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Rockweiler NB, Ramu A, Nagirnaja L, Wong WH, Noordam MJ, Drubin CW, Huang N, Miller B, Todres EZ, Vigh-Conrad KA, Zito A, Small KS, Ardlie KG, Cohen BA, Conrad DF. The origins and functional effects of postzygotic mutations throughout the human life span. Science 2023; 380:eabn7113. [PMID: 37053313 PMCID: PMC11246725 DOI: 10.1126/science.abn7113] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 03/17/2023] [Indexed: 04/15/2023]
Abstract
Postzygotic mutations (PZMs) begin to accrue in the human genome immediately after fertilization, but how and when PZMs affect development and lifetime health remain unclear. To study the origins and functional consequences of PZMs, we generated a multitissue atlas of PZMs spanning 54 tissue and cell types from 948 donors. Nearly half the variation in mutation burden among tissue samples can be explained by measured technical and biological effects, and 9% can be attributed to donor-specific effects. Through phylogenetic reconstruction of PZMs, we found that their type and predicted functional impact vary during prenatal development, across tissues, and through the germ cell life cycle. Thus, methods for interpreting effects across the body and the life span are needed to fully understand the consequences of genetic variants.
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Affiliation(s)
- Nicole B. Rockweiler
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Present address: Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Avinash Ramu
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Liina Nagirnaja
- Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, 97006, USA
| | - Wing H. Wong
- Department of Pediatrics, Division of Hematology and Oncology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Present Address: Departments of Genetics and Medicine, Stanford University, CA 94305, USA
| | - Michiel J. Noordam
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Casey W. Drubin
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Ni Huang
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Present Address: T-Therapeutics Ltd., Cambridge CB21 6AD, UK
| | - Brian Miller
- Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, 97006, USA
| | - Ellen Z. Todres
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Katinka A. Vigh-Conrad
- Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, 97006, USA
| | - Antonino Zito
- Department of Twin Research and Genetic Epidemiology, King’s College London, London SE1 7EH, UK
- Present Address: Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, 02114, USA; Department of Genetics, The Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Kerrin S. Small
- Department of Twin Research and Genetic Epidemiology, King’s College London, London SE1 7EH, UK
| | | | - Barak A. Cohen
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Donald F. Conrad
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, 97006, USA
- Center for Embryonic Cell & Gene Therapy, Oregon Health & Science University, Portland, OR, 97239, USA
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DeCoste R, Amemiya Y, Nersesian S, Westhaver L, Lee SN, Carter MD, Sapp HL, Stueck AE, Arnason T, Boudreau J, Seth A, Huang WY. PAXgene Fixation for Pancreatic Cancer: Implications for Molecular and Surgical Pathology. J Clin Med 2022; 11:jcm11144241. [PMID: 35888003 PMCID: PMC9319620 DOI: 10.3390/jcm11144241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/11/2022] [Accepted: 07/14/2022] [Indexed: 12/04/2022] Open
Abstract
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.
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Affiliation(s)
- Ryan DeCoste
- Department of Pathology & Laboratory Medicine, QEII Health Sciences Centre, Nova Scotia Health Authority (Central Zone), Halifax, NS B3H 1V8, Canada; (R.D.); (M.D.C.); (H.L.S.); (A.E.S.); (T.A.)
- Department of Pathology, Dalhousie University, Halifax, NS B3H 1V8, Canada; (L.W.); (J.B.)
| | - Yutaka Amemiya
- Sunnybrook Research Institute Genomics Core Facility, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada; (Y.A.); (A.S.)
| | - Sarah Nersesian
- Department of Microbiology & Immunology, Dalhousie University, Halifax, NS B3H 4R2, Canada; (S.N.); (S.N.L.)
| | - Lauren Westhaver
- Department of Pathology, Dalhousie University, Halifax, NS B3H 1V8, Canada; (L.W.); (J.B.)
| | - Stacey N. Lee
- Department of Microbiology & Immunology, Dalhousie University, Halifax, NS B3H 4R2, Canada; (S.N.); (S.N.L.)
| | - Michael D. Carter
- Department of Pathology & Laboratory Medicine, QEII Health Sciences Centre, Nova Scotia Health Authority (Central Zone), Halifax, NS B3H 1V8, Canada; (R.D.); (M.D.C.); (H.L.S.); (A.E.S.); (T.A.)
- Department of Pathology, Dalhousie University, Halifax, NS B3H 1V8, Canada; (L.W.); (J.B.)
| | - Heidi L. Sapp
- Department of Pathology & Laboratory Medicine, QEII Health Sciences Centre, Nova Scotia Health Authority (Central Zone), Halifax, NS B3H 1V8, Canada; (R.D.); (M.D.C.); (H.L.S.); (A.E.S.); (T.A.)
