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Liu Y, Hao S, Guo X, Fan L, Qiao Z, Wang Y, Wang X, Man J, Wang L, Wei X, Peng H, Peng Z, Sun Y, Song L. Accuracy and depth evaluation of clinical low pass genome sequencing in the detection of mosaic aneuploidies and CNVs. BMC Med Genomics 2023; 16:294. [PMID: 37978521 PMCID: PMC10656965 DOI: 10.1186/s12920-023-01703-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 10/14/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND Low-pass genome sequencing (LP GS) has shown distinct advantages over traditional methods for the detection of mosaicism. However, no study has systematically evaluated the accuracy of LP GS in the detection of mosaic aneuploidies and copy number variants (CNVs) in prenatal diagnosis. Moreover, the influence of sequencing depth on mosaicism detection of LP GS has not been fully evaluated. METHODS To evaluate the accuracy of LP GS in the detection of mosaic aneuploidies and mosaic CNVs, 27 samples with known aneuploidies and CNVs and 1 negative female sample were used to generate 6 simulated samples and 21 virtual samples, each sample contained 9 different mosaic levels. Mosaic levels were simulated by pooling reads or DNA from each positive sample and the negative sample according to a series of percentages (ranging from 3 to 40%). Then, the influence of sequencing depth on LP GS in the detection of mosaic aneuploidies and CNVs was evaluated by downsampling. RESULTS To evaluate the accuracy of LP GS in the detection of mosaic aneuploidies and CNVs, a comparative analysis of mosaic levels was performed using 6 simulated samples and 21 virtual samples with 35 M million (M) uniquely aligned high-quality reads (UAHRs). For mosaic levels > 30%, the average difference (detected mosaic levels vs. theoretical mosaic levels) of 6 mosaic CNVs in simulated samples was 4.0%, and the average difference (detected mosaic levels vs. mosaic levels of Y chromosome) of 6 mosaic aneuploidies and 15 mosaic CNVs in virtual samples was 2.7%. Furthermore, LP GS had a higher detection rate and accuracy for the detection of mosaic aneuploidies and CNVs of larger sizes, especially mosaic aneuploidies. For depth evaluation, the results of LP GS in downsampling samples were compared with those of LP GS using 35 M UAHRs. The detection sensitivity of LP GS for 6 mosaic aneuploidies and 15 mosaic CNVs in virtual samples increased with UAHR. For mosaic levels > 30%, the total detection sensitivity reached a plateau at 30 M UAHRs. With 30 M UAHRs, the total detection sensitivity was 99.2% for virtual samples. CONCLUSIONS We demonstrated the accuracy of LP GS in mosaicism detection using simulated data and virtual samples, respectively. Thirty M UAHRs (single-end 35 bp) were optimal for LP GS in the detection of mosaic aneuploidies and most mosaic CNVs larger than 1.48 Mb (Megabases) with mosaic levels > 30%. These results could provide a reference for laboratories that perform clinical LP GS in the detection of mosaic aneuploidies and CNVs.
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Affiliation(s)
- Yanqiu Liu
- Jiangxi Maternal and Child Health Hospital Affiliated to Nanchang Medical College, Nanchang, 33000, Jiangxi, China
| | - Shengju Hao
- Medical Genetics Center, Gansu Provincial Clinical Research Center for Birth Defects and Rare Diseases, Gansu Provincial Maternity and Child-care Hospital, Lanzhou, 730050, China
| | - Xueqin Guo
- Clin Lab, BGI Genomics, Wuhan, 430074, China
| | - Linlin Fan
- Clin Lab, BGI Genomics, Tianjin, 300308, China
| | | | | | - Xiaoli Wang
- Clin Lab, BGI Genomics, Shenzhen, 518083, China
| | - Jianfen Man
- Clin Lab, BGI Genomics, Wuhan, 430074, China
| | - Lina Wang
- Clin Lab, BGI Genomics, Wuhan, 430074, China
| | | | | | | | - Yan Sun
- BGI Genomics, Shenzhen, 518083, China.
| | - Lijie Song
- Clin Lab, BGI Genomics, Tianjin, 300308, China.
- DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, 2800, Denmark.
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Shen H, Liu Y, Wang C, Wang R, Di Z, Huang X, Zhang H, Liu M. Prenatal diagnosis of 46,XX testicular disorder of sex development with SRY-positive: A case report and review of the literature. Eur J Obstet Gynecol Reprod Biol 2023; 289:140-144. [PMID: 37660509 DOI: 10.1016/j.ejogrb.2023.08.393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 08/30/2023] [Indexed: 09/05/2023]
Abstract
We report a case of a fetus with 46,XX testicular disorder of sex development detected prenatally. This fetus was found abnormally due to non-invasive prenatal testing. Amniocentesis revealed SRY gene on the X chromosome of the fetus. The related literature was reviewed, and the advantages and limitations of various prenatal diagnostic techniques were discussed. The combination of non-invasive prenatal testing and various prenatal diagnostic techniques has enabled more fetuses with sex reversal to be detected.
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Affiliation(s)
- Huimin Shen
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Harbin Medical University, China
| | - Yu Liu
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Harbin Medical University, China
| | - Chao Wang
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Harbin Medical University, China
| | - Ruijing Wang
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Harbin Medical University, China
| | - Zhixin Di
- Department of Ultrasonic Medicine, The Second Affiliated Hospital of Harbin Medical University, China
| | - Xin Huang
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Harbin Medical University, China
| | - Haomiao Zhang
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Harbin Medical University, China
| | - Meimei Liu
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Harbin Medical University, China.
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Wang Z, Guo Y, Xu R. Attitude Disparity and Worrying Scenarios in Genetic Discrimination-Based on Questionnaires from China. Healthcare (Basel) 2023; 11:healthcare11020188. [PMID: 36673556 PMCID: PMC9859512 DOI: 10.3390/healthcare11020188] [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: 09/08/2022] [Revised: 12/12/2022] [Accepted: 01/06/2023] [Indexed: 01/10/2023] Open
Abstract
Objectives: As genetic testing is increasingly used in non-medical fields, the judgment of people's potential conditions based on predictive genetic information inevitably causes genetic discrimination (henceforth GD). This article aimed to systematically investigate the disparity in attitudes and worrying scenarios concerning GD in China. Methods: A questionnaire survey of 555 respondents was conducted. Statistical tests were used to examine disparity in attitudes between gender, age, and education. A descriptive analysis was also conducted to explore other worrying scenarios. Results: It shows that (1) men are more tolerant of GD compared to women, and (2) participants aged between 18 and 30 years old possess the highest objection to GD. However, (3) no indication can attest to the relationship between educational level and perspective on GD. In addition, (4) the acceptance of gene testing in the three most common scenarios is ranked in descending order as follows: partner choice, insurance services, and recruitment. Moreover, (5) worrying scenarios relating to GD include: education, social occasions, medical services, fertility, shopping, and so on. Conclusions: Based on the results, suggestions proposed include developing a blacklist mechanism in the field of genetic data application and strengthening the security regulations for the commercial use of genetic data.
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Affiliation(s)
- Zhong Wang
- School of Economics, Guangdong University of Technology, Guangzhou 510520, China
- Key Laboratory of Digital Economy and Data Governance, Guangdong University of Technology, Guangzhou 510520, China
| | - Yujun Guo
- LIESMARS, Wuhan University, Wuhan 430079, China
| | - Rui Xu
- School of Economics, Guangdong University of Technology, Guangzhou 510520, China
- Correspondence: ; Tel.: +86-20-3932-2722
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Ryšavý P, Kléma J, Merkerová MD. circGPA: circRNA functional annotation based on probability-generating functions. BMC Bioinformatics 2022; 23:392. [PMID: 36167495 PMCID: PMC9513885 DOI: 10.1186/s12859-022-04957-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 09/21/2022] [Indexed: 11/25/2022] Open
Abstract
Recent research has already shown that circular RNAs (circRNAs) are functional in gene expression regulation and potentially related to diseases. Due to their stability, circRNAs can also be used as biomarkers for diagnosis. However, the function of most circRNAs remains unknown, and it is expensive and time-consuming to discover it through biological experiments. In this paper, we predict circRNA annotations from the knowledge of their interaction with miRNAs and subsequent miRNA-mRNA interactions. First, we construct an interaction network for a target circRNA and secondly spread the information from the network nodes with the known function to the root circRNA node. This idea itself is not new; our main contribution lies in proposing an efficient and exact deterministic procedure based on the principle of probability-generating functions to calculate the p-value of association test between a circRNA and an annotation term. We show that our publicly available algorithm is both more effective and efficient than the commonly used Monte-Carlo sampling approach that may suffer from difficult quantification of sampling convergence and subsequent sampling inefficiency. We experimentally demonstrate that the new approach is two orders of magnitude faster than the Monte-Carlo sampling, which makes summary annotation of large circRNA files feasible; this includes their reannotation after periodical interaction network updates, for example. We provide a summary annotation of a current circRNA database as one of our outputs. The proposed algorithm could be generalized towards other types of RNA in way that is straightforward.
