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Brazdilova K, Prihoda D, Ton Q, Klock H, Bitton DA. TraceTrack, an open-source software for batch processing, alignment and visualization of sanger sequencing chromatograms. BIOINFORMATICS ADVANCES 2023; 3:vbad083. [PMID: 37456510 PMCID: PMC10348866 DOI: 10.1093/bioadv/vbad083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/23/2023] [Accepted: 07/11/2023] [Indexed: 07/18/2023]
Abstract
Motivation Despite the advent of next-generation sequencing technology and its widespread applications, Sanger sequencing remains instrumental for molecular biology subcloning work in biological and medical research and indispensable for drug discovery campaigns. Although Sanger sequencing technology has been long established, existing software for processing and visualization of trace file chromatograms is limited in terms of functionality, scalability and availability for commercial use. Results To fill this gap, we developed TraceTrack, an open-source web application tool for batch alignment, analysis and visualization of Sanger trace files. TraceTrack offers high-throughput matching of trace files to reference sequences, rapid identification of mutations and an intuitive chromatogram analysis. Comparative analysis between TraceTrack and existing software tools highlights the advantages of TraceTrack with regards to batch processing, visualization and export functionalities. Availability and implementation TraceTrack is available at https://github.com/MSDLLCpapers/TraceTrack and as a web application at https://tracetrack.dichlab.org. TraceTrack is a web application for batch processing and visualization of Sanger trace file chromatograms that meets the increasing demand of industrial sequence validation workflows in pharmaceutical settings. Supplementary information Supplementary data are available at Bioinformatics Advances online.
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Affiliation(s)
- Kveta Brazdilova
- Discovery Informatics, MSD Czech Republic s.r.o, Prague 150 00, Czech Republic
- Department of Informatics and Chemistry, Faculty of Chemical Technology, University of Chemistry and Technology, Prague 160 00, Czech Republic
| | - David Prihoda
- Discovery Informatics, MSD Czech Republic s.r.o, Prague 150 00, Czech Republic
- Department of Informatics and Chemistry, Faculty of Chemical Technology, University of Chemistry and Technology, Prague 160 00, Czech Republic
| | - Quynh Ton
- Protein Sciences, MRL, Merck & Co., Inc., Boston, MA 02115, USA
| | - Heath Klock
- Protein Sciences, MRL, Merck & Co., Inc., Boston, MA 02115, USA
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Yang L, Fu J, Cheng J, Zhou B, Chen M, Anuchapreeda S, Fu J. Novel, heterozygous, de novo pathogenic variant (c.4963delA: p.Thr1656Glnfs*42) of the NF1 gene in a Chinese family with neurofibromatosis type 1. BMC Med Genomics 2023; 16:85. [PMID: 37095468 PMCID: PMC10123994 DOI: 10.1186/s12920-023-01514-x] [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: 10/26/2022] [Accepted: 04/09/2023] [Indexed: 04/26/2023] Open
Abstract
Neurofibromatosis type 1 (NF1) presents an autosomal dominant, haploinsufficient, and multisystemic disorder with patches of skin café-au-lait spots, lisch nodules in the iris, even tumors in the peripheral nervous system or fibromatous skin. In this study, a Chinese young woman who suffered from NF1 disease with first-trimester spontaneous abortion was recruited. Analysis for whole exome sequencing (WES), Sanger sequencing, short tandem repeat (STR), and co-segregation was carried out. As results, a novel, heterozygous, de novo pathogenic variant (c.4963delA:p.Thr1656Glnfs*42) of the NF1 gene in the proband was identified. This pathogenic variant of the NF1 gene produced a truncated protein that lost more than one-third of the NF1 protein at the C-terminus including half of the CRAL-TRIO lipid-binding domain and nuclear localization signal (NLS), thus leading to pathogenicity (ACMG criteria: PVS1 + PM2 + PM2). Analysis for NF1 conservation in species revealed high conservation in different species. Analysis of NF1 mRNA levels in different human tissues showed low tissue specificity, which may affect multiple organs presenting other symptoms or phenotypes. Moreover, prenatal NF1 gene diagnosis showed both alleles as wild types. Thus, this NF1 novel variant probably underlays the NF1 pathogenesis in this pedigree, which would help for the diagnosis, genetic counseling, and clinical management of this disorder.
