1
|
Nano E, Gambella A, Paudice M, Garuti A, Pigozzi S, Valle L, Grillo F, Mastracci L. Be bold, start cold! cold formalin fixation of colorectal cancer specimens granted superior DNA and RNA quality for downstream molecular analysis. Histochem Cell Biol 2024; 162:541-550. [PMID: 39317804 PMCID: PMC11455702 DOI: 10.1007/s00418-024-02326-5] [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] [Accepted: 09/10/2024] [Indexed: 09/26/2024]
Abstract
The use of cold formalin fixation (CFF; i.e., fixating tissue samples with 4 °C precooled formalin) recently attracted further attention owing to its putative improved ability to preserve nucleic acid compared with standard room temperature formalin (SFF). In this study, we aimed to assess the effect of four formalin-based fixation protocols (SFF, CFF, delayed formalin fixation-DFF, and cold formalin hyperfixation; CFH) on both DNA and RNA quality. We collected 97 colorectal cancer (CRC) and analyzed 23 metrics of nucleic acid quantity and quality yield using a multiplatform approach by combining spectrophotometric, fluorimetric, electrophoretic, and polymerase chain reaction (PCR) assays. Following confirmation of fixation-protocol-related different effects via clustering analysis, CFF presented best metrics compared with all protocols, specifically positive coefficients of DV1000-60000, DV2/DV1, DNA λ ratio 260/230, and ABL gene expression absolute copies, and negative coefficient of DV150-1000. The SFF subgroup presented a positive coefficient of DV150-1000 and negative coefficients for DV1000-60000, DV2/DV1, RNA λ ratio 260/230, RNA QuBit concentration, DV100/200, RNA electrophoresis concentration and absolute quantity, and ABL copies. Overall, we confirmed the superior yield performances of CFF preservation for both DNA and RNA compared with the other protocols in our series of CRC samples. Pending further validations and clarification of the specific mechanisms behind these findings, our study supports the implementation of CFF in the pathology unit routine specimen management for tumor tissue molecular profiling.
Collapse
Affiliation(s)
- Ennio Nano
- Molecular Pathology Unit, IRCCS San Martino Policlinic Hospital of Genoa, Genoa, Italy
| | - Alessandro Gambella
- Pathology Unit, Department of Surgical Sciences and Integrated Diagnostics (DISC), University of Genoa, Genoa, Italy.
| | - Michele Paudice
- Pathology Unit, Department of Surgical Sciences and Integrated Diagnostics (DISC), University of Genoa, Genoa, Italy
- IRCCS San Martino Policlinic Hospital of Genoa, Genoa, Italy
| | - Anna Garuti
- Internal Medicine Clinic, IRCCS San Martino Policlinic Hospital of Genoa, Genoa, Italy
| | - Simona Pigozzi
- Pathology Unit, Department of Surgical Sciences and Integrated Diagnostics (DISC), University of Genoa, Genoa, Italy
- IRCCS San Martino Policlinic Hospital of Genoa, Genoa, Italy
| | - Luca Valle
- IRCCS San Martino Policlinic Hospital of Genoa, Genoa, Italy
| | - Federica Grillo
- Pathology Unit, Department of Surgical Sciences and Integrated Diagnostics (DISC), University of Genoa, Genoa, Italy
- IRCCS San Martino Policlinic Hospital of Genoa, Genoa, Italy
| | - Luca Mastracci
- Pathology Unit, Department of Surgical Sciences and Integrated Diagnostics (DISC), University of Genoa, Genoa, Italy
- IRCCS San Martino Policlinic Hospital of Genoa, Genoa, Italy
| |
Collapse
|
2
|
Merker Breyer G, De Carli S, Rocha Jacques Da Silva ME, Dias ME, Muterle Varela AP, Bertoni Mann M, Frazzon J, Quoos Mayer F, Góes Neto A, Maboni Siqueira F. Alternative amplicon-PCR protocol for maximizing bacterial and fungal sequencing in low-biomass samples. Anal Biochem 2024; 687:115449. [PMID: 38145697 DOI: 10.1016/j.ab.2023.115449] [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: 08/23/2023] [Revised: 12/20/2023] [Accepted: 12/22/2023] [Indexed: 12/27/2023]
Abstract
Determining bacterial and fungal communities from low-biomass samples remains a challenge for high-throughput sequencing. Due to the low microbial load and host contamination, some sites, including the female upper reproductive tract and the lower respiratory tract, were even considered sterile until recent years. Despite efforts to improve sampling and DNA isolation protocols, some samples provide insufficient microbial DNA input for library preparation and sequencing. Herein, we propose an alternative amplicon-PCR protocol to be used in bacterial and fungal sequencing in low-biomass samples, targeting 16S-rDNA and the internal transcribed spacer region (ITS), respectively. Similar to a nested-PCR, we performed two sequential PCR reactions to maximise the target amplicon. We compared metagenomic results from the original Illumina protocol (Protocol 1 - P1) and the alternative one (Protocol 2 - P2), using a mock community and clinical samples with different microbial loads. Our findings showed no significant differences in data generated by P1 and P2, indicating that the second amplification round does not bias the microbiota diversity rates. Thus, the alternative protocol can be applied for low-biomass samples when the original protocol results in spurious output, preventing library preparation and sequencing.
