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Li J, Schilit SLP, Liang S, Qin N, Teng X, Zhang J. Novel Loss-of-Function SYCP2 Variants in Infertile Males Upgrade the Gene-Disease Clinical Validity Classification for SYCP2 and Male Infertility to Strong. Genes (Basel) 2024; 15:1092. [PMID: 39202451 DOI: 10.3390/genes15081092] [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: 06/20/2024] [Revised: 08/13/2024] [Accepted: 08/16/2024] [Indexed: 09/03/2024] Open
Abstract
Male infertility affects approximately 7% of the male population, and about 15% of these cases are predicted to have a genetic etiology. One gene implicated in autosomal dominant male infertility, SYCP2, encodes a protein critical for the synapsis of homologous chromosomes during meiosis I, resulting in impaired spermatogenesis. However, the clinical validity of the gene-disease pair was previously categorized as on the border of limited and moderate due to few reported cases. This study investigates the genetic cause of infertility for three unrelated Chinese patients with oligoasthenozoospermia. Whole exome sequencing (WES) and subsequent Sanger sequencing revealed novel heterozygous loss-of-function (LOF) variants in SYCP2 (c.89dup, c.946_947del, and c.4378_4379del). These cases, combined with the previously reported cases, provide strong genetic evidence supporting an autosomal dominant inheritance pattern. The experimental evidence also demonstrates a critical role for SYCP2 in spermatogenesis. Collectively, this updated assessment of the genetic and experimental evidence upgrades the gene-disease association strength of SYCP2 and autosomal dominant male infertility from on the border of limited and moderate to strong. The reclassification improves SYCP2 variant interpretation and qualifies it for the inclusion on diagnostic male infertility gene panels and prioritization in whole exome or genome studies for related phenotypes. These findings therefore improve the clinical interpretation of SYCP2 LOF variants.
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Affiliation(s)
- Jinli Li
- Reproductive Medicine Center, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, 2699 West Gaoke Road, Shanghai 201204, China
| | | | - Shanshan Liang
- Reproductive Medicine Center, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, 2699 West Gaoke Road, Shanghai 201204, China
| | - Ningxin Qin
- Reproductive Medicine Center, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, 2699 West Gaoke Road, Shanghai 201204, China
| | - Xiaoming Teng
- Reproductive Medicine Center, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, 2699 West Gaoke Road, Shanghai 201204, China
| | - Junyu Zhang
- Reproductive Medicine Center, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, 2699 West Gaoke Road, Shanghai 201204, China
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To-Mai XH, Nguyen HT, Nguyen-Thi TT, Nguyen TV, Nguyen-Thi MN, Thai KQ, Lai MT, Nguyen TA. Prevalence of common autosomal recessive mutation carriers in women in the Southern Vietnam following the application of expanded carrier screening. Sci Rep 2024; 14:7461. [PMID: 38553482 PMCID: PMC10980709 DOI: 10.1038/s41598-024-57513-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 03/19/2024] [Indexed: 04/02/2024] Open
Abstract
The common autosomal recessive (AR) mutation carrier is still unknown in Vietnam. This study aims to identify the most common AR gene mutation carriers in women of reproductive age to build a Vietnamese-specific carrier screening panel for AR and X-linked disorders in the preconception and prenatal healthcare program. A cross-sectional study was conducted at University Medical Center-Branch 2 in Ho Chi Minh City from December 1st, 2020, to June 30th, 2023. 338 women have consented to take a 5 mL blood test to identify 540 recessive genes. The carrier screening panel was designed based on the American College of Medical Genetics and Genomics (ACMG)-recommended genes and suggestions from 104 clinical experts in Vietnam. Obstetricians and genetic experts counseled all positive testing results to discuss the possibility of recessive diseases in their offspring. The most common recessive disorders were defined at a prevalence of 1 in 60 or greater, and those were added to a Vietnamese-specific carrier screening panel. 338 non-pregnant and pregnant women underwent the expanded carrier screening (ECS). The carrier frequency was 63.6%, in which 215 women carried at least one AR gene mutation. GJB2 hearing impairment was identified as the most common chronic condition (1 in 5). The second most common AR disorder was beta-thalassemia (1 in 16), followed by cystic fibrosis (1 in 23), G6PD deficiency (1 in 28), Wilson's disease (1 in 31), Usher's syndrome (1 in 31), and glycogen storage disease (1 in 56). Seven common recessive genes were added in ethnic-based carrier screening. Women in the South of Vietnam have been carried for many recessive conditions at high frequency, such as hearing impairment, genetic anemia, and cystic fibrosis. It is necessary to implement a preconception and prenatal screening program by using seven widely popular AR genes in a Vietnamese-specific carrier screening panel to reduce the burden related to AR and X-linked disorders.
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Affiliation(s)
- Xuan-Hong To-Mai
- University of Alberta, Edmonton, Canada
- University of Nam Can Tho, Can Tho, Vietnam
| | - Huu-Trung Nguyen
- University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
- University Medical Center-Branch 2, Ho Chi Minh City, Vietnam
| | | | - Thuy-Vy Nguyen
- University of Science, Vietnam National University Ho Chi Minh, Ho Chi Minh City, Vietnam
- Ktest Company, Ho Chi Minh City, Vietnam
| | - My-Nuong Nguyen-Thi
- University of Science, Vietnam National University Ho Chi Minh, Ho Chi Minh City, Vietnam
- Ktest Company, Ho Chi Minh City, Vietnam
| | | | | | - Tuan-Anh Nguyen
- University Medical Center-Branch 2, Ho Chi Minh City, Vietnam.
- Molecular Biomedical Center, University Medical Center, Ho Chí Minh City, Vietnam.
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Birnbaum R, Ezer S, Lotan NS, Eilat A, Sternlicht K, Benyamini L, Reish O, Falik-Zaccai T, Ben-Gad G, Rod R, Segel R, Kim K, Burton B, Keegan CE, Wagner M, Henderson LB, Mor N, Barel O, Hirsch Y, Meiner V, Elpeleg O, Harel T, Mor-Shakad H. Intellectual disability syndrome associated with a homozygous founder variant in SGSM3 in Ashkenazi Jews. J Med Genet 2024; 61:289-293. [PMID: 37833060 DOI: 10.1136/jmg-2023-109504] [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: 07/10/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023]
Abstract
BACKGROUND Neurodevelopmental disorders (NDDs) impact both the development and functioning of the brain and exhibit clinical and genetic variability. RAP and RAB proteins, belonging to the RAS superfamily, are identified as established contributors to NDDs. However, the involvement of SGSM (small G protein signalling modulator), another member of the RAS family, in NDDs has not been previously documented. METHODS Proband-only or trio exome sequencing was performed on DNA samples obtained from affected individuals and available family members. The variant prioritisation process focused on identifying rare deleterious variants. International collaboration aided in the identification of additional affected individuals. RESULTS We identified 13 patients from 8 families of Ashkenazi Jewish origin who all carried the same homozygous frameshift variant in SGSM3 gene. The variant was predicted to cause a loss of function, potentially leading to impaired protein structure or function. The variant co-segregated with the disease in all available family members. The affected individuals displayed mild global developmental delay and mild to moderate intellectual disability. Additional prevalent phenotypes observed included hypotonia, behavioural challenges and short stature. CONCLUSIONS An Ashkenazi Jewish homozygous founder variant in SGSM3 was discovered in individuals with NDDs and short stature. This finding establishes a connection between another member of the RAS family and NDDs. Additional research is needed to uncover the specific molecular mechanisms by which SGSM3 influences neurodevelopmental processes and the regulation of growth.
