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Litviakov NV, Ibragimova MK, Tsyganov MM, Doroshenko AV, Garbukov EY, Slonimskaya EM. Neoadjuvant Chemotherapy Induces the Appearance of New Copy Number Aberrations in Breast Tumor and is Associated with Metastasis. Curr Cancer Drug Targets 2021; 20:681-688. [PMID: 31577208 DOI: 10.2174/1568009620666200506104523] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 03/02/2020] [Accepted: 03/10/2020] [Indexed: 12/13/2022]
Abstract
BACKGROUND In this study, we examined the CNA-genetic landscape (CNA - copy number aberration) of breast cancer prior to and following neoadjuvant chemotherapy (NAC) and correlated changes in the tumor landscape with chemotherapy efficiency as well as metastasis-free survival. OBJECTIVE Breast cancer patients (n = 30) with luminal B molecular subtypes were treated with anthracycline- based therapy. METHODS To study CNAs in breast tumors, microarray analysis was performed. RESULTS Three effects of NAC on tumor CNA landscape were identified: 1 - the number of CNAbearing tumor clones decreased following NAC; 2 - there were no alterations in the number of CNAcontaining clones after NAC; 3 - the treatment with NAC increased the number of CNA-bearing clones (new clones appeared). All NAC-treated patients who had new tumor clones with amplification (20%) had a 100% likelihood of metastasis formation. In these cases, NAC contributed to the emergence of potential metastatic clones. Our study identified the following loci - 5p, 6p, 7q, 8q, 9p, 10p, 10q22.1, 13q, 16p, 18Chr and 19p - that were amplified during the treatment with NAC and maybe the markers of potential metastatic clones. In other patients who showed total or partial elimination of CNA-bearing cell clones, no new amplification clones were observed after NAC, and no evidence of metastases was found with follow-up for 5 years (р = 0.00000). CONCLUSION Our data suggest that the main therapeutic result from NAC is the elimination of potential metastatic clones present in the tumor before treatment. The results showed the necessity of an intelligent approach to NAC to avoid metastasis stimulation.
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Affiliation(s)
- Nikolai V Litviakov
- Laboratory of Oncovirology, Cancer Research Institute, Tomsk National Research Medical Center, Russia Academy of Science, Tomsk, Russian Federation
| | - Marina K Ibragimova
- Laboratory of Oncovirology, Cancer Research Institute, Tomsk National Research Medical Center, Russia Academy of Science, Tomsk, Russian Federation
| | - Matvey M Tsyganov
- Laboratory of Oncovirology, Cancer Research Institute, Tomsk National Research Medical Center, Russia Academy of Science, Tomsk, Russian Federation
| | - Artem V Doroshenko
- Department of General Oncology, Cancer Research Institute, Tomsk National Research Medical Center, Russia Academy of Science, Tomsk, Russian Federation
| | - Eugeniy Y Garbukov
- Department of General Oncology, Cancer Research Institute, Tomsk National Research Medical Center, Russia Academy of Science, Tomsk, Russian Federation
| | - Elena M Slonimskaya
- Department of General Oncology, Cancer Research Institute, Tomsk National Research Medical Center, Russia Academy of Science, Tomsk, Russian Federation
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2
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MYBL2 amplification in breast cancer: Molecular mechanisms and therapeutic potential. Biochim Biophys Acta Rev Cancer 2020; 1874:188407. [DOI: 10.1016/j.bbcan.2020.188407] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/21/2020] [Accepted: 07/21/2020] [Indexed: 02/08/2023]