Collapse
Affiliation(s)
- Gabriela Merker Breyer
- Laboratório de Bacteriologia Veterinária (LaBacVet), Universidade Federal do Rio Grande do Sul, Departamento de Patologia Veterinária, Porto Alegre, Brazil; Programa de Pós-Graduação em Ciências Veterinárias, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Silvia De Carli
- Laboratório de Bacteriologia Veterinária (LaBacVet), Universidade Federal do Rio Grande do Sul, Departamento de Patologia Veterinária, Porto Alegre, Brazil; Programa de Pós-Graduação em Ciências Veterinárias, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Maria Eduarda Rocha Jacques Da Silva
- Laboratório de Bacteriologia Veterinária (LaBacVet), Universidade Federal do Rio Grande do Sul, Departamento de Patologia Veterinária, Porto Alegre, Brazil
| | - Maria Eduarda Dias
- Laboratório de Bacteriologia Veterinária (LaBacVet), Universidade Federal do Rio Grande do Sul, Departamento de Patologia Veterinária, Porto Alegre, Brazil
| | - Ana Paula Muterle Varela
- Programa de Pós-Graduação em Biociências, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, Brazil
| | - Michele Bertoni Mann
- Programa de Pós-Graduação em Microbiologia Agrícola e do Ambiente, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Jeverson Frazzon
- Programa de Pós-Graduação em Microbiologia Agrícola e do Ambiente, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil; Laboratório de Bioquímica e Biologia Molecular de Microrganismos, Departamento de Ciência de Alimentos, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Fabiana Quoos Mayer
- Centro de Pesquisa em Saúde Animal, Instituto de Pesquisas Veterinárias Desidério Finamor, Departamento de Diagnóstico e Pesquisa Agropecuária, Secretaria da Agricultura, Pecuária e Desenvolvimento Rural, Eldorado do Sul, Brazil
| | - Aristóteles Góes Neto
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Franciele Maboni Siqueira
- Laboratório de Bacteriologia Veterinária (LaBacVet), Universidade Federal do Rio Grande do Sul, Departamento de Patologia Veterinária, Porto Alegre, Brazil; Programa de Pós-Graduação em Ciências Veterinárias, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.
| |
Collapse
|
3
|
Hiramatsu K, Matsuda C, Masago K, Toriyama K, Sasaki E, Fujita Y, Haneda M, Ebi H, Shibata N, Hosoda W. Diagnostic utility of DNA integrity number as an indicator of sufficient DNA quality in next-generation sequencing-based genomic profiling. Am J Clin Pathol 2023; 160:261-267. [PMID: 37167067 DOI: 10.1093/ajcp/aqad046] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 03/29/2023] [Indexed: 05/13/2023] Open
Abstract
OBJECTIVES DNA integrity number (DIN) is a metric for assessing DNA degradation, calculated based on electrophoresis using the Agilent TapeStation System. The utility of DIN as a diagnostic indicator of sufficient DNA quality in clinical next-generation sequencing (NGS) has not been well described. METHODS We evaluated the DINs of 166 tumor formalin-fixed, paraffin-embedded (FFPE) tissue samples submitted for 124-gene panel sequencing. We also investigated a new metric on the electropherogram that could improve the predictive accuracy of the DIN. RESULTS A DIN cutoff of 2.5 discriminated samples with successful analysis (n = 143) from samples with failed analysis (n = 23), with a sensitivity of 0.84 and a specificity of 0.78 (area under the curve [AUC] = 0.88). The DIN was positively correlated with the mean coverage (r = 0.72, P < .0001) but could not discriminate success from failure when the DIN was below 2.5 (negative predictive value, 0.44). We introduced a new metric, the peak/base ratio, that distinguished success from failure with higher accuracy than the DIN (cutoff = 1.6; sensitivity = 0.98, specificity = 0.83, and AUC =0.96). CONCLUSIONS To predict successful NGS, the DNA quality of FFPE tissue can be easily and reliably assessed using the DIN and peak/base ratio.
Collapse
Affiliation(s)
- Kaho Hiramatsu
- Department of Pathology and Molecular Diagnostics, Aichi Cancer Center Hospital, Aichi, Japan
| | - Chiaki Matsuda
- Department of Pathology and Molecular Diagnostics, Aichi Cancer Center Hospital, Aichi, Japan
| | - Katsuhiro Masago
- Department of Pathology and Molecular Diagnostics, Aichi Cancer Center Hospital, Aichi, Japan
| | - Kazuhiro Toriyama
- Department of Pathology and Molecular Diagnostics, Aichi Cancer Center Hospital, Aichi, Japan
| | - Eiichi Sasaki
- Department of Pathology and Molecular Diagnostics, Aichi Cancer Center Hospital, Aichi, Japan
| | - Yasuko Fujita
- Department of Pathology and Molecular Diagnostics, Aichi Cancer Center Hospital, Aichi, Japan
| | - Masataka Haneda
- Department of Pathology and Molecular Diagnostics, Aichi Cancer Center Hospital, Aichi, Japan
| | - Hiromichi Ebi
- Division of Molecular Therapeutics, Aichi Cancer Center Research Institute, Aichi, Japan
| | - Noriko Shibata
- Department of Pathology and Molecular Diagnostics, Aichi Cancer Center Hospital, Aichi, Japan
| | - Waki Hosoda
- Department of Pathology and Molecular Diagnostics, Aichi Cancer Center Hospital, Aichi, Japan
| |
Collapse
|
4
|
Noda Y, Yamaka R, Atsumi N, Higasa K, Tsuta K. Areas of Crush Nuclear Streaming Should Be Included as Tumor Content in the Era of Molecular Diagnostics. Cancers (Basel) 2023; 15:cancers15061910. [PMID: 36980797 PMCID: PMC10099727 DOI: 10.3390/cancers15061910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 03/14/2023] [Accepted: 03/21/2023] [Indexed: 03/29/2023] Open
Abstract
Degenerated tissues are frequently observed in malignant tumors, but are not analyzed. We investigated whether nuclear streaming and necrosis samples could be used for genetic analysis to expand the sample pool. A total of 81 samples were extracted from small cell carcinoma and lymphoma FFPE tissue blocks and classified into three histological cohorts: 33 materials with well-preserved tumor morphology, 31 nuclear streaming samples, and 17 necrosis samples. DNA and RNA integrity numbers, percentage of RNA fragments with >200 nucleotides, and next-generation sequencing quality metrics were compared among the cohorts. DNA quality did not significantly differ between nuclear streaming materials and materials with well-preserved morphology, whereas that of the necrosis samples was inferior. RNA quality decreased in the following order: materials with well-preserved morphology > nuclear streaming > necrosis. The sequencing metrics did not differ significantly between the nuclear streaming samples and materials with well-preserved morphology, and reliable variants were detected. The necrosis samples extracted from resections exhibited sequencing failure and showed significantly fewer on-target aligned reads and variants. However, variant allele frequency did not differ among the cohorts. We revelated that DNA in nuclear streaming samples, especially within biopsies, could be used for genetic analysis. Moreover, degenerated non-tumor cells should be counted when evaluating tumor content to avoid misinterpreting the variant allele frequency.
