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Chen H, Yu F, Lu D, Huang S, Liu S, Zhang B, Shu K, Pu D. Enhanced Error Suppression for Accurate Detection of Low-Frequency Variants. Electrophoresis 2025; 46:65-75. [PMID: 39679747 DOI: 10.1002/elps.202400202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2024] [Revised: 10/21/2024] [Accepted: 11/15/2024] [Indexed: 12/17/2024]
Abstract
The identification of low-frequency variants remains challenging due to the inevitable high error rates of next-generation sequencing (NGS). Numerous promising strategies employ unique molecular identifiers (UMIs) for error suppression. However, their efficiency depends highly on redundant sequencing and quality control, leading to tremendous read waste and cost inefficiency. Here, we describe a novel approach, enhanced error suppression strategy (EES), that addresses these challenges by (1) optimizing data utilization and reducing read waste by utilizing single-read correction that reserves abundant single reads that complement other single reads or single-strand consensus sequences (SSCSs), and (2) effectively enhancing the accuracy of NGS by employing Bayes' theorem. EES significantly improves variant detection accuracy, achieving a background error rate of less than 4.4 × 10-5 per base pair. Additionally, the data utilization rate is dramatically increased, with a 22.9-fold enhancement in duplex consensus sequence (DCS) recovery compared to traditional methodologies. Furthermore, EES demonstrates superior error suppression performance across various base substitutions. In conclusion, EES represents a significant advancement in detecting low-frequency variants by improving data utilization and reducing sequencing errors. It potentially enhances the sensitivity and accuracy of NGS applications, proving highly valuable in clinical and research contexts where precise variant detection is critical.
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Affiliation(s)
- Huimin Chen
- Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing, China
| | - Fei Yu
- Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing, China
| | - Debin Lu
- Department of Neurology, The Second Affiliated Hospital of the Army Medical University of the People's Liberation Army, Chongqing, China
| | - Shiyue Huang
- Chongqing Yangjiaping Middle School, Chongqing, China
| | - Songrui Liu
- Chongqing Yangjiaping Middle School, Chongqing, China
| | - Boseng Zhang
- Chongqing Yangjiaping Middle School, Chongqing, China
| | - Kunxian Shu
- Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing, China
| | - Dan Pu
- Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing, China
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2
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Gilbert A, Tudor M, Delaunay A, Leman R, Levilly J, Atkinson A, Castéra L, Dinischiotu A, Savu DI, Valable S, Chevalier F. Radiosensitizing Effect of PARP Inhibition on Chondrosarcoma and Chondrocyte Cells Is Dependent on Radiation LET. Biomolecules 2024; 14:1071. [PMID: 39334838 PMCID: PMC11429578 DOI: 10.3390/biom14091071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2024] [Revised: 08/14/2024] [Accepted: 08/21/2024] [Indexed: 09/30/2024] Open
Abstract
Chondrosarcoma is a rare malignant tumor that forms in bone and cartilage. The primary treatment involves surgical removal of the tumor with a margin of healthy tissue. Especially if complete surgical removal is not possible, radiation therapy and chemotherapy are used in conjunction with surgery, but with a generally low efficiency. Ongoing researches are focused on understanding the genetic and molecular basis of chondrosarcoma following high linear energy transfer (LET) irradiation, which may lead to treatments that are more effective. The goal of this study is to evaluate the differential effects of DNA damage repair inhibitors and high LET irradiation on chondrosarcoma versus chondrocyte cells and the LET-dependency of the effects. Two chondrosarcoma cell lines with different IDH mutation status and one chondrocyte cell line were exposed to low LET (X-ray) and high LET (carbon ion) irradiation in combination with an Olaparib PARP inhibitor. Cell survival and DNA repair mechanisms were investigated. High LET irradiation drastically reduced cell survival, with a biological efficiency three times that of low LET. Olaparib significantly inhibited PARylation in all the tested cells. A significant reduction in cell survival of both chondrosarcoma and chondrocyte cells was observed following the treatment combining Olaparib and X-ray. PARP inhibition induced an increase in PARP-1 expression and a reduced effect on the cell survival of WT IDH chondrosarcoma cells. No radiosensitizing effect was observed in cells exposed to Olaparib paired with high LET irradiation. NHEJ was activated in response to high LET irradiation, neutralizing the PARP inhibition effect in both chondrosarcoma cell lines. When high LET irradiation is not available, PARP inhibition could be used in combination with low LET irradiation, with significant radiosensitizing effects on chondrosarcoma cells. Chondrocytes may be affected by the treatment combination too, showing the need to preserve normal tissues from radiation fields when this kind of treatment is suggested.
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Affiliation(s)
- Antoine Gilbert
- UMR6252 CIMAP, CEA-CNRS-ENSICAEN, Normandie Université, Team Applications in Radiobiology with Accelerated Ions, 14000 Caen, France
| | - Mihaela Tudor
- Department of Life and Environmental Physics, Horia Hulubei National Institute for R&D in Physics and Nuclear Engineering, Reactorului 30, 077125 Magurele, Romania
- Faculty of Biology, University of Bucharest, Splaiul Independentei 91-95, 050095 Bucharest, Romania
| | - Amandine Delaunay
- UMR6252 CIMAP, CEA-CNRS-ENSICAEN, Normandie Université, Team Applications in Radiobiology with Accelerated Ions, 14000 Caen, France
| | - Raphaël Leman
- Laboratoire de Biologie et de Génétique du Cancer, Centre François Baclesse, 14000 Caen, France
- Inserm U1245, Cancer Brain and Genome, Normandie Universite, UNICAEN, FHU G4 Genomique, 76000 Rouen, France
| | - Julien Levilly
- Laboratoire de Biologie et de Génétique du Cancer, Centre François Baclesse, 14000 Caen, France
- Inserm U1245, Cancer Brain and Genome, Normandie Universite, UNICAEN, FHU G4 Genomique, 76000 Rouen, France
| | - Alexandre Atkinson
- Laboratoire de Biologie et de Génétique du Cancer, Centre François Baclesse, 14000 Caen, France