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Affiliation(s)
- Rivka Birnbaum
- Department of Genetics, Hadassah Medical Center, Jerusalem, Israel
| | - Shlomit Ezer
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Nava Shaul Lotan
- Department of Genetics, Hadassah Medical Center, Jerusalem, Israel
| | - Avital Eilat
- Department of Genetics, Hadassah Medical Center, Jerusalem, Israel
| | | | | | - Orit Reish
- Genetics Institute, Shamir Medical Center, Tzrifin, Israel
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Tzipora Falik-Zaccai
- Institute of Human Genetics, Western Galilee Hospital-Nahariya, Nahariya, Israel
| | - Gali Ben-Gad
- Department of Child Development, Galilee Medical Center, Nahariya, Israel
| | - Raya Rod
- The Center for Child Development and Pediatric Neurology, Western Galilee Hospital-Naharyia, Nahariya, Israel
| | | | - Katherine Kim
- Genetics, Ann and Robert H Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
- Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Barabra Burton
- Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
| | - Catherine E Keegan
- Department of Pediatrics, University of Michigan, Ann Arbor, Michigan, USA
| | - Mallory Wagner
- Department of Pediatrics, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Nofar Mor
- The Genomic Unit, Sheba Cancer Research Center, Sheba Medical Center, Tel Hashomer, Israel
| | - Ortal Barel
- The Genomic Unit, Sheba Cancer Research Center, Sheba Medical Center, Tel Hashomer, Israel
| | - Yoel Hirsch
- Research, Dor Yeshroim, Brooklyn, New York, USA
- Dor Yeshorim, New York, New York, USA
| | - Vardiella Meiner
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
- Department of Genetics, Hadassah Medical Center, Jerusalem, Jerusalem, Israel
| | - Orly Elpeleg
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
- Department of Genetics, Hadassah Medical Center, Jerusalem, Jerusalem, Israel
| | - Tamar Harel
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
- Department of Genetics, Hadassah Medical Center, Jerusalem, Jerusalem, Israel
| | - Hagar Mor-Shakad
- Department of Genetics, Hadassah Medical Center, Jerusalem, Israel
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
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4
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Cahn A, Mor-Shaked H, Rosenberg-Fogler H, Pollack R, Tolhuis B, Sharma G, Schultz E, Yanovsky-Dagan S, Harel T. Complex rearrangement in TBC1D4 in an individual with diabetes due to severe insulin resistance syndrome. Eur J Hum Genet 2024; 32:232-237. [PMID: 38086948 PMCID: PMC10853276 DOI: 10.1038/s41431-023-01512-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 11/14/2023] [Accepted: 11/23/2023] [Indexed: 02/10/2024] Open
Abstract
Severe insulin resistance syndromes result from primary insulin signaling defects, adipose tissue abnormalities or other complex syndromes. Mutations in TBC1D4 lead to partial insulin signaling defects, characterized mainly by postprandial insulin resistance. We describe an individual with severe insulin-resistant diabetes unresponsive to multiple therapies, in whom exome and genome analyses identified a complex rearrangement in TBC1D4. The rearrangement was of the pattern DUP-TRP/INV-DUP, with mutational signatures suggestive of replicative repair and Alu-Alu recombination as the underlying mechanisms. TBC1D4 encodes the TBC1D4/AS160 RabGTPase activating protein (RabGAP) involved in the translocation of glucose transporter 4 (GLUT4) from the cytosol to the cell membrane. Although the precise functional mechanism underlying insulin resistance in the proband is yet to be determined, this case provides further support for the link between TBC1D4 and hereditary insulin-resistant diabetes.
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Affiliation(s)
- Avivit Cahn
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
- Diabetes Unit, Department of Endocrinology and Metabolism, Hadassah Medical Center, Jerusalem, Israel
| | - Hagar Mor-Shaked
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
- Department of Genetics, Hadassah Medical Center, Jerusalem, Israel
| | - Hallel Rosenberg-Fogler
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
- Department of Genetics, Hadassah Medical Center, Jerusalem, Israel
| | - Rena Pollack
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
- Diabetes Unit, Department of Endocrinology and Metabolism, Hadassah Medical Center, Jerusalem, Israel
| | | | | | | | | | - Tamar Harel
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel.
- Department of Genetics, Hadassah Medical Center, Jerusalem, Israel.
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5
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Tuncel T, Ak G, Güneş HV, Metintaş M. Complex Genomic Rearrangement Patterns in Malignant Pleural Mesothelioma due to Environmental Asbestos Exposure. J Environ Pathol Toxicol Oncol 2024; 43:13-27. [PMID: 38505910 DOI: 10.1615/jenvironpatholtoxicoloncol.2023046200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024] Open
Abstract
Malignant pleural mesothelioma (MPM) is a rare type of cancer, and its main risk factor is exposure to asbestos. Accordingly, our knowledge of the genomic structure of an MPM tumor is limited when compared to other cancers. In this study, we aimed to characterize complex genomic rearrangement patterns and variations to better understand the genomics of MPM tumors. We comparatively scanned 3 MPM tumor genomes by Whole-Genome Sequencing and High-Resolution SNP array. We also used various computational algorithms to detect both CNAs and complex chromosomal rearrangements. Genomic data obtained from each bioinformatics tool are interpreted comparatively to better understand CNAs and cancer-related Nucleotide variations in MPM tumors. In patients 1 and 2, we found pathogenic nucleotide variants of BAP1, RB1, and TP53. These two MPM genomes exhibited a highly rearranged chromosomal rearrangement pattern resembling Chromomanagesis particularly in the form of Chromoanasynthesis. In patient 3, we found nucleotide variants of important cancer-related genes, including TGFBR1, KMT2C, and PALLD, to have lower chromosomal rearrangement complexity compared with patients 1 and 2. We also detected several actionable nucleotide variants including XRCC1, ERCC2. We also discovered the SKA3-DDX10 fusion in two MPM genomes, which is a novel finding for MPM. We found that MPM genomes are very complex, suggesting that this highly rearranged pattern is strongly related to driver mutational status like BAP1, TP53 and RB1.
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Affiliation(s)
- Tunç Tuncel
- Health Institutes of Turkey, Turkish Biotechnology Institute, Ankara, Turkey
| | - Güntülü Ak
- Eskisehir Osmangazi University Medical Faculty, Department of Chest Diseases, Lung and Pleural Cancers Research and Clinical Center, Eskisehir, Turkey
| | - Hasan Veysi Güneş
- Eskisehir Osmangazi University Medical Faculty, Department of Medical Biology, Eskisehir, Turkey
| | - Muzaffer Metintaş
- Eskisehir Osmangazi University Medical Faculty, Department of Chest Diseases, Lung and Pleural Cancers Research and Clinical Center, Eskisehir, Turkey
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Sun YL, Zhao PP, Zhu CB, Li XM, Yuan B. Qingfei Formula Protects against Human Respiratory Syn cytial Virus-induced Lung Inflammatory Injury by Regulating the M APK Signaling Pathway. Comb Chem High Throughput Screen 2024; 27:969-983. [PMID: 37605417 PMCID: PMC11165710 DOI: 10.2174/1386207326666230821121358] [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: 12/13/2022] [Revised: 06/26/2023] [Accepted: 07/12/2023] [Indexed: 08/23/2023]
Abstract
OBJECTIVE Qingfei formula (QF) is an empirical formula that shows good clinical efficacy in treating human respiratory syncytial virus pneumonia (RSVP). However, the underlying mechanism remains unclear. This study explores the possible pharmacological actions of QF in RSVP treatment. METHODS We used a network pharmacology approach to identify the active ingredients of QF, forecast possible therapeutic targets, and analyze biological processes and pathways. Molecular docking simulation was used to evaluate the binding capability of active ingredients and therapeutic targets. Finally, in vivo experiments confirmed the reliability of network pharmacology-based prediction of underlying mechanisms. RESULTS The study identified 92 potential therapeutic targets and corresponding 131 active ingredients. Enrichment analysis showed that QF downregulated the MAPK signaling pathway and suppressed the inflammatory injury to the lungs induced by the RSV virus. Molecular docking simulations demonstrated that the core active ingredients of QF could stably bind to genes associated with the MAPK signaling pathway. QF had a protective effect against pneumonia in RSV-infected mice. The QF group exhibited a significant reduction in the levels of inflammatory mediators, interleukin- 6 (IL-6), interleukin-8 (CXCL8, IL-8), and P-STAT3, compared to the RSV-induced group. The QF group showed remarkably inhibited MAPK1+3(P-ERK1+2) and MAPK8(P-JNK) protein expression. CONCLUSION The current study showed that QF downregulated the MAPK signaling pathway, which inhibited pulmonary inflammation triggered by RSV infection. This study recommends the appropriate use of QF in the clinical management of RSVP.
