Reference Citation Analysis: Find an Article, Find a Category, Find a Journal, Find a Scholar

For: Stevenson M, Pagnamenta AT, Reichart S, Philpott C, Lines KE, Gorvin CM, Lhotta K, Taylor JC, Thakker RV. Whole genome sequence analysis identifies a PAX2 mutation to establish a correct diagnosis for a syndromic form of hyperuricemia. Am J Med Genet A 2020;182:2521-2528. [PMID: 32776440 PMCID: PMC7611017 DOI: 10.1002/ajmg.a.61814] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/04/2020] [Accepted: 07/07/2020] [Indexed: 01/13/2023]

For:	Stevenson M, Pagnamenta AT, Reichart S, Philpott C, Lines KE, Gorvin CM, Lhotta K, Taylor JC, Thakker RV. Whole genome sequence analysis identifies a PAX2 mutation to establish a correct diagnosis for a syndromic form of hyperuricemia. Am J Med Genet A 2020;182:2521-2528. [PMID: 32776440 PMCID: PMC7611017 DOI: 10.1002/ajmg.a.61814] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/04/2020] [Accepted: 07/07/2020] [Indexed: 01/13/2023]

Number

Cited by Other Article(s)

Pagnamenta AT, Camps C, Giacopuzzi E, Taylor JM, Hashim M, Calpena E, Kaisaki PJ, Hashimoto A, Yu J, Sanders E, Schwessinger R, Hughes JR, Lunter G, Dreau H, Ferla M, Lange L, Kesim Y, Ragoussis V, Vavoulis DV, Allroggen H, Ansorge O, Babbs C, Banka S, Baños-Piñero B, Beeson D, Ben-Ami T, Bennett DL, Bento C, Blair E, Brasch-Andersen C, Bull KR, Cario H, Cilliers D, Conti V, Davies EG, Dhalla F, Dacal BD, Dong Y, Dunford JE, Guerrini R, Harris AL, Hartley J, Hollander G, Javaid K, Kane M, Kelly D, Kelly D, Knight SJL, Kreins AY, Kvikstad EM, Langman CB, Lester T, Lines KE, Lord SR, Lu X, Mansour S, Manzur A, Maroofian R, Marsden B, Mason J, McGowan SJ, Mei D, Mlcochova H, Murakami Y, Németh AH, Okoli S, Ormondroyd E, Ousager LB, Palace J, Patel SY, Pentony MM, Pugh C, Rad A, Ramesh A, Riva SG, Roberts I, Roy N, Salminen O, Schilling KD, Scott C, Sen A, Smith C, Stevenson M, Thakker RV, Twigg SRF, Uhlig HH, van Wijk R, Vona B, Wall S, Wang J, Watkins H, Zak J, Schuh AH, Kini U, Wilkie AOM, Popitsch N, Taylor JC. Structural and non-coding variants increase the diagnostic yield of clinical whole genome sequencing for rare diseases. Genome Med 2023;15:94. [PMID: 37946251 PMCID: PMC10636885 DOI: 10.1186/s13073-023-01240-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 09/27/2023] [Indexed: 11/12/2023] Open

Abstract

BACKGROUND

Whole genome sequencing is increasingly being used for the diagnosis of patients with rare diseases. However, the diagnostic yields of many studies, particularly those conducted in a healthcare setting, are often disappointingly low, at 25-30%. This is in part because although entire genomes are sequenced, analysis is often confined to in silico gene panels or coding regions of the genome.

METHODS

We undertook WGS on a cohort of 122 unrelated rare disease patients and their relatives (300 genomes) who had been pre-screened by gene panels or arrays. Patients were recruited from a broad spectrum of clinical specialties. We applied a bioinformatics pipeline that would allow comprehensive analysis of all variant types. We combined established bioinformatics tools for phenotypic and genomic analysis with our novel algorithms (SVRare, ALTSPLICE and GREEN-DB) to detect and annotate structural, splice site and non-coding variants.

RESULTS

Our diagnostic yield was 43/122 cases (35%), although 47/122 cases (39%) were considered solved when considering novel candidate genes with supporting functional data into account. Structural, splice site and deep intronic variants contributed to 20/47 (43%) of our solved cases. Five genes that are novel, or were novel at the time of discovery, were identified, whilst a further three genes are putative novel disease genes with evidence of causality. We identified variants of uncertain significance in a further fourteen candidate genes. The phenotypic spectrum associated with RMND1 was expanded to include polymicrogyria. Two patients with secondary findings in FBN1 and KCNQ1 were confirmed to have previously unidentified Marfan and long QT syndromes, respectively, and were referred for further clinical interventions. Clinical diagnoses were changed in six patients and treatment adjustments made for eight individuals, which for five patients was considered life-saving.