- Inserm U1245, Cancer Brain and Genome, Normandie Universite, UNICAEN, FHU G4 Genomique, 76000 Rouen, France
| | - Laurent Castéra
- Laboratoire de Biologie et de Génétique du Cancer, Centre François Baclesse, 14000 Caen, France
- Inserm U1245, Cancer Brain and Genome, Normandie Universite, UNICAEN, FHU G4 Genomique, 76000 Rouen, France
| | - Anca Dinischiotu
- Faculty of Biology, University of Bucharest, Splaiul Independentei 91-95, 050095 Bucharest, Romania
| | - Diana Iulia Savu
- Department of Life and Environmental Physics, Horia Hulubei National Institute for R&D in Physics and Nuclear Engineering, Reactorului 30, 077125 Magurele, Romania
| | - Samuel Valable
- Université de Caen Normandie, CNRS, Normandie Université, ISTCT UMR6030, GIP CYCERON, 14000 Caen, France
| | - François Chevalier
- UMR6252 CIMAP, CEA-CNRS-ENSICAEN, Normandie Université, Team Applications in Radiobiology with Accelerated Ions, 14000 Caen, France
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3
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Xiang X, Lu B, Song D, Li J, Shu K, Pu D. Evaluating the performance of low-frequency variant calling tools for the detection of variants from short-read deep sequencing data. Sci Rep 2023; 13:20444. [PMID: 37993475 PMCID: PMC10665316 DOI: 10.1038/s41598-023-47135-3] [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: 08/11/2023] [Accepted: 11/09/2023] [Indexed: 11/24/2023] Open
Abstract
Detection of low-frequency variants with high accuracy plays an important role in biomedical research and clinical practice. However, it is challenging to do so with next-generation sequencing (NGS) approaches due to the high error rates of NGS. To accurately distinguish low-level true variants from these errors, many statistical variants calling tools for calling low-frequency variants have been proposed, but a systematic performance comparison of these tools has not yet been performed. Here, we evaluated four raw-reads-based variant callers (SiNVICT, outLyzer, Pisces, and LoFreq) and four UMI-based variant callers (DeepSNVMiner, MAGERI, smCounter2, and UMI-VarCal) considering their capability to call single nucleotide variants (SNVs) with allelic frequency as low as 0.025% in deep sequencing data. We analyzed a total of 54 simulated data with various sequencing depths and variant allele frequencies (VAFs), two reference data, and Horizon Tru-Q sample data. The results showed that the UMI-based callers, except smCounter2, outperformed the raw-reads-based callers regarding detection limit. Sequencing depth had almost no effect on the UMI-based callers but significantly influenced on the raw-reads-based callers. Regardless of the sequencing depth, MAGERI showed the fastest analysis, while smCounter2 consistently took the longest to finish the variant calling process. Overall, DeepSNVMiner and UMI-VarCal performed the best with considerably good sensitivity and precision of 88%, 100%, and 84%, 100%, respectively. In conclusion, the UMI-based callers, except smCounter2, outperformed the raw-reads-based callers in terms of sensitivity and precision. We recommend using DeepSNVMiner and UMI-VarCal for low-frequency variant detection. The results provide important information regarding future directions for reliable low-frequency variant detection and algorithm development, which is critical in genetics-based medical research and clinical applications.
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Affiliation(s)
- Xudong Xiang
- Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing, 400065, China
| | - Bowen Lu
- Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing, 400065, China
| | - Dongyang Song
- Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing, 400065, China
| | - Jie Li
- Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing, 400065, China
| | - Kunxian Shu
- Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing, 400065, China.
| | - Dan Pu
- Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing, 400065, China.
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4
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Leman R, Muller E, Legros A, Goardon N, Chentli I, Atkinson A, Tranchant A, Castera L, Krieger S, Ricou A, Boulouard F, Joly F, Boucly R, Dumont A, Basset N, Coulet F, Chevalier LM, Rouleau E, Leitner K, González-Martin A, Gargiulo P, Lück HJ, Genestie C, Ray-Coquard I, Pujade-Lauraine E, Vaur D. Validation of the Clinical Use of GIScar, an Academic-developed Genomic Instability Score Predicting Sensitivity to Maintenance Olaparib for Ovarian Cancer. Clin Cancer Res 2023; 29:4419-4429. [PMID: 37756555 PMCID: PMC10618649 DOI: 10.1158/1078-0432.ccr-23-0898] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 06/12/2023] [Accepted: 08/15/2023] [Indexed: 09/29/2023]
Abstract
PURPOSE The optimal application of maintenance PARP inhibitor therapy for ovarian cancer requires accessible, robust, and rapid testing of homologous recombination deficiency (HRD). However, in many countries, access to HRD testing is problematic and the failure rate is high. We developed an academic HRD test to support treatment decision-making. EXPERIMENTAL DESIGN Genomic Instability Scar (GIScar) was developed through targeted sequencing of a 127-gene panel to determine HRD status. GIScar was trained from a noninterventional study with 250 prospectively collected ovarian tumor samples. GIScar was validated on 469 DNA tumor samples from the PAOLA-1 trial evaluating maintenance olaparib for newly diagnosed ovarian cancer, and its predictive value was compared with Myriad Genetics MyChoice (MGMC). RESULTS GIScar showed significant correlation with MGMC HRD classification (kappa statistics: 0.780). From PAOLA-1 samples, more HRD-positive tumors were identified by GIScar (258) than MGMC (242), with a lower proportion of inconclusive results (1% vs. 9%, respectively). The HRs for progression-free survival (PFS) with olaparib versus placebo were 0.45 [95% confidence interval (CI), 0.33-0.62] in GIScar-identified HRD-positive BRCA-mutated tumors, 0.50 (95% CI, 0.31-0.80) in HRD-positive BRCA-wild-type tumors, and 1.02 (95% CI, 0.74-1.40) in HRD-negative tumors. Tumors identified as HRD positive by GIScar but HRD negative by MGMC had better PFS with olaparib (HR, 0.23; 95% CI, 0.07-0.72). CONCLUSIONS GIScar is a valuable diagnostic tool, reliably detecting HRD and predicting sensitivity to olaparib for ovarian cancer. GIScar showed high analytic concordance with MGMC test and fewer inconclusive results. GIScar is easily implemented into diagnostic laboratories with a rapid turnaround.
