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Zhao D, Sun H, Li H, Li C, Zhou B. A prediction model for the impact of environmental and genetic factors on cardiovascular events: development in a salt substitutes population. J Transl Med 2023; 21:62. [PMID: 36717874 PMCID: PMC9887817 DOI: 10.1186/s12967-023-03899-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 01/17/2023] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Cardiovascular disease (CVD) has evolved into a serious public health issue that demands the use of suitable methods to estimate the risk of the disease. As a result, in a sample of individuals who completed a 3-year low-sodium salt or conventional salt intervention in a hypertensive environment, we constructed a 13-year cardiovascular (CV) event risk prediction model with a 10-year follow-up. METHODS A Cox proportional hazards model was used to build a prediction model based on data from 306 participants who matched the inclusion criteria. Both the discriminating power and the calibration of the prediction models were assessed. The discriminative power of the prediction model was measured using the area under the curve (AUC). Brier scores and calibration plots were used to assess the prediction model's calibration. The model was internally validated using the tenfold cross-validation method. The nomogram served as a tool for visualising the model. RESULTS Among the 306 total individuals, there were 100 cases and 206 control. In the model, there were six predictors including age, smoking, LDL-C (low-density lipoprotein cholesterol), baseline SBP (systolic blood pressure), CVD (cardiovascular history), and CNV (genomic copy number variation) nsv483076. The fitted model has an AUC of 0.788, showing strong model discrimination, and a Brier score of 0.166, indicating that it was well-calibrated. According to the results of internal validation, the prediction model utilised in this study had a good level of repeatability. According to the model integrating the interaction of CNVs and baseline blood pressure, the effect of baseline SBP on CV events may be greater when nsv483076 was normal double copies than when nsv483076 was copy number variation. CONCLUSIONS The efficacy of risk prediction models for CV events that include environmental and genetic components is excellent, and they may be utilised as risk assessment tools for CV events in specific groups to offer a foundation for tailored intervention strategies.
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Affiliation(s)
- Dan Zhao
- grid.412636.40000 0004 1757 9485Department of Clinical Epidemiology and Evidence-Based Medicine, The First Hospital of China Medical University, No.155, Nanjing North Street, Heping District, Shenyang, Liaoning China ,grid.412449.e0000 0000 9678 1884School of Public Health, China Medical University, Shenyang, Liaoning China
| | - Hao Sun
- grid.412636.40000 0004 1757 9485Department of Clinical Epidemiology and Evidence-Based Medicine, The First Hospital of China Medical University, No.155, Nanjing North Street, Heping District, Shenyang, Liaoning China
| | - Huamin Li
- grid.412636.40000 0004 1757 9485Department of Clinical Epidemiology and Evidence-Based Medicine, The First Hospital of China Medical University, No.155, Nanjing North Street, Heping District, Shenyang, Liaoning China ,grid.412449.e0000 0000 9678 1884School of Public Health, China Medical University, Shenyang, Liaoning China
| | - Chaoxiu Li
- grid.412636.40000 0004 1757 9485Department of Clinical Epidemiology and Evidence-Based Medicine, The First Hospital of China Medical University, No.155, Nanjing North Street, Heping District, Shenyang, Liaoning China ,grid.412449.e0000 0000 9678 1884School of Public Health, China Medical University, Shenyang, Liaoning China
| | - Bo Zhou
- Department of Clinical Epidemiology and Evidence-Based Medicine, The First Hospital of China Medical University, No.155, Nanjing North Street, Heping District, Shenyang, Liaoning, China.
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2
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Droplet digital PCR enabled by microfluidic impact printing for absolute gene quantification. Talanta 2020; 211:120680. [DOI: 10.1016/j.talanta.2019.120680] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 12/20/2019] [Accepted: 12/24/2019] [Indexed: 01/01/2023]
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3
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Ahmed P H, V V, More RP, Viswanath B, Jain S, Rao MS, Mukherjee O. INDEX-db: The Indian Exome Reference Database (Phase I). J Comput Biol 2019; 26:225-234. [PMID: 30615482 PMCID: PMC6441288 DOI: 10.1089/cmb.2018.0199] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Deep sequencing-based genetic mapping has greatly enhanced the ability to catalog variants with plausible disease association. Confirming how these identified variants contribute to specific disease conditions, across human populations, poses the next challenge. Differential selection pressure may impact the frequency of genetic variations, and thus detection of association with disease conditions, across populations. To understand genotype to phenotype correlations, it thus becomes important to first understand the spectrum of genetic variation within a population by creating a reference map. In this study, we report the development of phase I of a new database of genetic variations called INDian EXome database (INDEX-db), from the Indian population, with an aim to establish a centralized database of integrated information. This could be useful for researchers involved in studying disease mechanisms at clinical, genetic, and cellular levels.
