Targeted next-generation sequencing assays using triplet samples of normal breast tissue, primary breast cancer, and recurrent/metastatic lesions

Abstract Background Next-generation sequencing (NGS) has shown that recurrent/metastatic breast cancer lesions may have additional genetic changes compared with the primary tumor. These additional changes may be related to tumor progression and/or drug resistance. However, breast cancer-targeted NGS is not still widely used in clinical practice to compare the genomic profiles of primary breast cancer and recurrent/metastatic lesions. Methods Triplet samples of genomic DNA were extracted from each patient’s normal breast tissue, primary breast cancer, and recurrent/metastatic lesion(s). A DNA library was constructed using the QIAseq Human Breast Cancer Panel (93 genes, Qiagen) and then sequenced using MiSeq (Illumina). The Qiagen web portal was utilized for data analysis. Results Successful results for three or four samples (normal breast tissue, primary tumor, and at least one metastatic/recurrent lesion) were obtained for 11 of 35 breast cancer patients with recurrence/metastases (36 samples). We detected shared somatic mutations in all but one patient, who had a germline mutation in TP53. Additional mutations that were detected in recurrent/metastatic lesions compared with primary tumor were in genes including TP53 (three patients) and one case each of ATR, BLM, CBFB, EP300, ERBB2, MUC16, PBRM1, and PIK3CA. Actionable mutations and/or copy number variations (CNVs) were detected in 73% (8/11) of recurrent/metastatic breast cancer lesions. Conclusions The QIAseq Human Breast Cancer Panel assay showed that recurrent/metastatic breast cancers sometimes acquired additional mutations and CNV. Such additional genomic changes could provide therapeutic target.

Download Full-text

Targeted next-generation sequencing assays using triplet samples of normal breast tissue, primary breast cancer, and recurrent/metastatic lesions

10.21203/rs.2.16536/v3 ◽

2020 ◽

Author(s):

Toshiaki Akahane ◽

Naoki Kanomata ◽

Oi Harada ◽

Tetsumasa Yamashita ◽

Junichi Kurebayashi ◽

...

Keyword(s):

Breast Cancer ◽

Primary Tumor ◽

Primary Breast Cancer ◽

Breast Tissue ◽

Normal Breast Tissue ◽

Metastatic Breast ◽

Normal Breast ◽

Human Breast ◽

Metastatic Lesions ◽

Generation Sequencing

Abstract Background: Next-generation sequencing (NGS) has shown that recurrent/metastatic breast cancer lesions may have additional genetic changes compared with the primary tumor. These additional changes may be related to tumor progression and/or drug resistance. However, breast cancer-targeted NGS is not still widely used in clinical practice to compare the genomic profiles of primary breast cancer and recurrent/metastatic lesions.Methods: Triplet samples of genomic DNA were extracted from each patient’s normal breast tissue, primary breast cancer, and recurrent/metastatic lesion(s). A DNA library was constructed using the QIAseq Human Breast Cancer Panel (93 genes, Qiagen) and then sequenced using MiSeq (Illumina). The Qiagen web portal was utilized for data analysis.Results: Successful results for three or four samples (normal breast tissue, primary tumor, and at least one metastatic/recurrent lesion) were obtained for 11 of 35 breast cancer patients with recurrence/metastases (36 samples). We detected shared somatic mutations in all but one patient, who had a germline mutation in TP53. Additional mutations that were detected in recurrent/metastatic lesions compared with primary tumor were in genes including TP53 (three patients) and one case each of ATR, BLM, CBFB, EP300, ERBB2, MUC16, PBRM1, and PIK3CA. Actionable mutations and/or copy number variations (CNVs) were detected in 73% (8/11) of recurrent/metastatic breast cancer lesions.Conclusions: The QIAseq Human Breast Cancer Panel assay showed that recurrent/metastatic breast cancers sometimes acquired additional mutations and CNV. Such additional genomic changes could provide therapeutic target.

Download Full-text

Targeted next-generation sequencing assays using triplet samples of normal breast tissue, primary breast cancer, and recurrent/metastatic lesions

10.21203/rs.2.16536/v5 ◽

2020 ◽

Author(s):

Toshiaki Akahane ◽

Naoki Kanomata ◽

Oi Harada ◽

Tetsumasa Yamashita ◽

Junichi Kurebayashi ◽

...