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Ibragimova MK, Tsyganov MM, Slonimskaya EM, Litviakov NV. Aberrations of the number of copies (CNA) in the genome of luminal B breast tumor. BULLETIN OF SIBERIAN MEDICINE 2020. [DOI: 10.20538/1682-0363-2020-3-22-28] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- M. K. Ibragimova
- Саnсеr Rеsеаrсh Institute, Tomsk National Research Medical Center of Russian Academy of Sciences
| | - M. M. Tsyganov
- Саnсеr Rеsеаrсh Institute, Tomsk National Research Medical Center of Russian Academy of Sciences
| | | | - N. V. Litviakov
- Саnсеr Rеsеаrсh Institute, Tomsk National Research Medical Center of Russian Academy of Sciences
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Resistance to Neoadjuvant Treatment in Breast Cancer: Clinicopathological and Molecular Predictors. Cancers (Basel) 2020; 12:cancers12082012. [PMID: 32708049 PMCID: PMC7463925 DOI: 10.3390/cancers12082012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 07/03/2020] [Accepted: 07/20/2020] [Indexed: 01/30/2023] Open
Abstract
Neoadjuvant Chemotherapy (NAC) in Breast Cancer (BC) has proved useful for the reduction in tumor burden prior to surgery, allowing for a more extensive breast preservation and the eradication of subjacent micrometastases. However, the impact on prognosis is highly dependent on the establishment of Pathological Complete Response (pCR), in particular for Triple Negative (TN) and Hormonal Receptor negative/Human Epidermal growth factor Receptor 2 positive (HR-/HER2+) subtypes. Several pCR predictors, such as PAM50, Integrative Cluster (IntClust), mutations in PI3KCA, or the Trastuzumab Risk model (TRAR), are useful molecular tools for estimating response to treatment and are prognostic. Major evolution events during BC NAC that feature the Residual Disease (RD) are the loss of HR and HER2, which are prognostic of bad outcome, and stemness and immune depletion-related gene expression aberrations. This dynamic nature of the determinants of response to BC NAC, together with the extensive heterogeneity of BC, raises the need to discern the individual and subtype-specific determinants of resistance. Moreover, refining the current approaches for a comprehensive monitoring of tumor evolution during treatment, RD, and eventual recurrences is essential for identifying new actionable alterations and the integral best management of the disease.
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Kunimasa K, Matsumoto S, Nishino K, Nakamura H, Kuhara H, Tamiya M, Inoue T, Kawamura T, Kawachi H, Kuno K, Kimura T, Maniwa T, Okami J, Nakatsuka SI, Goto K, Kumagai T. Improvement strategies for successful next-generation sequencing analysis of lung cancer. Future Oncol 2020; 16:1597-1606. [PMID: 32490705 DOI: 10.2217/fon-2020-0332] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Aim: We aimed to improve the success rate of NGS (next-generation sequencing) analysis through improved strategies of lung cancer sampling. Materials & methods: The improvement strategies are as follows. Surgically resected specimens were preferentially submitted in cooperation with pathologists and surgeons. In bronchoscopic samples, the size of the sample collection device and the number of samples collected was increased. Results: The strategies increased the success rate of NGS analysis of DNA from 69.3 to 91.1%, and that of RNA from 64.6 to 90.0%. Discussion: The introduction of strategies aimed at improving the success of NGS analysis resulted in an improvement in the success rate and brought us closer to the delivery of effective precision medicine in cancer therapy.
