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Zhang D, Wen Q, Zhang R, Kou K, Lin M, Zhang S, Yang J, Shi H, Yang Y, Tan X, Yin S, Ou X. From Cell to Gene: Deciphering the Mechanism of Heart Failure With Single-Cell Sequencing. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2308900. [PMID: 39159065 DOI: 10.1002/advs.202308900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 07/24/2024] [Indexed: 08/21/2024]
Abstract
Heart failure (HF) is a prevalent cardiovascular disease with significant morbidity and mortality rates worldwide. Due to the intricate structure of the heart, diverse cell types, and the complex pathogenesis of HF, further in-depth investigation into the underlying mechanisms is required. The elucidation of the heterogeneity of cardiomyocytes and the intercellular communication network is particularly important. Traditional high-throughput sequencing methods provide an average measure of gene expression, failing to capture the "heterogeneity" between cells and impacting the accuracy of gene function knowledge. In contrast, single-cell sequencing techniques allow for the amplification of the entire genome or transcriptome at the individual cell level, facilitating the examination of gene structure and expression with unparalleled precision. This approach offers valuable insights into disease mechanisms, enabling the identification of changes in cellular components and gene expressions during hypertrophy associated with HF. Moreover, it reveals distinct cell populations and their unique roles in the HF microenvironment, providing a comprehensive understanding of the cellular landscape that underpins HF pathogenesis. This review focuses on the insights provided by single-cell sequencing techniques into the mechanisms underlying HF and discusses the challenges encountered in current cardiovascular research.
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Affiliation(s)
- Dan Zhang
- Key Laboratory of Medical Electrophysiology of Ministry of Education, Institute of Cardiovascular Medicine, Department of Cardiology of the Affiliated Hospital, Southwest Medical University, Luzhou, Sichuan, 646000, China
- Department of Rehabilitation Medicine, Southwest Medical University, Luzhou, Sichuan, 646000, China
| | - Qiang Wen
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Rd, Wuhan, Hubei, 430022, China
| | - Rui Zhang
- Key Laboratory of Medical Electrophysiology of Ministry of Education, Institute of Cardiovascular Medicine, Department of Cardiology of the Affiliated Hospital, Southwest Medical University, Luzhou, Sichuan, 646000, China
| | - Kun Kou
- Key Laboratory of Medical Electrophysiology of Ministry of Education, Institute of Cardiovascular Medicine, Department of Cardiology of the Affiliated Hospital, Southwest Medical University, Luzhou, Sichuan, 646000, China
| | - Miao Lin
- Key Laboratory of Medical Electrophysiology of Ministry of Education, Institute of Cardiovascular Medicine, Department of Cardiology of the Affiliated Hospital, Southwest Medical University, Luzhou, Sichuan, 646000, China
| | - Shiyu Zhang
- Key Laboratory of Medical Electrophysiology of Ministry of Education, Institute of Cardiovascular Medicine, Department of Cardiology of the Affiliated Hospital, Southwest Medical University, Luzhou, Sichuan, 646000, China
| | - Jun Yang
- Key Laboratory of Medical Electrophysiology of Ministry of Education, Institute of Cardiovascular Medicine, Department of Cardiology of the Affiliated Hospital, Southwest Medical University, Luzhou, Sichuan, 646000, China
| | - Hangchuan Shi
- Department of Clinical & Translational Research, University of Rochester Medical Center, 265 Crittenden Blvd, Rochester, NY, 14642, USA
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, 601 Elmwood Ave, Rochester, NY, 14642, USA
| | - Yan Yang
- Key Laboratory of Medical Electrophysiology of Ministry of Education, Institute of Cardiovascular Medicine, Department of Cardiology of the Affiliated Hospital, Southwest Medical University, Luzhou, Sichuan, 646000, China
| | - Xiaoqiu Tan
- Key Laboratory of Medical Electrophysiology of Ministry of Education, Institute of Cardiovascular Medicine, Department of Cardiology of the Affiliated Hospital, Southwest Medical University, Luzhou, Sichuan, 646000, China
- Department of Physiology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, Sichuan, 646000, China
| | - Shigang Yin
- Luzhou Key Laboratory of Nervous system disease and Brain Function, Southwest Medical University, Luzhou, Sichuan, 646000, China
| | - Xianhong Ou
- Key Laboratory of Medical Electrophysiology of Ministry of Education, Institute of Cardiovascular Medicine, Department of Cardiology of the Affiliated Hospital, Southwest Medical University, Luzhou, Sichuan, 646000, China
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Guangxi Normal University, Guilin, Guangxi, 541004, China
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Ordóñez CD, Mayoral-Campos C, Egas C, Redrejo-Rodríguez M. A primer-independent DNA polymerase-based method for competent whole-genome amplification of intermediate to high GC sequences. NAR Genom Bioinform 2023; 5:lqad073. [PMID: 37608803 PMCID: PMC10440786 DOI: 10.1093/nargab/lqad073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 07/03/2023] [Accepted: 08/09/2023] [Indexed: 08/24/2023] Open
Abstract
Multiple displacement amplification (MDA) has proven to be a useful technique for obtaining large amounts of DNA from tiny samples in genomics and metagenomics. However, MDA has limitations, such as amplification artifacts and biases that can interfere with subsequent quantitative analysis. To overcome these challenges, alternative methods and engineered DNA polymerase variants have been developed. Here, we present new MDA protocols based on the primer-independent DNA polymerase (piPolB), a replicative-like DNA polymerase endowed with DNA priming and proofreading capacities. These new methods were tested on a genomes mixture containing diverse sequences with high-GC content, followed by deep sequencing. Protocols relying on piPolB as a single enzyme cannot achieve competent amplification due to its limited processivity and the presence of ab initio DNA synthesis. However, an alternative method called piMDA, which combines piPolB with Φ29 DNA polymerase, allows proficient and faithful amplification of the genomes. In addition, the prior denaturation step commonly performed in MDA protocols is dispensable, resulting in a more straightforward protocol. In summary, piMDA outperforms commercial methods in the amplification of genomes and metagenomes containing high GC sequences and exhibits similar profiling, error rate and variant determination as the non-amplified samples.