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Affiliation(s)
- Lisha Yang
- Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, 3-319, Zhongshan Rd, Luzhou, Sichuan, 646000, China
- Department of Obstetrics, the Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, 646000, China
| | - Jiewen Fu
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, 3-319, Zhongshan Rd, Luzhou, Sichuan, 646000, China
| | - Jingliang Cheng
- Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, 3-319, Zhongshan Rd, Luzhou, Sichuan, 646000, China
| | - Baixu Zhou
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, 3-319, Zhongshan Rd, Luzhou, Sichuan, 646000, China
- Department of Gynecology and Obstetrics, Guangdong Women and Children Hospital, Guangzhou, Guangdong, China
| | - Maomei Chen
- Department of Obstetrics, the Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, 646000, China
| | - Songyot Anuchapreeda
- Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand.
- Research Center of Pharmaceutical Nanotechnology, Chiang Mai University, Chiang Mai, 50200, Thailand.
| | - Junjiang Fu
- Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand.
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, 3-319, Zhongshan Rd, Luzhou, Sichuan, 646000, China.
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3
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Novel, heterozygous, pathogenic variant (c.4272delA: p.I1426Ffs*2) for the NF1 gene in a large Chinese family with neurofibromatosis type 1. Mol Biol Rep 2023; 50:1117-1123. [PMID: 36401065 DOI: 10.1007/s11033-022-08096-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 11/07/2022] [Indexed: 11/19/2022]
Abstract
BACKGROUND Neurofibromatosis type 1 (NF1) is an autosomal dominant with haploinsufficient, and multisystemic disorder including patches of skin Café-au-lait spots, Lisch nodules in the iris, and tumors in the peripheral nervous systems or fibromatous skin. METHODS Blood samples were collected and DNA was extracted from a large Chinese pedigree suffering from NF1 disease with three spontaneous abortions or death for proband. Analysis for whole exome sequencing (WES), Sanger sequencing, and co-segregation was carried out. Prenatal gene diagnosis was also carried out in amniotic fluid DNA. The expression of NF1 was conducted by bioinformatics. RESULTS A large Chinese pedigree with NF1 was recruited and a novel, heterozygous, variant (c.4272delA: p.I1426Ffs*2) for the NF1 gene in the proband was identified. This variant of NF1 produced a truncated protein that losses half of NF1 protein at the C-terminus including the CRAL-TRIO lipid-binding domain, NLS, and a small portion of Ras-GAP domain, thus leading to pathogenicity (ACMG criteria: PVS1 + PM2). NF1 expressions in different human tissues showed low tissue specificity, which may affect multiple organs presenting different phenotypes. Moreover, prenatal gene diagnosis for NF1 showed both alleles as wild types in the fetus of the proband. CONCLUSION We thus successfully identified a novel, pathogenic, heterozygous variant (c.4272delA:p.I1426Ffs*2) in the NF1 gene of NF1 disorder, expanding the NF1 mutation spectrum, that will help elucidate the molecular pathogenesis of NF1 disease and to contribute to the NF1 diagnosis, genetic counseling, clinical management in this large Chinese family.
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Cheng J, Song B, Fu J, Zheng X, He T, Fu J. Genetic polymorphism of 19 autosomal STR loci in the Yi ethnic minority of Liangshan Yi autonomous prefecture from Sichuan province in China. Sci Rep 2021; 11:16327. [PMID: 34381158 PMCID: PMC8357927 DOI: 10.1038/s41598-021-95883-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 08/02/2021] [Indexed: 01/10/2023] Open
Abstract
The Yi is one of fifty-six ethnic populations and one of the most ancient ethnic groups in China. The Liangshan Yi Autonomous Prefecture (LYAP) in Sichuan Province has the single largest Yi community in China. To establish a Yi population database in the LYAP of Sichuan in China, a Goldeneye™ DNA Identification System 20A Kit with 19 autosomal STRs (short tandem repeats) was used. As a result, the total discrimination power (TDP) and the cumulative probability of exclusion (CPE) for these STRs in 1016 unrelated individuals were 0.999999999999999999999897 and 0.9999999597, respectively. Totals of 273 alleles for 19 STRs and 8-22 alleles for each locus were found. The allelic frequencies ranged from 0.0005 to 0.5084. The forensic parameter averages of these STRs were as follows: observed heterozygosity (Hobs) of 78.44%, expected heterozygosity (Hexp) of 79.89%, discrimination power (DP) of 92.66%, and probability of exclusion (PE) of 57.68%. Penta E presented the highest levels of Hobs and DP, whereas TPOX showed the lowest Hobs and DP values. Nei's standard genetic distance matrix among 31 populations found that the nearest genetic distance to the Yi population was the Sichuan Han (0.0056). Altogether, we first reported the forensic parameters and allele frequencies of 19 autosomal STRs of the Yi group in Liangshan. These 19 STR makers could provide highly informative polymorphisms for individual identification, paternity testing and genetic population analyses.