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Affiliation(s)
- Kei Kunimasa
- Department of Thoracic Oncology, Osaka International Cancer Institute, Osaka, 541-8567, Japan
| | - Shingo Matsumoto
- Department of Thoracic Oncology, National Cancer Center Hospital East, Kashiwa, 277-8577, Japan
| | - Kazumi Nishino
- Department of Thoracic Oncology, Osaka International Cancer Institute, Osaka, 541-8567, Japan
| | - Harumi Nakamura
- Department of Diagnostic Pathology & Cytology, Osaka International Cancer Institute, Osaka, 541-8567, Japan
| | - Hanako Kuhara
- Department of Thoracic Oncology, Osaka International Cancer Institute, Osaka, 541-8567, Japan
| | - Motohiro Tamiya
- Department of Thoracic Oncology, Osaka International Cancer Institute, Osaka, 541-8567, Japan
| | - Takako Inoue
- Department of Thoracic Oncology, Osaka International Cancer Institute, Osaka, 541-8567, Japan
| | - Takahisa Kawamura
- Department of Thoracic Oncology, Osaka International Cancer Institute, Osaka, 541-8567, Japan
| | - Hayato Kawachi
- Department of Thoracic Oncology, Osaka International Cancer Institute, Osaka, 541-8567, Japan
| | - Kika Kuno
- Department of Thoracic Oncology, Osaka International Cancer Institute, Osaka, 541-8567, Japan
| | - Toru Kimura
- Department of General Thoracic Surgery, Osaka International Cancer Institute, Osaka, 541-8567, Japan
| | - Tomohiro Maniwa
- Department of General Thoracic Surgery, Osaka International Cancer Institute, Osaka, 541-8567, Japan
| | - Jiro Okami
- Department of General Thoracic Surgery, Osaka International Cancer Institute, Osaka, 541-8567, Japan
| | - Shin-Ichi Nakatsuka
- Department of Diagnostic Pathology & Cytology, Osaka International Cancer Institute, Osaka, 541-8567, Japan
| | - Koichi Goto
- Department of Thoracic Oncology, National Cancer Center Hospital East, Kashiwa, 277-8577, Japan
| | - Toru Kumagai
- Department of Thoracic Oncology, Osaka International Cancer Institute, Osaka, 541-8567, Japan
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Granados-Soler JL, Bornemann-Kolatzki K, Beck J, Brenig B, Schütz E, Betz D, Junginger J, Hewicker-Trautwein M, Murua Escobar H, Nolte I. Analysis of Copy-Number Variations and Feline Mammary Carcinoma Survival. Sci Rep 2020; 10:1003. [PMID: 31969654 PMCID: PMC6976565 DOI: 10.1038/s41598-020-57942-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 01/03/2020] [Indexed: 02/07/2023] Open
Abstract
Feline mammary carcinomas (FMCs) are highly malignant. As the disease-free survival (DFS) and overall survival (OS) are short, prognostication is crucial. Copy-number variations (CNVs) analysis by next-generation sequencing serves to identify critical cancer-related genomic regions. Thirty-three female cats with FMCs were followed during two years after surgery. Tumours represented tubulopapillary and solid carcinomas encompassing six molecular subtypes. Regardless of the histopathological diagnosis, molecular subtypes showed important differences in survival. Luminal A tumours exhibited the highest DFS (p = 0.002) and cancer-specific OS (p = 0.001), and the lowest amount of CNVs (p = 0.0001). In contrast, basal-like triple-negative FMCs had the worst outcome (DFS, p < 0.0001; and OS, p < 0.00001) and were the most aberrant (p = 0.05). In the multivariate analysis, copy-number losses (CNLs) in chromosome B1 (1-23 Mb) harbouring several tumour-repressors (e.g. CSMD1, MTUS1, MSR1, DBC2, and TUSC3) negatively influenced DFS. Whereas, copy-number gains (CNGs) in B4 (1-29 Mb) and F2 (64-82.3 Mb) comprising epithelial to mesenchymal transition genes and metastasis-promoting transcription factors (e.g. GATA3, VIM, ZEB1, and MYC) negatively influenced DFS and cancer-specific OS. These data evidence an association between specific CNVs in chromosomes B1, B4 and F2, and poor prognosis in FMCs.
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Affiliation(s)
- José Luis Granados-Soler
- Small Animal Clinic, University of Veterinary Medicine Hannover Foundation, Hannover, Germany
- Haematology, Oncology and Palliative Medicine, Clinic III, University of Rostock, Rostock, Germany
| | | | | | - Bertram Brenig
- Institute of Veterinary Medicine, University of Göttingen, Göttingen, Germany
| | | | - Daniela Betz
- Small Animal Clinic, University of Veterinary Medicine Hannover Foundation, Hannover, Germany
| | - Johannes Junginger
- Department of Pathology, University of Veterinary Medicine Hannover Foundation, Hannover, Germany
| | | | - Hugo Murua Escobar
- Haematology, Oncology and Palliative Medicine, Clinic III, University of Rostock, Rostock, Germany
| | - Ingo Nolte
- Small Animal Clinic, University of Veterinary Medicine Hannover Foundation, Hannover, Germany.
