Browsing by Author "Chen, Ruoying"

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    Comparison of whole genome sequencing and targeted sequencing for mitochondrial DNA
    (Elsevier, 2021) Chen, Ruoying; Aldred, Micheala A.; Xu, Weiling; Zein, Joe; Bazeley, Peter; Comhai, Suzy A. A.; Meyers, Deborah A.; Bleecker, Eugene R.; Liu, Chunyu; Erzurum, Serpil C.; Hu, Bo; NHLBI Severe Asthma Research Program (SARP); Medicine, School of Medicine
    Mitochondrial dysfunction has emerged to be associated with a broad spectrum of diseases, and there is an increasing demand for accurate detection of mitochondrial DNA (mtDNA) variants. Whole genome sequencing (WGS) has been the dominant sequencing approach to identify genetic variants in recent decades, but most studies focus on variants on the nuclear genome. Whole genome sequencing is also costly and time consuming. Sequencing specifically targeted for mtDNA is commonly used in the diagnostic settings and has lower costs. However, there is a lack of pairwise comparisons between these two sequencing approaches for calling mtDNA variants on a population basis. In this study, we compared WGS and mtDNA-targeted sequencing (targeted-seq) in analyzing mitochondrial DNA from 1499 participants recruited into the Severe Asthma Research Program (SARP). Our study reveals that targeted-sequencing and WGS have comparable capacity to determine genotypes and to call haplogroups and homoplasmies on mtDNA. However, there exists a large variability in calling heteroplasmies, especially for low-frequency heteroplasmies, which indicates that investigators should be cautious about heteroplasmies acquired from different sequencing methods. Further research is highly desired to improve variant detection methods for mitochondrial DNA.
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    Mitochondrial DNA Copy Number Variation in Asthma Risk, Severity, and Exacerbations
    (medRxiv, 2023-12-05) Xu, Weiling; Hong, Yun Soo; Hu, Bo; Comhair, Suzy A. A.; Janocha, Allison J.; Zein, Joe G.; Chen, Ruoying; Meyers, Deborah A.; Mauger, David T.; Ortega, Victor E.; Bleecker, Eugene R.; Castro, Mario; Denlinger, Loren C.; Fahy, John V.; Israel, Elliot; Levy, Bruce D.; Jarjour, Nizar N.; Moore, Wendy C.; Wenzel, Sally E.; Gaston, Benjamin; Liu, Chunyu; Arking, Dan E.; Erzurum, Serpil C.; National Heart, Lung, and Blood Institute (NHLBI) Severe Asthma Research Program (SARP) and TOPMed mtDNA Working Group in NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium; Pediatrics, School of Medicine
    Rationale: Although airway oxidative stress and inflammation are central to asthma pathogenesis, there is limited knowledge of the relationship of asthma risk, severity, or exacerbations to mitochondrial dysfunction, which is pivotal to oxidant generation and inflammation. Objectives: We investigated whether mitochondrial DNA copy number (mtDNA-CN) as a measure of mitochondrial function is associated with asthma diagnosis, severity, oxidative stress, and exacerbations. Methods: We measured mtDNA-CN in blood in two cohorts. In the UK Biobank (UKB), we compared mtDNA-CN in mild and moderate-severe asthmatics to non-asthmatics. In the Severe Asthma Research Program (SARP), we evaluated mtDNA-CN in relation to asthma severity, biomarkers of oxidative stress and inflammation, and exacerbations. Measures and main results: In UK Biobank, asthmatics (n = 29,768) have lower mtDNA-CN compared to non-asthmatics (n = 239,158) (beta, -0.026 [95% CI, -0.038 to -0.014], P = 2.46×10-5). While lower mtDNA-CN is associated with asthma, mtDNA-CN did not differ by asthma severity in either UKB or SARP. Biomarkers of inflammation show that asthmatics have higher white blood cells (WBC), neutrophils, eosinophils, fraction exhaled nitric oxide (FENO), and lower superoxide dismutase (SOD) than non-asthmatics, confirming greater oxidative stress in asthma. In one year follow-up in SARP, higher mtDNA-CN is associated with reduced risk of three or more exacerbations in the subsequent year (OR 0.352 [95% CI, 0.164 to 0.753], P = 0.007). Conclusions: Asthma is characterized by mitochondrial dysfunction. Higher mtDNA-CN identifies an exacerbation-resistant asthma phenotype, suggesting mitochondrial function is important in exacerbation risk.