Collapse
Affiliation(s)
- Yuri Noda
- Department of Pathology, Kansai Medical University, 2-5-1 Shin-machi, Hirakata 573-1010, Osaka, Japan
- Department of Pathology and Laboratory Medicine, Kansai Medical University Hospital, 2-3-1 Shin-machi, Hirakata 573-1191, Osaka, Japan
- Correspondence:
| | - Ryosuke Yamaka
- Department of Pathology and Laboratory Medicine, Kansai Medical University Hospital, 2-3-1 Shin-machi, Hirakata 573-1191, Osaka, Japan
| | - Naho Atsumi
- Department of Pathology, Kansai Medical University, 2-5-1 Shin-machi, Hirakata 573-1010, Osaka, Japan
| | - Koichiro Higasa
- Department of Genome Analysis, Institute of Biomedical Science, Kansai Medical University, 2-5-1 Shin-machi, Hirakata 573-1010, Osaka, Japan
| | - Koji Tsuta
- Department of Pathology, Kansai Medical University, 2-5-1 Shin-machi, Hirakata 573-1010, Osaka, Japan
- Department of Pathology and Laboratory Medicine, Kansai Medical University Hospital, 2-3-1 Shin-machi, Hirakata 573-1191, Osaka, Japan
| |
Collapse
|
5
|
Leong TL, Aloe C, Aujla S, Wang H, Gayevskiy V, Asselin-Labat ML, Gray LA, Steinfort D, Bozinovski S. Heterogeneity of tumour mutational burden in metastatic NSCLC demonstrated by endobronchial ultrasound sampling. Front Oncol 2023; 13:1150349. [PMID: 36994206 PMCID: PMC10042177 DOI: 10.3389/fonc.2023.1150349] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 02/22/2023] [Indexed: 03/14/2023] Open
Abstract
IntroductionTumour mutational burden (TMB) is an important emerging biomarker for immune checkpoint inhibitors (ICI). The stability of TMB values across distinct EBUS tumour regions is not well defined in advanced lung cancer patients.MethodsThis study included a whole-genome sequencing cohort (n=11, LxG cohort) and a targeted Oncomine TML panel cohort (n=10, SxD cohort), where paired primary and metastatic samples were obtained by endobronchial ultrasound transbronchial needle aspiration (EBUS-TBNA).ResultsThe LxG cohort displayed a strong correlation between the paired primary and metastatic sites, with a median TMB score of 7.70 ± 5.39 and 8.31 ± 5.88 respectively. Evaluation of the SxD cohort demonstrated greater inter-tumoural TMB heterogeneity, where Spearman correlation between the primary and metastatic sites fell short of significance. Whilst median TMB scores were not significantly different between the two sites, 3 out of 10 paired samples were discordant when using a TMB cut-off of 10 mutations per Mb. In addition, PD-L1 copy number and KRAS mutations were assessed, demonstrating the feasibility of performing multiple molecular tests relevant to ICI treatment using a single EBUS sample. We also observed good consistency in PD-L1 copy number and KRAS mutation, where cut-off estimates were consistent across the primary and metastatic sites.ConclusionsAssessment of TMB acquired by EBUS from multiple sites is highly feasible and has the potential to improve accuracy of TMB panels as a companion diagnostic test. We demonstrate similar TMB values across primary and metastatic sites, however 3 out of 10 samples displayed inter-tumoural heterogeneity that would alter clinical management.
Collapse
Affiliation(s)
- Tracy L. Leong
- Department of Respiratory Medicine, Austin Health, Heidelberg, VIC, Australia
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Faculty of Medicine, University of Melbourne, Parkville, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Christian Aloe
- School of Health & Biomedical Sciences, RMIT University, Bundoora, VIC, Australia
| | - Savreet Aujla
- School of Health & Biomedical Sciences, RMIT University, Bundoora, VIC, Australia
| | - Hao Wang
- School of Health & Biomedical Sciences, RMIT University, Bundoora, VIC, Australia
| | - Velimir Gayevskiy
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Marie-Liesse Asselin-Labat
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Lesley-Ann Gray
- Australian Genome Research Facility Ltd., Melbourne, VIC, Australia
| | - Daniel Steinfort
- Faculty of Medicine, University of Melbourne, Parkville, VIC, Australia
- Department of Respiratory Medicine, Royal Melbourne Hospital, Melbourne, VIC, Australia
- *Correspondence: Steven Bozinovski, ; Daniel Steinfort,
| | - Steven Bozinovski
- School of Health & Biomedical Sciences, RMIT University, Bundoora, VIC, Australia
- *Correspondence: Steven Bozinovski, ; Daniel Steinfort,
| |
Collapse
|
6
|
Comprehensive Development and Implementation of Good Laboratory Practice for NGS Based Targeted Panel on Solid Tumor FFPE Tissues in Diagnostics. Diagnostics (Basel) 2022; 12:diagnostics12051291. [PMID: 35626446 PMCID: PMC9141409 DOI: 10.3390/diagnostics12051291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 05/03/2022] [Accepted: 05/09/2022] [Indexed: 11/25/2022] Open
Abstract
The speed, accuracy, and increasing affordability of next-generation sequencing (NGS) have revolutionized the advent of precision medicine. To date, standardized validation criteria for diagnostic accreditation do not exist due to variability across the multitude of NGS platforms and within NGS processes. In molecular diagnostics, it is necessary to ensure that the primary material of the FFPE sample has good quality and optimum quantity for the analysis, otherwise the laborious and expensive NGS test may result in unreliable information. Therefore, stringent quality control of DNA and RNA before, during, and after library preparation is an essential parameter. Considering the various challenges with the FFPE samples, we aimed to set a benchmark in QC metrics that can be utilized by molecular diagnostic laboratories for successful library preparation and high-quality NGS data output. In total, 144 DNA and 103 RNA samples of various cancer types with a maximum storage of 2 years were processed for 52 gene focus panels. During the making of DNA and RNA libraries, extensive QC check parameters were imposed at different checkpoints. The decision tree approach can be set as a benchmark for FFPE samples and as a guide to establishing a good clinical laboratory practice for targeted NGS panels.