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Affiliation(s)
- Jingliang Cheng
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China.,Laboratory of Forensic DNA, The Judicial Authentication Center, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Binghui Song
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China.,Laboratory of Forensic DNA, The Judicial Authentication Center, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Jiewen Fu
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China.,Laboratory of Forensic DNA, The Judicial Authentication Center, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Xiaoli Zheng
- Laboratory of Forensic DNA, The Judicial Authentication Center, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Tao He
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China. .,Laboratory of Forensic DNA, The Judicial Authentication Center, Southwest Medical University, Luzhou, 646000, Sichuan, China.
| | - Junjiang Fu
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China. .,Laboratory of Forensic DNA, The Judicial Authentication Center, Southwest Medical University, Luzhou, 646000, Sichuan, China.
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Fu J, Fu S, Yin S, Cheng J, Liu X, Jin Z, He T, Fu J. Technical note: multi-alleles at the DYS385ab locus with high frequency in a Han Chinese population from southwestern China. Int J Legal Med 2021; 135:1737-1741. [PMID: 33844081 DOI: 10.1007/s00414-021-02592-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 03/26/2021] [Indexed: 10/21/2022]
Abstract
Y-chromosome short tandem repeat (Y-STR) markers have been widely used in forensic applications and usually show monoallelic or diallelic genotypic patterns at certain double-copied loci. In this study, we have found 13 samples among 703 males with multi-alleles at the DYS385ab locus, including one with five mutant alleles, nine with four, and three with three. The frequency of abnormal DYS385ab genotypes was 1.85% (13/703), which is very high in the Han Chinese population. The percentage of samples with diallelic patterns at DYS385ab was higher than that of monoallelic patterns (80.23% vs. 17.92%). Additionally, the percentage of samples with tetra-allelic patterns at DYS385ab was higher than that of tri-allelic patterns (1.28% vs. 0.43%), suggesting that there are possibly two copies with duplicated events happening frequently on the Y chromosome. Interestingly, the peak height of allele 13 was two to three-folds higher than that of other alleles. The allele 18 peak height was also two-fold higher than others, which could potentially be explained by a duplication event mechanism. We also found that tri-allelic genotypes for alleles 13, 17, and 20, tetra-allelic genotypes for alleles 13, 14, 19, and 20, and tetra-allelic genotypes for alleles 12, 13, 19 and 21 were more common than others. Furthermore, all 13 samples had multi-alleles containing allele 13, implying a founder effect in this particular Chinese-specific ethnic group. Taken together, this study provides new information for this population and will be useful for paternal lineage identification, kinship analysis, and family relationship reconstruction using Y-STR forensic DNA analysis methods.
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Affiliation(s)
- Jiewen Fu
- Laboratory of Forensic DNA, the Judicial Authentication Center, Southwest Medical University, Luzhou, 646000, Sichuan, China.,Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Shangyi Fu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.,School of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Shiqiang Yin
- Judicial Authentication Institute, Luzhou Public Security Bureau, Luzhou, 646000, Sichuan, China
| | - Jingliang Cheng
- Laboratory of Forensic DNA, the Judicial Authentication Center, Southwest Medical University, Luzhou, 646000, Sichuan, China.,Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Xiaoyan Liu
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Zeming Jin
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China.
| | - Tao He
- Laboratory of Forensic DNA, the Judicial Authentication Center, Southwest Medical University, Luzhou, 646000, Sichuan, China. .,Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China.
| | - Junjiang Fu
- Laboratory of Forensic DNA, the Judicial Authentication Center, Southwest Medical University, Luzhou, 646000, Sichuan, China. .,Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China.