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Affiliation(s)
- Carlos D Ordóñez
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Madrid, Spain
| | - Carmen Mayoral-Campos
- Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM) and Instituto de Investigaciones Biomédicas Sols-Morreale (CSIC-UAM), Madrid, Spain
| | - Conceição Egas
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
- Biocant, Transfer Technology Association, Cantanhede, Portugal
| | - Modesto Redrejo-Rodríguez
- Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM) and Instituto de Investigaciones Biomédicas Sols-Morreale (CSIC-UAM), Madrid, Spain
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Yang J, Shi H, Niu W, Bao X, Liu H, Chen C, Jin H, Song W, Sun Y. Identification of carrier status of Xp22.31 microdeletions associated with X-linked ichthyosis at the single-cell level using haplotype linkage analysis by karyomapping. J Assist Reprod Genet 2023; 40:1735-1746. [PMID: 37154837 PMCID: PMC10352200 DOI: 10.1007/s10815-023-02812-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 04/18/2023] [Indexed: 05/10/2023] Open
Abstract
PURPOSE Currently, owing to the limitations of high-throughput sequencing depth and the allele dropout caused by the whole-genome amplification, detection of chromosomal variants in embryos with CNVs <5 Mb is unsatisfactory at the single-cell level using only conventional sequencing methods. Therefore, here we aimed to use a strategy of preimplantation genetic testing for monogenic (PGT-M) to compensate for the shortcomings of conventional sequencing methods. The purpose of this study is to report the effectiveness of haplotype linkage analysis by karyomapping for preimplantation diagnosis microdeletion diseases. METHODS Six couples carrying chromosomal microdeletions associated with X-linked ichthyosis were recruited, and all couples entered the PGT process. Multiple displacement amplification (MDA) method was used to amplify the whole-genome DNA of trophectoderm cells. Then karyomapping based on single nucleotide polymorphism (SNP) was used for haplotype linkage analysis to detect alleles carrying microdeletions, and CNVs of embryos were identified to determine euploid identity. Amniotic fluid tests were performed in the second trimester to verify the PGT-M results. RESULTS All couples were tested for chromosomal microdeletions, with deletion fragments ranging in size from 1.60 to 1.73 Mb, and one partner in each couple did not carry the microdeletion. Three couples successfully underwent PGT-M assisted conception and obtained healthy live births. CONCLUSION This study shows that haplotype linkage analysis by karyomapping could effectively detect the carrier status of embryos with microdeletions at the single-cell level. This approach may be applied to the preimplantation diagnosis of various chromosomal microvariation diseases.