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Affiliation(s)
- Ya-Lei Sun
- Department of Pediatrics, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210000, China
- Jiangsu Key Laboratory of Pediatric Respiratory Disease, Institute of Pediatrics, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210000, China
| | - Pei-Pei Zhao
- Department of Pediatrics, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210000, China
- Jiangsu Key Laboratory of Pediatric Respiratory Disease, Institute of Pediatrics, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210000, China
| | - Cheng-Bi Zhu
- Department of Pediatrics, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210000, China
- Jiangsu Key Laboratory of Pediatric Respiratory Disease, Institute of Pediatrics, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210000, China
| | - Xin-Min Li
- Henan University of Chinese Medicine, Zhengzhou, 450000, China
| | - Bin Yuan
- Department of Pediatrics, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210000, China
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Chen X, Yu B, Wang Z, Li Q, Dai C, Wei J. Two novel mutations within FREM1 gene in patients with bifid nose. BMC Pediatr 2023; 23:631. [PMID: 38097983 PMCID: PMC10720098 DOI: 10.1186/s12887-023-04453-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 11/30/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Bifid nose is a rare congenital deformity and the etiology is unknown. The purpose of this study was to report genetic variation in family of patients with bifid nose. METHODS Twenty-three consecutive patients who were diagnosed with mild bifid nose were operated with z-plasty from 2009 to 2021. Three underage patients (a pair of twins and a girl) from two family lines, who came to our hospital for surgical treatment, were enrolled. Whole exome sequencing and Sanger sequencing were conducted. Z-shaped flaps were created and the cartilago alaris major were re-stitched. Photographs and CT scan before and after surgery were obtained. Clinical outcomes, complications and patients' satisfaction were evaluated and analyzed. The follow-up time ranges from 2 to 3 years (2.4 ± 1.2 years). RESULTS Most patients were satisfied with the outcome (96.2%). The nasal deformities were corrected successfully with z-plasty technique in one-stage. FREM1 c.870_876del and c.2 T > C were detected with Whole exome sequencing, which have not been reported before. The results of Sanger sequencing were consistent with those of Whole exome sequencing. CONCLUSIONS The newly detected mutations of FREM1 have a certain heritability, and are helpful to make an accurate diagnosis and provide a better understanding of bifid nose mechanism. Z-plasty technique can be an effective technical approach for correcting mild bifid nose deformity.
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Affiliation(s)
- Xiaoxue Chen
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital Affiliated to Shanghai Jiaotong University School of Medicine, 639 Zhi Zao Ju Rd, Shanghai, 200011, People's Republic of China
| | - Baofu Yu
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital Affiliated to Shanghai Jiaotong University School of Medicine, 639 Zhi Zao Ju Rd, Shanghai, 200011, People's Republic of China
| | - Zi Wang
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital Affiliated to Shanghai Jiaotong University School of Medicine, 639 Zhi Zao Ju Rd, Shanghai, 200011, People's Republic of China
| | - Qingfeng Li
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital Affiliated to Shanghai Jiaotong University School of Medicine, 639 Zhi Zao Ju Rd, Shanghai, 200011, People's Republic of China.
| | - Chuanchang Dai
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital Affiliated to Shanghai Jiaotong University School of Medicine, 639 Zhi Zao Ju Rd, Shanghai, 200011, People's Republic of China.
| | - Jiao Wei
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital Affiliated to Shanghai Jiaotong University School of Medicine, 639 Zhi Zao Ju Rd, Shanghai, 200011, People's Republic of China.
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8
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Zhang J, Tang J, Li G, Li N, Wang J, Yao R, Yu T. SINE-VNTR-Alu retrotransposon insertion as a novel mutational event underlying Glanzmann thrombasthenia. J Thromb Haemost 2023; 21:3597-3607. [PMID: 37604334 DOI: 10.1016/j.jtha.2023.08.012] [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: 01/09/2023] [Revised: 08/01/2023] [Accepted: 08/06/2023] [Indexed: 08/23/2023]
Abstract
BACKGROUND Glanzmann thrombasthenia (GT) is an autosomal recessive platelet aggregation disorder caused by mutations in ITGA2B or ITGB3. OBJECTIVES We aimed to assess the phenotype and investigate the genetic etiology of a GT pedigree. METHODS A patient with bleeding manifestations and mild mental retardation was enrolled. Complete blood count, coagulation, and platelet aggregation tests were performed. Causal mutations were identified via whole exome and genome sequencing and subsequently confirmed through polymerase chain reaction and Sanger sequencing. The transcription of ITGB3 was characterized using RNA sequencing and reverse transcription polymerase chain reaction. The αⅡb and β3 biosynthesis was investigated via whole blood flow cytometry and in vitro studies. RESULTS GT was diagnosed in a patient with defective platelet aggregation. Novel compound heterozygous ITGB3 variants were identified, with a maternal nonsense mutation (c.2222G>A, p.Trp741∗) and a paternal SINE-VNTR-Alu (SVA) retrotransposon insertion. The 5' truncated SVA element was inserted in a sense orientation in intron 11 of ITGB3, resulting in aberrant splicing of ITGB3 and significantly reducing β3 protein content. Meanwhile, both the expression and transportation of β3 were damaged by the ITGB3 c.2222G>A. Almost no αⅡb and β3 expressions were detected on the patient's platelets surface. CONCLUSION Novel compound heterozygous ITGB3 mutations were identified in the GT pedigree, resulting in defects of αⅡbβ3 biosynthesis. This is the first report of SVA retrotransposon insertion in the genetic pathogenesis of GT. Our study highlights the importance of combining multiple high-throughput sequencing technologies for the molecular diagnosis of genetic disorders.
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Affiliation(s)
- Jiasheng Zhang
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jie Tang
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Guoqiang Li
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Niu Li
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jian Wang
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ruen Yao
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Tingting Yu
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
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Asatryan B, Bleijendaal H, Wilde AAM. Toward advanced diagnosis and management of inherited arrhythmia syndromes: Harnessing the capabilities of artificial intelligence and machine learning. Heart Rhythm 2023; 20:1399-1407. [PMID: 37442407 DOI: 10.1016/j.hrthm.2023.07.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/20/2023] [Accepted: 07/02/2023] [Indexed: 07/15/2023]
Abstract
The use of advanced computational technologies, such as artificial intelligence (AI), is now exerting a significant influence on various aspects of life, including health care and science. AI has garnered remarkable public notice with the release of deep learning models that can model anything from artwork to academic papers with minimal human intervention. Machine learning, a method that uses algorithms to extract information from raw data and represent it in a model, and deep learning, a method that uses multiple layers to progressively extract higher-level features from the raw input with minimal human intervention, are increasingly leveraged to tackle problems in the health sector, including utilization for clinical decision support in cardiovascular medicine. Inherited arrhythmia syndromes are a clinical domain where multiple unanswered questions remain despite unprecedented progress over the past 2 decades with the introduction of large panel genetic testing and the first steps in precision medicine. In particular, AI tools can help address gaps in clinical diagnosis by identifying individuals with concealed or transient phenotypes; enhance risk stratification by elevating recognition of underlying risk burden beyond widely recognized risk factors; improve prediction of response to therapy, and further prognostication. In this contemporary review, we provide a summary of the AI models developed to solve challenges in inherited arrhythmia syndromes and also outline gaps that can be filled with the development of intelligent AI models.
