Evaluation of next generation sequencing for detecting HER2 copy number in breast and gastric cancers.

e13004 Background: 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. Methods: 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. Results: 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 131 HER2 non-amplified FFPE samples. In breast cancer patients, the cut-off value was 2.910, with 95.28%, 99.23% 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 macro-dissection procedure was not effective for increasing sensitivity (57.14%). Thus indicated that HER2 copy number correlation between NGS and FISH in gastric cancer was different from breast cancer. Conclusions: 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. NGS-based HER2 assessment may decrease the equivocal HER2 determinations in breast cancer patients assessed by FISH/IHC. The greater discordance in gastric cancer may reflect the underlying biological mechanisms, and further study is warranted.

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Single Cell Genetic Profiling of Tumors of Breast Cancer Patients Aged 50 Years and Older Reveals Enormous Intratumor Heterogeneity Independent of Individual Prognosis

Cancers ◽

10.3390/cancers13133366 ◽

2021 ◽

Vol 13 (13) ◽

pp. 3366

Author(s):

Anna-Sophie Liegmann ◽

Kerstin Heselmeyer-Haddad ◽

Annette Lischka ◽

Daniela Hirsch ◽

Wei-Dong Chen ◽

...

Keyword(s):

Breast Cancer ◽

Cancer Patients ◽

Copy Number ◽

Genome Instability ◽

Single Cells ◽

Gene Mutations ◽

Intratumor Heterogeneity ◽

Breast Cancer Patients ◽

Luminal A ◽

Pik3ca Mutations

Purpose: Older breast cancer patients are underrepresented in cancer research even though the majority (81.4%) of women dying of breast cancer are 55 years and older. Here we study a common phenomenon observed in breast cancer which is a large inter- and intratumor heterogeneity; this poses a tremendous clinical challenge, for example with respect to treatment stratification. To further elucidate genomic instability and tumor heterogeneity in older patients, we analyzed the genetic aberration profiles of 39 breast cancer patients aged 50 years and older (median 67 years) with either short (median 2.4 years) or long survival (median 19 years). The analysis was based on copy number enumeration of eight breast cancer-associated genes using multiplex interphase fluorescence in situ hybridization (miFISH) of single cells, and by targeted next-generation sequencing of 563 cancer-related genes. Results: We detected enormous inter- and intratumor heterogeneity, yet maintenance of common cancer gene mutations and breast cancer specific chromosomal gains and losses. The gain of COX2 was most common (72%), followed by MYC (69%); losses were most prevalent for CDH1 (74%) and TP53 (69%). The degree of intratumor heterogeneity did not correlate with disease outcome. Comparing the miFISH results of diploid with aneuploid tumor samples significant differences were found: aneuploid tumors showed significantly higher average signal numbers, copy number alterations (CNAs) and instability indices. Mutations in PIKC3A were mostly restricted to luminal A tumors. Furthermore, a significant co-occurrence of CNAs of DBC2/MYC, HER2/DBC2 and HER2/TP53 and mutual exclusivity of CNAs of HER2 and PIK3CA mutations and CNAs of CCND1 and PIK3CA mutations were revealed. Conclusion: Our results provide a comprehensive picture of genome instability profiles with a large variety of inter- and intratumor heterogeneity in breast cancer patients aged 50 years and older. In most cases, the distribution of chromosomal aneuploidies was consistent with previous results; however, striking exceptions, such as tumors driven by exclusive loss of chromosomes, were identified.

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Next-generation sequencing of BRCA1/2 in breast cancer patients: potential effects on clinical decision-making using rapid, high-accuracy genetic results

Annals of Surgical Treatment and Research ◽

10.4174/astr.2017.92.5.331 ◽

2017 ◽

Vol 92 (5) ◽

pp. 331 ◽

Cited By ~ 5

Author(s):

Hyung Seok Park ◽

Seo-Jin Park ◽

Jee Ye Kim ◽

Sanghwa Kim ◽

Jaegyu Ryu ◽

...