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Affiliation(s)
- Raphaël Leman
- Laboratoire de Biologie et de Génétique du Cancer, Centre François Baclesse, Caen, France
- Inserm U1245, Cancer Brain and Genome, Normandie Université, UNICAEN, FHU G4 Génomique, Rouen, France
| | - Etienne Muller
- Laboratoire de Biologie et de Génétique du Cancer, Centre François Baclesse, Caen, France
- Inserm U1245, Cancer Brain and Genome, Normandie Université, UNICAEN, FHU G4 Génomique, Rouen, France
| | - Angelina Legros
- Laboratoire de Biologie et de Génétique du Cancer, Centre François Baclesse, Caen, France
| | - Nicolas Goardon
- Laboratoire de Biologie et de Génétique du Cancer, Centre François Baclesse, Caen, France
- Inserm U1245, Cancer Brain and Genome, Normandie Université, UNICAEN, FHU G4 Génomique, Rouen, France
| | - Imène Chentli
- Laboratoire de Biologie et de Génétique du Cancer, Centre François Baclesse, Caen, France
| | - Alexandre Atkinson
- Laboratoire de Biologie et de Génétique du Cancer, Centre François Baclesse, Caen, France
- Inserm U1245, Cancer Brain and Genome, Normandie Université, UNICAEN, FHU G4 Génomique, Rouen, France
| | - Aurore Tranchant
- Laboratoire de Biologie et de Génétique du Cancer, Centre François Baclesse, Caen, France
| | - Laurent Castera
- Laboratoire de Biologie et de Génétique du Cancer, Centre François Baclesse, Caen, France
- Inserm U1245, Cancer Brain and Genome, Normandie Université, UNICAEN, FHU G4 Génomique, Rouen, France
| | - Sophie Krieger
- Laboratoire de Biologie et de Génétique du Cancer, Centre François Baclesse, Caen, France
- Inserm U1245, Cancer Brain and Genome, Normandie Université, UNICAEN, FHU G4 Génomique, Rouen, France
| | - Agathe Ricou
- Laboratoire de Biologie et de Génétique du Cancer, Centre François Baclesse, Caen, France
- Inserm U1245, Cancer Brain and Genome, Normandie Université, UNICAEN, FHU G4 Génomique, Rouen, France
| | - Flavie Boulouard
- Laboratoire de Biologie et de Génétique du Cancer, Centre François Baclesse, Caen, France
- Inserm U1245, Cancer Brain and Genome, Normandie Université, UNICAEN, FHU G4 Génomique, Rouen, France
| | - Florence Joly
- Clinical Research, Centre François Baclesse, Caen, France
| | - Romain Boucly
- Unité d'Oncologie Moléculaire Humaine, Centre Oscar Lambret, Lille, France
| | - Aurélie Dumont
- Unité d'Oncologie Moléculaire Humaine, Centre Oscar Lambret, Lille, France
| | - Noémie Basset
- Département de Génétique Médicale, UF d'Onco-Angiogénétique et Génomique des Tumeurs Solides, Hôpital Pitié Salpêtrière APHP, Paris, France
- Sorbonne Université, Paris, France
| | - Florence Coulet
- Département de Génétique Médicale, UF d'Onco-Angiogénétique et Génomique des Tumeurs Solides, Hôpital Pitié Salpêtrière APHP, Paris, France
- Sorbonne Université, Paris, France
| | - Louise-Marie Chevalier
- Unité de Génomique Fonctionnelle, Institut de Cancérologie de l'Ouest, Angers, France
- Université Angers, Nantes Université, Inserm, CNRS, CRCI2NA, SFR ICAT, Angers, France
| | - Etienne Rouleau
- Service de Génétique des Tumeurs, Gustave Roussy, Villejuif, France
| | - Katharina Leitner
- Department of Obstetrics and Gynecology, Medical University Innsbruck, Innsbruck, Austria
- AGO Austria, Vienna, Austria
| | - Antonio González-Martin
- Department of Medical Oncology and Program in Solid Tumors-Cima, Cancer Center Clinica Universidad de Navarra, Madrid, Spain
- GEICO, Cádiz, Spain
| | - Piera Gargiulo
- Clinical Trials Unit, Istituto Nazionale Tumori IRCCS Fondazione G. Pascale, Naples, Italy
- MITO, Italy
| | - Hans-Joachim Lück
- Gynäkologisch-Onkologische Praxis Hannover, Hannover, Germany
- AGO, Wiesbaden, Germany
| | | | - Isabelle Ray-Coquard
- Association de Recherche Cancers Gynécologiques (ARCAGY), Paris, France
- Groupe d'Investigateurs Nationaux pour l'Etude des Cancers Ovariens et du sein (GINECO), France
| | - Eric Pujade-Lauraine
- Groupe d'Investigateurs Nationaux pour l'Etude des Cancers Ovariens et du sein (GINECO), France
| | - Dominique Vaur
- Laboratoire de Biologie et de Génétique du Cancer, Centre François Baclesse, Caen, France
- Inserm U1245, Cancer Brain and Genome, Normandie Université, UNICAEN, FHU G4 Génomique, Rouen, France
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5
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Steiert TA, Parra G, Gut M, Arnold N, Trotta JR, Tonda R, Moussy A, Gerber Z, Abuja P, Zatloukal K, Röcken C, Folseraas T, Grimsrud M, Vogel A, Goeppert B, Roessler S, Hinz S, Schafmayer C, Rosenstiel P, Deleuze JF, Gut I, Franke A, Forster M. A critical spotlight on the paradigms of FFPE-DNA sequencing. Nucleic Acids Res 2023; 51:7143-7162. [PMID: 37351572 PMCID: PMC10415133 DOI: 10.1093/nar/gkad519] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 05/24/2023] [Accepted: 06/05/2023] [Indexed: 06/24/2023] Open
Abstract
In the late 19th century, formalin fixation with paraffin-embedding (FFPE) of tissues was developed as a fixation and conservation method and is still used to this day in routine clinical and pathological practice. The implementation of state-of-the-art nucleic acid sequencing technologies has sparked much interest for using historical FFPE samples stored in biobanks as they hold promise in extracting new information from these valuable samples. However, formalin fixation chemically modifies DNA, which potentially leads to incorrect sequences or misinterpretations in downstream processing and data analysis. Many publications have concentrated on one type of DNA damage, but few have addressed the complete spectrum of FFPE-DNA damage. Here, we review mitigation strategies in (I) pre-analytical sample quality control, (II) DNA repair treatments, (III) analytical sample preparation and (IV) bioinformatic analysis of FFPE-DNA. We then provide recommendations that are tested and illustrated with DNA from 13-year-old liver specimens, one FFPE preserved and one fresh frozen, applying target-enriched sequencing. Thus, we show how DNA damage can be compensated, even when using low quantities (50 ng) of fragmented FFPE-DNA (DNA integrity number 2.0) that cannot be amplified well (Q129 bp/Q41 bp = 5%). Finally, we provide a checklist called 'ERROR-FFPE-DNA' that summarises recommendations for the minimal information in publications required for assessing fitness-for-purpose and inter-study comparison when using FFPE samples.