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Affiliation(s)
- Babken Asatryan
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland.
| | - Hidde Bleijendaal
- University of Amsterdam, Heart Center; Department of Clinical and Experimental Cardiology, Amsterdam Cardiovascular Sciences, Heart Failure and Arrhythmias, Amsterdam, The Netherlands; Department of Clinical Epidemiology, Biostatistics and Bioinformatics, University of Amsterdam, Amsterdam, The Netherlands
| | - Arthur A M Wilde
- University of Amsterdam, Heart Center; Department of Clinical and Experimental Cardiology, Amsterdam Cardiovascular Sciences, Heart Failure and Arrhythmias, Amsterdam, The Netherlands; Department of Clinical Epidemiology, Biostatistics and Bioinformatics, University of Amsterdam, Amsterdam, The Netherlands; European Reference Network for Rare and Low Prevalence Complex Diseases of the Heart (ERN GUARD-Heart)
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10
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Engal E, Oja KT, Maroofian R, Geminder O, Le TL, Mor E, Tzvi N, Elefant N, Zaki MS, Gleeson JG, Muru K, Pajusalu S, Wojcik MH, Pachat D, Elmaksoud MA, Jeong WC, Lee H, Bauer P, Zifarelli G, Houlden H, Elpeleg O, Gordon C, Harel T, Õunap K, Salton M, Mor-Shaked H. Biallelic loss of function variants in WBP4, encoding a spliceosome protein, result in a variable neurodevelopmental delay syndrome. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.06.19.23291425. [PMID: 37425688 PMCID: PMC10327195 DOI: 10.1101/2023.06.19.23291425] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Over two dozen spliceosome proteins are involved in human diseases, also referred to as spliceosomopathies. WBP4 (WW Domain Binding Protein 4) is part of the early spliceosomal complex, and was not described before in the context of human pathologies. Ascertained through GeneMatcher we identified eleven patients from eight families, with a severe neurodevelopmental syndrome with variable manifestations. Clinical manifestations included hypotonia, global developmental delay, severe intellectual disability, brain abnormalities, musculoskeletal and gastrointestinal abnormalities. Genetic analysis revealed overall five different homozygous loss-of-function variants in WBP4. Immunoblotting on fibroblasts from two affected individuals with different genetic variants demonstrated complete loss of protein, and RNA sequencing analysis uncovered shared abnormal splicing patterns, including enrichment for abnormalities of the nervous system and musculoskeletal system genes, suggesting that the overlapping differentially spliced genes are related to the common phenotypes of the probands. We conclude that biallelic variants in WBP4 cause a spliceosomopathy. Further functional studies are called for better understanding of the mechanism of pathogenicity.
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Affiliation(s)
- Eden Engal
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
- Department of Military Medicine and “Tzameret”, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Kaisa Teele Oja
- Genetics and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia
- Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Reza Maroofian
- Department of Neuromuscular Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Ophir Geminder
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
- Department of Military Medicine and “Tzameret”, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | | | - Evyatar Mor
- Department of computer science, Ben-Gurion University of the Negev
| | - Naama Tzvi
- Department of Genetics, Hadassah Medical Organization, Jerusalem, Israel
| | - Naama Elefant
- Department of Genetics, Hadassah Medical Organization, Jerusalem, Israel
| | - Maha S. Zaki
- Department of Clinical Genetics, Human Genetics and Genome Research Institute, Cairo, Egypt
| | - Joseph G. Gleeson
- Department of Neurosciences, University of California, San Diego, La Jolla, USA
- Rady Children’s Institute for Genomic Medicine, San Diego, La Jolla, USA
| | - Kai Muru
- Genetics and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia
- Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Sander Pajusalu
- Genetics and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia
- Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | | | | | - Marwa Abd Elmaksoud
- Neurology Unit, Alexandria University Children’s Hospital, Department of Pediatrics, Faculty of Medicine, Alexandria University, Alexandria, Egypt
| | | | | | - Peter Bauer
- CENTOGENE N.V., Am Strande 7, 18055 Rostock, Germany
| | | | - Henry Houlden
- Department of Neuromuscular Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Orly Elpeleg
- Department of Genetics, Hadassah Medical Organization, Jerusalem, Israel
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | | | - Tamar Harel
- Department of Genetics, Hadassah Medical Organization, Jerusalem, Israel
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Katrin Õunap
- Genetics and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia
- Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Maayan Salton
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Hagar Mor-Shaked
- Department of Genetics, Hadassah Medical Organization, Jerusalem, Israel
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
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11
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Salma M, Alaterre E, Moreaux J, Soler E. Var∣Decrypt: a novel and user-friendly tool to explore and prioritize variants in whole-exome sequencing data. Epigenetics Chromatin 2023; 16:23. [PMID: 37312221 DOI: 10.1186/s13072-023-00497-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 05/23/2023] [Indexed: 06/15/2023] Open
Abstract
BACKGROUND High-throughput sequencing (HTS) offers unprecedented opportunities for the discovery of causative gene variants in multiple human disorders including cancers, and has revolutionized clinical diagnostics. However, despite more than a decade of use of HTS-based assays, extracting relevant functional information from whole-exome sequencing (WES) data remains challenging, especially for non-specialists lacking in-depth bioinformatic skills. RESULTS To address this limitation, we developed Var∣Decrypt, a web-based tool designed to greatly facilitate WES data browsing and analysis. Var∣Decrypt offers a wide range of gene and variant filtering possibilities, clustering and enrichment tools, providing an efficient way to derive patient-specific functional information and to prioritize gene variants for functional analyses. We applied Var∣Decrypt on WES datasets of 10 acute erythroid leukemia patients, a rare and aggressive form of leukemia, and recovered known disease oncogenes in addition to novel putative drivers. We additionally validated the performance of Var∣Decrypt using an independent dataset of ~ 90 multiple myeloma WES, recapitulating the identified deregulated genes and pathways, showing the general applicability and versatility of Var∣Decrypt for WES analysis. CONCLUSION Despite years of use of WES in human health for diagnosis and discovery of disease drivers, WES data analysis still remains a complex task requiring advanced bioinformatic skills. In that context, there is a need for user-friendly all-in-one dedicated tools for data analysis, to allow biologists and clinicians to extract relevant biological information from patient datasets. Here, we provide Var∣Decrypt (trial version accessible here: https://vardecrypt.com/app/vardecrypt ), a simple and intuitive Rshiny application created to fill this gap. Source code and detailed user tutorial are available at https://gitlab.com/mohammadsalma/vardecrypt .
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Affiliation(s)
- Mohammad Salma
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier, France.
- Laboratory of Excellence GR-Ex, Université de Paris, Paris, France.
| | - Elina Alaterre
- Institute of Human Genetics, UMR 9002 CNRS-UM, Montpellier, France
| | - Jérôme Moreaux
- Department of Biological Hematology, CHU Montpellier, Montpellier, France
- Institute of Human Genetics, UMR 9002 CNRS-UM, Montpellier, France
- Institut Universitaire de France (IUF), Paris, France
| | - Eric Soler
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier, France.
- Laboratory of Excellence GR-Ex, Université de Paris, Paris, France.
