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Jiang X, Xie B, Li K, Zhou F. Prolonged Linear Amplification of qPCR for the Correction of Amplification Variation and the Absolute Quantification without Standard Curves. Anal Chem 2023; 95:18451-18459. [PMID: 38063082 DOI: 10.1021/acs.analchem.3c03637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
The variable amplification efficiency of each thermal cycle of qPCR obeys the Poisson distribution, and the qPCR system dynamically changes, so there must be a detection error in its quantitative analysis. Here, more than 20 cycles of the linear amplification of qPCR can be produced as the BSA hydrogel is introduced to achieve the controlled release of Taq DNA polymerase. There is a significant negative correlation between the slope of linear amplification and Ct values (r = -0.9455), and it is well evident that the slope can reflect the amplification efficiency and a linear positive correlation exists between them. Through the change in the concentration of primers in the qPCR system, an exponential equation between Ct values and the slopes can be fitted (R2 = 0.9995). The slopes and Ct values of each qPCR system can be corrected by using this equation to guarantee that there will be significant consistency in their amplification efficiency because the degree of linear fitting (R2) between Ct values and the logarithm of their corresponding concentration of the DNA template increased significantly. By this time, the accurate amplification efficiency can be calculated in a known multiple of two initial concentrations of DNA templates. With the aid of the relationship between the known primer concentration and the fluorescence intensity at the end of PCR (End RFU), the initial concentrations of DNA templates can be reversely calculated in the absence of standard curves.
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Affiliation(s)
- Xinglu Jiang
- Clinical Laboratory Medicine Department, College of Stomatology, Hospital of Stomatology, Guangxi Medical University, Nanning 530021, Guangxi, China
- Guangxi Key Laboratory of Oral and Maxillofacial Rehabilitation and Reconstruction, College of Stomatology, Hospital of Stomatology, Guangxi Medical University, Nanning 530021, Guangxi, China
| | - BeiBei Xie
- Guangxi Key Laboratory of Oral and Maxillofacial Rehabilitation and Reconstruction, College of Stomatology, Hospital of Stomatology, Guangxi Medical University, Nanning 530021, Guangxi, China
- Conservative Dentistry & Endodontics Department, College of Stomatology, Hospital of Stomatology, Guangxi Medical University, Nanning 530021, Guangxi, China
| | - Kangjing Li
- Guangxi Key Laboratory of Oral and Maxillofacial Rehabilitation and Reconstruction, College of Stomatology, Hospital of Stomatology, Guangxi Medical University, Nanning 530021, Guangxi, China
- Conservative Dentistry & Endodontics Department, College of Stomatology, Hospital of Stomatology, Guangxi Medical University, Nanning 530021, Guangxi, China
| | - Fengyuan Zhou
- Clinical Laboratory Medicine Department, College of Stomatology, Hospital of Stomatology, Guangxi Medical University, Nanning 530021, Guangxi, China
- Guangxi Key Laboratory of Oral and Maxillofacial Rehabilitation and Reconstruction, College of Stomatology, Hospital of Stomatology, Guangxi Medical University, Nanning 530021, Guangxi, China
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Liu X, Ma T, Yang C, Li J, Zhang Y, Zhao Y. Persistent dyslipidemia increases the longitudinal changes in telomere length. Lipids Health Dis 2023; 22:173. [PMID: 37853446 PMCID: PMC10585729 DOI: 10.1186/s12944-023-01938-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 10/09/2023] [Indexed: 10/20/2023] Open
Abstract
BACKGROUND AND AIMS Leukocyte telomere length (LTL) as a 'biological clock' of aging is closely related to human health, its association with an aging-related disease, dyslipidemia, has been less studied and mainly focused on cross-sectional investigations. METHODS Two rounds of information and blood collections were conducted on a cohort of 1624 individuals residing in rural Ningxia, located in northwest China, with an average time gap of 9.8 years. The relative telomere length (RTL) of peripheral blood leukocytes was assessed using real-time quantitative PCR. To investigate the association between dyslipidemia, blood lipid levels, and alterations in RTL, multiple linear regression and generalized linear models were employed. RESULTS After conducting the follow-up analysis, it was observed that 83.3% of the participants in the study exhibited a reduction in telomere length, while 16.7% experienced an increase in telomere length. The results suggested that dyslipidemia at baseline or follow-up may increase longitudinal changes in telomere length, but it was more significant in the healthy group, especially in those aged ≥ 60 years. Furthermore, HDL-C levels in baseline and follow-up were found to be associated with longitudinal changes in telomere length, and lower HDL-C levels may be associated with increased longitudinal changes in telomere length. CONCLUSIONS The change in telomere length is correlated with dyslipidemia and its lipid indicators especially HDL-C. Persistent dyslipidemia and a reduction in HDL-C levels may be associated with elevated longitudinal fluctuations in telomere length.