Collapse
|
7
|
Sung MT, Wang YH, Li CF. Open the Technical Black Box of Tumor Mutational Burden (TMB): Factors Affecting Harmonization and Standardization of Panel-Based TMB. Int J Mol Sci 2022; 23:ijms23095097. [PMID: 35563486 PMCID: PMC9103036 DOI: 10.3390/ijms23095097] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/30/2022] [Accepted: 05/02/2022] [Indexed: 01/25/2023] Open
Abstract
As tumor mutational burden (TMB) has been approved as a predictive biomarker for immune checkpoint inhibitors (ICIs), next-generation sequencing (NGS) TMB panels are being increasingly used clinically. However, only a few of them have been validated in clinical trials or authorized by administration. The harmonization and standardization of TMB panels are thus essential for clinical implementation. In this review, preanalytic, sequencing, bioinformatics and interpretative factors are summarized to provide a comprehensive picture of how the different factors affect the estimation of panel-based TMB. Among the factors, poor DNA quality, improper formalin fixation and residual germline variants after filtration may overestimate TMB, while low tumor purity may decrease the sensitivity of the TMB panel. In addition, a small panel size leads to more variability when comparing with true TMB values detected by whole-exome sequencing (WES). A panel covering a genomic region of more than 1Mb is more stable for harmonization and standardization. Because the TMB estimate reflects the sum of effects from multiple factors, deliberation based on laboratory and specimen quality, as well as clinical information, is essential for decision making.
Collapse
Affiliation(s)
- Meng-Ta Sung
- Division of Hematology and Oncology, Department of Internal Medicine, MacKay Memorial Hospital, Taipei 104217, Taiwan;
- Division of Hematology and Medical Oncology, Mennonite Christian Hospital, Hualien 970472, Taiwan
| | - Yeh-Han Wang
- Division of Pathology and Medical Informatics, ACT Genomics Co., Ltd., Taipei 114065, Taiwan
- ACT Precision Medicine Clinic, Taipei 114063, Taiwan
- College of Nursing, National Taipei University of Nursing and Health Sciences, Taipei 112303, Taiwan
- Institute of Public Health, National Yang Ming Chao Tung University, Taipei 112304, Taiwan
- Correspondence:
| | - Chien-Feng Li
- Department of Medical Research, Chi Mei Medical Center, Tainan 710402, Taiwan;
- Institute of Precision Medicine, National Sun Yat-Sen University, Kaohsiung 804201, Taiwan
- National Institute of Cancer Research, National Health Research Institutes, Tainan 704016, Taiwan
| |
Collapse
|
8
|
Human Papillomavirus Detection by Whole-Genome Next-Generation Sequencing: Importance of Validation and Quality Assurance Procedures. Viruses 2021; 13:v13071323. [PMID: 34372528 PMCID: PMC8310033 DOI: 10.3390/v13071323] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/04/2021] [Accepted: 06/18/2021] [Indexed: 12/27/2022] Open
Abstract
Next-generation sequencing (NGS) yields powerful opportunities for studying human papillomavirus (HPV) genomics for applications in epidemiology, public health, and clinical diagnostics. HPV genotypes, variants, and point mutations can be investigated in clinical materials and described in previously unprecedented detail. However, both the NGS laboratory analysis and bioinformatical approach require numerous steps and checks to ensure robust interpretation of results. Here, we provide a step-by-step review of recommendations for validation and quality assurance procedures of each step in the typical NGS workflow, with a focus on whole-genome sequencing approaches. The use of directed pilots and protocols to ensure optimization of sequencing data yield, followed by curated bioinformatical procedures, is particularly emphasized. Finally, the storage and sharing of data sets are discussed. The development of international standards for quality assurance should be a goal for the HPV NGS community, similar to what has been developed for other areas of sequencing efforts including microbiology and molecular pathology. We thus propose that it is time for NGS to be included in the global efforts on quality assurance and improvement of HPV-based testing and diagnostics.
Collapse
|
9
|
Kuwata T, Wakabayashi M, Hatanaka Y, Morii E, Oda Y, Taguchi K, Noguchi M, Ishikawa Y, Nakajima T, Sekine S, Nomura S, Okamoto W, Fujii S, Yoshino T. Impact of DNA integrity on the success rate of tissue-based next-generation sequencing: Lessons from nationwide cancer genome screening project SCRUM-Japan GI-SCREEN. Pathol Int 2020; 70:932-942. [PMID: 33030786 PMCID: PMC7820973 DOI: 10.1111/pin.13029] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 09/15/2020] [Indexed: 12/14/2022]
Abstract
In the nationwide cancer genome screening project SCRUM-Japan GI-SCREEN, 2590 archival formalin-fixed paraffin-embedded (FFPE) tumor tissues from 19 institutions were analyzed with two tissue-based next-generation sequencing (NGS) panels at the Clinical Laboratory Improvement Amendments (CLIA)-certified College of American Pathologists (CAP)-accredited central laboratory. The Oncomine Cancer Research Panel (OCP; 143 genes) succeeded in producing validated results for only 68.3% of the samples (%OCP-success). CE-IVD (25 genes) succeeded in 45.9% of the OCP-failed samples, leading to an overall NGS success (%combined-success) rate as high as 82.9%. Among 2573 samples, the DNA-integrity (ΔCt )-high (ΔCt < 4.4, n = 1253) samples showed significantly higher %OCP- and %combined-success rates (90.2% and 97.4%, respectively) than the DNA-integrity-intermediate (4.4 < ΔCt < 6.3, n = 911; 68.9% and 88.7%) and DNA-integrity-low ones (ΔCt > 6.3 or polymerase chain reaction-failed, n = 409; 5.6% and 24.7%). Other factors associated with NGS success included the FFPE-sample storage period (<4 years), the specimen type (surgical) and the primary tumor site (colorectal). Multivariable analysis revealed DNA integrity as the factor with the strongest independent association with NGS success, although it was suggested that other institution-specific factors contribute to the discordance of inter-institutional NGS success rates. Our results emphasize the importance of DNA quality in FFPE samples for NGS tests and the impact of DNA integrity on quality monitoring of pathology specimens for achieving successful NGS.
