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Genomic features of lung cancer patients in Indonesia’s National Cancer Center

Hanafi, Arif, Dharmais Cancer Hospital, https://orcid.org/0000-0002-1121-0180
Hanif, Muhammad, Dharmais Cancer Hospital
Pangaribuan, Mariska, Dharmais Cancer Hospital
Ariawan, Wily, Dharmais Cancer Hospital
Sutandyo, Noorwati, Dharmais Cancer Hospital
Kurniawati, Sri, Dharmais Cancer Hospital
Setiawan, Lyana, Dharmais Cancer Hospital
Cahyanti, Dian, Dharmais Cancer Hospital
Rayhani, Farilaila, Dharmais Cancer Hospital
Imelda, Priscillia, Dharmais Cancer Hospital
arif.r.hanafi@gmail.com, priscilliaechi@gmail.com
Published Jan 16, 2024 on Dryad. https://doi.org/10.5061/dryad.1vhhmgr1m

Cite this dataset

Hanafi, Arif et al. (2024). Genomic features of lung cancer patients in Indonesia’s National Cancer Center [Dataset]. Dryad. https://doi.org/10.5061/dryad.1vhhmgr1m

Abstract

Introduction: Advances in molecular biology bring advantages to lung cancer management. Moreover, high-throughput molecular tests are currently useful for revealing genetic variations among lung cancer patients. We investigated the genomics profile of the lung cancer patients at the National Cancer Centre of Indonesia.

Methods: A retrospective study enrolled 627 tissue biopsy samples using real time polymerase chain reaction (RT-PCR) and 80 circulating tumour DNA (ctDNA) liquid biopsy samples using next-generation sequencing (NGS) from lung cancer patients admitted to the Dharmais Cancer Hospital from January 2018 to December 2022. Data were obtained from medical records. Data statistically analysed with p<0.05 is considered significant.

Result: The EGFR test results revealed by RT-PCR were wild type (51.5%), single variant (38.8%), double variant (8.3%), and triple variant (1.4%), with 18.66% L85R, 18.22% Ex19del, and 11.08% L861Q variant. Liquid biopsy ctDNA using NGS showed only 2.5% EGFR wild type, 62.5% single variant and 35% co-variant, with EGFR/TP53 and EGFR/PIK3CA as the highest.

Conclusion: EGFR variants are the most found in our centre. Liquid biopsy with ctDNA using NGS examination could detect broad variants and co-variants that will influence the treatment planning.

README

This README file was generated on 2024-01-13 by Arif Riswahyudi Hanafi

General Information

  1. Title of Dataset:Genomic features of lung cancer patients in Indonesia’s National Cancer Center

  2. Author Information:
    Principal Investigator contact information:
    Name : Arif Riswahyudi Hanafi
    Institution : Dharmais Cancer Hospital, National Cancer Centre, Indonesia
    E-mail : arif.r.hanafi@gmail.com

  3. Date of data collection:2018-2022

  4. Geographic location of data collection:Indonesia

  5. Funding sources that support the collection of data:No funding

Data & File Overview

  1. File list:
    A) final_data_genomic_features_lung_cancer_indonesia.xlsx
    B) README.md

  2. Relationship between files, if important: None

  3. Additional related data collected that was not included in the current data package: None

  4. Are there multiple versions of the dataset? No

Data Specific information

for: final_data_genomic_features_lung_cancer_indonesia.xlsx

Sheet 1: PCR
1. Number of variables : 6
2. Number of rows : 628
3. Variable List:
* patient_code : code for all patients included in the study (coded randomly)
* age_range : patients'age categorize based on age range (0-39; 40-60; >60)
* sex : patient's sex (0= male; 1= female)
* diagnosis : patient's diagnosis when was included in the study (1= adenocarcinoma; 2= squamous cell carcinoma (SCC); 3= other non-small cell lung carcinoma (NSCLC); 4= small cell lung carcinoma (SCLC))
* smoking status: patient's smoking status (0= non-smoker; 1=smoker/passive smoker)
* result : genomic result based on the test (WT= wild-type; other results is written based on HGNC)
4. Missing data codes: None
5. Specialized formats or other abbreviations used: None

Sheet 2: NGS
1. Number of variables : 6
2. Number of rows : 81
3. Variable List:
* patient_code : code for all patients included in the study (coded randomly)
* age_range : patients'age categorize based on age range (0-39; 40-60; >60)
* sex : patient's sex (0= male; 1= female)
* diagnosis : patient's diagnosis when was included in the study (1= adenocarcinoma; 2= squamous cell carcinoma (SCC); 3= other non-small cell lung carcinoma (NSCLC); 4= small cell lung carcinoma (SCLC))
* smoking status: patient's smoking status (0= non-smoker; 1=smoker/passive smoker)
* result : genomic result based on the test (WT= wild-type; other genomic results is written based on HGNC)
4. Missing data codes: None
5. Specialized formats or other abbreviations used: None

Sharing/Access Information

  1. Licenses/restrictions placed on the data: CC0 1.0 Universal (CC0 1.0) Public Domain

  2. Links to publications that cite or use the data: Hanafi, AR et al. (2023). Genomic features of lung cancer patients in Indonesia’s National Cancer Center. BMC Pulmonary Medicine

  3. Links to other publicly accessible locations of the data: None

  4. Links/relationships to ancillary data sets: None

  5. Was data derived from another source? No

  6. Recommended citation for this dataset: Hanafi, Arif et al. (2024). Genomic features of lung cancer patients in Indonesia’s National Cancer Center [Dataset]. Dryad. https://doi.org/10.5061/dryad.1vhhmgr1m

Methods

The genomics data are secondary data from third-party company (a collaborative laboratory with Dharmais Cancer Hospital), while other data are extracted from medical records from the hospital database.