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Affiliation(s)
- Tim A Steiert
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Medical Center Schleswig-Holstein, Kiel 24105, Germany
| | - Genís Parra
- Center for Genomic Regulation, Centro Nacional de Análisis Genómico, Barcelona 08028, Spain
| | - Marta Gut
- Center for Genomic Regulation, Centro Nacional de Análisis Genómico, Barcelona 08028, Spain
| | - Norbert Arnold
- Department of Gynaecology and Obstetrics, University Medical Center Schleswig-Holstein, Campus Kiel, Kiel 24105, Germany
| | - Jean-Rémi Trotta
- Center for Genomic Regulation, Centro Nacional de Análisis Genómico, Barcelona 08028, Spain
| | - Raúl Tonda
- Center for Genomic Regulation, Centro Nacional de Análisis Genómico, Barcelona 08028, Spain
| | - Alice Moussy
- Le Centre de référence, d’innovation, d’expertise et de transfert (CRefIX), PFMG 2025, Évry 91057, France
| | - Zuzana Gerber
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Évry 91057, France
| | - Peter M Abuja
- Diagnostic & Research Center for Molecular Biomedicine, Diagnostic & Research Institute of Pathology, Medical University of Graz, Graz 8010, Austria
| | - Kurt Zatloukal
- Diagnostic & Research Center for Molecular Biomedicine, Diagnostic & Research Institute of Pathology, Medical University of Graz, Graz 8010, Austria
| | - Christoph Röcken
- Department of Pathology, University Medical Center Schleswig-Holstein, Campus Kiel, Kiel 24105, Germany
| | - Trine Folseraas
- Norwegian PSC Research Center Department of Transplantation Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital Rikshospitalet, Oslo 0372, Norway
- Section of Gastroenterology, Department of Transplantation Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet, Oslo 0372, Norway
| | - Marit M Grimsrud
- Norwegian PSC Research Center Department of Transplantation Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital Rikshospitalet, Oslo 0372, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo 0372, Norway
| | - Arndt Vogel
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hanover 30625, Germany
| | - Benjamin Goeppert
- Institute of Pathology, University Hospital Heidelberg, Heidelberg 69120, Germany
- Institute of Pathology and Neuropathology, RKH Klinikum Ludwigsburg, Ludwigsburg 71640, Germany
| | - Stephanie Roessler
- Institute of Pathology, University Hospital Heidelberg, Heidelberg 69120, Germany
| | - Sebastian Hinz
- Department of General Surgery, University Medicine Rostock, Rostock 18057, Germany
| | - Clemens Schafmayer
- Department of General Surgery, University Medicine Rostock, Rostock 18057, Germany
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Medical Center Schleswig-Holstein, Kiel 24105, Germany
| | - Jean-François Deleuze
- Le Centre de référence, d’innovation, d’expertise et de transfert (CRefIX), PFMG 2025, Évry 91057, France
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Évry 91057, France
| | - Ivo G Gut
- Center for Genomic Regulation, Centro Nacional de Análisis Genómico, Barcelona 08028, Spain
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Medical Center Schleswig-Holstein, Kiel 24105, Germany
| | - Michael Forster
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Medical Center Schleswig-Holstein, Kiel 24105, Germany
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6
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Nadeu F, Royo R, Massoni-Badosa R, Playa-Albinyana H, Garcia-Torre B, Duran-Ferrer M, Dawson KJ, Kulis M, Diaz-Navarro A, Villamor N, Melero JL, Chapaprieta V, Dueso-Barroso A, Delgado J, Moia R, Ruiz-Gil S, Marchese D, Giró A, Verdaguer-Dot N, Romo M, Clot G, Rozman M, Frigola G, Rivas-Delgado A, Baumann T, Alcoceba M, González M, Climent F, Abrisqueta P, Castellví J, Bosch F, Aymerich M, Enjuanes A, Ruiz-Gaspà S, López-Guillermo A, Jares P, Beà S, Capella-Gutierrez S, Gelpí JL, López-Bigas N, Torrents D, Campbell PJ, Gut I, Rossi D, Gaidano G, Puente XS, Garcia-Roves PM, Colomer D, Heyn H, Maura F, Martín-Subero JI, Campo E. Detection of early seeding of Richter transformation in chronic lymphocytic leukemia. Nat Med 2022; 28:1662-1671. [PMID: 35953718 PMCID: PMC9388377 DOI: 10.1038/s41591-022-01927-8] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 07/01/2022] [Indexed: 02/06/2023]
Abstract
Richter transformation (RT) is a paradigmatic evolution of chronic lymphocytic leukemia (CLL) into a very aggressive large B cell lymphoma conferring a dismal prognosis. The mechanisms driving RT remain largely unknown. We characterized the whole genome, epigenome and transcriptome, combined with single-cell DNA/RNA-sequencing analyses and functional experiments, of 19 cases of CLL developing RT. Studying 54 longitudinal samples covering up to 19 years of disease course, we uncovered minute subclones carrying genomic, immunogenetic and transcriptomic features of RT cells already at CLL diagnosis, which were dormant for up to 19 years before transformation. We also identified new driver alterations, discovered a new mutational signature (SBS-RT), recognized an oxidative phosphorylation (OXPHOS)high–B cell receptor (BCR)low-signaling transcriptional axis in RT and showed that OXPHOS inhibition reduces the proliferation of RT cells. These findings demonstrate the early seeding of subclones driving advanced stages of cancer evolution and uncover potential therapeutic targets for RT. Single-cell genomic and transcriptomic analyses of longitudinal samples of patients with Richter syndrome reveal the presence and dynamics of clones driving transformation from chronic lymphocytic leukemia years before clinical manifestation
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Affiliation(s)
- Ferran Nadeu
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain. .,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.
| | - Romina Royo
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | - Ramon Massoni-Badosa
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Heribert Playa-Albinyana
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Beatriz Garcia-Torre
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Martí Duran-Ferrer
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | | | - Marta Kulis
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Ander Diaz-Navarro
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología, Universidad de Oviedo, Oviedo, Spain
| | - Neus Villamor
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Hospital Clínic of Barcelona, Barcelona, Spain
| | | | - Vicente Chapaprieta
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | | | - Julio Delgado
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Hospital Clínic of Barcelona, Barcelona, Spain.,Universitat de Barcelona, Barcelona, Spain
| | - Riccardo Moia
- Division of Hematology, Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy
| | - Sara Ruiz-Gil
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Domenica Marchese
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Ariadna Giró
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Núria Verdaguer-Dot
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Mónica Romo
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Guillem Clot
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Maria Rozman
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Hospital Clínic of Barcelona, Barcelona, Spain
| | | | - Alfredo Rivas-Delgado
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Hospital Clínic of Barcelona, Barcelona, Spain
| | - Tycho Baumann
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Hospital Clínic of Barcelona, Barcelona, Spain.,Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Miguel Alcoceba
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Biología Molecular e Histocompatibilidad, IBSAL-Hospital Universitario, Centro de Investigación del Cáncer-IBMCC (USAL-CSIC), Salamanca, Spain
| | - Marcos González
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Biología Molecular e Histocompatibilidad, IBSAL-Hospital Universitario, Centro de Investigación del Cáncer-IBMCC (USAL-CSIC), Salamanca, Spain
| | - Fina Climent
- Hospital Universitari de Bellvitge-Institut d'Investigació Biomédica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Pau Abrisqueta
- Department of Hematology, Vall d'Hebron Institute of Oncology, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Josep Castellví
- Department of Hematology, Vall d'Hebron Institute of Oncology, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Francesc Bosch
- Department of Hematology, Vall d'Hebron Institute of Oncology, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Marta Aymerich
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Hospital Clínic of Barcelona, Barcelona, Spain
| | - Anna Enjuanes
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Sílvia Ruiz-Gaspà
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Armando López-Guillermo
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Hospital Clínic of Barcelona, Barcelona, Spain.,Universitat de Barcelona, Barcelona, Spain
| | - Pedro Jares
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Hospital Clínic of Barcelona, Barcelona, Spain.,Universitat de Barcelona, Barcelona, Spain
| | - Sílvia Beà
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Hospital Clínic of Barcelona, Barcelona, Spain.,Universitat de Barcelona, Barcelona, Spain
| | | | - Josep Ll Gelpí
- Barcelona Supercomputing Center (BSC), Barcelona, Spain.,Universitat de Barcelona, Barcelona, Spain
| | - Núria López-Bigas
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - David Torrents
- Barcelona Supercomputing Center (BSC), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | | | - Ivo Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Davide Rossi
- Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Gianluca Gaidano
- Division of Hematology, Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy
| | - Xose S Puente
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología, Universidad de Oviedo, Oviedo, Spain
| | - Pablo M Garcia-Roves
- Universitat de Barcelona, Barcelona, Spain.,Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Dolors Colomer
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Hospital Clínic of Barcelona, Barcelona, Spain.,Universitat de Barcelona, Barcelona, Spain
| | - Holger Heyn
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Francesco Maura
- Myeloma Service, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - José I Martín-Subero
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Universitat de Barcelona, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Elías Campo
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain. .,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain. .,Hospital Clínic of Barcelona, Barcelona, Spain. .,Universitat de Barcelona, Barcelona, Spain.