CONCLUSIONS

Genome sequencing is increasingly being considered as a first-line genetic test in routine clinical settings and can make a substantial contribution to rapidly identifying a causal aetiology for many patients, shortening their diagnostic odyssey. We have demonstrated that structural, splice site and intronic variants make a significant contribution to diagnostic yield and that comprehensive analysis of the entire genome is essential to maximise the value of clinical genome sequencing.

Collapse

Affiliation(s)

Alistair T Pagnamenta Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
Carme Camps Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
Edoardo Giacopuzzi Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK Human Technopole, Viale Rita Levi Montalcini 1, 20157, Milan, Italy
John M Taylor NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Old Road, Oxford, OX3 7LE, UK
Mona Hashim Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
Eduardo Calpena NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
Pamela J Kaisaki Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
Akiko Hashimoto MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
Jing Yu Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
Edward Sanders MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
Ron Schwessinger MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
Jim R Hughes MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
Gerton Lunter MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK University Medical Center Groningen, Groningen University, PO Box 72, 9700 AB, Groningen, The Netherlands
Helene Dreau NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK Department of Oncology, Oxford Molecular Diagnostics Centre, University of Oxford, Level 4, John Radcliffe Hospital, Headley Way, Oxford, OX3 9DU, UK
Matteo Ferla Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
Lukas Lange Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
Yesim Kesim Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
Vassilis Ragoussis Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
Dimitrios V Vavoulis Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK Department of Oncology, Oxford Molecular Diagnostics Centre, University of Oxford, Level 4, John Radcliffe Hospital, Headley Way, Oxford, OX3 9DU, UK
Holger Allroggen Neurosciences Department, UHCW NHS Trust, Clifford Bridge Road, Coventry, CV2 2DX, UK
Olaf Ansorge Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
Christian Babbs MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
Siddharth Banka Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK Manchester Centre for Genomic Medicine, Saint Mary's Hospital, Oxford Road, Manchester, M13 9WL, UK
Benito Baños-Piñero Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Old Road, Oxford, OX3 7LE, UK
David Beeson MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
Tal Ben-Ami Pediatric Hematology-Oncology Unit, Kaplan Medical Center, Rehovot, Israel
David L Bennett Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
Celeste Bento Hematology Department, Hospitais da Universidade de Coimbra, Coimbra, Portugal
Edward Blair NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 7LE, UK
Charlotte Brasch-Andersen Department of Clinical Genetics, Odense University Hospital and Department of Clinical Research, University of Southern Denmark, Odense, Denmark
Katherine R Bull Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
Holger Cario Department of Pediatrics and Adolescent Medicine, University Medical Center, Eythstrasse 24, 89075, Ulm, Germany
Deirdre Cilliers Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 7LE, UK
Valerio Conti Neuroscience Department, Meyer Children's Hospital IRCCS, Viale Pieraccini 24, 50139, Florence, Italy
E Graham Davies Department of Immunology, Great Ormond Street Hospital for Children NHS Trust and UCL Great Ormond Street Institute of Child Health, Zayed Centre for Research, 2Nd Floor, 20C Guilford Street, London, WC1N 1DZ, UK
Fatima Dhalla Department of Paediatrics, Institute of Developmental and Regenerative Medicine, IMS-Tetsuya Nakamura Building, Old Road Campus, Roosevelt Drive, Oxford, OX3 7TY, UK
Beatriz Diez Dacal Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Old Road, Oxford, OX3 7LE, UK
Yin Dong MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
James E Dunford Oxford NIHR Musculoskeletal BRC and Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Nuffield Orthopaedic Centre, Old Road, Oxford, OX3 7HE, UK
Renzo Guerrini Neuroscience Department, Meyer Children's Hospital IRCCS, Viale Pieraccini 24, 50139, Florence, Italy
Adrian L Harris Department of Oncology, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK
Jane Hartley Liver Unit, Birmingham Women's & Children's Hospital and University of Birmingham, Steelhouse Lane, Birmingham, B4 6NH, UK
Georg Hollander Department of Paediatrics, University of Oxford, Level 2, Children's Hospital, John Radcliffe Hospital, Oxford, OX3 9DU, UK
Kassim Javaid Oxford NIHR Musculoskeletal BRC and Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Nuffield Orthopaedic Centre, Old Road, Oxford, OX3 7HE, UK
Maureen Kane Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Pharmacy Hall North, Room 731, 20 N. Pine Street, Baltimore, MD, 21201, USA
Deirdre Kelly Liver Unit, Birmingham Women's & Children's Hospital and University of Birmingham, Steelhouse Lane, Birmingham, B4 6NH, UK
Dominic Kelly Children's Hospital, OUH NHS Foundation Trust, NIHR Oxford BRC, Headley Way, Oxford, OX3 9DU, UK
Samantha J L Knight Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
Alexandra Y Kreins Department of Immunology, Great Ormond Street Hospital for Children NHS Trust and UCL Great Ormond Street Institute of Child Health, Zayed Centre for Research, 2Nd Floor, 20C Guilford Street, London, WC1N 1DZ, UK