Collapse
Affiliation(s)
- Takeshi Kuwata
- Department of Genetic Medicine and ServicesNational Cancer Center Hospital EastChibaJapan
- Department of Pathology and Clinical LaboratoriesNational Cancer Center Hospital EastChibaJapan
| | - Masashi Wakabayashi
- Clinical Research Support OfficeNational Cancer Center Hospital EastChibaJapan
| | - Yutaka Hatanaka
- Research Division of Genome Companion DiagnosticsHokkaido University HospitalHokkaidoJapan
| | - Eiichi Morii
- Department of PathologyOsaka University Graduate School of MedicineOsakaJapan
| | - Yoshinao Oda
- Department of Anatomic Pathology, Pathological Sciences, Graduate School of Medical SciencesKyushu UniversityFukuokaJapan
| | - Kenichi Taguchi
- Department of PathologyNational Hospital Organization Kyushu Cancer CenterFukuokaJapan
| | - Masayuki Noguchi
- Department of Diagnostic Pathology, Faculty of MedicineUniversity of TsukubaIbarakiJapan
| | - Yuichi Ishikawa
- Department of Pathology, the Cancer InstituteJapanese Foundation for Cancer ResearchTokyoJapan
| | - Takashi Nakajima
- Division of Diagnostic PathologyShizuoka Cancer Center HospitalShizuokaJapan
| | - Shigeki Sekine
- Department of PathologyNational Cancer Center HospitalTokyoJapan
| | - Shogo Nomura
- Clinical Research Support OfficeNational Cancer Center Hospital EastChibaJapan
| | - Wataru Okamoto
- Translational Research Support SectionNational Cancer Center Hospital EastChibaJapan
- Cancer Treatment CenterHiroshima University HospitalHiroshimaJapan
| | - Satoshi Fujii
- Department of Pathology and Clinical LaboratoriesNational Cancer Center Hospital EastChibaJapan
- Department of Molecular PathologyYokohama City University Graduate School of MedicineKanagawaJapan
| | - Takayuki Yoshino
- Department of Gastrointestinal OncologyNational Cancer Center Hospital EastChibaJapan
| | | |
Collapse
|
10
|
Flores Bueso Y, Walker SP, Hogan G, Claesson MJ, Tangney M. Protoblock - A biological standard for formalin fixed samples. MICROBIOME 2020; 8:122. [PMID: 32828122 PMCID: PMC7443293 DOI: 10.1186/s40168-020-00901-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 07/24/2020] [Indexed: 05/16/2023]
Abstract
BACKGROUND Formalin-fixed, paraffin-embedded (FFPE) tissue is the gold standard in pathology tissue storage, representing the largest collections of patient material. Their reliable use for DNA analyses could open a trove of potential samples for research and are currently being recognised as a viable source material for bacterial analysis. There are several key features which limit bacterial-related data generation from this material: (i) DNA damage inherent to the fixing process, (ii) low bacterial biomass that increases the vulnerability to contamination and exacerbates the host DNA effects and (iii) lack of suitable DNA extraction methods, leading to data bias. The development and systematic use of reliable standards is a key priority for microbiome research. More than perhaps any other sample type, FFPE material urgently requires the development of standards to ensure the validity of results and to promote reproducibility. RESULTS To address these limitations and concerns, we have developed the Protoblock as a biological standard for FFPE tissue-based research and method optimisation. This is a novel system designed to generate bespoke mock FFPE 'blocks' with a cell content that is user-defined and which undergoes the same treatment conditions as clinical FFPE tissues. The 'Protoblock' features a mix of formalin-fixed cells, of known number, embedded in an agar matrix which is solidified to form a defined shape that is paraffin embedded. The contents of various Protoblocks populated with mammalian and bacterial cells were verified by microscopy. The quantity and condition of DNA purified from blocks was evaluated by qPCR, 16S rRNA gene amplicon sequencing and whole genome sequencing. These analyses validated the capability of the Protoblock system to determine the extent to which each of the three stated confounding features impacts on eventual analysis of cellular DNA present in FFPE samples. CONCLUSION The Protoblock provides a representation of biological material after FFPE treatment. Use of this standard will greatly assist the stratification of biological variations detected into those legitimately resulting from experimental conditions, and those that are artefacts of the processed nature of the samples, thus enabling users to relate the outputs of laboratory analyses to reality. Video Abstract.
Collapse
Affiliation(s)
- Yensi Flores Bueso
- CancerResearch@UCC, University College Cork, Cork, Ireland
- SynBioCentre, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Sidney P Walker
- CancerResearch@UCC, University College Cork, Cork, Ireland
- SynBioCentre, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Glenn Hogan
- CancerResearch@UCC, University College Cork, Cork, Ireland
- SynBioCentre, University College Cork, Cork, Ireland
| | - Marcus J Claesson
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Mark Tangney
- CancerResearch@UCC, University College Cork, Cork, Ireland.
- SynBioCentre, University College Cork, Cork, Ireland.
