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Gustav Smith

Associate professor

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Whole-genome sequencing based on formalin-fixed paraffin-embedded endomyocardial biopsies for genetic studies on outcomes after heart transplantation

Author

  • Gustav Zar
  • J. Gustav Smith
  • Maya Landenhed Smith
  • Bodil Andersson
  • Johan Nilsson

Summary, in English

Background Whole-genome sequencing (WGS) of heart transplant recipient- and donor-derived cardiac biopsies may facilitate organ matching, graft failure prediction, and immunotolerance research. The objective of this study was to determine the feasibility of WGS based on formalin-fixed paraffin-embedded endomyocardial biopsies. Methods and results The study included serial donor- and recipient samples from patients who had undergone heart transplantation at Skane University Hospital, Lund, Sweden, between 1988 and 2009. DNA extraction and WGS were conducted. Additional WGS sequencing quality metrics and coverage were obtained with the Genome Analysis Toolkit (GATK). 455 endomyocardial samples from 37 heart transplant recipients were acquired from routine rejection monitoring and stored as formalin-fixed paraffin-embedded samples. They were analyzed after 3–26 years of storage. DNA was extracted from 114 samples and WGS was run on 85 samples. DNA extraction yielded 313 ng (IQR 96–601) for all samples. A coverage of 11.3x (IQR 9.0–15.9) was recorded for all WGS samples. Three samples stored for > 25 years yielded a coverage of > 25x. Data were generated for 1.7 billion reads per sample (IQR 1.4–2.7). A Transition/Transversion (TiTv) ratio of 2.09 ± 0.05 was calculated for all WGS samples. No associations were found among storage time, DNA yield, or sequencing quality metrics. Conclusions The present study demonstrated the feasibility of whole-genome sequencing based on endomyocardial biopsies. This process could enable large-scale retrospective genomic studies using stored histopathological samples.

Department/s

  • Thoracic Surgery
  • Cardiology
  • EpiHealth: Epidemiology for Health
  • EXODIAB: Excellence of Diabetes Research in Sweden
  • Molecular Epidemiology and Cardiology
  • eSSENCE: The e-Science Collaboration
  • Surgery (Lund)
  • Artificial Intelligence and Bioinformatics in Cardiothoracic Sciences (AIBCTS)
  • Heart and Lung transplantation

Publishing year

2019

Language

English

Publication/Series

PLoS ONE

Volume

14

Issue

6

Document type

Journal article

Publisher

Public Library of Science (PLoS)

Topic

  • Biomedical Laboratory Science/Technology

Status

Published

Research group

  • Molecular Epidemiology and Cardiology
  • Artificial Intelligence and Bioinformatics in Cardiothoracic Sciences (AIBCTS)
  • Heart and Lung transplantation

ISBN/ISSN/Other

  • ISSN: 1932-6203