PAXgene Fixation for Pancreatic Cancer: Implications for Molecular and Surgical Pathology
Genomic profiling of pancreatic cancer using small core biopsies has taken an increasingly prominent role in precision medicine. However, if not appropriately preserved, nucleic acids (NA) from pancreatic tissues are known to be susceptible to degradation due to high intrinsic levels of nucleases. P...
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-07-01
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| Series: | Journal of Clinical Medicine |
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| Online Access: | https://www.mdpi.com/2077-0383/11/14/4241 |
| _version_ | 1797446172945678336 |
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| author | Ryan DeCoste Yutaka Amemiya Sarah Nersesian Lauren Westhaver Stacey N. Lee Michael D. Carter Heidi L. Sapp Ashley E. Stueck Thomas Arnason Jeanette Boudreau Arun Seth Weei-Yuarn Huang |
| author_facet | Ryan DeCoste Yutaka Amemiya Sarah Nersesian Lauren Westhaver Stacey N. Lee Michael D. Carter Heidi L. Sapp Ashley E. Stueck Thomas Arnason Jeanette Boudreau Arun Seth Weei-Yuarn Huang |
| author_sort | Ryan DeCoste |
| collection | DOAJ |
| description | Genomic profiling of pancreatic cancer using small core biopsies has taken an increasingly prominent role in precision medicine. However, if not appropriately preserved, nucleic acids (NA) from pancreatic tissues are known to be susceptible to degradation due to high intrinsic levels of nucleases. PAXgene fixation (PreAnalytix, Switzerland) represents a novel formalin-free tissue preservation method. We sought to compare the NA and histomorphological preservation of pancreatic cancer tissues preserved with PAXgene-fixed paraffin-embedding (PFPE) and formalin-fixed paraffin-embedding (FFPE). Tissues from 19 patients were obtained prospectively from pancreaticoduodenectomy specimens and evaluated by four gastrointestinal pathologists. The extracted NA were quantified by Nanodrop and Qubit and assessed for quality by qPCR, targeted next-generation sequencing (NGS) assay, and RNA-sequencing. Our results demonstrated that, when assessed blindly for morphological quality, the four pathologists deemed the PFPE slides adequate for diagnostic purposes. PFPE tissues enable greater yields of less fragmented and more amplifiable DNA. PFPE tissues demonstrated significantly improved quality control (QC) metrics in a targeted NGS assay including Median Absolute Pair-wise Difference (MAPD) scores. Our results support the use of PAXgene fixative for the processing of specimens from pancreatic cancers with the potential benefits of improved yields for more amplifiable DNA in low-yield biopsy specimens and its ideal use for amplicon-based NGS assays. |
| first_indexed | 2024-03-09T13:36:25Z |
| format | Article |
| id | doaj.art-c9fbe9a3348b4c28b0de0263bd8209af |
| institution | Directory Open Access Journal |
| issn | 2077-0383 |
| language | English |
| last_indexed | 2024-03-09T13:36:25Z |
| publishDate | 2022-07-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Journal of Clinical Medicine |
| spelling | doaj.art-c9fbe9a3348b4c28b0de0263bd8209af2023-11-30T21:11:59ZengMDPI AGJournal of Clinical Medicine2077-03832022-07-011114424110.3390/jcm11144241PAXgene Fixation for Pancreatic Cancer: Implications for Molecular and Surgical PathologyRyan DeCoste0Yutaka Amemiya1Sarah Nersesian2Lauren Westhaver3Stacey N. Lee4Michael D. Carter5Heidi L. Sapp6Ashley E. Stueck7Thomas Arnason8Jeanette Boudreau9Arun Seth10Weei-Yuarn Huang11Department of Pathology & Laboratory Medicine, QEII Health Sciences Centre, Nova Scotia Health Authority (Central Zone), Halifax, NS B3H 1V8, CanadaSunnybrook Research Institute Genomics Core Facility, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, CanadaDepartment of Microbiology & Immunology, Dalhousie University, Halifax, NS B3H 4R2, CanadaDepartment of