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Affiliation(s)
- Jingya Yang
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Henan Provincial Obstetrical and Gynecological Diseases (Reproductive Medicine) Clinical Research Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Henan Engineering Laboratory of Preimplantation Genetic Diagnosis and Screening, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Hao Shi
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Henan Provincial Obstetrical and Gynecological Diseases (Reproductive Medicine) Clinical Research Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Henan Engineering Laboratory of Preimplantation Genetic Diagnosis and Screening, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Wenbin Niu
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Henan Provincial Obstetrical and Gynecological Diseases (Reproductive Medicine) Clinical Research Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Henan Engineering Laboratory of Preimplantation Genetic Diagnosis and Screening, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Xiao Bao
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Henan Provincial Obstetrical and Gynecological Diseases (Reproductive Medicine) Clinical Research Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Henan Engineering Laboratory of Preimplantation Genetic Diagnosis and Screening, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Han Liu
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Henan Provincial Obstetrical and Gynecological Diseases (Reproductive Medicine) Clinical Research Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Henan Engineering Laboratory of Preimplantation Genetic Diagnosis and Screening, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Chuanju Chen
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Henan Provincial Obstetrical and Gynecological Diseases (Reproductive Medicine) Clinical Research Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Henan Engineering Laboratory of Preimplantation Genetic Diagnosis and Screening, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Haixia Jin
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Henan Provincial Obstetrical and Gynecological Diseases (Reproductive Medicine) Clinical Research Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Henan Engineering Laboratory of Preimplantation Genetic Diagnosis and Screening, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Wenyan Song
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Henan Provincial Obstetrical and Gynecological Diseases (Reproductive Medicine) Clinical Research Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Henan Engineering Laboratory of Preimplantation Genetic Diagnosis and Screening, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Yingpu Sun
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
- Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
- Henan Provincial Obstetrical and Gynecological Diseases (Reproductive Medicine) Clinical Research Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
- Henan Engineering Laboratory of Preimplantation Genetic Diagnosis and Screening, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
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Yamazaki M, Hosokawa M, Matsunaga H, Arikawa K, Takamochi K, Suzuki K, Hayashi T, Kambara H, Takeyama H. Integrated spatial analysis of gene mutation and gene expression for understanding tumor diversity in formalin-fixed paraffin-embedded lung adenocarcinoma. Front Oncol 2022; 12:936190. [PMID: 36505794 PMCID: PMC9731154 DOI: 10.3389/fonc.2022.936190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 10/31/2022] [Indexed: 11/26/2022] Open
Abstract
Introduction A deeper understanding of intratumoral heterogeneity is essential for prognosis prediction or accurate treatment plan decisions in clinical practice. However, due to the cross-links and degradation of biomolecules within formalin-fixed paraffin-embedded (FFPE) specimens, it is challenging to analyze them. In this study, we aimed to optimize the simultaneous extraction of mRNA and DNA from microdissected FFPE tissues (φ = 100 µm) and apply the method to analyze tumor diversity in lung adenocarcinoma before and after erlotinib administration. Method Two magnetic beads were used for the simultaneous extraction of mRNA and DNA. The decross-linking conditions were evaluated for gene mutation and gene expression analyses of microdissected FFPE tissues. Lung lymph nodes before treatment and lung adenocarcinoma after erlotinib administration were collected from the same patient and were preserved as FFPE specimens for 4 years. Gene expression and gene mutations between histologically classified regions of lung adenocarcinoma (pre-treatment tumor in lung lymph node biopsies and post-treatment tumor, normal lung, tumor stroma, and remission stroma, in resected lung tissue) were compared in a microdissection-based approach. Results Using the optimized simultaneous extraction of DNA and mRNA and whole-genome amplification, we detected approximately 4,000-10,000 expressed genes and the epidermal growth factor receptor (EGFR) driver gene mutations from microdissected FFPE tissues. We found the differences in the highly expressed cancer-associated genes and the positive rate of EGFR exon 19 deletions among the tumor before and after treatment and tumor stroma, even though they were collected from tumors of the same patient or close regions of the same specimen. Conclusion Our integrated spatial analysis method would be applied to various FFPE pathology specimens providing area-specific gene expression and gene mutation information.
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Affiliation(s)
- Miki Yamazaki
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan,Computational Bio Big-Data Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Masahito Hosokawa
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan,Computational Bio Big-Data Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan,Research Organization for Nano and Life Innovation, Waseda University, Tokyo, Japan,Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Waseda University, Tokyo, Japan
| | - Hiroko Matsunaga
- Research Organization for Nano and Life Innovation, Waseda University, Tokyo, Japan
| | - Koji Arikawa
- Research Organization for Nano and Life Innovation, Waseda University, Tokyo, Japan
| | - Kazuya Takamochi
- Department of Thoracic Surgery, Juntendo University School of Medicine, Tokyo, Japan
| | - Kenji Suzuki
- Department of Thoracic Surgery, Juntendo University School of Medicine, Tokyo, Japan
| | - Takuo Hayashi
- Department of Human Pathology, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Hideki Kambara
- Research Organization for Nano and Life Innovation, Waseda University, Tokyo, Japan,Frontier BioSystems Inc., Tokyo, Japan
| | - Haruko Takeyama
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan,Computational Bio Big-Data Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan,Research Organization for Nano and Life Innovation, Waseda University, Tokyo, Japan,Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Waseda University, Tokyo, Japan,*Correspondence: Haruko Takeyama,
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Wang X, Liu Y, Liu H, Pan W, Ren J, Zheng X, Tan Y, Chen Z, Deng Y, He N, Chen H, Li S. Recent advances and application of whole genome amplification in molecular diagnosis and medicine. MedComm (Beijing) 2022; 3:e116. [PMID: 35281794 PMCID: PMC8906466 DOI: 10.1002/mco2.116] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 01/11/2022] [Accepted: 01/12/2022] [Indexed: 11/30/2022] Open
Abstract
Whole genome amplification (WGA) is a technology for non-selective amplification of the whole genome sequence, first appearing in 1992. Its primary purpose is to amplify and reflect the whole genome of trace tissues and single cells without sequence bias and to provide sufficient DNA template for subsequent multigene and multilocus analysis, along with comprehensive genome research. WGA provides a method to obtain a large amount of genetic information from a small amount of DNA and provides a valuable tool for preserving limited samples in molecular biology. WGA technology is especially suitable for forensic identification and genetic disease research, along with new technologies such as next-generation sequencing (NGS). In addition, WGA is also widely used in single-cell sequencing. Due to the small amount of DNA in a single cell, it is often unable to meet the amount of samples needed for sequencing, so WGA is generally used to achieve the amplification of trace samples. This paper reviews WGA methods based on different principles, summarizes both amplification principle and amplification quality, and discusses the application prospects and challenges of WGA technology in molecular diagnosis and medicine.