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Affiliation(s)
- Xiaowei Liu
- Public Health School, Ningxia Medical University, Yinchuan, 750004, China
| | - Tao Ma
- Public Health School, Ningxia Medical University, Yinchuan, 750004, China
| | - Chan Yang
- School of Nursing, Ningxia Medical University, Yinchuan, 750004, China
| | - Juan Li
- Public Health School, Ningxia Medical University, Yinchuan, 750004, China
| | - Yuhong Zhang
- Public Health School, Ningxia Medical University, Yinchuan, 750004, China.
- NHC Key Laboratory of Metabolic Cardiovascular Diseases Research, Ningxia Medical University, Yinchuan, 750004, China.
- Key Laboratory of Environmental Factors and Chronic Disease Control, Yinchuan, 750004, China.
| | - Yi Zhao
- Public Health School, Ningxia Medical University, Yinchuan, 750004, China.
- NHC Key Laboratory of Metabolic Cardiovascular Diseases Research, Ningxia Medical University, Yinchuan, 750004, China.
- Key Laboratory of Environmental Factors and Chronic Disease Control, Yinchuan, 750004, China.
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Xu EY, Schneper LM, Notterman DA. A novel metric to improve mismatched primer selection and quantification accuracy in amplifying DNA repeats for quantitative polymerase chain reactions. PLoS One 2023; 18:e0292559. [PMID: 37812635 PMCID: PMC10561853 DOI: 10.1371/journal.pone.0292559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 09/23/2023] [Indexed: 10/11/2023] Open
Abstract
In quantitative polymerase chain reaction (qPCR) experiments, primers containing mismatches with respect to the template are widely used in measuring repetitive DNA elements. Primer-template mismatches may lead to underestimation of the input sample quantity due to inefficient annealing and amplification. But how primer-template mismatches affect quantification accuracy has not been rigorously investigated. In this study, we performed a series of qPCR experiments in which we tested three pairs of mismatched telomere primers (tel1/tel2, tel1b/tel2b and telg/telc) and two pairs of perfect-match reference gene primers (36B4-F/-R and IFNB1-F/-R) at three different primer concentrations under four cycling conditions. Templates used were genomic DNA from two human cell lines and oligo duplexes which contained telomere sequences, reference gene sequences, or both. We demonstrated that the underestimation of input sample quantity from reactions containing mismatched primers was not due to lower amplification efficiency (E), but due to ineffective usage of the input sample. We defined a novel concept of amplification efficacy (f) which quantifies the effectiveness of input sample amplification by primers. We have modified the conventional qPCR kinetic formula to include f, which corrects the effects of primer mismatches. We demonstrated that reactions containing mismatched telomere primer pairs had similar efficiency (E), but varying degrees of reduced efficacy (f) in comparison to those with the perfect-match gene primer pairs. Using the quantitative parameter f, underestimation of initial target by telomere primers can be adjusted to provide a more accurate measurement. Additionally, we found that the tel1b/tel2b primer set at concentration of 500 nM and 900 nM exhibited the best amplification efficacy f. This study provides a novel way to incorporate an evaluation of amplification efficacy into qPCR analysis. In turn, it improves mismatched primer selection and quantification accuracy in amplifying DNA repeats using qPCR methods.