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12
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Sun YL, Zhao PP, Zhu CB, Jiang MC, Li XM, Tao JL, Hu CC, Yuan B. Integrating metabolomics and network pharmacology to assess the effects of quercetin on lung inflammatory injury induced by human respiratory syncytial virus. Sci Rep 2023; 13:8051. [PMID: 37198253 DOI: 10.1038/s41598-023-35272-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 05/15/2023] [Indexed: 05/19/2023] Open
Abstract
Quercetin (QR) has significant anti-respiratory syncytial virus (RSV) effects. However, its therapeutic mechanism has not been thoroughly explored. In this study, a lung inflammatory injury model caused by RSV was established in mice. Untargeted lung tissue metabolomics was used to identify differential metabolites and metabolic pathways. Network pharmacology was used to predict potential therapeutic targets of QR and analyze biological functions and pathways modulated by QR. By overlapping the results of the metabolomics and the network pharmacology analyses, the common targets of QR that were likely to be involved in the amelioration of RSV-induced lung inflammatory injury by QR were identified. Metabolomics analysis identified 52 differential metabolites and 244 corresponding targets, while network pharmacology analysis identified 126 potential targets of QR. By intersecting these 244 targets with the 126 targets, hypoxanthine-guanine phosphoribosyltransferase (HPRT1), thymidine phosphorylase (TYMP), lactoperoxidase (LPO), myeloperoxidase (MPO), and cytochrome P450 19A1 (CYP19A1) were identified as the common targets. The key targets, HPRT1, TYMP, LPO, and MPO, were components of purine metabolic pathways. The present study demonstrated that QR effectively ameliorated RSV-induced lung inflammatory injury in the established mouse model. Combining metabolomics and network pharmacology showed that the anti-RSV effect of QR was closely associated with purine metabolism pathways.
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Affiliation(s)
- Ya-Lei Sun
- Department of Pediatrics, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
- Jiangsu Key Laboratory of Pediatric Respiratory Disease, Institute of Pediatrics, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Pei-Pei Zhao
- Department of Pediatrics, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
- Jiangsu Key Laboratory of Pediatric Respiratory Disease, Institute of Pediatrics, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Cheng-Bi Zhu
- Department of Pediatrics, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
- Jiangsu Key Laboratory of Pediatric Respiratory Disease, Institute of Pediatrics, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | | | - Xin-Min Li
- Henan University of Chinese Medicine, Zhengzhou, China
| | - Jia-Lei Tao
- Department of Pediatrics, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China.
| | - Chan-Chan Hu
- Department of Pediatrics, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China.
| | - Bin Yuan
- Department of Pediatrics, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China.
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13
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Application of Prenatal Whole Exome Sequencing for Structural Congenital Anomalies-Experience from a Local Prenatal Diagnostic Laboratory. Healthcare (Basel) 2022; 10:healthcare10122521. [PMID: 36554045 PMCID: PMC9778831 DOI: 10.3390/healthcare10122521] [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: 10/27/2022] [Revised: 12/05/2022] [Accepted: 12/07/2022] [Indexed: 12/15/2022] Open
Abstract
Fetal structural congenital abnormalities (SCAs) complicate 2-3% of all pregnancies. Whole-exome sequencing (WES) has been increasingly adopted prenatally when karyotyping and chromosomal microarray do not yield a diagnosis. This is a retrospective cohort study of 104 fetuses with SCAs identified on antenatal ultrasound in Hong Kong, where whole exome sequencing is performed. Molecular diagnosis was obtained in 25 of the 104 fetuses (24%). The highest diagnostic rate was found in fetuses with multiple SCAs (29.2%), particularly those with involvement of the cardiac and musculoskeletal systems. Variants of uncertain significance were detected in 8 out of the 104 fetuses (7.7%). Our study shows the utility of WES in the prenatal setting, and the extended use of the technology would be recommended in addition to conventional genetic workup.
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14
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Halim-Fikri H, Syed-Hassan SNRK, Wan-Juhari WK, Assyuhada MGSN, Hernaningsih Y, Yusoff NM, Merican AF, Zilfalil BA. Central resources of variant discovery and annotation and its role in precision medicine. ASIAN BIOMED 2022; 16:285-298. [PMID: 37551357 PMCID: PMC10392146 DOI: 10.2478/abm-2022-0032] [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] [Indexed: 08/09/2023]
Abstract
Rapid technological advancement in high-throughput genomics, microarray, and deep sequencing technologies has accelerated the possibility of more complex precision medicine research using large amounts of heterogeneous health-related data from patients, including genomic variants. Genomic variants can be identified and annotated based on the reference human genome either within the sequence as a whole or in a putative functional genomic element. The American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP) mutually created standards and guidelines for the appraisal of proof to expand consistency and straightforwardness in clinical variation interpretations. Various efforts toward precision medicine have been facilitated by many national and international public databases that classify and annotate genomic variation. In the present study, several resources are highlighted with recognition and data spreading of clinically important genetic variations.
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Affiliation(s)
- Hashim Halim-Fikri
- Malaysian Node of the Human Variome Project, School of Medical Sciences, Universiti Sains Malaysia, Kelantan16150, Malaysia
| | | | - Wan-Khairunnisa Wan-Juhari
- Malaysian Node of the Human Variome Project, School of Medical Sciences, Universiti Sains Malaysia, Kelantan16150, Malaysia
- Human Genome Centre, School of Medical Sciences, Universiti Sains Malaysia, Kelantan16150, Malaysia
| | - Mat Ghani Siti Nor Assyuhada
- Malaysian Node of the Human Variome Project, School of Medical Sciences, Universiti Sains Malaysia, Kelantan16150, Malaysia
| | - Yetti Hernaningsih
- Department of Clinical Pathology, Faculty of Medicine Universitas Airlangga, Dr. Soetomo Academic General Hospital, Surabaya, Indonesia
| | - Narazah Mohd Yusoff
- Department of Clinical Pathology, Faculty of Medicine Universitas Airlangga, Dr. Soetomo Academic General Hospital, Surabaya, Indonesia
- Clinical Diagnostic Laboratory, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Penang13200, Malaysia
| | - Amir Feisal Merican
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur50603, Malaysia
- Center of Research for Computational Sciences and Informatics in Biology, Bio Industry, Environment, Agriculture and Healthcare (CRYSTAL), University of Malaya, Kuala Lumpur50603, Malaysia
| | - Bin Alwi Zilfalil
- Malaysian Node of the Human Variome Project, School of Medical Sciences, Universiti Sains Malaysia, Kelantan16150, Malaysia
- Human Genome Centre, School of Medical Sciences, Universiti Sains Malaysia, Kelantan16150, Malaysia
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15
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Yu T, Zhang Y, Zheng WQ, Wu S, Li G, Zhang Y, Li N, Yao R, Fang P, Wang J, Zhou XL. Selective degradation of tRNASer(AGY) is the primary driver for mitochondrial seryl-tRNA synthetase-related disease. Nucleic Acids Res 2022; 50:11755-11774. [PMID: 36350636 PMCID: PMC9723649 DOI: 10.1093/nar/gkac1028] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 10/13/2022] [Accepted: 10/21/2022] [Indexed: 11/11/2022] Open
Abstract
Mitochondrial translation is of high significance for cellular energy homeostasis. Aminoacyl-tRNA synthetases (aaRSs) are crucial translational components. Mitochondrial aaRS variants cause various human diseases. However, the pathogenesis of the vast majority of these diseases remains unknown. Here, we identified two novel SARS2 (encoding mitochondrial seryl-tRNA synthetase) variants that cause a multisystem disorder. c.654-14T > A mutation induced mRNA mis-splicing, generating a peptide insertion in the active site; c.1519dupC swapped a critical tRNA-binding motif in the C-terminus due to stop codon readthrough. Both mutants exhibited severely diminished tRNA binding and aminoacylation capacities. A marked reduction in mitochondrial tRNASer(AGY) was observed due to RNA degradation in patient-derived induced pluripotent stem cells (iPSCs), causing impaired translation and comprehensive mitochondrial function deficiencies. These impairments were efficiently rescued by wild-type SARS2 overexpression. Either mutation caused early embryonic fatality in mice. Heterozygous mice displayed reduced muscle tissue-specific levels of tRNASers. Our findings elucidated the biochemical and cellular consequences of impaired translation mediated by SARS2, suggesting that reduced abundance of tRNASer(AGY) is a key determinant for development of SARS2-related diseases.