Pathology, Dalhousie University, Halifax, NS B3H 1V8, CanadaDepartment of Microbiology & Immunology, Dalhousie University, Halifax, NS B3H 4R2, CanadaDepartment of Pathology & Laboratory Medicine, QEII Health Sciences Centre, Nova Scotia Health Authority (Central Zone), Halifax, NS B3H 1V8, CanadaDepartment of Pathology & Laboratory Medicine, QEII Health Sciences Centre, Nova Scotia Health Authority (Central Zone), Halifax, NS B3H 1V8, CanadaDepartment of Pathology & Laboratory Medicine, QEII Health Sciences Centre, Nova Scotia Health Authority (Central Zone), Halifax, NS B3H 1V8, CanadaDepartment of Pathology & Laboratory Medicine, QEII Health Sciences Centre, Nova Scotia Health Authority (Central Zone), Halifax, NS B3H 1V8, CanadaDepartment of Pathology, Dalhousie University, Halifax, NS B3H 1V8, CanadaSunnybrook Research Institute Genomics Core Facility, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, CanadaDepartment of Laboratory Medicine & Molecular Diagnostics, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, CanadaGenomic profiling of pancreatic cancer using small core biopsies has taken an increasingly prominent role in precision medicine. However, if not appropriately preserved, nucleic acids (NA) from pancreatic tissues are known to be susceptible to degradation due to high intrinsic levels of nucleases. PAXgene fixation (PreAnalytix, Switzerland) represents a novel formalin-free tissue preservation method. We sought to compare the NA and histomorphological preservation of pancreatic cancer tissues preserved with PAXgene-fixed paraffin-embedding (PFPE) and formalin-fixed paraffin-embedding (FFPE). Tissues from 19 patients were obtained prospectively from pancreaticoduodenectomy specimens and evaluated by four gastrointestinal pathologists. The extracted NA were quantified by Nanodrop and Qubit and assessed for quality by qPCR, targeted next-generation sequencing (NGS) assay, and RNA-sequencing. Our results demonstrated that, when assessed blindly for morphological quality, the four pathologists deemed the PFPE slides adequate for diagnostic purposes. PFPE tissues enable greater yields of less fragmented and more amplifiable DNA. PFPE tissues demonstrated significantly improved quality control (QC) metrics in a targeted NGS assay including Median Absolute Pair-wise Difference (MAPD) scores. Our results support the use of PAXgene fixative for the processing of specimens from pancreatic cancers with the potential benefits of improved yields for more amplifiable DNA in low-yield biopsy specimens and its ideal use for amplicon-based NGS assays.https://www.mdpi.com/2077-0383/11/14/4241PAXgeneNGSpancreatic cancermolecular diagnosticssurgical pathology |
| spellingShingle | Ryan DeCoste Yutaka Amemiya Sarah Nersesian Lauren Westhaver Stacey N. Lee Michael D. Carter Heidi L. Sapp Ashley E. Stueck Thomas Arnason Jeanette Boudreau Arun Seth Weei-Yuarn Huang PAXgene Fixation for Pancreatic Cancer: Implications for Molecular and Surgical Pathology Journal of Clinical Medicine PAXgene NGS pancreatic cancer molecular diagnostics surgical pathology |
| title | PAXgene Fixation for Pancreatic Cancer: Implications for Molecular and Surgical Pathology |
| title_full | PAXgene Fixation for Pancreatic Cancer: Implications for Molecular and Surgical Pathology |
| title_fullStr | PAXgene Fixation for Pancreatic Cancer: Implications for Molecular and Surgical Pathology |
| title_full_unstemmed | PAXgene Fixation for Pancreatic Cancer: Implications for Molecular and Surgical Pathology |
| title_short | PAXgene Fixation for Pancreatic Cancer: Implications for Molecular and Surgical Pathology |
| title_sort | paxgene fixation for pancreatic cancer implications for molecular and surgical pathology |
| topic | PAXgene NGS pancreatic cancer molecular diagnostics surgical pathology |
| url | https://www.mdpi.com/2077-0383/11/14/4241 |
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