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Fu J, Cheng J, Wei C, Khan MA, Jin Z, Fu J. Assessing 23 Y-STR loci mutation rates in Chinese Han father-son pairs from southwestern China. Mol Biol Rep 2020; 47:7755-7760. [PMID: 32989501 DOI: 10.1007/s11033-020-05851-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 09/18/2020] [Indexed: 12/27/2022]
Abstract
In this study, we have analyzed 23 Y-chromosomal short tandem repeats (Y-STRs) (DYS576, DYS389I, DYS389II, DYS448, DYS19, DYS391, DYS481, DYS549, DYS533, DYS438, DYS437, DYS570, DYS635, DYS390, DYS439, DYS392, DYS643, DYS393, DYS458, DYS460, DYS385ab, DYS456 and Y-GATA-H4) in 175 father-son sample pairs using a Microreader™ 24Y Direct ID system. Sixteen repeat mutations of father-son pairs at 10 loci, including three mutations at DYS570, 2 mutations at DYS549, DYS460, DYS458, and DYS576, and 1 mutation at other five loci, were revealed. Furthermore, all of the observed repeat mutations were single repeat changes with 5 (31.25%) repeat insertions and 11 (68.75%) repeat deletions. The deletion rate is more than two fold higher than of insertions (11:5 = 2.2-fold). Locus-specific mutation rates estimated varied between 5.71 × 10-3 (CI from 0.1 × 10-3 to 31.4 × 10-3) and 1.71 × 10-2 (CI from 3.6 × 10-3 to 49.3 × 10-3) for the 23 Y-STRs. An average mutation rate across all 23 Y-STR markers was estimated as 3.97 × 10-3 (CI 2.3 × 10-3 to 6.4 × 10-3). Thus, locus-specific mutation rates in DYS460, DYS458, and DYS438, estimated are much higher than previously published comprehensive data, but an average mutation rate across all 23 Y-STR markers is similar to previous reports (3.97 × 10-3 vs 4.34 × 10-3). These results by characterizing Y-STR mutations will not only provided new information for Y-STR mutations but also might be important for paternal lineage identification, kinship analysis, and family relationship reconstruction in our forensic Y-STR analysis.
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Affiliation(s)
- Jiewen Fu
- Laboratory of Forensic DNA, the Judicial Authentication Center, Southwest Medical University, Luzhou, 646000, Sichuan, China.,Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Jingliang Cheng
- Laboratory of Forensic DNA, the Judicial Authentication Center, Southwest Medical University, Luzhou, 646000, Sichuan, China.,Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Chunli Wei
- Laboratory of Forensic DNA, the Judicial Authentication Center, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Md Asaduzzaman Khan
- Laboratory of Forensic DNA, the Judicial Authentication Center, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Zeming Jin
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Junjiang Fu
- Laboratory of Forensic DNA, the Judicial Authentication Center, Southwest Medical University, Luzhou, 646000, Sichuan, China. .,Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China.
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Fu J, Shen S, Cheng J, Lv H, Fu J. A case of Usher syndrome type IIA caused by a rare USH2A homozygous frameshift variant with maternal uniparental disomy (UPD) in a Chinese family. J Cell Mol Med 2020; 24:7743-7750. [PMID: 32449591 PMCID: PMC7348175 DOI: 10.1111/jcmm.15405] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Revised: 04/29/2020] [Accepted: 05/03/2020] [Indexed: 12/29/2022] Open
Abstract
Usher syndrome encompasses a group of genetically and clinically heterogeneous autosomal recessive disorders with hearing deficiencies and retinitis pigmentosa. The mechanisms underlying the Usher syndrome are highly variable. In the present study, a Chinese family with Usher syndrome was recruited. Whole exome sequencing (WES), Sanger sequencing, homozygosity mapping, short tandem repeat (STR) analysis and segregation analysis were performed. Functional domains of the pathogenic variant for USH2A were analysed. We identified a homozygous frameshift variant c.99_100insT (p.Arg34Serfs*41) in the USH2A gene in the proband that showed discordant segregation in the father. Further homozygosity mapping and STR analysis identified an unusual homozygous variant of proband that originated from maternal uniparental disomy (UPD). The p.Arg34Serfs*41 variant produced a predicted truncated protein that removes all functional domains of USH2A. The variant was not included in the 1000 Human Genomes Project database, ExAC database, HGMD or gnomAD database, but was included in the ClinVar databases as pathogenic. Although USH2A is an autosomal recessive disease, the effects of UPD should be informed in genetic counselling since the recurrence risk of an affected child is greatly reduced when the disease is due to the UPD mechanism. To test potential patients, WES, combined with STR analysis and homozygosity mapping, provides an accurate and useful strategy for genetic diagnosis. In summary, our discoveries can help further the understanding of the molecular pathogenesis of Usher syndrome type IIA to advance the prevention, diagnosis and therapy for this disorder.