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Pennock ND, Jindal S, Horton W, Sun D, Narasimhan J, Carbone L, Fei SS, Searles R, Harrington CA, Burchard J, Weinmann S, Schedin P, Xia Z. RNA-seq from archival FFPE breast cancer samples: molecular pathway fidelity and novel discovery. BMC Med Genomics 2019; 12:195. [PMID: 31856832 PMCID: PMC6924022 DOI: 10.1186/s12920-019-0643-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 12/08/2019] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Formalin-fixed, paraffin-embedded (FFPE) tissues for RNA-seq have advantages over fresh frozen tissue including abundance and availability, connection to rich clinical data, and association with patient outcomes. However, FFPE-derived RNA is highly degraded and chemically modified, which impacts its utility as a faithful source for biological inquiry. METHODS True archival FFPE breast cancer cases (n = 58), stored at room temperature for 2-23 years, were utilized to identify key steps in tissue selection, RNA isolation, and library choice. Gene expression fidelity was evaluated by comparing FFPE data to public data obtained from fresh tissues, and by employing single-gene, gene set and transcription network-based regulon analyses. RESULTS We report a single 10 μm section of breast tissue yields sufficient RNA for RNA-seq, and a relationship between RNA quality and block age that was not linear. We find single-gene analysis is limiting with FFPE tissues, while targeted gene set approaches effectively distinguish ER+ from ER- breast cancers. Novel utilization of regulon analysis identified the transcription factor KDM4B to associate with ER+ disease, with KDM4B regulon activity and gene expression having prognostic significance in an independent cohort of ER+ cases. CONCLUSION Our results, which outline a robust FFPE-RNA-seq pipeline for broad use, support utilizing FFPE tissues to address key questions in the breast cancer field, including the delineation between indolent and life-threatening disease, biological stratification and molecular mechanisms of treatment resistance.
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Affiliation(s)
- Nathan D Pennock
- Department of Cell, Developmental and Cancer Biology, Oregon Health & Science University, 2720 SW Moody Ave, Portland, OR, 97201, USA
| | - Sonali Jindal
- Department of Cell, Developmental and Cancer Biology, Oregon Health & Science University, 2720 SW Moody Ave, Portland, OR, 97201, USA
- Knight Cancer Institute, Oregon Health & Science University, 2720 SW Moody Ave, Portland, OR, 97201, USA
| | - Wesley Horton
- Department of Cell, Developmental and Cancer Biology, Oregon Health & Science University, 2720 SW Moody Ave, Portland, OR, 97201, USA
- Computational Biology Program, Oregon Health & Science University, Portland, OR, 97201, USA
| | - Duanchen Sun
- Computational Biology Program, Oregon Health & Science University, Portland, OR, 97201, USA
| | - Jayasri Narasimhan
- Department of Cell, Developmental and Cancer Biology, Oregon Health & Science University, 2720 SW Moody Ave, Portland, OR, 97201, USA
| | - Lucia Carbone
- Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, 97006, USA
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health & Science University, 3303 SW Bond Ave, Portland, OR, 97239, USA
| | - Suzanne S Fei
- Bioinformatics & Biostatistics Core, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, 97006, USA
| | - Robert Searles
- Integrated Genomics Laboratory, Knight Cancer Institute, Oregon Health & Science University Knight Cancer Institute, Portland, OR, 97239, USA
| | - Christina A Harrington
- Integrated Genomics Laboratory, Knight Cancer Institute, Oregon Health & Science University Knight Cancer Institute, Portland, OR, 97239, USA
| | - Julja Burchard
- Computational Biology Program, Oregon Health & Science University, Portland, OR, 97201, USA
| | - Sheila Weinmann
- Center for Health Research, Kaiser Permanente Northwest, Portland, OR, 97278, USA
| | - Pepper Schedin
- Department of Cell, Developmental and Cancer Biology, Oregon Health & Science University, 2720 SW Moody Ave, Portland, OR, 97201, USA.
- Knight Cancer Institute, Oregon Health & Science University, 2720 SW Moody Ave, Portland, OR, 97201, USA.