Keyword(s):

Breast Cancer ◽

Decision Making ◽

Next Generation Sequencing ◽

Cancer Patients ◽

Clinical Decision Making ◽

Clinical Decision ◽

High Accuracy ◽

Breast Cancer Patients ◽

Generation Sequencing ◽

Genetic Results

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Reduced mitochondrial DNA copy number is correlated with tumor progression and prognosis in Chinese breast cancer patients

IUBMB Life ◽

10.1080/15216540701509955 ◽

2007 ◽

Vol 59 (7) ◽

pp. 450-457 ◽

Cited By ~ 156

Author(s):

Man Yu ◽

Yunli Zhou ◽

Yurong Shi ◽

Liansheng Ning ◽

Yi Yang ◽

...

Keyword(s):

Breast Cancer ◽

Mitochondrial Dna ◽

Tumor Progression ◽

Cancer Patients ◽

Copy Number ◽

Breast Cancer Patients ◽

Dna Copy Number ◽

Mitochondrial Dna Copy Number

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Genome-Wide Dna Copy Number Profiles Identify Lapatinib Sensitivity in Metastatic Breast Cancer Patients

Annals of Oncology ◽

10.1093/annonc/mdt083.8 ◽

2013 ◽

Vol 24 ◽

pp. iii25

Author(s):

M. Xie ◽

C. He

Keyword(s):

Breast Cancer ◽

Metastatic Breast Cancer ◽

Cancer Patients ◽

Copy Number ◽

Metastatic Breast ◽

Breast Cancer Patients ◽

Dna Copy Number ◽

Genome Wide

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In situ analysis of FGFR2 mRNA and comparison with FGFR2 gene copy number by dual-color in situ hybridization in a large cohort of gastric cancer patients

Gastric Cancer ◽

10.1007/s10120-017-0758-x ◽

2017 ◽

Vol 21 (3) ◽

pp. 401-412 ◽

Cited By ~ 4

Author(s):

Yasutoshi Kuboki ◽

Christoph A. Schatz ◽

Karl Koechert ◽

Sabine Schubert ◽

Janine Feng ◽

...

Keyword(s):

Gastric Cancer ◽

In Situ Hybridization ◽

Cancer Patients ◽

Copy Number ◽

Gene Copy Number ◽

In Situ Analysis ◽

Gene Copy ◽

Fgfr2 Gene ◽

Gastric Cancer Patients

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ILDR1 Is a Prognostic Biomarker and Associated With Immune Inﬁltration in Gastric Cancer

10.21203/rs.3.rs-944596/v1 ◽

2021 ◽

Author(s):

Yanling Ma ◽

WenBo Qi ◽

BaoHong Gu ◽

XueMei Li ◽

ZhenYu Yin ◽

...

Keyword(s):

Gastric Cancer ◽

T Cells ◽

Dendritic Cells ◽

Cancer Patients ◽

Cd8 T Cells ◽

Immune Cells ◽

Copy Number ◽

Sequencing Data ◽

Number Variation ◽

Gastric Cancer Patients

Abstract Objective: To investigate the association between ILDR1 and prognosis and immune infiltration in gastric cancer. Methods: We analyzed the RNA sequencing data of 9736 tumor tissues and 8587 normal tissues in the TCGA and GTEx databases through the GEPIA2 platform. The expression of ILDR1 in gastric cancer and normal gastric mucosa tissues with GEPIA and TIMER. Clinical subgroup analysis was made through Kaplan-Meier analysis. Analyzed the correlation between ILDR1 and VEGFA expression in gastric cancer, through the gene sequencing data of gastric cancer in TCGA. Explored the relationship between ILDR1 methylation and the prognosis of gastric cancer patients through the MethSurv database. The correlation between ILDR1 and immune cells and the correlation of copy number variation were explored through the TIMER database. Results: ILDR1-high GC patients had a lower PFS and OS. High ILDR1 expression was significantly correlated with tumor grade. There was a negative correlation between the ILDR1 expression and the abundances of CD8+ T, Macrophages and DC and etc. The methylation level of ILDR1 is associated with a good prognosis of gastric cancer. ILDR1 copy number variation was correlated with immune cells, IDLR1 arm-loss was associated with the infiltration of B cells, CD8+ T cells, CD4+ T cells, macrophages, neutrophils, and dendritic cells, and arm-duplication was associated with the infiltration of B cells, CD8+ T cells, CD4+ T cells, macrophages, neutrophils and dendritic cells. Conclusion: The increased expression of ILDR1 is associated with poor prognosis in patients with gastric cancer. ILDR1 can be used as a novel predictive biomarker to provide a new therapeutic target for gastric cancer patients.

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