Abstract
BackgroundWhole-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 resultsThe 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.ConclusionsThe 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.
Highlights
Post-heart transplantation survival has improved over the last three decades
The objective of this study was to determine the feasibility of Whole-genome sequencing (WGS) based on formalin-fixed paraffin-embedded endomyocardial biopsies
455 endomyocardial samples from 37 heart transplant recipients were acquired from routine rejection monitoring and stored as formalin-fixed paraffin-embedded samples
Summary
Post-heart transplantation survival has improved over the last three decades. Management of long-term complications such as malignancy underscores the importance of customizing immunosuppression in transplant patients [2]. Graft failure remains the most common cause of death and is often the result of immune-mediated rejection [3]. Whole-genome sequencing (WGS) technologies comprehensively characterizes human leukocyte antigen (HLA) genes located on chromosome 6 and other genomic regions determining immune tolerance. Elucidation of the genetic predisposition to rejection may help tailor immunosuppressive therapy and lower the incidence of malignancies in closely matched patients. 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.
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