- Department of Pathology, Dalhousie University, Halifax, NS B3H 1V8, Canada; (L.W.); (J.B.)
| | - Ashley E. Stueck
- Department of Pathology & Laboratory Medicine, QEII Health Sciences Centre, Nova Scotia Health Authority (Central Zone), Halifax, NS B3H 1V8, Canada; (R.D.); (M.D.C.); (H.L.S.); (A.E.S.); (T.A.)
- Department of Pathology, Dalhousie University, Halifax, NS B3H 1V8, Canada; (L.W.); (J.B.)
| | - Thomas Arnason
- Department of Pathology & Laboratory Medicine, QEII Health Sciences Centre, Nova Scotia Health Authority (Central Zone), Halifax, NS B3H 1V8, Canada; (R.D.); (M.D.C.); (H.L.S.); (A.E.S.); (T.A.)
- Department of Pathology, Dalhousie University, Halifax, NS B3H 1V8, Canada; (L.W.); (J.B.)
| | - Jeanette Boudreau
- Department of Pathology, Dalhousie University, Halifax, NS B3H 1V8, Canada; (L.W.); (J.B.)
- Department of Microbiology & Immunology, Dalhousie University, Halifax, NS B3H 4R2, Canada; (S.N.); (S.N.L.)
| | - Arun Seth
- Sunnybrook Research Institute Genomics Core Facility, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada; (Y.A.); (A.S.)
- Department of Laboratory Medicine & Molecular Diagnostics, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Weei-Yuarn Huang
- Department of Laboratory Medicine & Molecular Diagnostics, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
- Correspondence:
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Frasquilho SG, Sanchez I, Yoo C, Antunes L, Bellora C, Mathieson W. Do Tissues Fixed in a Non-crosslinking Fixative Require a Dedicated Formalin-free Processor? J Histochem Cytochem 2021; 69:389-405. [PMID: 34010071 DOI: 10.1369/00221554211017859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
We evaluate the consequences of processing alcohol-fixed tissue in a processor previously used for formalin-fixed tissue. Biospecimens fixed in PAXgene Tissue Fixative were cut into three pieces then processed in a flushed tissue processor previously used for formalin-fixed, paraffin-embedded (FFPE) blocks (neutral buffered formalin [NBF]+ve), a formalin-free system (NBF-ve), or left unprocessed. Histomorphology and immunohistochemistry were compared using hematoxylin/eosin staining and antibodies for MLH-1, Ki-67, and CK-7. Nucleic acid was extracted using the PAXgene Tissue RNA/DNA kits and an FFPE RNA extraction kit. RNA integrity was assessed using RNA integrity number (RIN), reverse transcription polymerase chain reaction (RT-PCR) (four amplicons), and quantitative RT-PCR (three genes). For DNA, multiplex PCR, quantitative PCR, DNA integrity number, and gel electrophoresis were used. Compared with NBF-ve, RNA from NBF+ve blocks had 88% lower yield and poorer purity; average RIN reduced from 5.0 to 3.8, amplicon length was 408 base pairs shorter, and Cq numbers were 1.9-2.4 higher. Using the FFPE extraction kit rescued yield and purity, but RIN further declined by 1.1 units. Differences between NBF+ve and NBF-ve in respect of DNA, histomorphology, and immunohistochemistry were either non-existent or small in magnitude. Formalin contamination of a tissue processor and its reagents therefore critically reduce RNA yield and integrity. We discuss the available options users can adopt to ameliorate this problem.