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Affiliation(s)
- Eugenia Y. Xu
- Department of Molecular Biology, Princeton University, Princeton, NJ, United States of America
| | - Lisa M. Schneper
- Department of Molecular Biology, Princeton University, Princeton, NJ, United States of America
| | - Daniel A. Notterman
- Department of Molecular Biology, Princeton University, Princeton, NJ, United States of America
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Ye Q, Apsley AT, Etzel L, Hastings WJ, Kozlosky JT, Walker C, Wolf SE, Shalev I. Telomere length and chronological age across the human lifespan: A systematic review and meta-analysis of 414 study samples including 743,019 individuals. Ageing Res Rev 2023; 90:102031. [PMID: 37567392 PMCID: PMC10529491 DOI: 10.1016/j.arr.2023.102031] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 07/27/2023] [Accepted: 08/07/2023] [Indexed: 08/13/2023]
Abstract
Telomere attrition is a proposed hallmark of aging. To evaluate the association of telomere length (TL) with chronological age across the human lifespan, we conducted a systematic review and meta-analysis of 414 study samples comprising 743,019 individuals aged 0-112 years. We examined both cross-sectional and longitudinal data, and evaluated the impact of various biological and methodological factors including sex, health status, tissue types, DNA extraction procedures, and TL measurement methods. The pooled corrected correlation between TL and age from cross-sectional samples was -0.19 (95%CI: -0.22 to -0.15), which weakened with increased chronological age (β = 0.003, p < 0.001). Z-score change rates of TL across the lifespan showed a gradual decrease in shortening rate until around age 50 and remained at a relatively stable rate towards the elderly period. A greater attrition rate was observed in longitudinal than cross-sectional evaluations. For TL measured in base pairs, the median change rate of TL was -23 bp/year in cross-sectional samples and -38 bp/year in longitudinal samples. Methodological factors including TL measurement methods and tissue types impacted the TL-age correlation, while sex or disease status did not. This meta-analysis revealed the non-linear shortening trend of TL across the human lifespan and provides a reference value for future studies. Results also highlight the importance of methodological considerations when using TL as an aging biomarker.
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Affiliation(s)
- Qiaofeng Ye
- Department of Biobehavioral Health, The Pennsylvania State University, University Park, PA 16802, USA.
| | - Abner T Apsley
- Department of Biobehavioral Health, The Pennsylvania State University, University Park, PA 16802, USA; Department of Molecular, Cellular and Integrative Biological Sciences, The Pennsylvania State University, University Park, PA 16802, USA.
| | - Laura Etzel
- Department of Biobehavioral Health, The Pennsylvania State University, University Park, PA 16802, USA.
| | - Waylon J Hastings
- Department of Psychiatry and Behavioral Science, Tulane University School of Medicine, LA 70112, USA.
| | - John T Kozlosky
- Department of Biobehavioral Health, The Pennsylvania State University, University Park, PA 16802, USA.
| | - Cade Walker
- Department of Biobehavioral Health, The Pennsylvania State University, University Park, PA 16802, USA.
| | - Sarah E Wolf
- Department of Biobehavioral Health, The Pennsylvania State University, University Park, PA 16802, USA.
| | - Idan Shalev
- Department of Biobehavioral Health, The Pennsylvania State University, University Park, PA 16802, USA.
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Allaire P, He J, Mayer J, Moat L, Gerstenberger P, Wilhorn R, Strutz S, Kim DS, Zeng C, Cox N, Shay JW, Denny J, Bastarache L, Hebbring S. Genetic and clinical determinants of telomere length. HGG ADVANCES 2023; 4:100201. [PMID: 37216007 PMCID: PMC10199259 DOI: 10.1016/j.xhgg.2023.100201] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 04/21/2023] [Indexed: 05/24/2023] Open
Abstract
Many epidemiologic studies have identified important relationships between leukocyte telomere length (LTL) with genetics and health. Most of these studies have been significantly limited in scope by focusing predominantly on individual diseases or restricted to GWAS analysis. Using two large patient populations derived from Vanderbilt University and Marshfield Clinic biobanks linked to genomic and phenomic data from medical records, we investigated the inter-relationship between LTL, genomics, and human health. Our GWAS confirmed 11 genetic loci previously associated with LTL and two novel loci in SCNN1D and PITPNM1. PheWAS of LTL identified 67 distinct clinical phenotypes associated with both short and long LTL. We demonstrated that several diseases associated with LTL were related to one another but were largely independent from LTL genetics. Age of death was correlated with LTL independent of age. Those with very short LTL (<-1.5 standard deviation [SD]) died 10.4 years (p < 0.0001) younger than those with average LTL (±0.5 SD; mean age of death = 74.2 years). Likewise, those with very long LTL (>1.5 SD) died 1.9 years (p = 0.0175) younger than those with average LTL. This is consistent with the PheWAS results showing diseases associating with both short and long LTL. Finally, we estimated that the genome (12.8%) and age (8.5%) explain the largest proportion of LTL variance, whereas the phenome (1.5%) and sex (0.9%) explained a smaller fraction. In total, 23.7% of LTL variance was explained. These observations provide the rationale for expanded research to understand the multifaceted correlations between TL biology and human health over time, leading to effective LTL usage in medical applications.