- Young Women's Breast Cancer Translational Program, University of Colorado Anschutz Medical Campus, 1665 Aurora Court, USA, Aurora, CO, 80045, USA.
| | - Zheng Xia
- Computational Biology Program, Oregon Health & Science University, Portland, OR, 97201, USA.
- Department of Molecular Microbiology and Immunology Oregon Health & Science University, Portland, OR, 97273, USA.
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Enblad M, Graf W, Terman A, Pucholt P, Viklund B, Isaksson A, Birgisson H. Gains of Chromosome 1p and 15q are Associated with Poor Survival After Cytoreductive Surgery and HIPEC for Treating Colorectal Peritoneal Metastases. Ann Surg Oncol 2019; 26:4835-4842. [PMID: 31620944 PMCID: PMC6863794 DOI: 10.1245/s10434-019-07923-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Indexed: 12/21/2022]
Abstract
Purpose Genetic alterations in colorectal peritoneal metastases (PM) are largely unknown. This study was designed to analyze whole-genome copy number alterations (CNA) in colorectal PM and to identify alterations associated with prognosis after cytoreductive surgery (CRS) and hyperthermic intraperitoneal chemotherapy (HIPEC). Methods All patients with PM, originating from a colorectal adenocarcinoma, who were treated with CRS and HIPEC in Uppsala Sweden, between 2004 and 2015, were included (n = 114). DNA derived from formalin-fixed paraffin-embedded (FFPE) specimens were analyzed for CNA using molecular inversion probe arrays. Results There were extensive but varying degrees of CNA, ranging from minimal CNA to total aneuploidy. In particular, gain of parts of chromosome 1p and major parts of 15q were associated with poor survival. A combination of gains of 1p and 15q was associated with poor survival, also after adjustment for differences in peritoneal cancer index and completeness of cytoreduction score [hazard ratio (HR) 5.96; 95% confidence interval (CI) 2.19–16.18]. These patients had a mean copy number (CN) of 3.19 compared with 2.24 in patients without gains. Complete CN analysis was performed in 53 patients. Analysis was unsuccessful for the remaining patients due to insufficient amounts of DNA and signals caused by interstitial components and normal cells. There was no difference in survival between patients with successful and unsuccessful CN analysis. Conclusions This study shows that gains of parts of chromosome 1p and of major parts of chromosome 15q were significantly associated with poor survival after CRS and HIPEC, which could represent future prognostic biomarkers. Electronic supplementary material The online version of this article (10.1245/s10434-019-07923-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Malin Enblad
- Department of Surgical Sciences, Colorectal Surgery, Uppsala University, Uppsala, Sweden.
| | - Wilhelm Graf
- Department of Surgical Sciences, Colorectal Surgery, Uppsala University, Uppsala, Sweden
| | - Alexei Terman
- Department of Immunology, Genetics and Pathology, Experimental Pathology, Uppsala University, Uppsala, Sweden
| | - Pascal Pucholt
- Department of Medical Sciences, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Björn Viklund
- Department of Medical Sciences, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Anders Isaksson
- Department of Medical Sciences, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Helgi Birgisson
- Department of Surgical Sciences, Colorectal Surgery, Uppsala University, Uppsala, Sweden
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Bao X, Duan J, Yan Y, Ma X, Zhang Y, Wang H, Ni D, Wu S, Peng C, Fan Y, Gao Y, Li X, Chen J, Du Q, Zhang F, Zhang X. Upregulation of long noncoding RNA PVT1 predicts unfavorable prognosis in patients with clear cell renal cell carcinoma. Cancer Biomark 2018; 21:55-63. [PMID: 29081406 DOI: 10.3233/cbm-170251] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
BACKGROUND Renal cell carcinoma (RCC) is one of the most malignant genitourinary diseases worldwide. Long noncoding RNAs (lncRNAs) are a class of noncoding RNAs in the human genome that are involved in RCC initiation and progression. OBJECTIVE To investigate the expression of PVT1 in ccRCC and evaluate its correlation with clinicopathologic characteristics and patients' survival. METHODS Quantitative real-time PCR was performed to examine PVT1 expression in 129 ccRCC tissue samples and matched adjacent normal tissue samples. The relationship of PVT1 expression with clinicopathologic characteristics and clinical outcome was evaluated. RESULTS We identified the lncRNA PVT1, which was upregulated in clear cell renal cell carcinoma (ccRCC) tissues when compared with corresponding controls. Furthermore, PVT1 expression was positively associated with gender, tumor size, pT stage, TNM stage, and Fuhrman grade. Kaplan-Meier survival analysis showed that patients with high PVT1 expression had shorter disease-free survival (DFS) and overall-survival (OS) than those with low PVT1 expression, and multivariate analysis identified PVT1 as an independent prognostic factor in ccRCC. CONCLUSIONS PVT1 may be an oncogene as well as may promote metastasis in ccRCC and could serve as a potential biomarker to predict the prognosis of ccRCC patients.