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Affiliation(s)
- Husayn Ahmed P
- Accelerator Program for Discovery in Brain Disorders Using Stem Cells (ADBS), National Centre for Biological Sciences, Tata Institute of Fundamental Research (NCBS-TIFR), Bengaluru, India
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru, India
| | - Vidhya V
- Accelerator Program for Discovery in Brain Disorders Using Stem Cells (ADBS), Centre for Brain Development and Repair (CBDR), Institute for Stem Cell Biology and Regenerative Medicine (InStem), Bengaluru, India
| | - Ravi Prabhakar More
- Accelerator Program for Discovery in Brain Disorders Using Stem Cells (ADBS), National Centre for Biological Sciences, Tata Institute of Fundamental Research (NCBS-TIFR), Bengaluru, India
| | - Biju Viswanath
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences (NIMHANS), Bengaluru, India
| | - Sanjeev Jain
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences (NIMHANS), Bengaluru, India
| | - Mahendra S. Rao
- Accelerator Program for Discovery in Brain Disorders Using Stem Cells (ADBS), Centre for Brain Development and Repair (CBDR), Institute for Stem Cell Biology and Regenerative Medicine (InStem), Bengaluru, India
| | - Odity Mukherjee
- Address correspondence to: Dr. Odity Mukherjee, Investigator & Chief Technologist, Accelerator Program for Discovery in Brain Disorders Using Stem Cells (ADBS), Centre for Brain Development and Repair (CBDR), Institute for Stem Cell Biology and Regenerative Medicine (InStem), Bellary Road, Bengaluru–560065, Karnataka, India
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Vijay A, Garg I, Ashraf MZ. Perspective: DNA Copy Number Variations in Cardiovascular Diseases. Epigenet Insights 2018; 11:2516865718818839. [PMID: 30560231 PMCID: PMC6291864 DOI: 10.1177/2516865718818839] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 11/08/2018] [Indexed: 12/27/2022] Open
Abstract
Human genome contains many variations, often called mutations, which are difficult to detect and have remained a challenge for years. A substantial part of the genome encompasses repeats and when such repeats are in the coding region they may lead to change in the gene expression profile followed by pathological conditions. Structural variants are alterations which change one or more sequence feature in the chromosome such as change in the copy number, rearrangements, and translocations of a sequence and can be balanced or unbalanced. Copy number variants (CNVs) may increase or decrease the copies of a given region and have a pivotal role in the onset of many diseases including cardiovascular disorders. Cardiovascular disorders have a magnitude of well-established risk factors and etiology, but their correlation with CNVs is still being studied. In this article, we have discussed history of CNVs and a summary on the diseases associated with CNVs. To detect such variations, we shed light on the number of techniques introduced so far and their limitations. The lack of studies on cardiovascular diseases to determine the frequency of such variants needs clinical studies with larger cohorts. This review is a compilation of articles suggesting the importance of CNVs in multitude of cardiovascular anomalies. Finally, future perspectives for better understanding of CNVs and cardiovascular disorders have also been discussed.
