Whole-genome sequencing based on formalin-fixed paraffin-embedded endomyocardial biopsies for genetic studies on outcomes after heart transplantation
(2019) In PLoS ONE 14(6).- Abstract
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... (More)
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.
(Less)
- author
- Zar, Gustav LU ; Gustav Smith, J. LU ; Smith, Maya Landenhed LU ; Andersson, Bodil LU and Nilsson, Johan LU
- organization
-
- Thoracic Surgery
- Cardiology
- EpiHealth: Epidemiology for Health
- EXODIAB: Excellence of Diabetes Research in Sweden
- Molecular Epidemiology and Cardiology (research group)
- eSSENCE: The e-Science Collaboration
- Surgery (Lund)
- Artificial Intelligence and Bioinformatics in Cardiothoracic Sciences (AIBCTS) (research group)
- Heart and Lung transplantation (research group)
- publishing date
- 2019
- type
- Contribution to journal
- publication status
- published
- subject
- in
- PLoS ONE
- volume
- 14
- issue
- 6
- article number
- e0217747
- publisher
- Public Library of Science (PLoS)
- external identifiers
-
- scopus:85066784013
- pmid:31166960
- ISSN
- 1932-6203
- DOI
- 10.1371/journal.pone.0217747
- language
- English
- LU publication?
- yes
- id
- 370c7f7f-ab70-4e3c-9cc4-2633cef0d3cf
- date added to LUP
- 2019-07-05 13:11:01
- date last changed
- 2024-09-18 06:26:34
@article{370c7f7f-ab70-4e3c-9cc4-2633cef0d3cf, abstract = {{<p>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.</p>}}, author = {{Zar, Gustav and Gustav Smith, J. and Smith, Maya Landenhed and Andersson, Bodil and Nilsson, Johan}}, issn = {{1932-6203}}, language = {{eng}}, number = {{6}}, publisher = {{Public Library of Science (PLoS)}}, series = {{PLoS ONE}}, title = {{Whole-genome sequencing based on formalin-fixed paraffin-embedded endomyocardial biopsies for genetic studies on outcomes after heart transplantation}}, url = {{http://dx.doi.org/10.1371/journal.pone.0217747}}, doi = {{10.1371/journal.pone.0217747}}, volume = {{14}}, year = {{2019}}, }