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7
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Dodani DD, Nguyen MH, Morin RD, Marra MA, Corbett RD. Combinatorial and Machine Learning Approaches for Improved Somatic Variant Calling From Formalin-Fixed Paraffin-Embedded Genome Sequence Data. Front Genet 2022; 13:834764. [PMID: 35571031 PMCID: PMC9092826 DOI: 10.3389/fgene.2022.834764] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 03/18/2022] [Indexed: 11/13/2022] Open
Abstract
Formalin fixation of paraffin-embedded tissue samples is a well-established method for preserving tissue and is routinely used in clinical settings. Although formalin-fixed, paraffin-embedded (FFPE) tissues are deemed crucial for research and clinical applications, the fixation process results in molecular damage to nucleic acids, thus confounding their use in genome sequence analysis. Methods to improve genomic data quality from FFPE tissues have emerged, but there remains significant room for improvement. Here, we use whole-genome sequencing (WGS) data from matched Fresh Frozen (FF) and FFPE tissue samples to optimize a sensitive and precise FFPE single nucleotide variant (SNV) calling approach. We present methods to reduce the prevalence of false-positive SNVs by applying combinatorial techniques to five publicly available variant callers. We also introduce FFPolish, a novel variant classification method that efficiently classifies FFPE-specific false-positive variants. Our combinatorial and statistical techniques improve precision and F1 scores compared to the results of publicly available tools when tested individually.
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Affiliation(s)
- Dollina D Dodani
- The Bioinformatics Graduate Program, University of British Columbia, Vancouver, BC, Canada
| | - Matthew H Nguyen
- The Bioinformatics Graduate Program, University of British Columbia, Vancouver, BC, Canada
| | - Ryan D Morin
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Provincial Health Services Authority, Vancouver, BC, Canada.,Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Provincial Health Services Authority, Vancouver, BC, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Richard D Corbett
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Provincial Health Services Authority, Vancouver, BC, Canada
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8
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Sater V, Viailly PJ, Lecroq T, Prieur-Gaston É, Bohers É, Viennot M, Ruminy P, Dauchel H, Vera P, Jardin F. UMI-Varcal: A Low-Frequency Variant Caller for UMI-Tagged Paired-End Sequencing Data. Methods Mol Biol 2022; 2493:235-245. [PMID: 35751818 DOI: 10.1007/978-1-0716-2293-3_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The rapid transition from traditional sequencing methods to Next-Generation Sequencing (NGS) has allowed for a faster and more accurate detection of somatic variants (Single-Nucleotide Variant (SNV) and Copy Number Variation (CNV)) in tumor cells. NGS technologies require a succession of steps during which false variants can be silently added at low frequencies. Filtering these artifacts can be a rather difficult task especially when the experiments are designed to look for very low frequency variants. Recently, adding unique molecular barcodes called UMI (Unique Molecular Identifier) to the DNA fragments appears to be a very effective strategy to specifically filter out false variants from the variant calling results (Kukita et al. DNA Res 22(4):269-277, 2015; Newman et al. Nat Biotechnol 34(5):547-555, 2016; Schmitt et al. Proc Natl Acad Sci U S A 109(36):14508-14513). Here, we describe UMI-VarCal (Sater et al. Bioinformatics 36:2718-2724, 2020), which can use the UMI information from UMI-tagged reads to offer a faster and more accurate variant calling analysis.
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Affiliation(s)
- Vincent Sater
- Normandie Univ, UNIROUEN, LITIS EA 4108, Rouen, France.
| | - Pierre-Julien Viailly
- Department of Pathology, Centre Henri Becquerel, Rouen, France
- INSERM U1245, University of Normandie UNIROUEN, Rouen, France
| | | | | | - Élodie Bohers
- Department of Pathology, Centre Henri Becquerel, Rouen, France
- INSERM U1245, University of Normandie UNIROUEN, Rouen, France
| | - Mathieu Viennot
- Department of Pathology, Centre Henri Becquerel, Rouen, France
- INSERM U1245, University of Normandie UNIROUEN, Rouen, France
| | - Philippe Ruminy
- Department of Pathology, Centre Henri Becquerel, Rouen, France
- INSERM U1245, University of Normandie UNIROUEN, Rouen, France
| | | | - Pierre Vera
- Normandie Univ, UNIROUEN, LITIS EA 4108, Rouen, France
- Department of Pathology, Centre Henri Becquerel, Rouen, France
| | - Fabrice Jardin
- Department of Pathology, Centre Henri Becquerel, Rouen, France
- INSERM U1245, University of Normandie UNIROUEN, Rouen, France
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9
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Woerner AE, Mandape S, King JL, Muenzler M, Crysup B, Budowle B. Reducing noise and stutter in short tandem repeat loci with unique molecular identifiers. Forensic Sci Int Genet 2020; 51:102459. [PMID: 33429137 DOI: 10.1016/j.fsigen.2020.102459] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 10/28/2020] [Accepted: 12/21/2020] [Indexed: 12/24/2022]
Abstract
Unique molecular identifiers (UMIs) are a promising approach to contend with errors generated during PCR and massively parallel sequencing (MPS). With UMI technology, random molecular barcodes are ligated to template DNA molecules prior to PCR, allowing PCR and sequencing error to be tracked and corrected bioinformatically. UMIs have the potential to be particularly informative for the interpretation of short tandem repeats (STRs). Traditional MPS approaches may simply lead to the observation of alleles that are consistent with the hypotheses of stutter, while with UMIs stutter products bioinformatically may be re-associated with their parental alleles and subsequently removed. Herein, a bioinformatics pipeline named strumi is described that is designed for the analysis of STRs that are tagged with UMIs. Unlike other tools, strumi is an alignment-free machine learning driven algorithm that clusters individual MPS reads into UMI families, infers consensus super-reads that represent each family and provides an estimate the resulting haplotype's accuracy. Super-reads, in turn, approximate independent measurements not of the PCR products, but of the original template molecules, both in terms of quantity and sequence identity. Provisional assessments show that naïve threshold-based approaches generate super-reads that are accurate (∼97 % haplotype accuracy, compared to ∼78 % when UMIs are not used), and the application of a more nuanced machine learning approach increases the accuracy to ∼99.5 % depending on the level of certainty desired. With these features, UMIs may greatly simplify probabilistic genotyping systems and reduce uncertainty. However, the ability to interpret alleles at trace levels also permits the interpretation, characterization and quantification of contamination as well as somatic variation (including somatic stutter), which may present newfound challenges.