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Affiliation(s)
| | | | - Changyoung Yoo
- The Catholic University of Korea, St. Vincent's Hospital, Seoul, Korea
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Smith J, Faria CSAA, Qvist CC, Melchior LC, Lauridsen T. Prolonging fixation time of an alternative fixative to formalin for dermatological samples using standard laboratory protocols. J Clin Pathol 2020; 74:149-156. [PMID: 32669366 DOI: 10.1136/jclinpath-2020-206612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 05/15/2020] [Accepted: 05/28/2020] [Indexed: 11/03/2022]
Abstract
AIMS Though formalin remains to be the gold standard fixative in pathology departments, analytical challenges persist for nucleic acid evaluations. In our laboratory, formalin fixation of skin samples in particular impairs diagnostic accuracy and demands repetition of biopsies and analytical procedures. PAXgene Tissue Systems may be an alternative; however, according to manufacturer specifications it only allows fixation for 48 hours before having to add a stabiliser. This may be a challenge in laboratories, which are closed in weekends and bank holidays. Our aim was to validate this alternative fixative for dermatological samples with prolonged fixation times using standard laboratory protocols developed for formalin-fixed specimens. We compared the results with gold standard formalin fixation. METHODS Skin specimens were formalin or PAXgene fixed for either 2 hours, 24 hours, 3 days or 7 days, paraffin-embedded, analysed and scored by observers. RESULTS Generally, formalin outperformed PAXgene fixation in H&E stains and fluorescence in situ hybridisation (FISH), but both seem usable for diagnostics. Time of PAXgene fixation did not have an impact on alcian blue-Van Gieson (ABVG), H&E (p=0.48), nor immunohistochemistry (p=0.74). There was a tendency towards best PAXgene performance at 24 hours of fixation for FISH, and for DNA integrity analysis 24 hours or 3 days. CONCLUSIONS Prolonging PAXgene fixation time to 3 days before adding stabiliser does not seem to have major impact on performance of general diagnostic analysis, but our preliminary results show optimisation of internal protocols are needed. PAXgene is an expensive alternative and may be confined to some dermatological samples.
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Affiliation(s)
- Julie Smith
- Department of Technology, Faculty of Health and Technology, University College Copenhagen, Copenhagen, Denmark
| | | | - Camilla Christine Qvist
- Department of Pathology, Copenhagen University Hospital (Rigshospitalet), Copenhagen, Denmark
| | - Linea C Melchior
- Department of Pathology, Copenhagen University Hospital (Rigshospitalet), Copenhagen, Denmark
| | - Thomas Lauridsen
- Department of Pathology, Copenhagen University Hospital (Rigshospitalet), Copenhagen, Denmark.,Department of Pathology, Zealand University Hospital, Roskilde, Denmark
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The impact of crosslinking and non-crosslinking fixatives on antigen retrieval and immunohistochemistry. N Biotechnol 2019; 52:69-83. [PMID: 31082574 DOI: 10.1016/j.nbt.2019.05.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 05/08/2019] [Accepted: 05/09/2019] [Indexed: 12/29/2022]
Abstract
Pre-analytical factors can greatly influence the outcome of molecular analyses in medical diagnostics and research. This also applies to in situ staining techniques such as immunohistochemistry (IHC), where different types of tissue fixation methods lead to different modifications of proteins and thus can affect differently the detection by antibodies. For formalin-fixed paraffin-embedded (FFPE) tissue, antigen retrieval is applied in order to reverse the negative effects of formalin and re-establish immunoreactivity. Most antibodies and protocols used in IHC are optimized for FFPE tissue, but not for paraffin-embedded tissue treated with other fixatives such as non-crosslinking fixatives. We report results from systematic studies on distinct pre-analytical conditions in IHC, immunofluorescence and electron microscopy. Parameters investigated are the impact of crosslinking and non-crosslinking fixatives (comparing formalin and PAXgene Tissue fixation) on whole tissue, subcellular structures and organelles, as well as on ultrastructure. The results generated show that minor changes in antigen retrieval conditions may have a major impact on IHC results and that protocols optimized for crosslinking fixatives may not be used for other fixatives without re-validation. Key antigen retrieval parameters such as buffers with different pH and duration of microwave treatment must be tested systematically for each antibody and fixation protocol.
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Morley-Bunker A, Pearson J, Currie MJ, Morrin H, Whitehead MR, Eglinton T, Walker LC. Assessment of intra-tumoural colorectal cancer prognostic biomarkers using RNA in situ hybridisation. Oncotarget 2019; 10:1425-1439. [PMID: 30858927 PMCID: PMC6402718 DOI: 10.18632/oncotarget.26675] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 02/01/2019] [Indexed: 01/01/2023] Open
Abstract
Genome-wide expression studies using microarrays and RNAseq have increased our understanding of colorectal cancer development. Translating potential gene biomarkers from these studies for clinical utility has typically relied on PCR-based technology and immunohistochemistry. Results from these techniques are limited by tumour sample heterogeneity and the lack of correlation between mRNA transcript abundance and corresponding protein levels. The aim of this research was to investigate the clinical utility of the RNA in situ hybridisation technique, RNAscope®, for measuring intra-tumoural gene expression of potential prognostic markers in a colorectal cancer cohort. Two candidate gene markers (GFI1 and TNFRSF11A) assessed in this study were identified from a previous study led by the The Cancer Genome Atlas (TCGA) Network, and analysis was performed on 112 consecutively collected, archival FFPE colorectal cancer tumour samples. Consistent with the TCGA Network study, we found reduced GFI1 expression was associated with high-grade and left-sided tumours, and reduced TNFRSF11A expression was associated with metastasis and high nodal involvement. RNAscope® combined with image analysis also enabled quantification of GFI1 and TNFRSF11A mRNA expression levels at the single cell level, allowing cell-type determination. These data showed that reduced mRNA transcript abundance measured in patients with poorer prognosis occurred in carcinoma cells, and not lymphocytes, stromal cells or normal epithelial cells. To our knowledge, this is the first study to assess the intra-tumoural expression patterns of GFI1 and TNFRSF11A and to validate their microarray expression profiles using RNAscope. We also demonstrate the utility of RNAscope® technology to show that expression differences are derived from carcinoma cells rather than from cells located in the tumour microenvironment.