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Affiliation(s)
- Xu Bao
- School of Medicine, Nankai University, Tianjin 300071, China
| | - Junyao Duan
- Department of Urology, Dongzhimen Hospital Affiliated to Beijing University of Chinese Medicine, Beijing 100700, China.,School of Medicine, Nankai University, Tianjin 300071, China
| | - Yongji Yan
- Department of Urology, Dongzhimen Hospital Affiliated to Beijing University of Chinese Medicine, Beijing 100700, China
| | - Xin Ma
- Department of Urology, State Key Laboratory of Kidney Diseases, Chinese People's Liberation Army General Hospital, PLA Medical School, Beijing 100853, China
| | - Yu Zhang
- Department of Urology, State Key Laboratory of Kidney Diseases, Chinese People's Liberation Army General Hospital, PLA Medical School, Beijing 100853, China
| | - Hanfeng Wang
- Department of Urology, State Key Laboratory of Kidney Diseases, Chinese People's Liberation Army General Hospital, PLA Medical School, Beijing 100853, China
| | - Dong Ni
- Department of Urology, State Key Laboratory of Kidney Diseases, Chinese People's Liberation Army General Hospital, PLA Medical School, Beijing 100853, China
| | - Shengpan Wu
- Department of Urology, State Key Laboratory of Kidney Diseases, Chinese People's Liberation Army General Hospital, PLA Medical School, Beijing 100853, China
| | - Cheng Peng
- Department of Urology, State Key Laboratory of Kidney Diseases, Chinese People's Liberation Army General Hospital, PLA Medical School, Beijing 100853, China
| | - Yang Fan
- Department of Urology, State Key Laboratory of Kidney Diseases, Chinese People's Liberation Army General Hospital, PLA Medical School, Beijing 100853, China
| | - Yu Gao
- Department of Urology, State Key Laboratory of Kidney Diseases, Chinese People's Liberation Army General Hospital, PLA Medical School, Beijing 100853, China
| | - Xintao Li
- Department of Urology, State Key Laboratory of Kidney Diseases, Chinese People's Liberation Army General Hospital, PLA Medical School, Beijing 100853, China
| | - Jianwen Chen
- Department of Urology, State Key Laboratory of Kidney Diseases, Chinese People's Liberation Army General Hospital, PLA Medical School, Beijing 100853, China
| | - Qingshan Du
- Department of Urology, State Key Laboratory of Kidney Diseases, Chinese People's Liberation Army General Hospital, PLA Medical School, Beijing 100853, China
| | - Fan Zhang
- Department of Urology, State Key Laboratory of Kidney Diseases, Chinese People's Liberation Army General Hospital, PLA Medical School, Beijing 100853, China
| | - Xu Zhang
- Department of Urology, State Key Laboratory of Kidney Diseases, Chinese People's Liberation Army General Hospital, PLA Medical School, Beijing 100853, China
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Chin SF, Santonja A, Grzelak M, Ahn S, Sammut SJ, Clifford H, Rueda OM, Pugh M, Goldgraben MA, Bardwell HA, Cho EY, Provenzano E, Rojo F, Alba E, Caldas C. Shallow whole genome sequencing for robust copy number profiling of formalin-fixed paraffin-embedded breast cancers. Exp Mol Pathol 2018; 104:161-169. [PMID: 29608913 PMCID: PMC5993858 DOI: 10.1016/j.yexmp.2018.03.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 03/29/2018] [Indexed: 12/14/2022]
Abstract
Pathology archives with linked clinical data are an invaluable resource for translational research, with the limitation that most cancer samples are formalin-fixed paraffin-embedded (FFPE) tissues. Therefore, FFPE tissues are an important resource for genomic profiling studies but are under-utilised due to the low amount and quality of extracted nucleic acids. We profiled the copy number landscape of 356 breast cancer patients using DNA extracted FFPE tissues by shallow whole genome sequencing. We generated a total of 491 sequencing libraries from 2 kits and obtained data from 98.4% of libraries with 86.4% being of good quality. We generated libraries from as low as 3.8 ng of input DNA and found that the success was independent of input DNA amount and quality, processing site and age of the fixed tissues. Since copy number alterations (CNA) play a major role in breast cancer, it is imperative that we are able to use FFPE archives and we have shown in this study that sWGS is a robust method to do such profiling.