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Affiliation(s)
- August E Woerner
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA; Department of Microbiology, Immunology and Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA.
| | - Sammed Mandape
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA
| | - Jonathan L King
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA
| | - Melissa Muenzler
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA
| | - Benjamin Crysup
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA
| | - Bruce Budowle
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA; Department of Microbiology, Immunology and Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA
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10
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Sater V, Viailly PJ, Lecroq T, Prieur-Gaston É, Bohers É, Viennot M, Ruminy P, Dauchel H, Vera P, Jardin F. UMI-VarCal: a new UMI-based variant caller that efficiently improves low-frequency variant detection in paired-end sequencing NGS libraries. Bioinformatics 2020; 36:2718-2724. [PMID: 31985795 DOI: 10.1093/bioinformatics/btaa053] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 11/18/2019] [Accepted: 01/20/2020] [Indexed: 01/03/2023] Open
Abstract
MOTIVATION Next-generation sequencing has become the go-to standard method for the detection of single-nucleotide variants in tumor cells. The use of such technologies requires a PCR amplification step and a sequencing step, steps in which artifacts are introduced at very low frequencies. These artifacts are often confused with true low-frequency variants that can be found in tumor cells and cell-free DNA. The recent use of unique molecular identifiers (UMI) in targeted sequencing protocols has offered a trustworthy approach to filter out artefactual variants and accurately call low-frequency variants. However, the integration of UMI analysis in the variant calling process led to developing tools that are significantly slower and more memory consuming than raw-reads-based variant callers. RESULTS We present UMI-VarCal, a UMI-based variant caller for targeted sequencing data with better sensitivity compared to other variant callers. Being developed with performance in mind, UMI-VarCal stands out from the crowd by being one of the few variant callers that do not rely on SAMtools to do their pileup. Instead, at its core runs an innovative homemade pileup algorithm specifically designed to treat the UMI tags in the reads. After the pileup, a Poisson statistical test is applied at every position to determine if the frequency of the variant is significantly higher than the background error noise. Finally, an analysis of UMI tags is performed, a strand bias and a homopolymer length filter are applied to achieve better accuracy. We illustrate the results obtained using UMI-VarCal through the sequencing of tumor samples and we show how UMI-VarCal is both faster and more sensitive than other publicly available solutions. AVAILABILITY AND IMPLEMENTATION The entire pipeline is available at https://gitlab.com/vincent-sater/umi-varcal-master under MIT license. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Pierre-Julien Viailly
- Department of Pathology, Centre Henri Becquerel.,INSERM U1245, University of Normandie UNIROUEN, Rouen 76000, France
| | | | | | - Élodie Bohers
- Department of Pathology, Centre Henri Becquerel.,INSERM U1245, University of Normandie UNIROUEN, Rouen 76000, France
| | - Mathieu Viennot
- Department of Pathology, Centre Henri Becquerel.,INSERM U1245, University of Normandie UNIROUEN, Rouen 76000, France
| | - Philippe Ruminy
- Department of Pathology, Centre Henri Becquerel.,INSERM U1245, University of Normandie UNIROUEN, Rouen 76000, France
| | - Hélène Dauchel
- Department of Pathology, Centre Henri Becquerel.,INSERM U1245, University of Normandie UNIROUEN, Rouen 76000, France
| | - Pierre Vera
- University of Normandie UNIROUEN, LITIS EA 4108.,Department of Pathology, Centre Henri Becquerel
| | - Fabrice Jardin
- Department of Pathology, Centre Henri Becquerel.,INSERM U1245, University of Normandie UNIROUEN, Rouen 76000, France
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11
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Sater V, Viailly PJ, Lecroq T, Ruminy P, Bérard C, Prieur-Gaston É, Jardin F. UMI-Gen: A UMI-based read simulator for variant calling evaluation in paired-end sequencing NGS libraries. Comput Struct Biotechnol J 2020; 18:2270-2280. [PMID: 32952940 PMCID: PMC7484502 DOI: 10.1016/j.csbj.2020.08.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 08/03/2020] [Accepted: 08/05/2020] [Indexed: 11/02/2022] Open
Abstract
Motivation With Next Generation Sequencing becoming more affordable every year, NGS technologies asserted themselves as the fastest and most reliable way to detect Single Nucleotide Variants (SNV) and Copy Number Variations (CNV) in cancer patients. These technologies can be used to sequence DNA at very high depths thus allowing to detect abnormalities in tumor cells with very low frequencies. Multiple variant callers are publicly available and are usually efficient at calling out variants. However, when frequencies begin to drop under 1%, the specificity of these tools suffers greatly as true variants at very low frequencies can be easily confused with sequencing or PCR artifacts. The recent use of Unique Molecular Identifiers (UMI) in NGS experiments has offered a way to accurately separate true variants from artifacts. UMI-based variant callers are slowly replacing raw-read based variant callers as the standard method for an accurate detection of variants at very low frequencies. However, benchmarking done in the tools publication are usually realized on real biological data in which real variants are not known, making it difficult to assess their accuracy. Results We present UMI-Gen, a UMI-based read simulator for targeted sequencing paired-end data. UMI-Gen generates reference reads covering the targeted regions at a user customizable depth. After that, using a number of control files, it estimates the background error rate at each position and then modifies the generated reads to mimic real biological data. Finally, it will insert real variants in the reads from a list provided by the user. Availability The entire pipeline is available at https://gitlab.com/vincent-sater/umigen under MIT license.
