Research on high-throughput detection of plasma cell-free DNA for targeted therapy-related genes screening and prognosis prediction in non-small cell lung cancer patients

Qiling DENG; Di SONG; Kexin XI; Xiaoting XIE; Xiaoyan WU; Wei ZHAO

doi:10.19401/j.cnki.1007-3639.2025.04.003

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Research on high-throughput detection of plasma cell-free DNA for targeted therapy-related genes screening and prognosis prediction in non-small cell lung cancer patients

Article | 更新时间：2025-12-31

- Research on high-throughput detection of plasma cell-free DNA for targeted therapy-related genes screening and prognosis prediction in non-small cell lung cancer patients
- China Oncology Vol. 35, Issue 4, Pages: 355-364(2025)
- 作者机构：
  
  1. 华南恶性肿瘤防治全国重点实验室，广东省恶性肿瘤临床医学研究中心，中山大学肿瘤防治中心分子诊断科，广东广州 510060
  2. 南方医科大学广东省热带病研究重点实验室BSL-3实验室，广东广州 510515
- 作者简介：
- 基金信息：
  
  Science and Technology Project of Guangdong Province(2021B1212030014)
- DOI：10.19401/j.cnki.1007-3639.2025.04.003
  CLC：
- Received：21 January 2025，
  
  Revised：2025-05-28，
  
  Published：30 April 2025
- 稿件说明：
移动端阅览
Qiling DENG, Di SONG, Kexin XI, et al. Research on high-throughput detection of plasma cell-free DNA for targeted therapy-related genes screening and prognosis prediction in non-small cell lung cancer patients[J]. China Oncology, 2025, 35(4): 355-364.
DOI：

Qiling DENG, Di SONG, Kexin XI, et al. Research on high-throughput detection of plasma cell-free DNA for targeted therapy-related genes screening and prognosis prediction in non-small cell lung cancer patients[J]. China Oncology, 2025, 35(4): 355-364. DOI： 10.19401/j.cnki.1007-3639.2025.04.003.

摘要

背景与目的：

肿瘤患者血浆游离DNA（cell-free DNA，cfDNA）高通量检测广泛用于肿瘤靶向治疗相关基因的筛选。本研究探讨cfDNA中Ⅰ类及Ⅱ类靶向治疗相关基因变异类型及数量与非小细胞肺癌（non-small cell lung cancer，NSCLC）患癌预后的关系。

方法：

收集2021年—2023年在中山大学肿瘤防治中心进行血浆cfDNA高通量测序项目的NSCLC患者的测序结果及临床资料，并对入组患者从2021年6月1日采集血浆当天开始截至2024年5月27日进行生存随访，并使用GraphPad Prism 8.0及SPSS Statistics 25.0对患者生存期与临床资料及测序结果中Ⅰ类与Ⅱ类靶向治疗相关基因类型及数目进行单因素及多因素统计学分析（伦理批号：B2024-359-01）。

结果：

313例NSCLC患者中确诊时分期Ⅰ期25例（7.98%）、Ⅱ期20例（6.39%）、Ⅲ期38例（12.14%）和Ⅳ期230例（73.48%）；组内NSCLC分型包含腺癌（90.10%），鳞癌（5.11%），大细胞癌（2.87%）及其他分型（1.92%）；入组的NSCLC患者血浆cfDNA中Ⅰ类与Ⅱ类靶向治疗相关基因数及占比分别为：0个（25.24%）、1个（17.57%）、2个（19.17%）、3个（14.38%）、4个（8.31%）、5个及以上（15.34%）。患者血浆cfDNA高通量测序检测结果中，突变频率最高的3个基因分别为

EGFR

、

TP53

、

ERBB2

基因，其中

EGFR

基因突变频率为36.04%，

TP53

基因突变频率为30.63%，

ERBB2

基因突变频率为4.95%。患者生存期不仅与热点靶向基因表达情况相关，与血浆cfDNA高通量测序中Ⅰ类和Ⅱ类靶向相关位点基因变异个数也呈正相关。经过治疗后无靶向治疗相关基因的位点变异比有靶向治疗相关基因的位点变异的患者的生存期长，死亡风险可降低63.2%。而单纯一个基因位点变异比多个驱动基因位点变异的患者的生存期长，死亡风险更低，所测得的Ⅰ类及Ⅱ类靶向治疗药物在3个基因数以内

，基因数目越少，患者的生存期越长。

结论：

血浆cfDNA高通量测序中Ⅰ类和Ⅱ类靶向相关位点基因变异个数对经过治疗后的NSCLC患者的生存期有影响。血浆cfDNA高通量测序检测可作为患者预后的评估指标。

Abstract

Background and purpose:

High-throughput detection of plasma cell-free DNA (cfDNA) is widely used for multi-cancer targeted therapy drug screening

and this study investigated the relationship between the type and number of plasma cfDNA class Ⅰ and Ⅱ targeted therapy-related gene variants and cancer survival in patients with non-small cell lung cancer (NSCLC).

Methods:

The sequencing results and clinical data of NSCLC patients who underwent tumor plasma cfDNA high-throughput sequencing projects in Sun Yat-sen University Cancer Center from 2021 to 2023 were collected. The survival follow-up of enrolled patients was carried out from the day of plasma collection on June 1

2021 to May 27

2024

and GraphPad Prism 8.0 and SPSS Statistics 25.0 were used. Univariate and multivariate statistical analyses were conducted on the types and numbers of class Ⅰ and class Ⅱ targeted therapy-related genes in the survival and clinical data of patients and sequencing results (Ethical approval: B2024-359-01).

Results:

A total of 313 patients included in this study with NSCLC were categorized into stage Ⅰ 25 patients (7.98%)

stage Ⅱ 20 patients (6.39%)

stage Ⅲ 38patients (12.14%)

and stage Ⅳ 230 patients (73.48%). Pathological diagnosis results showed that adenocarcinoma accounted for 90.10%

squamous cell carcinoma accounted for 5.11%

large cell carcinoma accounted for 2.87% and other classifications accounted for 1.92%. The number and the percentage of class Ⅰ and class Ⅱ targeted therapy drug-related genes in the plasma cfDNA NSCLC patients were 0 (25.24%)

1 (17.57%)

2 (19.17%)

3 (14.38%)

4 (8.31%)

and 5 or more (15.34%). The results of statistical analysis showed that 3 genes with the highest mutation frequencies were

EGFR

TP53

and

ERBB2

and the muta

tion frequency of

EGFR

gene was 36.04%. The mutation frequency of

TP53

gene was 30.63%. The mutation frequency of

ERBB2

gene was 4.95%. The survival time of patients is related to not only the expression of hotspot targeted genes

but also the number of class Ⅰ and Ⅱ target-related gene variants detected by plasma cfDNA high-throughput sequencing. The survival time of the patients with no targeted therapy-related locus variants after treatment was longer compares with targeted therapy-related locus variants

which can reduce the risk of death by 63.2%. However

patients with a single gene locus variant had longer survival time and lower risk of death than those with multiple driver locus variants

and the measured class Ⅰ and Ⅱ targeted therapy drugs were within 3 genes. Overall

the smaller the number of genes

the longer the survival.

Conclusions:

The number of class Ⅰ and class Ⅱ targeted therapy-related gene variants in plasma cfDNA high-throughput sequencing also has an effect on the survival of patients after treatment. Plasma cfDNA level detected by high-throughput sequencing could be a prognostic factor for the NSCLC patients.

关键词

Keywords

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