Keyword(s):

Breast Cancer ◽

Primary Tumor ◽

Primary Breast Cancer ◽

Breast Tissue ◽

Normal Breast Tissue ◽

Metastatic Breast ◽

Normal Breast ◽

Human Breast ◽

Metastatic Lesions ◽

Generation Sequencing

Abstract Background: Next-generation sequencing (NGS) has shown that recurrent/metastatic breast cancer lesions may have additional genetic changes compared with the primary tumor. These additional changes may be related to tumor progression and/or drug resistance. However, breast cancer-targeted NGS is not still widely used in clinical practice to compare the genomic profiles of primary breast cancer and recurrent/metastatic lesions.Methods: Triplet samples of genomic DNA were extracted from each patient’s normal breast tissue, primary breast cancer, and recurrent/metastatic lesion(s). A DNA library was constructed using the QIAseq Human Breast Cancer Panel (93 genes, Qiagen) and then sequenced using MiSeq (Illumina). The Qiagen web portal was utilized for data analysis.Results: Successful results for three or four samples (normal breast tissue, primary tumor, and at least one metastatic/recurrent lesion) were obtained for 11 of 35 breast cancer patients with recurrence/metastases (36 samples). We detected shared somatic mutations in all but onepatient, who had a germline mutation in TP53. Additional mutations that were detected in recurrent/metastatic lesions compared with primary tumor were in genes including TP53 (three patients) and one case each of ATR, BLM, CBFB, EP300, ERBB2, MUC16, PBRM1, and PIK3CA. Actionable mutations and/or copy number variations (CNVs) were detected in 73% (8/11) of recurrent/metastatic breast cancer lesions.Conclusions: The QIAseq Human Breast Cancer Panel assay showed that recurrent/metastatic breast cancers sometimes acquired additional mutations and CNV. Such additional genomic changes could provide therapeutic target.

Download Full-text

Targeted next-generation sequencing assays using triplet samples of normal breast tissue, primary breast cancer, and recurrent/metastatic lesions

10.21203/rs.2.16536/v4 ◽

2020 ◽

Author(s):

Toshiaki Akahane ◽

Naoki Kanomata ◽

Oi Harada ◽

Tetsumasa Yamashita ◽

Junichi Kurebayashi ◽

...

Keyword(s):

Breast Cancer ◽

Primary Tumor ◽

Primary Breast Cancer ◽

Breast Tissue ◽

Normal Breast Tissue ◽

Metastatic Breast ◽

Normal Breast ◽

Human Breast ◽

Metastatic Lesions ◽

Generation Sequencing

Download Full-text

Targeted next generation sequencing assays using triplet samples of normal breast tissue, primary breast cancer, and recurrent/metastatic lesions

10.21203/rs.2.16536/v1 ◽

2019 ◽

Author(s):

Toshiaki Akahane ◽

Naoki Kanomata ◽

Oi Harada ◽

Tetsumasa Yamashita ◽

Junichi Kurebayashi ◽

...

Keyword(s):

Breast Cancer ◽

Primary Breast Cancer ◽

Breast Tissue ◽

Normal Breast Tissue ◽

Primary Tumour ◽

Metastatic Breast ◽

Normal Breast ◽

Human Breast ◽

Metastatic Lesions ◽

Generation Sequencing

Abstract Background Next generation sequencing (NGS) has shown that recurrent/metastatic breast cancer lesions may have additional genetic changes compared with the primary tumour. These additional changes may be related to tumour progression and/or drug resistance. The breast cancer-targeted NGS, however, is not still widely used for comparing genomic profile of primary breast cancer and recurrent/metastatic lesions in clinical practice.Methods Genomic DNA was extracted from normal breast tissue, primary breast cancer, and recurrent/metastatic lesion(s) from the same patient. A DNA library was constructed using the QIAseq Human Breast Cancer Panel (93 genes, Qiagen) and then sequenced by a MiSeq (Illumina). The Qiagen web portal was utilized for data analysis.Results Of 107 breast cancer cases with recurrence/metastases, successful results for three or four samples (normal breast tissue, primary tumour, and at least one metastatic/recurrent lesion) were obtained for 11 patients (36 samples). We detected shared somatic mutations in all but one patient, who had germline mutations in TP53 and KMT2C . Additional mutations were detected in recurrent/metastatic lesions compared with primary tumour in genes including TP53 (three patients) and one case each of ATR , BLM , CBFB , EP300 , ERBB2 , MUC16 , PBRM1, and PIK3CA . More copy number variations (CNVs) was detected in distant metastases than in local recurrence ( P =0.030).Conclusions The QIAseq Human Breast Cancer Panel assay could identify driver mutations in both primary breast tumour tissue and recurrent/metastatic lesions in almost all patients. This method can assist in identifying drug-targetable mutations and CNV in metastatic breast cancers.

