Detection and analysis of copy number of HER2 gene in breast cancer tissue samples

doi:10.3969/j.issn.1674-8115.2022.11.011

Abstract

Abstract:

Objective ·A copy number detection system of HER2 genes in FFPE samples and plasma samples of breast cancer patients was established by using droplet digital PCR system (ddPCR), and then the performance of the detection system was evaluated to provide a scientific basis for clinical auxiliary diagnosis and treatment. Methods ·To evaluate the detection system, 12 tissue samples of breast cancer patients and 4 paired plasma samples were collected from the Department of General Surgery, Jiading District Central Hospital, Shanghai University of Medicine & Health Sciences from January 2020 to June 2021. In the same period, 24 plasma samples of healthy volunteers and 77 tissue sections of breast cancer patients were collected to extract nucleic acids, to establish limit of blank (LoB) and performance evaluation of detection system respectively. The detection system was designed and screened, and subsequently LoB, precision, sensitivity and linear range were also evaluated. We used next generation sequencing (NGS) to verify the consistency of ddPCR detection system, and compared the accuracy of the detection system with fluorescence in-situ hybridization (IHC)/immunohistochemistry (FISH) gold standard method. χ ² test and matched samples t-test were used for comparison of quantitative data. Poisson probability function was used to analyze the blank detection limit of the system, the coefficient of variation (CV) was used to evaluate the sensitivity and precision, and linear regression correlation coefficient ( R ² ) was used to evaluate the linear range. Results ·The ddPCR platform was used to establish the quantitative and amplification detection system of HER2 gene copy number in tissue section DNA of breast cancer patients. Compared with the results of tissue nucleic acid and plasma free nucleic acid samples detected by NGS method, the correlation coefficient of copy number detection results was 0.987, and the consistency of amplification was 100%. The intra assay precision and inter assay precision of the evaluation system were 6.8% and 9.4%, respectively. The sensitivity was 1 ng and the linearity was good ( R²>0.98). Compared with the traditional IHC/FISH method, the sensitivity and specificity were 84.6% (95% CI 64.3%~95.0%) and 76.5% (95% CI 62.2%~86.8%), Kappa was 0.57, and the consistency rate was 79.2%. Conclusion ·A copy number detection system for HER2 in breast cancer patients is established by using ddPCR platform, with good consistency in clinical detection, providing auxiliary means for the diagnosis, treatment and prognosis of breast cancer patients.

Key words: breast cancer, formalin-fixed paraffin embedded (FFPE), plasma, droplet digital PCR (ddPCR), HER2 copy number

CLC Number:

R446.1

SUN Yameng, MA Ye, GUO Runsheng. Detection and analysis of copy number of HER2 gene in breast cancer tissue samples[J]. Journal of Shanghai Jiao Tong University (Medical Science), 2022, 42(11): 1589-1597.

Figures/Tables 12

TrendMD

References 25

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Gene	Forword primer （5′→3′）	Reverse primer （5′→3′）	Probe sequence （5′→3′）
HER2	TCACTCATATCCTCCTCTTTCTGC	AATTTTCACATTCTCCCCATCAG	FAM-CAGGGCATCTGGATC-MGB
EIF2C1	GCTGCTAGGCTTTCCTGTTC	GCCTATTTTCCTGCATCTTCT	HEX-AGGCCCCAAAACCCTAAAC-MGB

Gene	Forword primer （5′→3′）	Reverse primer （5′→3′）	Probe sequence （5′→3′）
HER2	TCACTCATATCCTCCTCTTTCTGC	AATTTTCACATTCTCCCCATCAG	FAM-CAGGGCATCTGGATC-MGB
EIF2C1	GCTGCTAGGCTTTCCTGTTC	GCCTATTTTCCTGCATCTTCT	HEX-AGGCCCCAAAACCCTAAAC-MGB

Sample	Detection System 1			BC-HER2-2019
Sample	HER2 gene copy number （copies）	Reference gene copy number （copies）	Copy amplification ［（ HER2/Reference）］×2	HER2 gene copy number （copies）	Reference gene copy number （copies）	Copy amplification ［（ HER2/Reference）］×2
HV-1	2 400	3 600	1.33	3 180	3 200	1.99
HV-2	2 150	3 450	1.25	3 050	3 100	1.97
HV-3	2 600	3 700	1.41	3 200	3 280	2.05

Sample	Detection System 1			BC-HER2-2019
Sample	HER2 gene copy number （copies）	Reference gene copy number （copies）	Copy amplification ［（ HER2/Reference）］×2	HER2 gene copy number （copies）	Reference gene copy number （copies）	Copy amplification ［（ HER2/Reference）］×2
HV-1	2 400	3 600	1.33	3 180	3 200	1.99
HV-2	2 150	3 450	1.25	3 050	3 100	1.97
HV-3	2 600	3 700	1.41	3 200	3 280	2.05

Sample No.	Concentration/（ng·μL ^-1）	HER2 Gene copy	Sample No.	Concentration/（ng·μL ^-1）	HER2 Gene copy
1	0.44	1.80	13	0.21	2.24
2	0.19	2.20	14	0.10	2.20
3	0.54	2.08	15	0.16	2.22
4	0.26	2.01	16	0.10	1.20
5	0.95	2.58	17	0.38	2.37
6	0.62	2.00	18	0.13	1.87
7	0.23	2.90	19	0.49	1.99
8	0.29	2.27	20	0.32	1.62
9	0.32	1.99	21	0.10	2.40
10	0.21	2.28	22	0.24	1.75
11	0.23	2.08	23	0.19	2.19
12	0.38	2.17	24	0.74	1.69