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Affiliation(s)
| | | | - Wen-Qiang Zheng
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
| | - Siqi Wu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Guoqiang Li
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Key Laboratory of Clinical Molecular Diagnostics for Pediatrics, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, 1678 Dong Fang Road, Shanghai 200127, China
| | - Yong Zhang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
| | - Niu Li
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Key Laboratory of Clinical Molecular Diagnostics for Pediatrics, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, 1678 Dong Fang Road, Shanghai 200127, China
| | - Ruen Yao
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Key Laboratory of Clinical Molecular Diagnostics for Pediatrics, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, 1678 Dong Fang Road, Shanghai 200127, China
| | - Pengfei Fang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Jian Wang
- Correspondence may also be addressed to Jian Wang. Tel: +86 21 3808 7371;
| | - Xiao-Long Zhou
- To whom correspondence should be addressed. Tel: +86 21 5492 1247; Fax: +86 21 5492 1011;
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16
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Exploration of Tools for the Interpretation of Human Non-Coding Variants. Int J Mol Sci 2022; 23:ijms232112977. [PMID: 36361767 PMCID: PMC9654743 DOI: 10.3390/ijms232112977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/17/2022] [Accepted: 10/23/2022] [Indexed: 02/01/2023] Open
Abstract
The advent of Whole Genome Sequencing (WGS) broadened the genetic variation detection range, revealing the presence of variants even in non-coding regions of the genome, which would have been missed using targeted approaches. One of the most challenging issues in WGS analysis regards the interpretation of annotated variants. This review focuses on tools suitable for the functional annotation of variants falling into non-coding regions. It couples the description of non-coding genomic areas with the results and performance of existing tools for a functional interpretation of the effect of variants in these regions. Tools were tested in a controlled genomic scenario, representing the ground-truth and allowing us to determine software performance.
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17
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Whole Genome Sequencing Applied in Familial Hamartomatous Polyposis Identifies Novel Structural Variations. Genes (Basel) 2022; 13:genes13081408. [PMID: 36011318 PMCID: PMC9407864 DOI: 10.3390/genes13081408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 08/03/2022] [Accepted: 08/04/2022] [Indexed: 11/25/2022] Open
Abstract
Hamartomatous polyposis syndromes (HPS) are rare cancer-predisposing disorders including Juvenile polyposis (JPS), Peutz–Jeghers (PJS) and PTEN hamartomatous syndromes (PHS). Penetrant mutations in corresponding genes (SMAD4, BMPR1A, STK11, PTEN and AKT1), are usually diagnosed via a next-generation-sequencing gene panel (NGS-GP) for tailored surveillance and preimplantation testing for monogenic disorders (PGT-M). Five probands with HPS phenotype, with no genetic diagnosis per genetic workup, underwent whole-genome sequencing (WGS) that identified structural genetic alterations: two novel inversions in BMPRA1 and STK11, two BMPR1A-deletions, known as founders among Bukharan Jews, and BMPR1A microdeletion. BMPR1A inversion was validated by “junction fragment” amplification and direct testing. PGT-M was performed via multiplex-PCR and enabled successful birth of a non-carrier baby. WGS may be considered for HPS patients with no NGS-GP findings to exclude structural alterations.
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18
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Mechanism of Action of Zhi Gan Cao Decoction for Atrial Fibrillation and Myocardial Fibrosis in a Mouse Model of Atrial Fibrillation: A Network Pharmacology-Based Study. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:4525873. [PMID: 35720023 PMCID: PMC9203184 DOI: 10.1155/2022/4525873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 05/06/2022] [Accepted: 05/11/2022] [Indexed: 11/29/2022]
Abstract
Atrial fibrillation (AF), a commonly seen cardiac disease without optimal curative treatment option, is usually treated by traditional Chinese medicine in China. The Zhi-Gan-Cao decoction (ZGCD) is an alternative medicine for clinical use and has definitive effects. It remains to be defined regarding the specific components and related mechanisms of ZGCD for the treatment of AF. We determined the primary constituents and major targets of the herbs in ZGCD using the TCMSP, HERB, and BATMAN-TCM databases. The UniProt databank database amended and combined the prospective names to supply objective data and records. Every target connected to AF was generated using the GeneCards databank, Drugbank database, TTD, Disgenet database, and OMIM. After identifying possible common targets between ZGCD and AF, the interface network illustration “ZGCD component-AF-target” was created using Cytoscape. We obtained 175 constituents and 839 targets for seven herbal drug categories in the ZGCD and identified 1008 targets of AF. After merging and removing repetitions, 136 collective targets between the ZGCD and AF were removed using the Cytoscape system. These renowned targets were generated from 38 suitable components from among the 157 components. GO enhancement examination and KEGG enrichment analysis by Metascape identified the close connection between the critical target genes and 20 signaling pathways. Then, we injected isoproterenol subcutaneously into the mouse and gave gavage with roasted licorice soup. Two weeks later, mouse were processed and sampled for testing. The results of HE and Masson staining showed that ZGCD effectively alleviated the degree of myocardial fibrosis. As indicated by qRT-PCR and Western blotting, ZGCD significantly reduced COL1A1, COL1A2, COL3A1, and TGF-β1 in myocardial fibrotic tissue to reduce myocardial fibrosis and treat AF by interfering with the expression of COL1A1, COL1A2, COL3A1, and TGF-β1 in myocardial tissue. ZGCD may treat AF by lowering the degree of myocardial fibrosis.
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19
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Matthews H, de Jong G, Maal T, Claes P. Static and Motion Facial Analysis for Craniofacial Assessment and Diagnosing Diseases. Annu Rev Biomed Data Sci 2022; 5:19-42. [PMID: 35440145 DOI: 10.1146/annurev-biodatasci-122120-111413] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Deviation from a normal facial shape and symmetry can arise from numerous sources, including physical injury and congenital birth defects. Such abnormalities can have important aesthetic and functional consequences. Furthermore, in clinical genetics distinctive facial appearances are often associated with clinical or genetic diagnoses; the recognition of a characteristic facial appearance can substantially narrow the search space of potential diagnoses for the clinician. Unusual patterns of facial movement and expression can indicate disturbances to normal mechanical functioning or emotional affect. Computational analyses of static and moving 2D and 3D images can serve clinicians and researchers by detecting and describing facial structural, mechanical, and affective abnormalities objectively. In this review we survey traditional and emerging methods of facial analysis, including statistical shape modeling, syndrome classification, modeling clinical face phenotype spaces, and analysis of facial motion and affect. Expected final online publication date for the Annual Review of Biomedical Data Science, Volume 5 is August 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Harold Matthews
- Department of Human Genetics, KU Leuven, Leuven, Belgium; .,Medical Imaging Research Center, UZ Leuven, Leuven, Belgium.,Facial Sciences Research Group, Murdoch Children's Research Institute, Parkville, Australia
| | - Guido de Jong
- 3D Lab, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Thomas Maal
- 3D Lab, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Peter Claes
- Department of Human Genetics, KU Leuven, Leuven, Belgium; .,Medical Imaging Research Center, UZ Leuven, Leuven, Belgium.,Facial Sciences Research Group, Murdoch Children's Research Institute, Parkville, Australia.,Processing Speech and Images (PSI), Department of Electrical Engineering (ESAT), KU Leuven, Leuven, Belgium
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20
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A machine learning approach based on ACMG/AMP guidelines for genomic variant classification and prioritization. Sci Rep 2022; 12:2517. [PMID: 35169226 PMCID: PMC8847497 DOI: 10.1038/s41598-022-06547-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 01/07/2022] [Indexed: 01/19/2023] Open
Abstract
Genomic variant interpretation is a critical step of the diagnostic procedure, often supported by the application of tools that may predict the damaging impact of each variant or provide a guidelines-based classification. We propose the application of Machine Learning methodologies, in particular Penalized Logistic Regression, to support variant classification and prioritization. Our approach combines ACMG/AMP guidelines for germline variant interpretation as well as variant annotation features and provides a probabilistic score of pathogenicity, thus supporting the prioritization and classification of variants that would be interpreted as uncertain by the ACMG/AMP guidelines. We compared different approaches in terms of variant prioritization and classification on different datasets, showing that our data-driven approach is able to solve more variant of uncertain significance (VUS) cases in comparison with guidelines-based approaches and in silico prediction tools.
