Abstract 5746
Background
The next-generation sequencing (NGS) technology has increased the number of genes and types of genomic alterations detectable by a high-throughput assay and has become an essential part of clinical decision-making. We aimed to verify the analytical specifications of TruSight™ Tumor 170 (TST170, Illumina Inc.) panel for detecting 5% variant allele frequency (VAF) and reliable amplifications (copy number variants, CNVs) for ensuring high quality of sequencing results.
Methods
We use well-characterized human cancer cell lines mixtures with known specific gene mutations to evaluate the specifications given by TST170 and defined thresholds for each type of genomic alterations intended to detect. We performed the following mixing studies by using the lung adenocarcinoma cell lines H1975 and H1299 to acquired proportions: 100%, 33%, 10% and 2% H1975. H1975 harbors EGFR p.Thr790Met (c.2369C>T), p.Leu858Arg (c.2573T>G), TP53 p.Arg273His (c.818G>A), CDKN2A p.Glu69Ter (c.205G>T) and PIK3CA p.Gly118Asp (c.353G>A). H1299 harbors an EGFR, CDKN2A, PIK3CA wild type and a homozygous partial deletion of the TP53 gene. We extracted DNA and performed NGS TST170 analysis with each diluted sample.
Results
When we calculated the correlation between the expected and observed VAFs by linear regression analysis, the coefficient of determination was 0.99 in hotspot NSCLC genes. This result further supports the reliability of this system for variant identification. Mutations with a low VAF (<5%) were identified in half of the mutations and all mutations with >5% VAF were detected without exception. In the CNV analysis, the number of copies seen in the undiluted cell line (100% H1975) were found in all 33% dilution cases, in one third of the 10% dilution cases and in no case in the 2% dilution, independently of undiluted cell line fold changes.
Conclusions
Our analytical verification determines the ability of TST170 pipeline to detect 5% VAF with high confidence and CNVs in samples of tumor purity at 33% or more.
Clinical trial identification
Editorial acknowledgement
Legal entity responsible for the study
The authors.
Funding
Has not received any funding.
Disclosure
All authors have declared no conflicts of interest.
Resources from the same session
4868 - Evaluation of markers associated with efficacy of abiraterone acetate plus prednisone (AAP) in patients (pts) with castration-sensitive prostate cancer (mCSPC) from the LATITUDE study
Presenter: Kim Chi
Session: Poster Display session 3
Resources:
Abstract
4837 - LRP2, a potential new biomarker for Chinese younger aged intrahepatic cholangiocarcinoma patients
Presenter: Xiaoliang Shi
Session: Poster Display session 3
Resources:
Abstract
1286 - Reanalysis of the efficacy of molecular targeted agents (MTAs) given in the randomized trial SHIVA01 according to the ESMO ESCAT scale of actionability
Presenter: Aurelie Moreira
Session: Poster Display session 3
Resources:
Abstract
2736 - Comparison of Platforms for Determining Tumor Mutational Burden (TMB) From Blood Samples in Patients With Non-Small Cell Lung Cancer (NSCLC)
Presenter: Jonathan Baden
Session: Poster Display session 3
Resources:
Abstract
5045 - Comprehensive Pan-Cancer analysis of somatic mutations in drug transporters to reveal acquired and intrinsic drug resistance in 3149 metastatic cancer patients
Presenter: Sander Bins
Session: Poster Display session 3
Resources:
Abstract
4577 - Pan-Cancer Genomic Landscape of the Cyclin D1/FGF3,4,19 (11q13) Amplicon Including Associations with HPV Status, and ESR1 and AR Alterations
Presenter: Jennifer Johnson
Session: Poster Display session 3
Resources:
Abstract
5366 - Co-occurrence of NTRK fusions with other genomic biomarkers in cancer patients
Presenter: Xiaolong Jiao
Session: Poster Display session 3
Resources:
Abstract
4084 - Prospective comparative study of next-generation sequencing on fine needle aspirations versus core needle biopsies in cancer patients included in SHIVA02 trial
Presenter: Julien Masliah-Planchon
Session: Poster Display session 3
Resources:
Abstract
6017 - First national External Quality Assessement for the interpretation of somatic variants: assessment of 25 variants in colorectal, lung, ovarian cancers and melanoma in France
Presenter: Etienne Rouleau
Session: Poster Display session 3
Resources:
Abstract
2283 - Prospective testing of circulating tumor DNA in metastatic breast cancer facilitates clinical trial enrollment and precision oncology
Presenter: Andjelija Bujak
Session: Poster Display session 3
Resources:
Abstract