Erika M Kvikstad Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
Craig B Langman Feinberg School of Medicine, Northwestern University, 211 E Chicago Avenue, Chicago, IL, MS37, USA
Tracy Lester Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Old Road, Oxford, OX3 7LE, UK
Kate E Lines NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK University of Oxford, Academic Endocrine Unit, OCDEM, Churchill Hospital, Oxford, OX3 7LJ, UK
Simon R Lord Early Phase Clinical Trials Unit, Department of Oncology, University of Oxford, Cancer and Haematology Centre, Level 2 Administration Area, Churchill Hospital, Oxford, OX3 7LJ, UK
Xin Lu Nuffield Department of Clinical Medicine, Ludwig Institute for Cancer Research, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK
Sahar Mansour St George's University Hospitals NHS Foundation Trust, Blackshore Road, Tooting, London, SW17 0QT, UK
Adnan Manzur MRC Centre for Neuromuscular Diseases, National Hospital for Neurology and Neurosurgery, Queen Square, London, WC1N 3BG, UK
Reza Maroofian Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, WC1N 3BG, UK
Brian Marsden Nuffield Department of Medicine, Kennedy Institute, University of Oxford, Oxford, OX3 7BN, UK
Joanne Mason Yourgene Health Headquarters, Skelton House, Lloyd Street North, Manchester Science Park, Manchester, M15 6SH, UK
Simon J McGowan MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
Davide Mei Neuroscience Department, Meyer Children's Hospital IRCCS, Viale Pieraccini 24, 50139, Florence, Italy
Hana Mlcochova MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
Yoshiko Murakami Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
Andrea H Németh Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 7LE, UK
Steven Okoli Imperial College NHS Trust, Department of Haematology, Hammersmith Hospital, Du Cane Road, London, W12 0HS, UK
Elizabeth Ormondroyd NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK University of Oxford, Level 6 West Wing, Oxford, OX3 9DU, JR, UK
Lilian Bomme Ousager Department of Clinical Genetics, Odense University Hospital and Department of Clinical Research, University of Southern Denmark, Odense, Denmark
Jacqueline Palace Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
Smita Y Patel Clinical Immunology, John Radcliffe Hospital, Level 4A, Oxford, OX3 9DU, UK
Melissa M Pentony Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
Chris Pugh Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
Aboulfazl Rad Department of Otolaryngology-Head & Neck Surgery, Tübingen Hearing Research Centre, Eberhard Karls University, Elfriede-Aulhorn-Str. 5, 72076, Tübingen, Germany
Archana Ramesh Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
Simone G Riva MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
Irene Roberts MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK Department of Paediatrics, University of Oxford, Level 2, Children's Hospital, John Radcliffe Hospital, Oxford, OX3 9DU, UK
Noémi Roy Department of Haematology, Oxford University Hospitals NHS Foundation Trust, Level 4, Haematology, John Radcliffe Hospital, Oxford, OX3 9DU, UK
Outi Salminen NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK Department of Oncology, Oxford Molecular Diagnostics Centre, University of Oxford, Level 4, John Radcliffe Hospital, Headley Way, Oxford, OX3 9DU, UK
Kyleen D Schilling Ann & Robert H. Lurie Children's Hospital of Chicago, 225 E Chicago Avenue, Chicago, IL, 60611, USA
Caroline Scott MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
Arjune Sen Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
Conrad Smith Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Old Road, Oxford, OX3 7LE, UK
Mark Stevenson University of Oxford, Academic Endocrine Unit, OCDEM, Churchill Hospital, Oxford, OX3 7LJ, UK
Rajesh V Thakker University of Oxford, Academic Endocrine Unit, OCDEM, Churchill Hospital, Oxford, OX3 7LJ, UK
Stephen R F Twigg MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
Holm H Uhlig NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK Department of Paediatrics, University of Oxford, Level 2, Children's Hospital, John Radcliffe Hospital, Oxford, OX3 9DU, UK Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford, OX3 9DU, UK
Richard van Wijk UMC Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
Barbara Vona Department of Otolaryngology-Head & Neck Surgery, Tübingen Hearing Research Centre, Eberhard Karls University, Elfriede-Aulhorn-Str. 5, 72076, Tübingen, Germany Institute of Human Genetics, University Medical Center Göttingen, Heinrich-Düker-Weg 12, 37073, Göttingen, Germany Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany
Steven Wall Oxford Craniofacial Unit, John Radcliffe Hospital, Level LG1, West Wing, Oxford, OX3 9DU, UK
Jing Wang Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
Hugh Watkins NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK University of Oxford, Level 6 West Wing, Oxford, OX3 9DU, JR, UK
Jaroslav Zak Nuffield Department of Clinical Medicine, Ludwig Institute for Cancer Research, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK Department of Immunology and Microbiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
Anna H Schuh Department of Oncology, Oxford Molecular Diagnostics Centre, University of Oxford, Level 4, John Radcliffe Hospital, Headley Way, Oxford, OX3 9DU, UK
Usha Kini NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 7LE, UK
Andrew O M Wilkie NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
Niko Popitsch Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna BioCenter(VBC), Dr.-Bohr-Gasse 9, 1030, Vienna, Austria
Jenny C Taylor Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK. NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK.