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21
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Piryaei Z, Salehi Z, Tahsili MR, Ebrahimie E, Ebrahimi M, Kavousi K. Agonist/antagonist compounds' mechanism of action on estrogen receptor-positive breast cancer: A system-level investigation assisted by meta-analysis. INFORMATICS IN MEDICINE UNLOCKED 2022. [DOI: 10.1016/j.imu.2022.100985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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22
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He D, Li Y, Yang W, Chen S, Sun H, Li P, Zhang M, Ban B. Molecular diagnosis for growth hormone deficiency in Chinese children and adolescents and evaluation of impact of rare genetic variants on treatment efficacy of growth hormone. Clin Chim Acta 2022; 524:1-10. [PMID: 34826401 DOI: 10.1016/j.cca.2021.11.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 11/20/2021] [Indexed: 11/19/2022]
Abstract
BACKGROUND Growth hormone is an effective therapy for growth hormone deficiency (GHD) but with a rather variable individual sensitivity. It is unclear whether rare genetic variants may contribute to the differential GH responsiveness. METHODS The present study aims to investigate the molecular etiology of GHD in Chinese children and adolescents and evaluate the impact of rare variants on therapeutic efficacies of GH. RESULTS Twenty-one rare heterozygous variant were classified as promising uncertain significance (n = 14), pathogenic (n = 5) or likely pathogenic (n = 2) for 21 of the 93 GHD patients. After GHD patients harboring these rare variants were excluded, inter-individual variability in the response to GH therapy obviously reduced and the negative correlation between initiation age of treatment and height SDS change became stronger in the group without rare variants. Among rare variants, 7 (likely) pathogenic variants (7.5%, 7/93) involved a total of 6 genes not only associated with GH secretion (PROKR2, LZTR1), but also growth plate chondrocyte signaling (ACAN, FBN1, COL9A1) or genetic syndromes (PTPN11). CONCLUSIONS Rare genetic variants are an important factor contributing to differential GH responsiveness and genetic testing should be factored into accurate diagnosis and treatment decision making in the future. CLINICAL TRIAL REGISTRATION NUMBER ChiCTR1900026510.
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Affiliation(s)
- Dongye He
- Department of Endocrinology, Genetics and Metabolism, Affiliated Hospital of Jining Medical University, Jining, PR China; Medical Research Center, Affiliated Hospital of Jining Medical University, Jining, PR China; Chinese Research Center for Behavior Medicine in Growth and Development, Jining, PR China
| | - Yanying Li
- Department of Endocrinology, Genetics and Metabolism, Affiliated Hospital of Jining Medical University, Jining, PR China; Chinese Research Center for Behavior Medicine in Growth and Development, Jining, PR China
| | - Wanling Yang
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, PR China
| | - Shuxiong Chen
- Department of Endocrinology, Genetics and Metabolism, Affiliated Hospital of Jining Medical University, Jining, PR China; Medical Research Center, Affiliated Hospital of Jining Medical University, Jining, PR China; Chinese Research Center for Behavior Medicine in Growth and Development, Jining, PR China
| | - Hailing Sun
- Department of Endocrinology, Genetics and Metabolism, Affiliated Hospital of Jining Medical University, Jining, PR China; Chinese Research Center for Behavior Medicine in Growth and Development, Jining, PR China
| | - Ping Li
- Department of Endocrinology, Genetics and Metabolism, Affiliated Hospital of Jining Medical University, Jining, PR China; Chinese Research Center for Behavior Medicine in Growth and Development, Jining, PR China
| | - Mei Zhang
- Department of Endocrinology, Genetics and Metabolism, Affiliated Hospital of Jining Medical University, Jining, PR China; Chinese Research Center for Behavior Medicine in Growth and Development, Jining, PR China.
| | - Bo Ban
- Department of Endocrinology, Genetics and Metabolism, Affiliated Hospital of Jining Medical University, Jining, PR China; Medical Research Center, Affiliated Hospital of Jining Medical University, Jining, PR China; Chinese Research Center for Behavior Medicine in Growth and Development, Jining, PR China.
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23
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Deng L, Xu J, Chen W, Guo S, Steiner RD, Chen Q, Cheng Z, Xu Y, Yao B, Li X, Wang X, Deng K, Schrodi SJ, Zhang D, Xin H. Remediation of ABCG5-Linked Macrothrombocytopenia With Ezetimibe Therapy. Front Genet 2021; 12:769699. [PMID: 34880906 PMCID: PMC8645579 DOI: 10.3389/fgene.2021.769699] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 10/21/2021] [Indexed: 11/29/2022] Open
Abstract
To investigate refractory hypercholesterolemia, a female patient and relatives were subjected to whole-genome sequencing. The proband was found to have compound heterozygous substitutions p. Arg446Gln and c.1118+3G>T in ABCG5, one of two genes causing sitosterolemia. When tracing these variants in the full pedigree, all maternally related heterozygotes for the intronic ABCG5 variant exhibited large platelets (over 30 fl), which segregated in an autosomal dominant manner, consistent with macrothrombocytopenia, or large platelet syndrome which may be associated with a bleeding tendency. In vitro cell-line and in vivo rat model experiments supported a pathogenic role for the variant and the macrothrombocytopenia was recapitulated in heterozygous rats and human cell lines exhibiting that single variant. Ezetimibe treatment successfully ameliorated all the symptoms of the proband with sitosterolemia and resolved the macrothrombocytopenia of the treated heterozygote relatives. Subsequently, in follow up these observations, platelet size, and size distribution were measured in 1,180 individuals; 30 were found to be clinically abnormal, three of which carried a single known pathogenic ABCG5 variant (p.Arg446Ter) and two individuals carried novel ABCG5 variants of uncertain significance. In this study, we discovered that identification of large platelets and therefore a possible macrothrombocytopenia diagnosis could easily be inadvertently missed in clinical practice due to variable instrument settings. These findings suggest that ABCG5 heterozygosity may cause macrothrombocytopenia, that Ezetimibe treatment may resolve macrothrombocytopenia in such individuals, and that increased attention to platelet size on complete blood counts can aid in the identification of candidates for ABCG5 genetic testing who might benefit from Ezetimibe treatment.