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Affiliation(s)
- Aatira Vijay
- Genomics Division, Defence Institute of Physiology & Allied Sciences, Delhi, India
| | - Iti Garg
- Genomics Division, Defence Institute of Physiology & Allied Sciences, Delhi, India
| | - Mohammad Zahid Ashraf
- Genomics Division, Defence Institute of Physiology and Allied Sciences, DRDO, Delhi, India
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5
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Fina F, Barets D, Colin C, Bouvier C, Padovani L, Nanni-Metellus I, Ouafik L, Scavarda D, Korshunov A, Jones DTW, Figarella-Branger D. Droplet digital PCR is a powerful technique to demonstrate frequent FGFR1 duplication in dysembryoplastic neuroepithelial tumors. Oncotarget 2018; 8:2104-2113. [PMID: 27791984 PMCID: PMC5356784 DOI: 10.18632/oncotarget.12881] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 10/13/2016] [Indexed: 01/23/2023] Open
Abstract
Dysembryoplastic neuroepithelial tumors (DNT) share V600E mutation in the BRAF gene with other low grade neuroepithelial tumors (LGNTs). FGFR1 internal tandem duplication of the tyrosine-kinase domain (FGFR1-ITD), another genetic alteration that also leads to MAP kinase pathway alteration, has been previously reported in LGNTs by whole-genome sequencing. In the present study we searched for FGFR1-ITD by droplet digital PCR (DDPCR™) and for FGFR1 point mutations by HRM-sequencing in a series of formalin-fixed paraffin-embedded (FFPE) LGNTs including 12 DNT, 2 oligodendrogliomas lacking IDH mutation and 1p/19q co- deletion (pediatric-type oligodendrogliomas; PTOs), 3 pediatric diffuse astrocytomas (PDAs), 14 gangliogliomas (GGs) and 5 pilocytic astrocytomas (PAs). We showed by DDPCR™ that 5/12 DNT, but none of the other LGNTs, demonstrated FGFR1-ITD. In addition, these cases also accumulated phosphorylated-FGFR1 protein as shown by immunohistochemistry. FGFR1G539R point mutation was only recorded in one DNT that also showed FGFR1-ITD. Interestingly, these FGFR1 alterations were mutually exclusive from BRAFV600E mutation that was recorded in 13 LGNTs (3 DNTs, 1 PTO, 2 PDAs, 5 GGs and 2 PAs). Therefore, FGFR1 alteration mainly represented by FGFR1-ITD is a frequent event in DNT. DDPCR™ is an easy and alternative method than whole-genome sequencing to detect FGFR1-ITD in FFPE brain tumors, in routine practice.
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Affiliation(s)
- Frédéric Fina
- Assistance Publique Hôpitaux de Marseille (AP-HM), Hôpital Nord, Service de Transfert d'Oncologie Biologique, Laboratoire de Biologie Médicale Marseille, France
| | - Doriane Barets
- APHM, Hôpital de la Timone, Service d'Anatomie Pathologique et de Neuropathologie, Marseille, France
| | - Carole Colin
- Aix-Marseille Université, Inserm, CRO2 UMR_S 911, Marseille, France
| | - Corinne Bouvier
- APHM, Hôpital de la Timone, Service d'Anatomie Pathologique et de Neuropathologie, Marseille, France.,Aix-Marseille Université, Inserm, CRO2 UMR_S 911, Marseille, France
| | - Laëtitia Padovani
- APHM, Hôpital de la Timone, Service de Radiothérapie, Marseille, France
| | - Isabelle Nanni-Metellus
- Assistance Publique Hôpitaux de Marseille (AP-HM), Hôpital Nord, Service de Transfert d'Oncologie Biologique, Laboratoire de Biologie Médicale Marseille, France
| | - L'Houcine Ouafik
- Assistance Publique Hôpitaux de Marseille (AP-HM), Hôpital Nord, Service de Transfert d'Oncologie Biologique, Laboratoire de Biologie Médicale Marseille, France
| | - Didier Scavarda
- APHM, Hôpital de la Timone, Service de Neurochirurgie Pédiatrique, Marseille, France
| | - Andrey Korshunov
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David T W Jones
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dominique Figarella-Branger
- APHM, Hôpital de la Timone, Service d'Anatomie Pathologique et de Neuropathologie, Marseille, France.,Aix-Marseille Université, Inserm, CRO2 UMR_S 911, Marseille, France
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6
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Prestes PR, Charchar FJ. Is there a link between mitochondrial DNA and blood pressure? J Hum Hypertens 2017; 31:761-762. [DOI: 10.1038/jhh.2017.73] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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7
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Zhu Q, Xu Y, Qiu L, Ma C, Yu B, Song Q, Jin W, Jin Q, Liu J, Mu Y. A scalable self-priming fractal branching microchannel net chip for digital PCR. LAB ON A CHIP 2017; 17:1655-1665. [PMID: 28418438 DOI: 10.1039/c7lc00267j] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
As an absolute quantification method at the single-molecule level, digital PCR has been widely used in many bioresearch fields, such as next generation sequencing, single cell analysis, gene editing detection and so on. However, existing digital PCR methods still have some disadvantages, including high cost, sample loss, and complicated operation. In this work, we develop an exquisite scalable self-priming fractal branching microchannel net digital PCR chip. This chip with a special design inspired by natural fractal-tree systems has an even distribution and 100% compartmentalization of the sample without any sample loss, which is not available in existing chip-based digital PCR methods. A special 10 nm nano-waterproof layer was created to prevent the solution from evaporating. A vacuum pre-packaging method called self-priming reagent introduction is used to passively drive the reagent flow into the microchannel nets, so that this chip can realize sequential reagent loading and isolation within a couple of minutes, which is very suitable for point-of-care detection. When the number of positive microwells stays in the range of 100 to 4000, the relative uncertainty is below 5%, which means that one panel can detect an average of 101 to 15 374 molecules by the Poisson distribution. This chip is proved to have an excellent ability for single molecule detection and quantification of low expression of hHF-MSC stem cell markers. Due to its potential for high throughput, high density, low cost, lack of sample and reagent loss, self-priming even compartmentalization and simple operation, we envision that this device will significantly expand and extend the application range of digital PCR involving rare samples, liquid biopsy detection and point-of-care detection with higher sensitivity and accuracy.