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Affiliation(s)
- Jiewen Fu
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, China
| | - Shiyi Shen
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, China
| | - Jingliang Cheng
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, China
| | - Hongbin Lv
- Department of Ophthalmology, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Junjiang Fu
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, China
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Expressions and significances of the angiotensin-converting enzyme 2 gene, the receptor of SARS-CoV-2 for COVID-19. Mol Biol Rep 2020; 47:4383-4392. [PMID: 32410141 PMCID: PMC7224351 DOI: 10.1007/s11033-020-05478-4] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 04/28/2020] [Indexed: 12/28/2022]
Abstract
The ACE2 gene is a receptor of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) for COVID-19 (coronavirus disease 2019). To analyze the expression profiles and clinical significances for this gene in humans, RNA-seq data representing 27 different tissues were analyzed using NCBI; total RNA was extracted from different tissues of mouse and semi-quantitative reverse transcriptional-polymerase chain reaction (Q-RT-PCR) was carried out. Immunohistochemistry expression profiles in normal tissues and cancer tissues and TCGA survival analysis in renal and liver cancer were conducted. ACE2 was highly conserved in different species. In normal tissues, ACE2 expression distributions were organ-specific, mainly in the kidney, male testis and female breast, and cardiovascular and gastrointestinal systems. High level of expression in testis, cardiovascular and gastrointestinal system indicated that SARS-CoV-2 might not only attack the lungs, but also affect other organs, particularly the testes, thus it may severely damage male sexual development for younger male and lead to infertility in an adult male, if he contracted COVID-19. On the other side, high expression of ACE2 was correlated with increased survival rate in renal and liver cancer, indicating that ACE2 is a prognostic marker in both renal cancer and liver cancers. Thus, the ACE2 is a functional receptor for SARS-CoV-2 and has a potential anti-tumor role in cancer. Taken together, this study may not only provide potential clues for further medical pathogenesis of COVID-19 and male fertility, but also indicate the clinical significance of the role of the ACE2 gene in cancer.
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Liu X, Du J, Khan MA, Cheng J, Wei C, Mei Z, Chen H, He T, Fu J. Analysis of genetic diversity and similarities between different Lycium varieties based on ISSR analysis and RAMP‑PCR markers. WORLD ACADEMY OF SCIENCES JOURNAL 2020. [DOI: 10.3892/wasj.2020.39] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/28/2024]
Affiliation(s)
- Xiaoyan Liu
- Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Jun Du
- Department of Chemistry, School of Basic Sciences, Southwest Medical University, Luzhou, Sichuan 646000,
| | - Md. Asaduzzaman Khan
- Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Jingliang Cheng
- Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Chunli Wei
- Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Zhiqiang Mei
- Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Hanchun Chen
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Central South University, Changsha, Hunan 410013, P.R. China
| | - Tao He
- Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Junjiang Fu
- Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
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10
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Cheng J, Peng J, Fu J, Khan MA, Tan P, Wei C, Deng X, Chen H, Fu J. Identification of a novel germline BRCA2 variant in a Chinese breast cancer family. J Cell Mol Med 2020; 24:1676-1683. [PMID: 31782247 PMCID: PMC6991642 DOI: 10.1111/jcmm.14861] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 09/06/2019] [Accepted: 11/09/2019] [Indexed: 12/24/2022] Open
Abstract
Breast cancer is the most frequently diagnosed cancer and the leading cause of cancer-related deaths in women worldwide. In this study, a large Chinese pedigree with breast cancer including a proband and two female patients was recruited and a familial history of breast cancer was collected by questionnaire. Clinicopathological assessments and neoadjuvant therapy-related information were obtained for the proband. Blood samples were taken, and gDNA was extracted. The BRCA1/2 and PALB2 genes were screened using next-generation sequencing by a targeted gene panel. We have successfully identified a novel, germline heterozygous, missense mutation of the gene BRCA2: c.7007G>T, p.R2336L, which is likely to be pathogenic in the proband and her elder sister who both had breast cancer. Furthermore, the risk factors for developing breast cancer in this family are discussed. Thus, genetic counselling and long-term follow-up should be provided for this family of breast cancer patients as well as carriers carrying a germline variant of BRCA2: c.7007G>T (p.R2336L).
