic profiling Next-generation sequencing Precision oncology Targeted therapy Immunotherapy Multidisciplinary molecular tumor board |
| url | https://doi.org/10.1038/s41598-025-94762-z |
| work_keys_str_mv | AT mithuaghosh comprehensivegenomicprofilingrevealsauniquegenomiclandscapeinsolidtumorsinanindiancancercohortof1000patientsasingleinstitutionalexperience AT sheelamysorelingaraju comprehensivegenomicprofilingrevealsauniquegenomiclandscapeinsolidtumorsinanindiancancercohortof1000patientsasingleinstitutionalexperience AT krishnacr comprehensivegenomicprofilingrevealsauniquegenomiclandscapeinsolidtumorsinanindiancancercohortof1000patientsasingleinstitutionalexperience AT gautambalaram comprehensivegenomicprofilingrevealsauniquegenomiclandscapeinsolidtumorsinanindiancancercohortof1000patientsasingleinstitutionalexperience AT ramyakodandapani comprehensivegenomicprofilingrevealsauniquegenomiclandscapeinsolidtumorsinanindiancancercohortof1000patientsasingleinstitutionalexperience AT vijaye comprehensivegenomicprofilingrevealsauniquegenomiclandscapeinsolidtumorsinanindiancancercohortof1000patientsasingleinstitutionalexperience AT vijayk comprehensivegenomicprofilingrevealsauniquegenomiclandscapeinsolidtumorsinanindiancancercohortof1000patientsasingleinstitutionalexperience AT suhasn comprehensivegenomicprofilingrevealsauniquegenomiclandscapeinsolidtumorsinanindiancancercohortof1000patientsasingleinstitutionalexperience AT devikah comprehensivegenomicprofilingrevealsauniquegenomiclandscapeinsolidtumorsinanindiancancercohortof1000patientsasingleinstitutionalexperience AT shekarpatil comprehensivegenomicprofilingrevealsauniquegenomiclandscapeinsolidtumorsinanindiancancercohortof1000patientsasingleinstitutionalexperience AT satheeshchiradonithungappa comprehensivegenomicprofilingrevealsauniquegenomiclandscapeinsolidtumorsinanindiancancercohortof1000patientsasingleinstitutionalexperience AT somoratbhattacharjee comprehensivegenomicprofilingrevealsauniquegenomiclandscapeinsolidtumorsinanindiancancercohortof1000patientsasingleinstitutionalexperience AT sridharps comprehensivegenomicprofilingrevealsauniquegenomiclandscapeinsolidtumorsinanindiancancercohortof1000patientsasingleinstitutionalexperience AT roshnidasgupta comprehensivegenomicprofilingrevealsauniquegenomiclandscapeinsolidtumorsinanindiancancercohortof1000patientsasingleinstitutionalexperience AT mohammednaseer comprehensivegenomicprofilingrevealsauniquegenomiclandscapeinsolidtumorsinanindiancancercohortof1000patientsasingleinstitutionalexperience AT srinivasbj comprehensivegenomicprofilingrevealsauniquegenomiclandscapeinsolidtumorsinanindiancancercohortof1000patientsasingleinstitutionalexperience AT vishalrao comprehensivegenomicprofilingrevealsauniquegenomiclandscapeinsolidtumorsinanindiancancercohortof1000patientsasingleinstitutionalexperience AT veenaramaswamy comprehensivegenomicprofilingrevealsauniquegenomiclandscapeinsolidtumorsinanindiancancercohortof1000patientsasingleinstitutionalexperience AT radheshyamnaik comprehensivegenomicprofilingrevealsauniquegenomiclandscapeinsolidtumorsinanindiancancercohortof1000patientsasingleinstitutionalexperience AT govindbabu comprehensivegenomicprofilingrevealsauniquegenomiclandscapeinsolidtumorsinanindiancancercohortof1000patientsasingleinstitutionalexperience AT aarthiravichandran comprehensivegenomicprofilingrevealsauniquegenomiclandscapeinsolidtumorsinanindiancancercohortof1000patientsasingleinstitutionalexperience AT urvashibahadur comprehensivegenomicprofilingrevealsauniquegenomiclandscapeinsolidtumorsinanindiancancercohortof1000patientsasingleinstitutionalexperience AT krithikamurugan comprehensivegenomicprofilingrevealsauniquegenomiclandscapeinsolidtumorsinanindiancancercohortof1000patientsasingleinstitutionalexperience AT maheshb comprehensivegenomicprofilingrevealsauniquegenomiclandscapeinsolidtumorsinanindiancancercohortof1000patientsasingleinstitutionalexperience AT lohithreddy comprehensivegenomicprofilingrevealsauniquegenomiclandscapeinsolidtumorsinanindiancancercohortof1000patientsasingleinstitutionalexperience AT ajaikumarbasavalingas comprehensivegenomicprofilingrevealsauniquegenomiclandscapeinsolidtumorsinanindiancancercohortof1000patientsasingleinstitutionalexperience |