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Affiliation(s)
- Qiangyuan Zhu
- Research Center for Analytical Instrumentation, Institute of Cyber Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China.
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8
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Tessitore MV, Sottini A, Roccaro AM, Ghidini C, Bernardi S, Martellosio G, Serana F, Imberti L. Detection of newly produced T and B lymphocytes by digital PCR in blood stored dry on nylon flocked swabs. J Transl Med 2017; 15:70. [PMID: 28381232 PMCID: PMC5381048 DOI: 10.1186/s12967-017-1169-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 03/23/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND A normal number of T-cell receptor excision circles (TRECs) and K-deleting recombination excision circles (KRECs) is considered a biomarker for adequate new T- and B-cell production. In newborns, detection of TRECs and KRECs by real time PCR from dried blood spotted on filter paper is used for the screening of severe immunodeficiency. In adults, elderly and during diseases, where the number of TRECs is lower than in newborns and children, a large amount of DNA and a sensitive method of amplification are necessary to identify newly produced lymphocytes. METHODS DNA was prepared from blood of 203 healthy adults (range: 18-91 years old) absorbed for 10 s on flocked swabs and let to dry, or from peripheral blood mononuclear cells. DNA was subjected to digital PCR and to well established conventional real time PCR-based method using TREC- and KREC-specific primers and probes. The number of TRECs and KRECs was expressed per mL of blood. Statistical analysis was performed by nested ANOVA, Pearson coefficient of determination, and by linear regression tests. RESULTS The novel method for the storage of dried blood on nylon flocked swabs and the use of digital PCR allow quantification of TRECs and KRECs with high degree of sensitivity, specificity, accuracy, and precision. TRECs and KRECs were amplified by digital PCR in all tested blood samples, including those obtained from elderly individuals (>70 years old) and that were negative by real time PCR. Furthermore, values of TRECs and KRECs obtained by digital PCR were in the range of those acquired by real time PCR. CONCLUSIONS Our findings demonstrate that DNA isolation from dried blood on flocked swabs followed by digital PCR-based analysis represents a useful tool for studying new lymphocyte production in adults and elderly individuals. This suggests the potential use of the methodology when monitoring of clinical variables is limited by the number of molecules that can be amplified and detected, such as in patients with immunodeficiency or under immunosuppressive therapies.