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Affiliation(s)
- Arthur Morley-Bunker
- Mackenzie Cancer Research Group, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - John Pearson
- Biostatistics and Computational Biology Unit, University of Otago, Christchurch, New Zealand
| | - Margaret J Currie
- Mackenzie Cancer Research Group, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Helen Morrin
- Mackenzie Cancer Research Group, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand.,Cancer Society Tissue Bank, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Martin R Whitehead
- Canterbury Health Laboratories, Christchurch Hospital, Christchurch, New Zealand
| | - Tim Eglinton
- Department of Surgery, University of Otago, Christchurch, New Zealand
| | - Logan C Walker
- Mackenzie Cancer Research Group, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
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Impact of storage conditions on the quality of nucleic acids in paraffin embedded tissues. PLoS One 2018; 13:e0203608. [PMID: 30192857 PMCID: PMC6128582 DOI: 10.1371/journal.pone.0203608] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 08/23/2018] [Indexed: 01/02/2023] Open
Abstract
RNA and DNA analyses from paraffin-embedded tissues (PET) are an important diagnostic tool for characterization of a disease, exploring biomarkers and treatment options. Since nucleic acids from formalin-fixed and paraffin-embedded (FFPE) tissue are of limited use for molecular analyses due to chemical modifications of biomolecules alternate, formalin-free fixation reagents such as the PAXgene Tissue system are of evolving interest. Furthermore, biomedical research and biomarker development critically relies on using long-term stored PET from medical archives or biobanks to correlate molecular features with long-term disease outcomes. We therefore performed a comparative study to evaluate the effect of long term storage of FFPE and PAXgene Tissue-fixed and paraffin-embedded (PFPE) tissue at different temperatures on nucleic acid stability and usability in PCR. Matched FFPE and PFPE human tissues from routine clinical setting or rat tissues from a highly controlled animal model were stored at room temperature and 4°C, as well as in case of animal tissues frozen at -20°C and -80°C. RNA and DNA were extracted in intervals for up to nine years, and examined for integrity, and usability in quantitative RT-PCR (RT-qPCR) or PCR (qPCR) assays. PET storage at room temperature led to a degradation of nucleic acids which was slowed down by storage at 4°C and prevented by storage at -20°C or -80°C. Degradation was associated with an amplicon length depending decrease of RT-qPCR and qPCR efficiency. Storage at 4°C improved amplifiability in RT-qPCR and qPCR profoundly. Chemically unmodified nucleic acids from PFPE tissue performed superior compared to FFPE tissue, regardless of storage time and temperature in both human and rat tissues. In conclusion molecular analyses from PET can be greatly improved by using a non-crosslinking fixative and storage at lower temperatures such as 4°C, which should be considered in prospective clinical studies.
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Biomedical analysis of formalin-fixed, paraffin-embedded tissue samples: The Holy Grail for molecular diagnostics. J Pharm Biomed Anal 2018; 155:125-134. [PMID: 29627729 DOI: 10.1016/j.jpba.2018.03.065] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 03/30/2018] [Accepted: 03/31/2018] [Indexed: 02/07/2023]
Abstract
More than a century ago in 1893, a revolutionary idea about fixing biological tissue specimens was introduced by Ferdinand Blum, a German physician. Since then, a plethora of fixation methods have been investigated and used. Formalin fixation with paraffin embedment became the most widely used types of fixation and preservation method, due to its proper architectural conservation of tissue structures and cellular shape. The huge collection of formalin-fixed, paraffin-embedded (FFPE) sample archives worldwide holds a large amount of unearthed information about diseases that could be the Holy Grail in contemporary biomarker research utilizing analytical omics based molecular diagnostics. The aim of this review is to critically evaluate the omics options for FFPE tissue sample analysis in the molecular diagnostics field.
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