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Affiliation(s)
- Petr Ryšavý
- Department of Computer Science, Faculty of Electrical Engineering, Czech Technical University in Prague, Prague, Czech Republic
| | - Jiří Kléma
- Department of Computer Science, Faculty of Electrical Engineering, Czech Technical University in Prague, Prague, Czech Republic
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Dubey PK, Patil M, Singh S, Dubey S, Ahuja P, Verma SK, Krishnamurthy P. Increased m6A-RNA methylation and FTO suppression is associated with myocardial inflammation and dysfunction during endotoxemia in mice. Mol Cell Biochem 2022; 477:129-141. [PMID: 34581943 PMCID: PMC8758538 DOI: 10.1007/s11010-021-04267-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 09/17/2021] [Indexed: 01/03/2023]
Abstract
Endotoxemia triggers life-threatening immune and cardiovascular response that leads to tissue damage, multi-organ failure, and death. The understanding of underlying molecular mechanisms is still evolving. N6-methyladenosine (m6A)-RNA modification plays key regulatory role in numerous biological processes. However, it remains unclear whether endotoxemia alters RNA methylation in the myocardium. In the current study, we investigated the effect of lipopolysaccharide (LPS)-induced endotoxemia on m6A-RNA methylation and its implications on myocardial inflammation and left ventricular (LV) function. Following LPS administration, mice showed increases in m6A-RNA methylation in the myocardium with a corresponding decrease in the expression of fat mass and obesity-associated protein (FTO, an m6A eraser/demethylase). The changes were associated with a significant increase in expression of myocardial inflammatory cytokine genes, such as IL-6, TNF-α, IL-1β, and reduced LV function. Moreover, rat cardiomyoblasts (H9c2) exposed to LPS showed similar changes (with increase in m6A-RNA methylation and inflammatory cytokine genes, whereas downregulation of FTO). Furthermore, methylated RNA immunoprecipitation assay showed hypermethylation and increase in the expression of IL-6 and TNF-α genes in LPS-treated H9c2 cells as compared to untreated cells. Interestingly, FTO knockdown in cardiomyocytes mimicked the above effects. Taken together, these data suggest that endotoxemia-induced m6A methylation might play a critical role in expression of cardiac proinflammatory cytokines, and modulation of m6A methylation might limit myocardial inflammation and dysfunction during endotoxemia.
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Affiliation(s)
- Praveen K Dubey
- Department of Biomedical Engineering, School of Medicine and School of Engineering, The University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Mallikarjun Patil
- Department of Biomedical Engineering, School of Medicine and School of Engineering, The University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Sarojini Singh
- Department of Biomedical Engineering, School of Medicine and School of Engineering, The University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Shubham Dubey
- Department of Biomedical Engineering, School of Medicine and School of Engineering, The University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Paras Ahuja
- Science and Technology Honors College, The University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Suresh Kumar Verma
- Division of Cardiovascular Disease, School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Prasanna Krishnamurthy
- Department of Biomedical Engineering, School of Medicine and School of Engineering, The University of Alabama at Birmingham, Birmingham, AL, 35294, USA.
