초록접수 현황
| 21F-212 | 구연 발표 |
Virus identification in DCMP patients using metagenomic next-generation sequencing (mNGS)
Soojin Park1†, Uram Jin2†, Do Jung Kim1, Sang-Hyun Lim1*, You-Sun Hong1 and Joon-Han Shin2*
1Department of Thoracic and Cardiovascular Surgery, Ajou University School of Medicine, Suwon, Korea., 2Department of Cardiology, Ajou University School of Medicine, Suwon, Korea
Purpose : Dilated cardiomyopathy (DCMP) is the most common cause of heart failure and indication for heart transplantation. Myocarditis is a disease that develops into DCMP in about 20% of cases, and viral infection is known to be the main cause. In this study, Coxsackievirus (CV), common causes of viral myocarditis, was identified using metagenomic next-generation sequencing (mNGS) in the heart tissue of DCMP patients.
Methods : We downloaded the raw data of RNA extracted from the heart tissue of DCMP patients uploaded in the European nucleotide archive and checked how much CV was observed in DCMP patients. mNGS was performed using the Burrows-Wheeler Aligner and SAMtools program for the RNA sequence in the FASTQ data form.
Results : First, for validation of this study method, mNGS was performed on RNA data extracted from cells after CV was infected in the cell line. It was confirmed that the RNA sequence corresponding to 14.91% of the extracted RNA was CV origin. Next, a total of 436 DCMP patient RNAs published by 14 study groups were analyzed in the same way, but as a result, no CV was detected.
Conclusion : mNGS is a hypothesis-free and unbiased method for quantifying organisms as the latest method for diagnosing infectious diseases. However, there are several limitations regarding viral infection, so a definitive methodology has not yet been established. It will be necessary to compare diagnostic thresholds of traditional methods such as PCR and methods through mNGS and optimize RNA sequencing and genome analysis methods through invitro in vivo experiments.
Methods : We downloaded the raw data of RNA extracted from the heart tissue of DCMP patients uploaded in the European nucleotide archive and checked how much CV was observed in DCMP patients. mNGS was performed using the Burrows-Wheeler Aligner and SAMtools program for the RNA sequence in the FASTQ data form.
Results : First, for validation of this study method, mNGS was performed on RNA data extracted from cells after CV was infected in the cell line. It was confirmed that the RNA sequence corresponding to 14.91% of the extracted RNA was CV origin. Next, a total of 436 DCMP patient RNAs published by 14 study groups were analyzed in the same way, but as a result, no CV was detected.
Conclusion : mNGS is a hypothesis-free and unbiased method for quantifying organisms as the latest method for diagnosing infectious diseases. However, there are several limitations regarding viral infection, so a definitive methodology has not yet been established. It will be necessary to compare diagnostic thresholds of traditional methods such as PCR and methods through mNGS and optimize RNA sequencing and genome analysis methods through invitro in vivo experiments.
책임저자: Sang-Hyun Lim
Department of Thoracic and Cardiovascular Surgery, Ajou University School of Medicine, Suwon, Korea
발표자: Soojin Park, E-mail : soojinima@gmail.com