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Affiliation(s)
- Marion Vaglio Tessitore
- Centro di Ricerca Emato-oncologica AIL (CREA), ASST Spedali Civili, P.le Spedali Civili, 1, 25123, Brescia, Italy
| | - Alessandra Sottini
- Centro di Ricerca Emato-oncologica AIL (CREA), ASST Spedali Civili, P.le Spedali Civili, 1, 25123, Brescia, Italy
| | - Aldo M Roccaro
- Centro di Ricerca Emato-oncologica AIL (CREA), ASST Spedali Civili, P.le Spedali Civili, 1, 25123, Brescia, Italy
| | - Claudia Ghidini
- Centro di Ricerca Emato-oncologica AIL (CREA), ASST Spedali Civili, P.le Spedali Civili, 1, 25123, Brescia, Italy
| | - Simona Bernardi
- Centro di Ricerca Emato-oncologica AIL (CREA), ASST Spedali Civili, P.le Spedali Civili, 1, 25123, Brescia, Italy
| | - Giovanni Martellosio
- Centro di Ricerca Emato-oncologica AIL (CREA), ASST Spedali Civili, P.le Spedali Civili, 1, 25123, Brescia, Italy
| | - Federico Serana
- Centro di Ricerca Emato-oncologica AIL (CREA), ASST Spedali Civili, P.le Spedali Civili, 1, 25123, Brescia, Italy
| | - Luisa Imberti
- Centro di Ricerca Emato-oncologica AIL (CREA), ASST Spedali Civili, P.le Spedali Civili, 1, 25123, Brescia, Italy.
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9
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Borzi C, Calzolari L, Conte D, Sozzi G, Fortunato O. Detection of microRNAs Using Chip-Based QuantStudio 3D Digital PCR. Methods Mol Biol 2017; 1580:239-247. [PMID: 28439837 DOI: 10.1007/978-1-4939-6866-4_16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Digital PCR (dPCR) is an innovative approach for detection and quantification of nucleic acid that offers an alternative method to conventional real-time quantitative PCR for absolute quantification. dPCR is a highly precise and sensitive technique that does not require a standard reference, making it a suitable method for the detection of microRNAs. The potential of these small noncoding RNA as biomarkers is on the rise, especially due to their presence in body fluids, making them easily accessible. Nevertheless, the problem of lack of consensus regarding an optimal method for miRNAs normalization compromises their use. Here, we describe an innovative method for the absolute quantification of miRNAs across different types of biological samples using a chip-based platform, the QuantStudio 3D digital PCR.
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Affiliation(s)
- Cristina Borzi
- Tumor Genomics Unit, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, via Venezian 1, 20133, Milan, Italy
| | - Linda Calzolari
- Tumor Genomics Unit, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, via Venezian 1, 20133, Milan, Italy
| | - Davide Conte
- Tumor Genomics Unit, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, via Venezian 1, 20133, Milan, Italy
| | - Gabriella Sozzi
- Tumor Genomics Unit, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, via Venezian 1, 20133, Milan, Italy.
| | - Orazio Fortunato
- Tumor Genomics Unit, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, via Venezian 1, 20133, Milan, Italy
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10
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Shrine N, Tobin MD, Schurmann C, Soler Artigas M, Hui J, Lehtimäki T, Raitakari OT, Pennell CE, Ang QW, Strachan DP, Homuth G, Gläser S, Felix SB, Evans DM, Henderson J, Granell R, Palmer LJ, Huffman J, Hayward C, Scotland G, Malarstig A, Musk B, James AL, Wain LV. Genome-wide association study of copy number variation with lung function identifies a novel signal of association near BANP for forced vital capacity. BMC Genet 2016; 17:116. [PMID: 27514831 PMCID: PMC4981989 DOI: 10.1186/s12863-016-0423-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 07/29/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genome-wide association studies of Single Nucleotide Polymorphisms (SNPs) have identified 55 SNPs associated with lung function. However, little is known about the effect of copy number variants (CNVs) on lung function, although CNVs represent a significant proportion of human genetic polymorphism. To assess the effect of CNVs on lung function quantitative traits, we measured copy number at 2788 previously characterised, common copy number variable regions in 6 independent cohorts (n = 24,237) using intensity data from SNP genotyping experiments. We developed a pipeline for genome-wide association analysis and meta-analysis of CNV genotypes measured across multiple studies using SNP genotype array intensity data from different platform technologies. We then undertook cohort-level genome-wide association studies of CNV with lung function in a subset of 4 cohorts (n < =12,403) with lung function measurements and meta-analysed the results. Follow-up was undertaken for CNVs which were well tagged by SNPs, in up to 146,871 individuals. RESULTS We generated robust copy number calls for 1962 out of 2788 (70 %) known CNV regions genome-wide, with 1103 measured with compatible class frequencies in at least 2 cohorts. We report a novel CNV association (discovery P = 0.0007) with Forced Vital Capacity (FVC) downstream of BANP on chromosome 16 that shows evidence of replication by a tag SNP in two independent studies (replication P = 0.004). In addition, we provide suggestive evidence (discovery P = 0.0002) for a role of complex copy number variation at a previously reported lung function locus, containing the rootletin gene CROCC, that is not tagged by SNPs. CONCLUSIONS We demonstrate how common CNV regions can be reliably and consistently called across cohorts, using an existing calling algorithm and rigorous quality control steps, using SNP genotyping array intensity data. Although many common biallelic CNV regions were well-tagged by common SNPs, we also identified associations with untagged mulitallelic CNV regions thereby illustrating the potential of our approach to identify some of the missing heritability of complex traits.