- APC Microbiome Ireland, University College Cork, Cork, Ireland.
| |
Collapse
|
11
|
Berrino E, Annaratone L, Miglio U, Maldi E, Piccinelli C, Peano E, Balmativola D, Cassoni P, Pisacane A, Sarotto I, Venesio T, Sapino A, Marchiò C. Cold Formalin Fixation Guarantees DNA Integrity in Formalin Fixed Paraffin Embedded Tissues: Premises for a Better Quality of Diagnostic and Experimental Pathology With a Specific Impact on Breast Cancer. Front Oncol 2020; 10:173. [PMID: 32140450 PMCID: PMC7042205 DOI: 10.3389/fonc.2020.00173] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 01/31/2020] [Indexed: 11/29/2022] Open
Abstract
Formalin fixation and paraffin embedding (FFPE) represent the standard method to preserve tissue specimens for diagnostic pathology, however formalin fixation induces severe fragmentation of nucleic acids. We investigated whether formalin fixation at 4°C could preserve DNA integrity in FFPE specimens. Paired samples from 38 specimens were formalin fixed at room temperature (stdFFPE) and at 4°C (coldFFPE), respectively. Two independent cohorts were prospectively collected, cohort A (collected 6 years prior to the study, n = 21), cohort B (collected at time of the study, n = 17). DNA was extracted and its integrity evaluated with a qPCR-based assay that produces a normalized integrity index, the QC score (ratio between the quantity of a long and a short amplicon of the same gene). We observed higher QC scores in coldFFPE compared to stdFFPE samples (mean values: 0.69 vs. 0.36, p < 0.0001) and stdFFPE breast cancer specimens showed the most detrimental effect overall. Comparable QC scores were obtained between coldFFPE tissues of both cohorts; conversely, DNA integrity of stdFFPE was significantly lower in cohort A compared to cohort B (p < 0.0001). Of note, QC scores of stdFFPE (but not of coldFFPE) samples were significantly reduced following 6 months of storage (p = 0.0001). Monitored formalin fixation at 4°C outperforms standard fixation in ensuring high-quality DNA, which is key to feasibility of downstream high-throughput molecular analyses. An important effect was observed over storage time, thus suggesting a likely better preservation of archival samples when this cold fixation protocol is used.
Collapse
Affiliation(s)
- Enrico Berrino
- Department of Medical Sciences, University of Turin, Turin, Italy.,Pathology Unit, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Laura Annaratone
- Department of Medical Sciences, University of Turin, Turin, Italy.,Pathology Unit, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Umberto Miglio
- Pathology Unit, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Elena Maldi
- Pathology Unit, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Chiara Piccinelli
- Pathology Unit, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Erica Peano
- Pathology Unit, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | | | - Paola Cassoni
- Department of Medical Sciences, University of Turin, Turin, Italy.,Pathology Unit, Città Della Salute e Della Scienza di Torino, Turin, Italy
| | - Alberto Pisacane
- Pathology Unit, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Ivana Sarotto
- Pathology Unit, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Tiziana Venesio
- Pathology Unit, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Anna Sapino
- Department of Medical Sciences, University of Turin, Turin, Italy.,Pathology Unit, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Caterina Marchiò
- Department of Medical Sciences, University of Turin, Turin, Italy.,Pathology Unit, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| |
Collapse
|
12
|
Fujii S, Yoshino T, Yamazaki K, Muro K, Yamaguchi K, Nishina T, Yuki S, Shinozaki E, Shitara K, Bando H, Mimaki S, Nakai C, Matsushima K, Suzuki Y, Akagi K, Yamanaka T, Nomura S, Esumi H, Sugiyama M, Nishida N, Mizokami M, Koh Y, Abe Y, Ohtsu A, Tsuchihara K. Histopathological factors affecting the extraction of high quality genomic DNA from tissue sections for next-generation sequencing. Biomed Rep 2019; 11:171-180. [PMID: 31565223 DOI: 10.3892/br.2019.1235] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 06/28/2019] [Indexed: 01/03/2023] Open
Abstract
To enable the widespread application of genomic medicine, the extraction of genomic DNA from thin sections of archived formalin-fixed and paraffin-embedded (FFPE) tissue blocks for next-generation sequencing (NGS) is often necessary. However, there are currently no guidelines available on which specific regions of the microtome sections to use for macrodissection with respect to the histopathological factors observed under microscopic examination. The aim of this study was to clarify the relationship between histopathological factors and DNA quality, and to standardize the macrodissection method for more efficient implementation of NGS. FFPE tissue specimens of 218 patients from the Biomarker Research for Anti-EGFR Monoclonal Antibodies by Comprehensive Cancer Genomics study were used to investigate the relationship between 15 histopathological factors and the quantitative ratio of double-stranded DNA (dsDNA) to total nucleic acids, as well as the ∆ crossing point value of each tissue specimen. Multivariate logistic regression analysis revealed that specimen storage of ≥3 years was negatively associated with dsDNA quality (P=0.0007, OR: 4.30, 95% CI: 1.85-10.04). In contrast, the presence of a mucus pool was positively associated with dsDNA quality (P=0.0308, OR: 0.23, 95% CI: 0.06-0.87). Metastatic tumors and longer specimen storage periods were significantly associated with lower ∆Cp values (P=0.0007, OR: 4.43, 95% CI: 1.87-10.49; and P=0.0003, OR: 5.51, 95% CI: 2.18-13.95, respectively). Therefore, macrodissection should not be performed on specimens exhibiting histopathological factors associated with poor DNA quality. In particular, the use of tissue blocks with a storage period of <3 years allows the extraction of genomic DNA suitable for NGS.