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Affiliation(s)
- Suet-Feung Chin
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK; Department of Oncology, University of Cambridge, Cambridge CB2 2QQ, UK; Cancer Research UK Cambridge Cancer Centre, Cambridge CB2 0QQ, UK.
| | - Angela Santonja
- Medical Oncology Service, Hospital Universitario Regional y Virgen de la Victoria, Instituto de Investigación Biomédica de Málaga (IBIMA), Málaga, Spain; Laboratorio de Biología Molecular del Cáncer, Centro de Investigaciones Médico-Sanitarias (CIMES), Universidad de Málaga, Málaga, Spain
| | - Marta Grzelak
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK
| | - Soomin Ahn
- Department of Pathology, Seoul National University Bundang Hospital, 82, Gumi-ro 173 Beon-gil, Bundang-gu, Seongnam, Gyeonggi 13620, Republic of Korea; Inivata, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Stephen-John Sammut
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK; Department of Oncology, University of Cambridge, Cambridge CB2 2QQ, UK; Cancer Research UK Cambridge Cancer Centre, Cambridge CB2 0QQ, UK
| | - Harry Clifford
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK
| | - Oscar M Rueda
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK; Cancer Research UK Cambridge Cancer Centre, Cambridge CB2 0QQ, UK
| | - Michelle Pugh
- Inivata UK, The Portway Building, Granta Park, Cambridge CB21 6GS, UK
| | - Mae A Goldgraben
- Department of Medical Genetics, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Helen A Bardwell
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK
| | - Eun Yoon Cho
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, 50 Irwon-dong, Gangnam-gu, Seoul 135-710, Republic of Korea
| | - Elena Provenzano
- Cambridge Breast Unit, Addenbrooke's Hospital, Cambridge University Hospital NHS Foundation Trust, NIHR Cambridge Biomedical Research Centre, Cambridge CB2 2QQ, UK; Cancer Research UK Cambridge Cancer Centre, Cambridge CB2 0QQ, UK
| | - Federico Rojo
- Pathology Department, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD), Madrid, Spain; GEICAM-Spanish Breast Cancer Research Group, Madrid, Spain
| | - Emilio Alba
- Medical Oncology Service, Hospital Universitario Regional y Virgen de la Victoria, Instituto de Investigación Biomédica de Málaga (IBIMA), Málaga, Spain; GEICAM-Spanish Breast Cancer Research Group, Madrid, Spain; Laboratorio de Biología Molecular del Cáncer, Centro de Investigaciones Médico-Sanitarias (CIMES), Universidad de Málaga, Málaga, Spain
| | - Carlos Caldas
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK; Department of Oncology, University of Cambridge, Cambridge CB2 2QQ, UK; Cambridge Breast Unit, Addenbrooke's Hospital, Cambridge University Hospital NHS Foundation Trust, NIHR Cambridge Biomedical Research Centre, Cambridge CB2 2QQ, UK; Cancer Research UK Cambridge Cancer Centre, Cambridge CB2 0QQ, UK.
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