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Affiliation(s)
- Patrick Allaire
- Marshfield Clinic Research Institute, Center for Precision Medicine Research, Marshfield, WI, USA
| | - Jing He
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - John Mayer
- Marshfield Clinic Research Institute, Office of Research Computing and Analytics, Marshfield, WI, USA
| | - Luke Moat
- Marshfield Clinic Research Institute, Center for Precision Medicine Research, Marshfield, WI, USA
| | - Peter Gerstenberger
- Marshfield Clinic Research Institute, Center for Precision Medicine Research, Marshfield, WI, USA
| | - Reynor Wilhorn
- Marshfield Clinic Research Institute, Center for Precision Medicine Research, Marshfield, WI, USA
| | - Sierra Strutz
- Marshfield Clinic Research Institute, Center for Precision Medicine Research, Marshfield, WI, USA
| | - David S.L. Kim
- Marshfield Clinic Health System, Pathology, Marshfield, WI, USA
| | - Chenjie Zeng
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Nancy Cox
- Vanderbilt Genetics Institute, Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jerry W. Shay
- University of Texas Southwestern Medical Center, Department of Cell Biology and the Simmons Comprehensive Cancer Center, Dallas, TX, USA
| | - Joshua Denny
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lisa Bastarache
- Center for Precision Medicine, Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Scott Hebbring
- Marshfield Clinic Research Institute, Center for Precision Medicine Research, Marshfield, WI, USA
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Hastings WJ, Etzel L, Heim CM, Noll JG, Rose EJ, Schreier HMC, Shenk CE, Tang X, Shalev I. Comparing qPCR and DNA methylation-based measurements of telomere length in a high-risk pediatric cohort. Aging (Albany NY) 2022; 14:660-677. [PMID: 35077392 PMCID: PMC8833135 DOI: 10.18632/aging.203849] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 01/17/2022] [Indexed: 11/25/2022]
Abstract
Various approaches exist to assess population differences in biological aging. Telomere length (TL) is one such measure, and is associated with disease, disability and early mortality. Yet, issues surrounding precision and reproducibility are a concern for TL measurement. An alternative method to estimate TL using DNA methylation (DNAmTL) was recently developed. Although DNAmTL has been characterized in adult and elderly cohorts, its utility in pediatric populations remains unknown. We examined the comparability of leukocyte TL measurements generated using qPCR (absolute TL; aTL) to those estimated using DNAmTL in a high-risk pediatric cohort (N = 269; age: 8–13 years, 83% investigated for maltreatment). aTL and DNAmTL measurements were correlated with one another (r = 0.20, p = 0.001), but exhibited poor measurement agreement and were significantly different in paired-sample t-tests (Cohen’s d = 0.77, p < 0.001). Shorter DNAmTL was associated with older age (r = −0.25, p < 0.001), male sex (β = −0.27, p = 0.029), and White race (β = −0.74, p = 0.008). By contrast, aTL was less strongly associated with age (r = −0.13, p = 0.040), was longer in males (β = 0.31, p = 0.012), and was not associated with race (p = 0.820). These findings highlight strengths and limitations of high-throughput measures of TL; although DNAmTL replicated hypothesized associations, aTL measurements were positively skewed and did not replicate associations with external validity measures. These results also extend previous research in adults and suggest that DNAmTL is a sensitive TL measure for use in pediatric populations.
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Affiliation(s)
- Waylon J Hastings
- Department of Biobehavioral Health, The Pennsylvania State University, University Park, PA 16802, USA
| | - Laura Etzel
- Department of Biobehavioral Health, The Pennsylvania State University, University Park, PA 16802, USA
| | - Christine M Heim
- Department of Biobehavioral Health, The Pennsylvania State University, University Park, PA 16802, USA.,Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Institute of Medical Psychology, Berlin, Germany
| | - Jennie G Noll
- Department of Human Development and Family Studies, The Pennsylvania State University, University Park, PA 16802, USA
| | - Emma J Rose
- Department of Human Development and Family Studies, The Pennsylvania State University, University Park, PA 16802, USA.,The Edna Bennett Pierce Prevention Research Center, The Pennsylvania State University, University Park, PA 16802, USA
| | - Hannah M C Schreier
- Department of Biobehavioral Health, The Pennsylvania State University, University Park, PA 16802, USA
| | - Chad E Shenk
- Department of Human Development and Family Studies, The Pennsylvania State University, University Park, PA 16802, USA.,Department of Pediatrics, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Xin Tang
- Department of Biobehavioral Health, The Pennsylvania State University, University Park, PA 16802, USA
| | - Idan Shalev
- Department of Biobehavioral Health, The Pennsylvania State University, University Park, PA 16802, USA
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