Collapse

Wang Z, Guo Y, Jin Y, Zhang X, Geng H, Xie G, Ye D, Yu Y, Liu D, Zhou D, Li B, Luo Y, Peng S, Li J. Establishment and drug screening of patient-derived extrahepatic biliary tract carcinoma organoids. Cancer Cell Int 2021;21:519. [PMID: 34600546 PMCID: PMC8487492 DOI: 10.1186/s12935-021-02219-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 09/20/2021] [Indexed: 11/21/2022] Open

Abstract

BACKGROUND

Patient-derived organoids (PDO) have been proposed as a novel in vitro method of drug screening for different types of cancer. However, to date, extrahepatic biliary tract carcinoma (eBTC) PDOs have not yet been fully established.

METHODS

We collected six samples of gallbladder carcinoma (GBC) and one sample of extrahepatic cholangiocarcinoma (eCCA) from seven patients to attempt to establish eBTC PDOs for drug screening. We successfully established five GBC and one eCCA PDOs. Histological staining was used to compare structural features between the original tissues and cancer PDOs. Whole exome sequencing (WES) was performed to analyze the genetic profiles of original tissues and cancer PDOs. Drug screening, including gemcitabine, 5-fluorouracil, cisplatin, paclitaxel, infigratinib, and ivosidenib, was measured and verified by clinical effects in certain cases.

RESULTS

Different PDOs exhibited diverse growth rates during in vitro culture. Hematoxylin and eosin staining demonstrated that the structures of most cancer PDOs retained the original structures of adenocarcinoma. Immunohistological and periodic acid-schiff staining revealed that marker expression in cancer PDOs was similar to that of the original specimens. Genetic profiles from the four original specimens, as well as paired cancer PDOs, were analyzed using whole exome sequencing. Three of the four PDOs exhibited a high degree of similarity when compared to the original specimens, except for GBC2 PDO, which only had a concordance of 74% in the proportion of single nucleotide polymorphisms in the coding sequence. In general, gemcitabine was found to be the most efficient drug for eBTC treatment, as it showed moderate or significant inhibitory impact on cancer growth. Results from drug screening were confirmed to a certain extent by three clinical cases.

CONCLUSIONS

Our study successfully established a series of eBTC PDOs, which contributed to the field of eBTC PDOs. Additional enhancements should be explored to improve the growth rate of PDOs and to preserve their immune microenvironment.

Collapse

Affiliation(s)

Zhiwei Wang Department of Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
Yinghao Guo Department of Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
Yun Jin Department of Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
Xiaoxiao Zhang Department of Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
Hao Geng Department of Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
Guangyuan Xie Department of Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
Dan Ye Department of Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
Yuanquan Yu Department of Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
Daren Liu Department of Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
Donger Zhou Department of Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
Baizhou Li Department of Pathology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
Yan Luo Department of Biochemistry and Cancer Institute of the Second Affiliated Hospital (Key Laboratory of Cancer Prevention and Intervention of China National MOE), Zhejiang University School of Medicine, Hangzhou, Zhejiang, China Department of Pharmacy, Tongde Hospital of Zhejiang Province, Hangzhou, Zhejiang, China
Shuyou Peng Department of Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
Jiangtao Li Department of Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China.

Collapse