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Affiliation(s)
- Vincent Sater
- University of Rouen Normandy UNIROUEN, LITIS EA 4108, 76000 Rouen, France.,INSERM U1245, University of Rouen Normandy UNIROUEN, 76000 Rouen, France
| | - Pierre-Julien Viailly
- Department of Pathology, Centre Henri Becquerel, 76000 Rouen, France.,INSERM U1245, University of Rouen Normandy UNIROUEN, 76000 Rouen, France
| | - Thierry Lecroq
- University of Rouen Normandy UNIROUEN, LITIS EA 4108, 76000 Rouen, France
| | - Philippe Ruminy
- Department of Pathology, Centre Henri Becquerel, 76000 Rouen, France.,INSERM U1245, University of Rouen Normandy UNIROUEN, 76000 Rouen, France
| | - Caroline Bérard
- University of Rouen Normandy UNIROUEN, LITIS EA 4108, 76000 Rouen, France
| | | | - Fabrice Jardin
- Department of Pathology, Centre Henri Becquerel, 76000 Rouen, France.,INSERM U1245, University of Rouen Normandy UNIROUEN, 76000 Rouen, France
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12
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Butz H, Nyírő G, Kurucz PA, Likó I, Patócs A. Molecular genetic diagnostics of hypogonadotropic hypogonadism: from panel design towards result interpretation in clinical practice. Hum Genet 2020; 140:113-134. [PMID: 32222824 PMCID: PMC7864839 DOI: 10.1007/s00439-020-02148-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 03/05/2020] [Indexed: 12/13/2022]
Abstract
Congenital hypogonadotropic hypogonadism (CHH) is a clinically and genetically heterogeneous congenital disease. Symptoms cover a wide spectrum from mild forms to complex phenotypes due to gonadotropin-releasing hormone (GnRH) deficiency. To date, more than 40 genes have been identified as pathogenic cause of CHH. These genes could be grouped into two major categories: genes controlling development and GnRH neuron migration and genes being responsible for neuroendocrine regulation and GnRH neuron function. High-throughput, next-generation sequencing (NGS) allows to analyze numerous gene sequences at the same time. Nowadays, whole exome or whole genome datasets could be investigated in clinical genetic diagnostics due to their favorable cost-benefit. The increasing genetic data generated by NGS reveal novel candidate genes and gene variants with unknown significance (VUSs). To provide clinically valuable genetic results, complex clinical and bioinformatics work are needed. The multifaceted genetics of CHH, the variable mode of inheritance, the incomplete penetrance, variable expressivity and oligogenic characteristics further complicate the interpretation of the genetic variants detected. The objective of this work, apart from reviewing the currently known genes associated with CHH, was to summarize the advantages and disadvantages of the NGS-based platforms and through the authors' own practice to guide through the whole workflow starting from gene panel design, performance analysis and result interpretation. Based on our results, a genetic diagnosis was clearly identified in 21% of cases tested (8/38).
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Affiliation(s)
- Henriett Butz
- Department of Laboratory Medicine, Semmelweis University, Nagyvárad tér 4, Budapest, 1089, Hungary.,Hereditary Tumours Research Group, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary.,Department of Molecular Genetics, National Institute of Oncology, Budapest, Hungary
| | - Gábor Nyírő
- Department of Laboratory Medicine, Semmelweis University, Nagyvárad tér 4, Budapest, 1089, Hungary.,Molecular Medicine Research Group, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary.,2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
| | - Petra Anna Kurucz
- Department of Laboratory Medicine, Semmelweis University, Nagyvárad tér 4, Budapest, 1089, Hungary
| | - István Likó
- Hereditary Tumours Research Group, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary
| | - Attila Patócs
- Department of Laboratory Medicine, Semmelweis University, Nagyvárad tér 4, Budapest, 1089, Hungary. .,Hereditary Tumours Research Group, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary. .,Department of Molecular Genetics, National Institute of Oncology, Budapest, Hungary.
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13
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Friedlaender A, Nouspikel T, Christinat Y, Ho L, McKee T, Addeo A. Tissue-Plasma TMB Comparison and Plasma TMB Monitoring in Patients With Metastatic Non-small Cell Lung Cancer Receiving Immune Checkpoint Inhibitors. Front Oncol 2020; 10:142. [PMID: 32117779 PMCID: PMC7028749 DOI: 10.3389/fonc.2020.00142] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 01/27/2020] [Indexed: 12/13/2022] Open
Abstract
Immuno-oncology is an ever growing field that has seen important progress across the spectrum of cancers. Responses can be deep and durable. However, as only a minority of patients respond to checkpoint inhibition, predictive biomarkers are needed. Cancer is a genetic disease arising from the accumulation of somatic mutations in the DNA of affected cells. Tumor mutational burden (TMB), represents the number of somatic mutations in a tumor that form neoantigens, responsible for the immunogenicity of tumors. Randomized controlled trials have so far failed to show a survival benefit when stratifying patients by tissue TMB. TMB has also been evaluated in plasma (PTMB). PTMB is anticipated to represent the biology of the entire cancer, whereas obtaining tissue of an amenable primary or a metastatic lesion may be prone to sampling bias because of tumor heterogeneity. For this reason, we are evaluating the correlation between TMB and PTMB, and prospectively evaluating the impact of these biomarkers on clinical outcomes. We also discuss the technical difficulties inherent to performing and comparing these analyses. Furthermore, we evaluate the correlation between the evolution of PTMB during an immunotherapy treatment and response at 3 and 6 months, as we believe PTMB may be a dynamic biomarker. In this paper, we present results from the first 4 patients in this project.
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Affiliation(s)
- Alex Friedlaender
- Department of Oncology, University Hospital of Geneva (HUG), Geneva, Switzerland
| | - Thierry Nouspikel
- Service of Medical Genetics, Diagnostics Department, University Hospital of Geneva, Geneva, Switzerland
| | - Yann Christinat
- Department of Pathology, University Hospital of Geneva, Geneva, Switzerland
| | - Liza Ho
- Department of Pathology, University Hospital of Geneva, Geneva, Switzerland
| | - Thomas McKee
- Department of Pathology, University Hospital of Geneva, Geneva, Switzerland
| | - Alfredo Addeo
- Department of Oncology, University Hospital of Geneva (HUG), Geneva, Switzerland
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14
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Sensitization of chondrosarcoma cells with PARP inhibitor and high-LET radiation. J Bone Oncol 2019; 17:100246. [PMID: 31312595 PMCID: PMC6609837 DOI: 10.1016/j.jbo.2019.100246] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 06/04/2019] [Accepted: 06/18/2019] [Indexed: 12/11/2022] Open
Abstract
Chondrosarcoma is a malignant tumor that arises from cartilaginous tissue and is radioresistant and chemoresistant to conventional treatments. The preferred treatment consists of surgical resection, which might cause severe disabilities for the patient; in addition, this procedure might be impossible for inoperable locations, such as the skull base. Carbon ion irradiation (hadron therapy) has been proposed as an alternative treatment, primarily due to its greater biological effectiveness and improved ballistic properties compared with conventional radiotherapy with X-rays. The goal of this study was to characterize the genetic mutations of a grade III chondrosarcoma cell line (CH2879) and examine the cellular responses to conventional radiotherapy (X-rays) and hadron therapy (proton and carbon ions) in the presence of the PARP inhibitor Olaparib. To better understand PARP inhibition, we first analyzed the formation of poly-ADP ribose chains by western blot; we observed an increase in its signal after irradiation, which disappeared on addition of the PARP inhibitor. PARPi enhanced ratio of approximately 1.3, 1.8, and 1.5 following irradiation of cells with X-rays, protons, and C-ions, respectively, as detected by clonogenic assay. The decrease in cell survival was confirmed by proliferation assay. The radiosensitivity of CH2879 cells was associated with mutations in homologous recombination repair genes, such as RAD50, SMARCA2 and NBN. This study demonstrates the capacity of the PARP inhibitor Olaparib to radiosensitize mutated chondrosarcoma cells to conventional photon irradiation, proton and carbon ion irradiation.