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Affiliation(s)
- Nick Shrine
- Department of Health Sciences, University of Leicester, University Road, Leicester, LE1 7RH UK
| | - Martin D. Tobin
- Department of Health Sciences, University of Leicester, University Road, Leicester, LE1 7RH UK
- National Institute for Health Research (NIHR) Leicester Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, LE3 9QP UK
| | - Claudia Schurmann
- Department of Functional Genomics, University Medicine Greifswald, Interfaculty Institute for Genetics and Functional Genomics, Greifswald, Germany
- DZHK (German Center for Cardiovascular Research), partner site Greifswald, 17475 Greifswald, Germany
| | - María Soler Artigas
- Department of Health Sciences, University of Leicester, University Road, Leicester, LE1 7RH UK
| | - Jennie Hui
- Busselton Population Medical Research Institute, Sir Charles Gairdner Hospital, Nedlands, Australia
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, University of Tampere and Tampere University Hospital, Tampere, 33521 Finland
| | - Olli T. Raitakari
- Department of Clinical Physiology, Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku University Hospital, Turku, 20521 Finland
| | - Craig E. Pennell
- School of Women’s and Infants’ Health, The University of Western Australia, Perth, Australia
| | - Qi Wei Ang
- School of Women’s and Infants’ Health, The University of Western Australia, Perth, Australia
| | - David P. Strachan
- Division of Population Health Sciences, St. George’s University of London, London, UK
| | - Georg Homuth
- Department of Functional Genomics, University Medicine Greifswald, Interfaculty Institute for Genetics and Functional Genomics, Greifswald, Germany
| | - Sven Gläser
- Department of Internal Medicine B – Pulmonary Medicine, Weaning and Infectious Diseases and Scientific Division of Pneumology and Pneumological Epidemiology, University Medicine Greifswald, Greifswald, Germany
| | - Stephan B. Felix
- Department of Functional Genomics, University Medicine Greifswald, Interfaculty Institute for Genetics and Functional Genomics, Greifswald, Germany
- Department of Internal Medicine B – Cardiology, University Medicine Greifswald, Greifswald, Germany
| | - David M. Evans
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- School of Social and Community Medicine, University of Bristol, Bristol, UK
- University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland Australia
| | - John Henderson
- School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Raquel Granell
- School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Lyle J. Palmer
- School of Public Health, University of Adelaide, Adelaide, Australia
| | - Jennifer Huffman
- Institute of Genetics and Molecular Medicine, University of Edinburgh Western General Hospital, Crewe Road, Edinburgh, EH4 2XU UK
| | - Caroline Hayward
- Institute of Genetics and Molecular Medicine, University of Edinburgh Western General Hospital, Crewe Road, Edinburgh, EH4 2XU UK
| | - Generation Scotland
- Institute of Genetics and Molecular Medicine, University of Edinburgh Western General Hospital, Crewe Road, Edinburgh, EH4 2XU UK
| | | | - Bill Musk
- Busselton Population Medical Research Institute, Sir Charles Gairdner Hospital, Nedlands, Australia
- Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Nedlands, Australia
| | - Alan L. James
- Busselton Population Medical Research Institute, Sir Charles Gairdner Hospital, Nedlands, Australia
- Department of Pulmonary Physiology and Sleep Medicine, Sir Charles Gairdner Hospital, Nedlands, Australia
| | - UK BiLEVE
- Department of Health Sciences, University of Leicester, University Road, Leicester, LE1 7RH UK
- National Institute for Health Research (NIHR) Leicester Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, LE3 9QP UK
- Department of Functional Genomics, University Medicine Greifswald, Interfaculty Institute for Genetics and Functional Genomics, Greifswald, Germany