Download Full-text

Targeted next generation sequencing assays using triplet samples of normal breast tissue, primary breast cancer, and recurrent/metastatic lesions

10.21203/rs.2.16536/v2 ◽

2020 ◽

Author(s):

Toshiaki Akahane ◽

Naoki Kanomata ◽

Oi Harada ◽

Tetsumasa Yamashita ◽

Junichi Kurebayashi ◽

...

Keyword(s):

Breast Cancer ◽

Primary Breast Cancer ◽

Breast Tissue ◽

Normal Breast Tissue ◽

Primary Tumour ◽

Metastatic Breast ◽

Normal Breast ◽

Human Breast ◽

Metastatic Lesions ◽

Generation Sequencing

Abstract Background: Next generation sequencing (NGS) has shown that recurrent/metastatic breast cancer lesions may have additional genetic changes compared with the primary tumour. These additional changes may be related to tumour progression and/or drug resistance. The breast cancer-targeted NGS, however, is not still widely used for comparing genomic profile of primary breast cancer and recurrent/metastatic lesions in clinical practice.Methods: Genomic DNA was extracted from normal breast tissue, primary breast cancer, and recurrent/metastatic lesion(s) from the same patient. A DNA library was constructed using the QIAseq Human Breast Cancer Panel (93 genes, Qiagen) and then sequenced by a MiSeq (Illumina). The Qiagen web portal was utilized for data analysis.Results: Of 35 breast cancer cases with recurrence/metastases, successful results for three or four samples (normal breast tissue, primary tumour, and at least one metastatic/recurrent lesion) were obtained for 11 patients (36 samples). We detected shared somatic mutations in all but one patient, who had germline mutation in TP53. Additional mutations were detected in recurrent/metastatic lesions compared with primary tumour in genes including TP53 (three patients) and one case each of ATR, BLM, CBFB, EP300, ERBB2, MUC16, PBRM1, and PIK3CA. Actionable mutations and/or copy number variations (CNVs) were detected in 82% (9/11) of recurrent/metastatic breast cancer cases.Conclusions: The QIAseq Human Breast Cancer Panel assay could identify driver mutations in both primary breast tumour tissue and recurrent/metastatic lesions in almost all patients. This method can assist in identifying drug-targetable mutation and CNV in metastatic breast cancers.

Download Full-text

Ezrin expression in primary breast cancer, metastatic lymph nodes and normal breast tissue

Geburtshilfe und Frauenheilkunde ◽

10.1055/s-0030-1254964 ◽

2010 ◽

Vol 70 (05) ◽

Author(s):

D Gschwantler-Kaulich ◽

C Natter ◽

S Steurer ◽

I Walter ◽

C Singer

Keyword(s):

Breast Cancer ◽

Lymph Nodes ◽

Primary Breast Cancer ◽

Breast Tissue ◽

Normal Breast Tissue ◽

Normal Breast ◽

Metastatic Lymph Nodes ◽

Metastatic Lymph ◽

Ezrin Expression

Download Full-text

Enhancer of the rudimentary gene homologue (ERH) expression pattern in sporadic human breast cancer and normal breast tissue

BMC Cancer ◽

10.1186/1471-2407-8-145 ◽

2008 ◽

Vol 8 (1) ◽

Cited By ~ 10

Author(s):

Menelaos Zafrakas ◽

Inge Losen ◽

Ruth Knüchel ◽

Edgar Dahl

Keyword(s):

Breast Cancer ◽

Expression Pattern ◽

Human Breast Cancer ◽

Breast Tissue ◽

Normal Breast Tissue ◽

Normal Breast ◽

Human Breast ◽

Gene Homologue

Download Full-text

The role of low keV virtual monochromatic imaging in increasing the conspicuity of primary breast cancer in dual-energy spectral thoracic CT examination for staging purposes

Acta Radiologica ◽

10.1177/0284185119858040 ◽

2019 ◽

Vol 61 (2) ◽

pp. 168-174 ◽

Cited By ~ 3

Author(s):

Yavuz Metin ◽

Nurgül Orhan Metin ◽

Oğuzhan Özdemir ◽

Filiz Taşçı ◽

Sibel Kul

Keyword(s):