Collapse
Affiliation(s)
- Satoshi Fujii
- Division of Pathology, Exploratory Oncology Research & Clinical Trial Center, National Cancer Center, Kashiwa, Chiba 277-8577, Japan
| | - Takayuki Yoshino
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Kashiwa, Chiba 277-8577, Japan
| | - Kentaro Yamazaki
- Division of Gastrointestinal Oncology, Shizuoka Cancer Center, Nagaizumi, Shizuoka 411-8777, Japan
| | - Kei Muro
- Department of Clinical Oncology, Aichi Cancer Center Hospital, Nagoya, Aichi 464-8681, Japan
| | - Kensei Yamaguchi
- Department of Gastrointestinal Chemotherapy, Cancer Institute Hospital of Japanese Foundation for Cancer Research, Tokyo 135-0063, Japan
| | - Tomohiro Nishina
- Department of Gastrointestinal Medical Oncology, National Hospital Organization Shikoku Cancer Center, Matsuyama, Ehime 791-0280, Japan
| | - Satoshi Yuki
- Department of Gastroenterology and Hepatology, Hokkaido University Hospital, Sapporo, Hokkaido 060-8648, Japan
| | - Eiji Shinozaki
- Department of Gastrointestinal Chemotherapy, Cancer Institute Hospital of Japanese Foundation for Cancer Research, Tokyo 135-0063, Japan
| | - Kohei Shitara
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Kashiwa, Chiba 277-8577, Japan
| | - Hideaki Bando
- Department of Clinical Oncology, Aichi Cancer Center Hospital, Nagoya, Aichi 464-8681, Japan
| | - Sachiyo Mimaki
- Division of Translational Informatics, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Kashiwa, Chiba 277-8577, Japan
| | | | | | - Yutaka Suzuki
- Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Kiwamu Akagi
- Division of Molecular Diagnosis and Cancer Prevention, Saitama Cancer Center, Saitama 362-0806, Japan
| | - Takeharu Yamanaka
- Department of Biostatistics, Yokohama City University School of Medicine, Yokohama, Kanagawa 236-0004, Japan
| | - Shogo Nomura
- Biostatistics Division, Center for Research and Administration and Support, National Cancer Center, Kashiwa, Chiba 277-8577, Japan
| | - Hiroyasu Esumi
- Research Institute for Biomedical Sciences, Tokyo University of Science, Noda, Chiba 278-0022, Japan
| | - Masaya Sugiyama
- Genome Medical Sciences Project, National Center for Global Health and Medicine, Chiba 277-8516, Japan
| | - Nao Nishida
- Genome Medical Sciences Project, National Center for Global Health and Medicine, Chiba 277-8516, Japan
| | - Masashi Mizokami
- Genome Medical Sciences Project, National Center for Global Health and Medicine, Chiba 277-8516, Japan
| | - Yasuhiro Koh
- Third Department of Internal Medicine, Wakayama Medical University, Wakayama 641-8509, Japan
| | - Yukiko Abe
- G&G Science Co. Ltd., Fukushima 960-1242, Japan
| | - Atsushi Ohtsu
- National Cancer Center Hospital East, Kashiwa, Chiba 277-8577, Japan
| | - Katsuya Tsuchihara
- Division of Translational Informatics, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Kashiwa, Chiba 277-8577, Japan
| |
Collapse
|
13
|
Wu S, Shi X, Si X, Liu Y, Lu T, Zhang L, Liang Z, Zeng X. EGFR T790M detection in formalin-fixed paraffin-embedded tissues of patients with lung cancer using RNA-based in situ hybridization: A preliminary feasibility study. Thorac Cancer 2019; 10:1936-1944. [PMID: 31407509 PMCID: PMC6775006 DOI: 10.1111/1759-7714.13169] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 07/28/2019] [Accepted: 07/29/2019] [Indexed: 12/13/2022] Open
Abstract
Background Following drug resistance in patients with lung cancer treated by EGFR TKIs, a biopsy is required to obtain sufficient cancer tissue for T790M detection in order to select potential beneficiaries suitable for third‐generation EGFR TKIs, such as osimertinib. The purpose of this study was to explore the feasibility of using a new in situ analysis technique based on RNA target sequences to detect EGFR T790M in lung cancer. Methods A total of 28 formalin‐fixed paraffin‐embedded (FFPE) samples from 24 lung adenocarcinoma patients archived in Peking Union Medical College Hospital from 2015 to 2016 were collected. The BaseScope T790M detection technique by in situ hybridization on FFPE slides was used to analyze the mutation of EGFR T790M, and then the results were compared with the data acquired by Scorpions ARMS assay, which is the so‐called gold standard for EGFR gene mutation testing. The sensitivity and specificity of the BaseScope T790M detection technique were preliminarily evaluated. Results Of the 28 FFPE specimens, the average proportion of T790M‐positive cells was 35.78% ± 17.68% in 18 samples with EGFR T790M, confirmed by Scorpions ARMS assay, Compared with real‐time PCR assay, the sensitivity and specificity of BaseScope T790M were all 100% in our cohort. Conclusion BaseScope T790M assay could be completed on only one FFPE slide and the visualized molecular result overplayed with histomorphological information perfectly, so it may be the alternative method for EGFR T790M evaluation. BaseScope assay has potential clinical utility, and it will be necessary to carry out validation with a large number of cases.