- DZHK (German Center for Cardiovascular Research), partner site Greifswald, 17475 Greifswald, Germany
- Busselton Population Medical Research Institute, Sir Charles Gairdner Hospital, Nedlands, Australia
- Department of Clinical Chemistry, Fimlab Laboratories, University of Tampere and Tampere University Hospital, Tampere, 33521 Finland
- Department of Clinical Physiology, Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku University Hospital, Turku, 20521 Finland
- School of Women’s and Infants’ Health, The University of Western Australia, Perth, Australia
- Division of Population Health Sciences, St. George’s University of London, London, UK
- Department of Internal Medicine B – Pulmonary Medicine, Weaning and Infectious Diseases and Scientific Division of Pneumology and Pneumological Epidemiology, University Medicine Greifswald, Greifswald, Germany
- Department of Internal Medicine B – Cardiology, University Medicine Greifswald, Greifswald, Germany
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- School of Social and Community Medicine, University of Bristol, Bristol, UK
- University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland Australia
- School of Public Health, University of Adelaide, Adelaide, Australia
- Institute of Genetics and Molecular Medicine, University of Edinburgh Western General Hospital, Crewe Road, Edinburgh, EH4 2XU UK
- Pfizer Worldwide Research and Development, Sollentuna, Sweden
- Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Nedlands, Australia
- Department of Pulmonary Physiology and Sleep Medicine, Sir Charles Gairdner Hospital, Nedlands, Australia
| | - Louise V. Wain
- Department of Health Sciences, University of Leicester, University Road, Leicester, LE1 7RH UK
- National Institute for Health Research (NIHR) Leicester Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, LE3 9QP UK
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11
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Liu X, Hu C, Bao M, Li J, Liu X, Tan X, Zhou Y, Chen Y, Wu S, Chen S, Zhang R, Jiang F, Jia W, Wang X, Yang X, Cai J. Genome Wide Association Study Identifies L3MBTL4 as a Novel Susceptibility Gene for Hypertension. Sci Rep 2016; 6:30811. [PMID: 27480026 PMCID: PMC4969609 DOI: 10.1038/srep30811] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 07/08/2016] [Indexed: 02/05/2023] Open
Abstract
Hypertension is a major global health burden and a leading risk factor for cardiovascular diseases. Although its heritability has been documented previously, contributing loci identified to date account for only a small fraction of blood pressure (BP) variation, which strongly suggests the existence of undiscovered variants. To identify novel variants, we conducted a three staged genetic study in 21,990 hypertensive cases and normotensive controls. Four single nucleotide polymorphisms (SNPs) at three new genes (L3MBTL4 rs403814, Pmeta = 6.128 × 10(-9); LOC729251, and TCEANC) and seven SNPs at five previously reported genes were identified as being significantly associated with hypertension. Through functional analysis, we found that L3MBTL4 is predominantly expressed in vascular smooth muscle cells and up-regulated in spontaneously hypertensive rats. Rats with ubiquitous over-expression of L3MBTL4 exhibited significantly elevated BP, increased thickness of the vascular media layer and cardiac hypertrophy. Mechanistically, L3MBTL4 over-expression could lead to down-regulation of latent transforming growth factor-β binding protein 1 (LTBP1), and phosphorylation activation of the mitogen-activated protein kinases (MAPK) signaling pathway, which is known to trigger the pathological progression of vascular remodeling and BP elevation. These findings pinpointed L3MBTL4 as a critical contributor to the development and progression of hypertension and uncovers a novel target for therapeutic intervention.