Breast Cancer ◽

Primary Breast Cancer ◽

Breast Tissue ◽

Normal Breast Tissue ◽

Energy Levels ◽

Iodine Content ◽

Pectoral Muscle ◽

Dual Energy ◽

Normal Breast

Background The additive value of dual-energy spectral computerized tomography (DESCT) in breast cancer imaging is still unknown. Purpose To investigate the role of DESCT in improving the conspicuity of primary breast cancer. Material and Methods Twenty-nine patients who were histopathologically diagnosed with breast cancer and underwent DESCT for staging of lung metastasis were evaluated retrospectively. The visual conspicuity of breast cancer was scored by two readers separately in reconstructed virtual monochromatic images obtained at 40, 60, 80, and 100 keV. A circular region of interest slightly smaller than the maximum contrasted portion of the primary breast cancer was manually placed. Iodine enhancement (HU) and iodine content (mg/mL) values of tumor, normal breast tissue and pectoral muscle, and contrast-to-noise values of images at four different energy levels were calculated. Results The lesion conspicuity score peaked at 40-keV series for both readers and was significantly higher than those at other energy levels (all P < 0.001). Lesion iodine enhancement was highest at 40-keV virtual monochromatic image reconstructions ( P < 0.001). The iodine content was significantly higher in tumor than normal breast tissue, and pectoral muscle ( P < 0.001). The highest contrast-to-noise value was obtained at 60 keV (4.0 ± 2.5), followed by 40 keV (3.9 ± 2.2), without a significant difference ( P = 0.33). Conclusion The conspicuity of primary breast cancer was significantly higher in low keV virtual monochromatic images obtained by DESCT. This gives us hope that DESCT may play an effective role in detecting incidental breast lesions. It also raises the question of whether quantitative values obtained by DESCT can be used for characterization of primary breast lesion.

Download Full-text

Evaluation of the expression levels of nm23-h1 mRNA in primary breast cancer, benign breast disease, axillary lymph nodes and normal breast tissue

Pathology ◽

10.1080/00313029400169122 ◽

1994 ◽

Vol 26 (4) ◽

pp. 423-428 ◽

Cited By ~ 12

Author(s):

Rebecca J. Goodall ◽

Hugh J.S. Dawkins ◽

Peter D. Robbins ◽

Erika Hähnel ◽

Mohinder Sarna ◽

...

Keyword(s):

Breast Cancer ◽

Lymph Nodes ◽

Primary Breast Cancer ◽

Breast Tissue ◽

Benign Breast Disease ◽

Normal Breast Tissue ◽

Breast Disease ◽

Normal Breast ◽

Axillary Lymph Nodes ◽

Axillary Lymph

Download Full-text

Lipid Markers of Breast Tissue for the Diagnosis of Regional Metastatic Lesion

10.21203/rs.3.rs-396953/v1 ◽

2021 ◽

Author(s):

Vitaliy Chagovets ◽

Alisa Tokareva ◽

Natalia Starodubtseva ◽

Vlada Kometova ◽

Maria Rodionova ◽

...

Keyword(s):

Breast Cancer ◽

Breast Tissue ◽

Tumor Tissue ◽

Normal Breast Tissue ◽

Normal Breast ◽

Diagnostic Model ◽

Regional Lymph Nodes ◽

Metastatic Lesions ◽

P 16 ◽

Lipid Markers

Abstract The development of minimally invasive, non-traumatic and stable approaches for the diagnosis of metastatic lesions of regional lymph nodes upon breast cancer is of great urgency. Here we recorded lipid profiles of normal breast tissue and malignant tissue to reveal potential lipid markers of metastatic lesions of regional lymph nodes. Lipid identification was done using the Lipid Match package. The search for lipid markers was carried out using the Mann-Whitney test. Lipids for the construction of a diagnostic logistic regression were selected according to the Akaike information criterion. For normal breast tissue, a diagnostic model was obtained with the area under the curve (AUC) of 0.83; for tumor tissue, a model with AUC = 0.86 was obtained. The species PC 14:0_20:4, PE 18:1_20:1, PC P-16:0/20:4, PC P-16:0/20:4, PE P-16:0/22:4, SM d18:1/18 0, SM d18:1/22:0 were determined as markers for normal breast tissue. The species PC 18:2_22:6, PC O-18:0/20:2, SM d16:1/18:1, SM d22:0/20:2, SM d16:0/18:2 were determined as markers for tumor tissue. The high AUC values for the developed diagnostic model indicate the potential significance of the revealed marker species for the diagnosis of breast cancer metastasis and indicate the need for further research in this direction.

Download Full-text