PMID- 32621174 OWN - NLM STAT- MEDLINE DCOM- 20210621 LR - 20210621 IS - 1532-2807 (Electronic) IS - 1219-4956 (Print) IS - 1219-4956 (Linking) VI - 26 IP - 4 DP - 2020 Oct TI - Evaluation of Next Generation Sequencing for Detecting HER2 Copy Number in Breast and Gastric Cancers. PG - 2577-2585 LID - 10.1007/s12253-020-00844-w [doi] AB - Amplicon-based next generation sequencing (NGS) approaches have been preferentially adopted by the clinical laboratories on the basis of a short turnaround time (TAT) and small DNA input needs. However, little work has been done to assess the amplicon-based NGS methods for copy number variation (CNV) detection in comparison with current standard methods like immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH). The correlation between NGS based CNV detection and the later standard methods has remained unexplored. We developed an amplicon-based panel to detect human epidermal receptor growth factor (HER2) amplification in formalin-fixed paraffin-embedded (FFPE) tumor tissue samples from 280 breast cancer and 50 gastric cancer patients. Assessment by IHC and FISH was conducted in parallel, and descriptive statistics were used to assess the concordance. The copy number detected by NGS was correlated with either the average HER2 copy number (signals/cell) (r = 0.844; p < 0.001) or the HER2/CEP17 ratio (r = 0.815; p < 0.001). We determined a cut-off value for NGS to categorize HER2 amplification status by using 151 HER2 non-amplified FFPE samples. In breast cancer patients, the cut-off value was 2.910, with 95.35%, 98.67% and 97.29% sensitivity, specificity and concordance, respectively. However, this cut-off value displayed low sensitivity in gastric cancer patients (64.71%), and the following macrodissection procedure was not effective for increasing sensitivity (57.14%). Evaluation of HER2 copy number with NGS in our study was comparable with IHC and FISH in breast cancer patients, but concordance in gastric cancer was only moderate. The greater discordance in gastric cancer may reflect the underlying biological mechanisms, and further study is warranted. NGS-based HER2 assessment may decrease the equivocal HER2 determinations in breast cancer patients assessed by FISH/IHC. FAU - Niu, Dongfeng AU - Niu D AD - Department of Pathology, Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China. FAU - Li, Lei AU - Li L AD - Beijing Novogene Bioinformatics Technology Co., Ltd, Beijing, China. FAU - Yu, Yang AU - Yu Y AD - Beijing Novogene Bioinformatics Technology Co., Ltd, Beijing, China. FAU - Zang, Wanchun AU - Zang W AD - Beijing Novogene Bioinformatics Technology Co., Ltd, Beijing, China. FAU - Li, Zhongwu AU - Li Z AD - Department of Pathology, Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China. FAU - Zhou, Lixin AU - Zhou L AD - Department of Pathology, Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China. FAU - Jia, Ling AU - Jia L AD - Department of Pathology, Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China. FAU - Rao, Guanhua AU - Rao G AD - Beijing Novogene Bioinformatics Technology Co., Ltd, Beijing, China. FAU - Gao, Lianju AU - Gao L AD - Beijing Novogene Bioinformatics Technology Co., Ltd, Beijing, China. FAU - Cheng, Gang AU - Cheng G AD - Beijing Novogene Bioinformatics Technology Co., Ltd, Beijing, China. FAU - Ji, Ke AU - Ji K AD - Department of Gastrointestinal Surgery, Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China. ji_jiafu@hotmail.com. FAU - Lin, Dongmei AU - Lin D AD - Department of Pathology, Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China. Dongm_lin@126.com. LA - eng GR - 81472743/Natural Science Foundation of China/ PT - Journal Article DEP - 20200703 PL - Switzerland TA - Pathol Oncol Res JT - Pathology oncology research : POR JID - 9706087 RN - 0 (Biomarkers, Tumor) RN - EC 2.7.10.1 (ERBB2 protein, human) RN - EC 2.7.10.1 (Receptor, ErbB-2) SB - IM MH - Biomarkers, Tumor/analysis/genetics MH - Breast Neoplasms/*genetics MH - DNA Copy Number Variations MH - Female MH - High-Throughput Nucleotide Sequencing/*methods MH - Humans MH - Receptor, ErbB-2/*genetics MH - Sequence Analysis, DNA/*methods MH - Stomach Neoplasms/*genetics PMC - PMC7471150 OTO - NOTNLM OT - Breast cancer OT - FISH/IHC OT - Gastric cancer OT - HER2 amplification OT - Next generation sequencing COIS- Lei Li, Wanchun Zang, Lianju Gao, Guanhua Rao, Yun Gao, Gang Cheng and Yang Yu were employee of Novogene Bioinformatics Technology Co., Ltd., Beijing, China. No potential conflicts of interest were disclosed by the other authors. SJK has received consulting/advisory fees from Lilly Oncology, Astellas, Boston Biomedical and Foundation Medicine, Inc. SJK has stock/equity in TP Therapeutics and receives institutional research funding from Merck, Leap therapeutics, and Astellas Pharmaceuticals. EDAT- 2020/07/06 06:00 MHDA- 2021/06/22 06:00 PMCR- 2020/07/03 CRDT- 2020/07/05 06:00 PHST- 2020/05/25 00:00 [received] PHST- 2020/06/10 00:00 [accepted] PHST- 2020/07/06 06:00 [pubmed] PHST- 2021/06/22 06:00 [medline] PHST- 2020/07/05 06:00 [entrez] PHST- 2020/07/03 00:00 [pmc-release] AID - 10.1007/s12253-020-00844-w [pii] AID - 844 [pii] AID - 10.1007/s12253-020-00844-w [doi] PST - ppublish SO - Pathol Oncol Res. 2020 Oct;26(4):2577-2585. doi: 10.1007/s12253-020-00844-w. Epub 2020 Jul 3.