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Affiliation(s)
- Xiaoyu Wang
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
| | - Yapeng Liu
- School of Early‐Childhood Education, Nanjing Xiaozhuang UniversityNanjingChina
| | - Hongna Liu
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
| | - Wenjing Pan
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
| | - Jie Ren
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
| | - Xiangming Zheng
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
| | - Yimin Tan
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
| | - Zhu Chen
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
| | - Yan Deng
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
| | - Nongyue He
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
- State Key Laboratory of BioelectronicsSoutheast UniversityNanjingChina
| | - Hui Chen
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
| | - Song Li
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
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Filia A, Droop A, Harland M, Thygesen H, Randerson-Moor J, Snowden H, Taylor C, Diaz JMS, Pozniak J, Nsengimana J, Laye J, Newton-Bishop JA, Bishop DT. High-Resolution Copy Number Patterns From Clinically Relevant FFPE Material. Sci Rep 2019; 9:8908. [PMID: 31222134 PMCID: PMC6586881 DOI: 10.1038/s41598-019-45210-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 05/07/2019] [Indexed: 11/09/2022] Open
Abstract
Systematic tumour profiling is essential for biomarker research and clinically for assessing response to therapy. Solving the challenge of delivering informative copy number (CN) profiles from formalin-fixed paraffin embedded (FFPE) material, the only likely readily available biospecimen for most cancers, involves successful processing of small quantities of degraded DNA. To investigate the potential for analysis of such lesions, whole-genome CNVseq was applied to 300 FFPE primary tumour samples, obtained from a large-scale epidemiological study of melanoma. The quality and the discriminatory power of CNVseq was assessed. Libraries were successfully generated for 93% of blocks, with input DNA quantity being the only predictor of success (success rate dropped to 65% if <20 ng available); 3% of libraries were dropped because of low sequence alignment rates. Technical replicates showed high reproducibility. Comparison with targeted CN assessment showed consistency with the Next Generation Sequencing (NGS) analysis. We were able to detect and distinguish CN changes with a resolution of ≤10 kb. To demonstrate performance, we report the spectrum of genomic CN alterations (CNAs) detected at 9p21, the major site of CN change in melanoma. This successful analysis of CN in FFPE material using NGS provides proof of principle for intensive examination of population-based samples.
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Affiliation(s)
- Anastasia Filia
- Section of Epidemiology and Biostatistics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom
- Centre for Translational Research, Biomedical Research Foundation of the Academy of Athens (BRFAA), Athens, Greece
| | - Alastair Droop
- MRC Medical Bioinformatics Centre, Leeds Institute of Data Analytics, University of Leeds, Leeds, United Kingdom
| | - Mark Harland
- Section of Epidemiology and Biostatistics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom
| | - Helene Thygesen
- Section of Epidemiology and Biostatistics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom
| | - Juliette Randerson-Moor
- Section of Epidemiology and Biostatistics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom
| | - Helen Snowden
- Section of Epidemiology and Biostatistics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom
| | - Claire Taylor
- Section of Epidemiology and Biostatistics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom
| | - Joey Mark S Diaz
- Section of Epidemiology and Biostatistics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom
| | - Joanna Pozniak
- Section of Epidemiology and Biostatistics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom
| | - Jérémie Nsengimana
- Section of Epidemiology and Biostatistics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom
| | - Jon Laye
- Section of Epidemiology and Biostatistics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom
| | - Julia A Newton-Bishop
- Section of Epidemiology and Biostatistics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom
| | - D Timothy Bishop
- Section of Epidemiology and Biostatistics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom.
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