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Fumonisin B 1 alters global m6A RNA methylation and epigenetically regulates Keap1-Nrf2 signaling in human hepatoma (HepG2) cells. Arch Toxicol 2021; 95:1367-1378. [PMID: 33496827 DOI: 10.1007/s00204-021-02986-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 01/14/2021] [Indexed: 12/29/2022]
Abstract
FB1 is a common contaminant of cereal grains that affects human and animal health. It has become increasingly evident that epigenetic changes are implicated in FB1 toxicity. N6-methyladenosine (m6A), the most abundant post-transcriptional RNA modification, is influenced by fluctuations in redox status. Since oxidative stress is a characteristic of FB1 exposure, we determined if there is cross-talk between oxidative stress and m6A in FB1-exposed HepG2 cells. Briefly, HepG2 cells were treated with FB1 (0, 5, 50, 100, 200 µM; 24 h) and ROS, LDH and m6A levels were quantified. qPCR was used to determine the expression of m6A modulators, Nrf2, Keap1 and miR-27b, while western blotting was used to quantify Keap1 and Nrf2 protein expression. Methylation status of Keap1 and Nrf2 promoters was assessed and RNA immunoprecipitation quantified m6A-Keap1 and m6A-Nrf2 levels. FB1 induced accumulation of intracellular ROS (p ≤ 0.001) and LDH leakage (p ≤ 0.001). Elevated m6A levels (p ≤ 0.05) were accompanied by an increase in m6A "writers" [METLL3 (p ≤ 0.01) and METLL14 (p ≤ 0.01)], and "readers" [YTHDF1 (p ≤ 0.01), YTHDF2 (p ≤ 0.01), YTHDF3 (p ≤ 0.001) and YTHDC2 (p ≤ 0.01)] and a decrease in m6A "erasers" [ALKBH5 (p ≤ 0.001) and FTO (p ≤ 0.001)]. Hypermethylation and hypomethylation occurred at Keap1 (p ≤ 0.001) and Nrf2 (p ≤ 0.001) promoters, respectively. MiR-27b was reduced (p ≤ 0.001); however, m6A-Keap1 (p ≤ 0.05) and m6A-Nrf2 (p ≤ 0.01) levels were upregulated. This resulted in the ultimate decrease in Keap1 (p ≤ 0.001) and increase in Nrf2 (p ≤ 0.001) expression. Our findings reveal that m6A RNA methylation can be modified by exposure to FB1, and a cross-talk between m6A and redox regulators does occur.
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Saberiyan M, Mirfakhraie R, Moghni M, Teimori H. Study of Linc00574 Regulatory Effect on the TCTE3 Expression in Sperm Motility. Reprod Sci 2020; 28:159-165. [PMID: 32749594 DOI: 10.1007/s43032-020-00275-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 07/23/2020] [Indexed: 10/23/2022]
Abstract
We investigated the relationship of t-complex-associated-testis-expressed 3 (TCTE3) and linc00574 expression levels with sperm motility and morphology in patients with asthenozoospermia (AZ) and terato-asthenozoospermia (TAZ). The study population consisted of 31 AZ patients, 31 TAZ patients, and 32 normozoospermia (NZ) as controls. Quantitative real-time PCR was conducted to evaluate the expression levels of TCTE3 and linc00574. Bioinformatics investigations were performed using databases to find molecular pathway. TCTE3 expression was reduced significantly in AZ and TAZ patients (P < 0.05). Linc00574 expression level increased only in the AZ patients (P < 0.05). The subsequent analyses showed a significantly positive correlation between TCTE3 and linc00574 expression levels (P < 0.05). In addition, a significantly positive relationship was observed between TCTE3 expression level and sperm motility and morphology (P < 0.05). The present study suggests that TCTE3 expression is regulated by linc00574 through a negative self-regulating mechanism and therefore may affect the flagella structure and function.
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Affiliation(s)
- Mohammadreza Saberiyan
- Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Rahmatiyeh, Shahrekord, 8813833435, Iran
| | - Reza Mirfakhraie
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mandana Moghni
- Department of pathology, Faculty of Medicine, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Hossein Teimori
- Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Rahmatiyeh, Shahrekord, 8813833435, Iran.
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