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Affiliation(s)
- Jingliang Cheng
- Key Laboratory of Epigenetics and OncologyThe Research Center for Preclinical MedicineSouthwest Medical UniversityLuzhouChina
| | - Jiangzhou Peng
- Department of Thoracic SurgeryThe Third Affiliated Hospital of Southern Medical UniversityGuangzhouChina
| | - Jiewen Fu
- Key Laboratory of Epigenetics and OncologyThe Research Center for Preclinical MedicineSouthwest Medical UniversityLuzhouChina
| | - Md. Asaduzzaman Khan
- Key Laboratory of Epigenetics and OncologyThe Research Center for Preclinical MedicineSouthwest Medical UniversityLuzhouChina
| | - Pingping Tan
- Department of PathologyHunan Cancer HospitalChangshaChina
| | - Chunli Wei
- Key Laboratory of Epigenetics and OncologyThe Research Center for Preclinical MedicineSouthwest Medical UniversityLuzhouChina
| | - Xiyun Deng
- Departments of Pathology and PathophysiologyHunan Normal University School of MedicineChangshaChina
| | - Hanchun Chen
- Department of BiochemistrySchool of Life Sciences & the State Key Laboratory of Medical GeneticsCentral South UniversityChangshaChina
| | - Junjiang Fu
- Key Laboratory of Epigenetics and OncologyThe Research Center for Preclinical MedicineSouthwest Medical UniversityLuzhouChina
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11
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Del Pino M, Martí C, Gaber J, Svanholm-Barrie C, Rodríguez-Carunchio L, Rodriguez-Trujillo A, Carreras N, Fuertes I, Barnadas E, Marimón L, Blanco JL, Persing DH, Torné A, Ordi J. mRNA Detection in Anal Cytology: A Feasible Approach for Anal Cancer Screening in Men Who Have Sex with Men Living With HIV. Diagnostics (Basel) 2019; 9:diagnostics9040173. [PMID: 31684110 PMCID: PMC6963475 DOI: 10.3390/diagnostics9040173] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 09/13/2019] [Accepted: 09/23/2019] [Indexed: 12/17/2022] Open
Abstract
There is growing interest in anal cancer screening strategies. However, cytological/molecular evaluation of anal samples is challenging. We aimed to determine the feasibility of detecting, in anal liquid-based cytologies, the expression of biomarkers involved in the cell cycle disturbance elicited by human papillomavirus (HPV). The accuracy of this approach in the identification of high-grade squamous intraepithelial lesions/anal intraepithelial neoplasia grade2-3 (HSIL/AIN2-3) was also evaluated. 215 anal cytologies from men having sex with men living with human immunodeficiency virus were evaluated. Patients showing concordant cytological and anoscopy-directed biopsy diagnosis were selected: 70 with negative cytology and HPV test, 70 with low-grade SIL (LSIL/AIN1) cytology and biopsy, and 75 with cytology and biopsy of HSIL/AIN2-3. CDKN2A/p16, MKI67 and TOP2A mRNA expression was analyzed. HPV detection was performed with Xpert HPV Assay (Cepheid, Sunnyvale, CA, USA). HSIL/AIN2-3 showed higher expression for the biomarkers than LSIL/AIN1 or negative samples. The specificity for HSIL/AIN2-3 detection for a sensitivity established at 70% was 44.7% (95%confidence interval [CI] 36.5-53.2) for TOP2A and MKI67 and 54.5% (95%CI 46.0-62.8%) for CDKN2A/p16. mRNA detection of cell biomarkers in anal liquid-based cytology is feasible. Further studies are warranted to confirm if strategies based on mRNA detection have any role in anal cancer screening.