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Affiliation(s)
- Xin Liu
- National Research Institute for Family Planning, Beijing, China
- Beijing Hypertension League Institute, Beijing, China
| | - Cheng Hu
- Shanghai Diabetes Institute, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai, China
- Institute for Metabolic Diseases, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital South Campus, Shanghai, China
| | - Minghui Bao
- Department of Cardiology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Jing Li
- Department of Cardiology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Hypertension, Beijing, China
| | - Xiaoyan Liu
- Medical Research Center, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Xuerui Tan
- Department of Cardiology, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Yong Zhou
- Department of Cardiology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Yequn Chen
- Department of Cardiology, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Shouling Wu
- Department of Cardiology, Kailuan General Hospital, Hebei Union University, Tangshan, Hebei, China
| | - Shuohua Chen
- Department of Cardiology, Kailuan General Hospital, Hebei Union University, Tangshan, Hebei, China
| | - Rong Zhang
- Shanghai Diabetes Institute, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai, China
| | - Feng Jiang
- Shanghai Diabetes Institute, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai, China
| | - Weiping Jia
- Shanghai Diabetes Institute, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai, China
| | - Xingyu Wang
- National Research Institute for Family Planning, Beijing, China
- Beijing Hypertension League Institute, Beijing, China
| | - Xinchun Yang
- Department of Cardiology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Jun Cai
- Department of Hypertension, Fuwai Hospital, Beijing, China
- State Key Laboratory of Cardiovascular Disease, Beijing, China
- National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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12
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Conte D, Verri C, Borzi C, Suatoni P, Pastorino U, Sozzi G, Fortunato O. Novel method to detect microRNAs using chip-based QuantStudio 3D digital PCR. BMC Genomics 2015; 16:849. [PMID: 26493562 PMCID: PMC4619272 DOI: 10.1186/s12864-015-2097-9] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 10/16/2015] [Indexed: 12/22/2022] Open
Abstract
Background Research efforts for the management of cancer, in particular for lung cancer, are directed to identify new strategies for its early detection. MicroRNAs (miRNAs) are a new promising class of circulating biomarkers for cancer detection, but lack of consensus on data normalization methods has affected the diagnostic potential of circulating miRNAs. There is a growing interest in techniques that allow an absolute quantification of miRNAs which could be useful for early diagnosis. Recently, digital PCR, mainly based on droplets generation, emerged as an affordable technology for precise and absolute quantification of nucleic acids. Results In this work, we described a new interesting approach for profiling circulating miRNAs in plasma samples using a chip-based platform, the QuantStudio 3D digital PCR. The proposed method was validated using synthethic oligonucleotide at serial dilutions in plasma samples of lung cancer patients and in lung tissues and cell lines. Conclusion Given its reproducibility and reliability, our approach could be potentially applied for the identification and quantification of miRNAs in other biological samples such as circulating exosomes or protein complexes. As chip-digital PCR becomes more established, it would be a robust tool for quantitative assessment of miRNA copy number for diagnosis of lung cancer and other diseases. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2097-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Davide Conte
- Tumor Genomics Unit, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, via Venezian 1, 20133, Milan, Italy.
| | - Carla Verri
- Tumor Genomics Unit, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, via Venezian 1, 20133, Milan, Italy.
| | - Cristina Borzi
- Tumor Genomics Unit, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, via Venezian 1, 20133, Milan, Italy.
| | - Paola Suatoni
- Thoracic Surgery Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, via Venezian 1, 20133, Milan, Italy.
| | - Ugo Pastorino
- Thoracic Surgery Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, via Venezian 1, 20133, Milan, Italy.
| | - Gabriella Sozzi
- Tumor Genomics Unit, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, via Venezian 1, 20133, Milan, Italy.
| | - Orazio Fortunato
- Tumor Genomics Unit, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, via Venezian 1, 20133, Milan, Italy.
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13
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Abstract
Hundreds of copy number variants are complex and multi-allelic, in that they have many structural alleles and have rearranged multiple times in the ancestors who contributed chromosomes to current humans. Not only are the relationships of these multi-allelic CNVs (mCNVs) to phenotypes generally unknown, but many mCNVs have not yet been described at the basic levels—alleles, allele frequencies, structural features—that support genetic investigation. To date, most reported disease associations to these variants have been ascertained through candidate gene studies. However, only a few associations have reached the level of acceptance defined by durable replications in many cohorts. This likely stems from longstanding challenges in making precise molecular measurements of the alleles individuals have at these loci. However, approaches for mCNV analysis are improving quickly, and some of the unique characteristics of mCNVs may assist future association studies. Their various structural alleles are likely to have different magnitudes of effect, creating a natural allelic series of growing phenotypic impact and giving investigators a set of natural predictions and testable hypotheses about the extent to which each allele of an mCNV predisposes to a phenotype. Also, mCNVs’ low-to-modest correlation to individual single-nucleotide polymorphisms (SNPs) may make it easier to distinguish between mCNVs and nearby SNPs as the drivers of an association signal, and perhaps, make it possible to preliminarily screen candidate loci, or the entire genome, for the many mCNV–disease relationships that remain to be discovered.
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