Collapse
Affiliation(s)
- Shafei Wu
- Molecular Pathology Research Center, Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Xiaohua Shi
- Molecular Pathology Research Center, Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Xiaoyan Si
- Department of Respiratory Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Yuanyuan Liu
- Molecular Pathology Research Center, Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Tao Lu
- Molecular Pathology Research Center, Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Li Zhang
- Department of Respiratory Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Zhiyong Liang
- Molecular Pathology Research Center, Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Xuan Zeng
- Molecular Pathology Research Center, Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| |
Collapse
|
14
|
Quy PN, Kanai M, Fukuyama K, Kou T, Kondo T, Yamamoto Y, Matsubara J, Hiroshima A, Mochizuki H, Sakuma T, Kamada M, Nakatsui M, Eso Y, Seno H, Masui T, Takaori K, Minamiguchi S, Matsumoto S, Muto M. Association Between Preanalytical Factors and Tumor Mutational Burden Estimated by Next-Generation Sequencing-Based Multiplex Gene Panel Assay. Oncologist 2019; 24:e1401-e1408. [PMID: 31186376 DOI: 10.1634/theoncologist.2018-0587] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 05/09/2019] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Tumor mutational burden (TMB) measured via next-generation sequencing (NGS)-based gene panel is a promising biomarker for response to immune checkpoint inhibitors (ICIs) in solid tumors. However, little is known about the preanalytical factors that can affect the TMB score. MATERIALS AND METHODS Data of 199 patients with solid tumors who underwent multiplex NGS gene panel (OncoPrime), which was commercially provided by a Clinical Laboratory Improvement Amendments-licensed laboratory and covered 0.78 megabase (Mb) of capture size relevant to the TMB calculation, were reviewed. Associations between the TMB score and preanalytical factors, including sample DNA quality, sample type, sampling site, and storage period, were analyzed. Clinical outcomes of patients with a high TMB score (≥10 mutations per megabase) who received anti-programmed cell death protein 1 antibodies (n = 22) were also analyzed. RESULTS Low DNA library concentration (<5 nM), formalin-fixed paraffin-embedded tissue (FFPE), and the prolonged sample storage period (range, 0.9-58.1 months) correlated with a higher TMB score. After excluding low DNA library samples from the analysis, FFPE samples, but not the sample storage period, exhibited a marked correlation with a high TMB score. Of 22 patients with a high TMB score, we observed the partial response in 2 patients (9.1%). CONCLUSION Our results indicate that the TMB score estimated via NGS-based gene panel could be affected by the DNA library concentration and sample type. These factors could potentially increase the false-positive and/or artifactual variant calls. As each gene panel has its own pipeline for variant calling, it is unknown whether these factors have a significant effect in other platforms. IMPLICATIONS FOR PRACTICE A high tumor mutational burden score, as estimated via next-generation sequencing-based gene panel testing, should be carefully interpreted as it could be affected by the DNA library concentration and sample type.
Collapse
Affiliation(s)
- Pham Nguyen Quy
- Department of Medical Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masashi Kanai
- Department of Medical Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Keita Fukuyama
- Division of Hepato-Biliary-Pancreatic Surgery and Transplantation, Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Tadayuki Kou
- Department of Medical Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Tomohiro Kondo
- Department of Medical Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yoshihiro Yamamoto
- Department of Medical Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Junichi Matsubara
- Department of Medical Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Akinori Hiroshima
- Biomedical Department, Mitsui Knowledge Industry Co., Ltd., Tokyo, Japan
| | - Hiroaki Mochizuki
- Biomedical Department, Mitsui Knowledge Industry Co., Ltd., Tokyo, Japan
| | - Tomohiro Sakuma
- Biomedical Department, Mitsui Knowledge Industry Co., Ltd., Tokyo, Japan
| | - Mayumi Kamada
- Department of Biomedical Data Intelligence, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masahiko Nakatsui
- Department of Biomedical Data Intelligence, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yuji Eso
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiroshi Seno
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Toshihiko Masui
- Division of Hepato-Biliary-Pancreatic Surgery and Transplantation, Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kyoichi Takaori
- Division of Hepato-Biliary-Pancreatic Surgery and Transplantation, Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Sachiko Minamiguchi
- Department of Diagnostic Pathology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Shigemi Matsumoto
- Department of Medical Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Manabu Muto
- Department of Medical Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| |
Collapse
|
15
|
Amemiya K, Hirotsu Y, Oyama T, Omata M. Relationship between formalin reagent and success rate of targeted sequencing analysis using formalin fixed paraffin embedded tissues. Clin Chim Acta 2018; 488:129-134. [PMID: 30395866 DOI: 10.1016/j.cca.2018.11.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 10/23/2018] [Accepted: 11/02/2018] [Indexed: 11/26/2022]
Abstract
BACKGROUND Tumor genetic alterations are determined to aid in selecting therapy and predicting prognosis. In routine clinical practice, targeted sequencing analysis is performed using formalin-fixed paraffin embedded (FFPE) tissues. However, successful genetic analysis remains challenging because FFPE DNA is fragmented during the sample preparation process. METHODS Real-time PCR was performed to assess DNA quality and quantities. Targeted sequencing was performed using FFPE tissues fixed with different types of formalin. RESULTS DNA was less fragmented from samples fixed in low formalin concentration (10% vs. 20%) and neutral buffered conditions (neutral buffered vs. non-neutral). DNA fragmentation increased over the fixation time. In a preliminary test study, we compared fixation using 10% neutral buffered formalin (n = 180) and 20% formalin (n = 26). The success rate of targeted analysis was higher using 10% neutral formalin (98.3%; 177/180) compared with 20% formalin (34.6%; 9/26). In a validation study with additional formalin-fixed paraffin embedded tissues fixed with 10% neutral buffered formalin (n = 860), we reproduced these results and achieved a high success rate for targeted sequencing analysis (98.4%; 846/860). CONCLUSION Our data show that 10% neutral buffered formalin is recommended for fixation of formalin-fixed paraffin embedded samples to achieve high success rate of targeted sequencing analysis.
Collapse
Affiliation(s)
- Kenji Amemiya
- Genome Analysis Center, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi 400-8506, Japan
| | - Yosuke Hirotsu
- Genome Analysis Center, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi 400-8506, Japan.
| | - Toshio Oyama
- Department of Pathology, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi 400-8506, Japan
| | - Masao Omata
- Genome Analysis Center, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi 400-8506, Japan; The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| |
Collapse
|
16
|
Suitability of melanoma FFPE samples for NGS libraries: time and quality thresholds for downstream molecular tests. Biotechniques 2018; 65:79-85. [PMID: 30091391 DOI: 10.2144/btn-2018-0016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The use of NGS in clinical practice for precision diagnosis requires a quality starting material. Despite the broadly established use of formalin-fixed paraffin-embedded (FFPE) samples in molecular testing, these usually have low-quality DNA. We established a method to determine the suitability of melanoma FFPE samples for an amplicon-based NGS custom panel analysis. DNA was extracted from unstained melanoma samples and wide local excision samples. Amplicon-based libraries were constructed and tested using time and quality parameters as variables. Time elapsed from sample retrieval >7 years, a quality control value > 5.63 and a DNA integrity value < 2.05 indicated samples were not suitable. A decision tree is provided with rate of samples suitable for analysis according to the combination of these parameters.
Collapse
|