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Affiliation(s)
- Marta Del Pino
- Institute Clinic of Gynaecology, Obstetrics, and Neonatology, Hospital Clínic-Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, 08036 Barcelona, Spain.
| | - Cristina Martí
- Institute Clinic of Gynaecology, Obstetrics, and Neonatology, Hospital Clínic-Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, 08036 Barcelona, Spain.
| | | | | | | | - Adriano Rodriguez-Trujillo
- Institute Clinic of Gynaecology, Obstetrics, and Neonatology, Hospital Clínic-Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, 08036 Barcelona, Spain.
| | - Núria Carreras
- Institute Clinic of Gynaecology, Obstetrics, and Neonatology, Hospital Clínic-Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, 08036 Barcelona, Spain.
| | - Irene Fuertes
- Department of Dermatology, Hospital Clinic of Barcelona, University of Barcelona, 08036 Barcelona, Spain.
| | - Esther Barnadas
- Department of Pathology, Hospital Clínic, University of Barcelona, 08036 Barcelona, Spain.
| | - Lorena Marimón
- Department of Pathology, Hospital Clínic, University of Barcelona, 08036 Barcelona, Spain.
| | - Jose Luis Blanco
- Department of Dermatology, Hospital Clinic of Barcelona, University of Barcelona, 08036 Barcelona, Spain.
| | | | - Aureli Torné
- Institute Clinic of Gynaecology, Obstetrics, and Neonatology, Hospital Clínic-Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, 08036 Barcelona, Spain.
| | - Jaume Ordi
- Department of Pathology, Hospital Clínic, University of Barcelona, 08036 Barcelona, Spain.
- Institut de Salut Global de Barcelona (ISGlobal), 08036 Barcelona, Spain.
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Imani S, Cheng J, Fu J, Mobasher-Jannat A, Wei C, Mohazzab-Torabi S, Jadidi K, Khosravi MH, Shasaltaneh MD, Yang L, Khan MA, Fu J. Novel splicing variant c. 208+2T>C in BBS5 segregates with Bardet-Biedl syndrome in an Iranian family by targeted exome sequencing. Biosci Rep 2019; 39:BSR20181544. [PMID: 30850397 PMCID: PMC6438871 DOI: 10.1042/bsr20181544] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 02/20/2019] [Accepted: 03/01/2019] [Indexed: 01/13/2023] Open
Abstract
Bardet-Biedl syndrome (BBS) is a rare genetically heterogeneous ciliopathy which accompanies retinitis pigmentosa (RP). However, the BBS5 mutation remains unclear in Iranians with BBS. The purpose of study is to evaluate genetic analyses of a BBS Iranian family using targetted exome sequencing (TES). A male 11-year-old proband and three related family members were recruited. Biochemical tests, electrocardiography and visual acuity testing, such as funduscopic, fundus photography (FP), optical coherence tomography (OCT), and standard electroretinography, were conducted. Molecular analysis and high-throughput DNA sequence analysis were performed. The proband was diagnosed with possible BBS based on the presence of three primary features and two secondary features. The TES analysis of the proband with BBS resulted in the identification of a novel, homozygous splicing variant c. 208+2T>C of the BBS5 gene (NM_152384.2) in this Iranian BBS family. This variant was confirmed and was completely co-segregated with the disease in this family by Sanger sequencing. Thus, we report a novel, homozygous splicing site variant c.208+2T>C in the BBS5 gene for the first time in the Iranian family.
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Affiliation(s)
- Saber Imani
- Key Laboratory of Epigenetics and Oncology, Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, Sichuan, China
| | - Jingliang Cheng
- Key Laboratory of Epigenetics and Oncology, Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, Sichuan, China
| | - Jiewen Fu
- Key Laboratory of Epigenetics and Oncology, Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, Sichuan, China
- Institute of Medical Technology, Xiangtan Medicine and Health Vocational College, Xiangtan, Hunan, China
| | | | - Chunli Wei
- Key Laboratory of Epigenetics and Oncology, Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, Sichuan, China
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau (SAR), China
| | | | - Khosrow Jadidi
- Department of Ophthalmology, Bina Eye Hospital Research Center, Tehran, Iran
| | | | | | - Lisha Yang
- Key Laboratory of Epigenetics and Oncology, Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, Sichuan, China
| | - Md Asaduzzaman Khan
- Key Laboratory of Epigenetics and Oncology, Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, Sichuan, China
| | - Junjiang Fu
- Key Laboratory of Epigenetics and Oncology, Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, Sichuan, China
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau (SAR), China
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