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Calling Variants in the Clinic: Informed Variant Calling Decisions Based on Biological, Clinical, and Laboratory Variables. Comput Struct Biotechnol J 2019; 17:561-569. [PMID: 31049166 PMCID: PMC6482431 DOI: 10.1016/j.csbj.2019.04.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 03/12/2019] [Accepted: 04/03/2019] [Indexed: 01/10/2023] Open
Abstract
Deep sequencing genomic analysis is becoming increasingly common in clinical research and practice, enabling accurate identification of diagnostic, prognostic, and predictive determinants. Variant calling, distinguishing between true mutations and experimental errors, is a central task of genomic analysis and often requires sophisticated statistical, computational, and/or heuristic techniques. Although variant callers seek to overcome noise inherent in biological experiments, variant calling can be significantly affected by outside factors including those used to prepare, store, and analyze samples. The goal of this review is to discuss known experimental features, such as sample preparation, library preparation, and sequencing, alongside diverse biological and clinical variables, and evaluate their effect on variant caller selection and optimization.
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What Does This Mutation Mean? The Tools and Pitfalls of Variant Interpretation in Lymphoid Malignancies. Int J Mol Sci 2018; 19:ijms19041251. [PMID: 29677173 PMCID: PMC5979354 DOI: 10.3390/ijms19041251] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 04/09/2018] [Accepted: 04/14/2018] [Indexed: 01/21/2023] Open
Abstract
High throughput sequencing (HTS) is increasingly important in determining cancer diagnoses, with subsequent prognostic and therapeutic implications. The biology of cancer is becoming increasingly deciphered and it is clear that therapy needs to be individually tailored. Whilst translational research plays an important role in lymphoid malignancies, few guidelines exist to guide biologists and routine laboratories through this constantly evolving field. In this article, we review the challenges of interpreting HTS in lymphoid malignancies and provide a toolkit to interpret single nucleotide variants obtained from HTS. We define the pre-analytical issues such as sequencing DNA obtained from formalin-fixed and paraffin-embedded tissue (FFPE), the acquisition of germline DNA, or the bioinformatic pitfalls, the analytical issues encountered and how to manage them. We describe the main constitutional and cancer databases, their characteristics and limitations, with an emphasis on variant interpretation in lymphoid malignancies. Finally, we discuss the challenges of predictions that one can make using in silico or in vitro modelling, pharmacogenomic screening, and the limits of those prediction tools. This description of the current status in genomic interpretation highlights the need for new large databases and international collaboration in the lymphoma field.
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Lesueur P, Chevalier F, El-Habr EA, Junier MP, Chneiweiss H, Castera L, Müller E, Stefan D, Saintigny Y. Radiosensitization Effect of Talazoparib, a Parp Inhibitor, on Glioblastoma Stem Cells Exposed to Low and High Linear Energy Transfer Radiation. Sci Rep 2018; 8:3664. [PMID: 29483558 PMCID: PMC5826933 DOI: 10.1038/s41598-018-22022-4] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 02/15/2018] [Indexed: 11/09/2022] Open
Abstract
Despite continuous improvements in treatment of glioblastoma, tumor recurrence and therapy resistance still occur in a high proportion of patients. One underlying reason for this radioresistance might be the presence of glioblastoma cancer stem cells (GSCs), which feature high DNA repair capability. PARP protein plays an important cellular role by detecting the presence of damaged DNA and then activating signaling pathways that promote appropriate cellular responses. Thus, PARP inhibitors (PARPi) have recently emerged as potential radiosensitizing agents. In this study, we investigated the preclinical efficacy of talazoparib, a new PARPi, in association with low and high linear energy transfer (LET) irradiation in two GSC cell lines. Reduction of GSC fraction, impact on cell proliferation, and cell cycle arrest were evaluated for each condition. All combinations were compared with a reference schedule: photonic irradiation combined with temozolomide. The use of PARPi combined with photon beam and even more carbon beam irradiation drastically reduced the GSC frequency of GBM cell lines in vitro. Furthermore, talazoparib combined with irradiation induced a marked and prolonged G2/M block, and decreased proliferation. These results show that talazoparib is a new candidate that effects radiosensitization in radioresistant GSCs, and its combination with high LET irradiation, is promising.
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Affiliation(s)
- Paul Lesueur
- LARIA, iRCM, François Jacob Institute, DRF-CEA, Caen, France.
- UMR6252 CIMAP, CEA - CNRS - ENSICAEN - Université de Caen Normandie, Caen, France.
- Radiotherapy Department, Centre François Baclesse, Caen, France.
| | - François Chevalier
- LARIA, iRCM, François Jacob Institute, DRF-CEA, Caen, France
- UMR6252 CIMAP, CEA - CNRS - ENSICAEN - Université de Caen Normandie, Caen, France
| | - Elias A El-Habr
- CNRS UMR8246, Inserm U1130, UPMC, Neuroscience Seine-IBPS, Sorbonne Universities, 75005, Paris, France
| | - Marie-Pierre Junier
- CNRS UMR8246, Inserm U1130, UPMC, Neuroscience Seine-IBPS, Sorbonne Universities, 75005, Paris, France
| | - Hervé Chneiweiss
- CNRS UMR8246, Inserm U1130, UPMC, Neuroscience Seine-IBPS, Sorbonne Universities, 75005, Paris, France
| | - Laurent Castera
- Plateforme de sequencage haut debit, Centre François Baclesse, Caen, France
| | - Etienne Müller
- Plateforme de sequencage haut debit, Centre François Baclesse, Caen, France
| | - Dinu Stefan
- Radiotherapy Department, Centre François Baclesse, Caen, France
| | - Yannick Saintigny
- LARIA, iRCM, François Jacob Institute, DRF-CEA, Caen, France
- UMR6252 CIMAP, CEA - CNRS - ENSICAEN - Université de Caen Normandie, Caen, France
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Xu C. A review of somatic single nucleotide variant calling algorithms for next-generation sequencing data. Comput Struct Biotechnol J 2018; 16:15-24. [PMID: 29552334 PMCID: PMC5852328 DOI: 10.1016/j.csbj.2018.01.003] [Citation(s) in RCA: 153] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 01/20/2018] [Accepted: 01/28/2018] [Indexed: 02/06/2023] Open
Abstract
Detection of somatic mutations holds great potential in cancer treatment and has been a very active research field in the past few years, especially since the breakthrough of the next-generation sequencing technology. A collection of variant calling pipelines have been developed with different underlying models, filters, input data requirements, and targeted applications. This review aims to enumerate these unique features of the state-of-the-art variant callers, in the hope to provide a practical guide for selecting the appropriate pipeline for specific applications. We will focus on the detection of somatic single nucleotide variants, ranging from traditional variant callers based on whole genome or exome sequencing of paired tumor-normal samples to recent low-frequency variant callers designed for targeted sequencing protocols with unique molecular identifiers. The variant callers have been extensively benchmarked with inconsistent performances across these studies. We will review the reference materials, datasets, and performance metrics that have been used in the benchmarking studies. In the end, we will discuss emerging trends and future directions of the variant calling algorithms.
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Affiliation(s)
- Chang Xu
- Life Science Research and Foundation, Qiagen Sciences, Inc., 6951 Executive Way, Frederick, Maryland 21703, USA
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