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Affiliation(s)
- Libin Deng
- The Second Affiliated Hospital of Nanchang University, Nanchang, China.,Institute of Translational Medicine, Nanchang University, Nanchang, China.,Jiangxi Provincial Key Laboratory of Preventive Medicine, School of Public Health, Nanchang University, Nanchang, China
| | - Jingsong Xu
- The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Wei Chen
- Key Laboratory of Biomechanics and Mechanobiology, Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, China
| | - Shicheng Guo
- Department of Medical Genetics, University of Wisconsin-Madison, Madison, WI, United States
| | - Robert D Steiner
- Department of Pediatrics, University of Wisconsin-Madison, Madison, WI, United States
| | - Qi Chen
- The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Zhujun Cheng
- Institute of Translational Medicine, Nanchang University, Nanchang, China
| | - Yanmei Xu
- The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Bei Yao
- Department of Clinical Laboratory, Peking University Third Hospital, Beijing, China
| | - Xiaoyan Li
- Beijing Institute of Heart, Lung & Blood Vessel Disease, Beijing Anzhen Hospital, Capital Medical University, Beijing, China
| | - Xiaozhong Wang
- The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Keyu Deng
- Institute of Translational Medicine, Nanchang University, Nanchang, China
| | - Steven J Schrodi
- Department of Medical Genetics, University of Wisconsin-Madison, Madison, WI, United States
| | - Dake Zhang
- Key Laboratory of Biomechanics and Mechanobiology, Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, China
| | - Hongbo Xin
- Institute of Translational Medicine, Nanchang University, Nanchang, China
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24
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Borchert F, Mock A, Tomczak A, Hügel J, Alkarkoukly S, Knurr A, Volckmar AL, Stenzinger A, Schirmacher P, Debus J, Jäger D, Longerich T, Fröhling S, Eils R, Bougatf N, Sax U, Schapranow MP. Knowledge bases and software support for variant interpretation in precision oncology. Brief Bioinform 2021; 22:bbab134. [PMID: 33971666 PMCID: PMC8574624 DOI: 10.1093/bib/bbab134] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 03/10/2021] [Accepted: 03/30/2021] [Indexed: 12/12/2022] Open
Abstract
Precision oncology is a rapidly evolving interdisciplinary medical specialty. Comprehensive cancer panels are becoming increasingly available at pathology departments worldwide, creating the urgent need for scalable cancer variant annotation and molecularly informed treatment recommendations. A wealth of mainly academia-driven knowledge bases calls for software tools supporting the multi-step diagnostic process. We derive a comprehensive list of knowledge bases relevant for variant interpretation by a review of existing literature followed by a survey among medical experts from university hospitals in Germany. In addition, we review cancer variant interpretation tools, which integrate multiple knowledge bases. We categorize the knowledge bases along the diagnostic process in precision oncology and analyze programmatic access options as well as the integration of knowledge bases into software tools. The most commonly used knowledge bases provide good programmatic access options and have been integrated into a range of software tools. For the wider set of knowledge bases, access options vary across different parts of the diagnostic process. Programmatic access is limited for information regarding clinical classifications of variants and for therapy recommendations. The main issue for databases used for biological classification of pathogenic variants and pathway context information is the lack of standardized interfaces. There is no single cancer variant interpretation tool that integrates all identified knowledge bases. Specialized tools are available and need to be further developed for different steps in the diagnostic process.
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Affiliation(s)
- Florian Borchert
- Digital Health Center, Hasso Plattner Institute (HPI), University of Potsdam, Prof.-Dr.-Helmert-Str. 2-3, 14482 Potsdam, Germany
| | - Andreas Mock
- Department of Translational Medical Oncology (TMO), National Center for Tumor Diseases (NCT) Heidelberg, German Cancer Research Center (DKFZ) Heidelberg, Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
- Department of Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg University Hospital, Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
| | - Aurelie Tomczak
- Institute of Pathology Heidelberg, Heidelberg University Hospital, Im Neuenheimer Feld 224, 69120 Heidelberg, Germany
- Liver Cancer Center Heidelberg, Heidelberg University Hospital, Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
| | - Jonas Hügel
- Department of Medical Informatics, University Medical Center Göttingen, Von-Siebold-Str. 3, 37099 Göttingen, Germany
- Campus Institute Data Science, Göttingen, Germany
| | - Samer Alkarkoukly
- CECAD, Faculty of Medicine and University Hospital Cologne, University of Cologne, Joseph-Stelzmann-Straße 26, 50931 Cologne
| | - Alexander Knurr
- Division of Medical Informatics for Translational Oncology, German Cancer Research Center (DKFZ) Heidelberg, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Anna-Lena Volckmar
- Institute of Pathology Heidelberg, Heidelberg University Hospital, Im Neuenheimer Feld 224, 69120 Heidelberg, Germany
| | - Albrecht Stenzinger
- Institute of Pathology Heidelberg, Heidelberg University Hospital, Im Neuenheimer Feld 224, 69120 Heidelberg, Germany
| | - Peter Schirmacher
- Institute of Pathology Heidelberg, Heidelberg University Hospital, Im Neuenheimer Feld 224, 69120 Heidelberg, Germany
- Liver Cancer Center Heidelberg, Heidelberg University Hospital, Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
| | - Jürgen Debus
- Department of Radiation Oncology, Heidelberg University Hospital, Im Neuenheimer Feld 400, 69120 Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg University Hospital, Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
- Clinical Cooperation Unit Radiation Oncology, German Cancer Research Center (DKFZ) Heidelberg, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
- Heidelberg Ion-Beam Therapy Center (HIT), Department of Radiation Oncology, Heidelberg University Hospital, Im Neuenheimer Feld 450, 69120 Heidelberg, Germany
- Heidelberg Institute of Radiation Oncology (HIRO), Heidelberg University Hospital, Im Neuenheimer Feld 400, 69120 Heidelberg, Germany
| | - Dirk Jäger
- Department of Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg University Hospital, Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
- Clinical Coorporation Unit Applied Tumor-Immunity, German Cancer Research Center (DKFZ) Heidelberg, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Thomas Longerich
- Institute of Pathology Heidelberg, Heidelberg University Hospital, Im Neuenheimer Feld 224, 69120 Heidelberg, Germany
- Liver Cancer Center Heidelberg, Heidelberg University Hospital, Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
| | - Stefan Fröhling
- Department of Translational Medical Oncology (TMO), National Center for Tumor Diseases (NCT) Heidelberg, German Cancer Research Center (DKFZ) Heidelberg, Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Roland Eils
- Health Data Science Unit, Heidelberg University Hospital, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
- Center for Digital Health, Berlin Institute of Health and Charité Universitötsmedizin Berlin, Kapelle-Ufer 2, 10117 Berlin, Germany
| | - Nina Bougatf
- Department of Radiation Oncology, Heidelberg University Hospital, Im Neuenheimer Feld 400, 69120 Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg University Hospital, Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
- Clinical Cooperation Unit Radiation Oncology, German Cancer Research Center (DKFZ) Heidelberg, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
- Heidelberg Ion-Beam Therapy Center (HIT), Department of Radiation Oncology, Heidelberg University Hospital, Im Neuenheimer Feld 450, 69120 Heidelberg, Germany
- Heidelberg Institute of Radiation Oncology (HIRO), Heidelberg University Hospital, Im Neuenheimer Feld 400, 69120 Heidelberg, Germany
| | - Ulrich Sax
- Department of Medical Informatics, University Medical Center Göttingen, Von-Siebold-Str. 3, 37099 Göttingen, Germany
- Campus Institute Data Science, Göttingen, Germany
| | - Matthieu-P Schapranow
- Digital Health Center, Hasso Plattner Institute (HPI), University of Potsdam, Prof.-Dr.-Helmert-Str. 2-3, 14482 Potsdam, Germany
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25
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Kim SY, Lee S, Seo GH, Kim BJ, Oh DY, Han JH, Park MK, Lee SM, Kim B, Yi N, Kim NJ, Koh DH, Hwang S, Keum C, Choi BY. Powerful use of automated prioritization of candidate variants in genetic hearing loss with extreme etiologic heterogeneity. Sci Rep 2021; 11:19476. [PMID: 34593925 PMCID: PMC8484668 DOI: 10.1038/s41598-021-99007-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 08/17/2021] [Indexed: 01/02/2023] Open
Abstract
Variant prioritization of exome sequencing (ES) data for molecular diagnosis of sensorineural hearing loss (SNHL) with extreme etiologic heterogeneity poses a significant challenge. This study used an automated variant prioritization system (“EVIDENCE”) to analyze SNHL patient data and assess its diagnostic accuracy. We performed ES of 263 probands manifesting mild to moderate or higher degrees of SNHL. Candidate variants were classified according to the 2015 American College of Medical Genetics guidelines, and we compared the accuracy, call rates, and efficiency of variant prioritizations performed manually by humans or using EVIDENCE. In our in silico panel, 21 synthetic cases were successfully analyzed by EVIDENCE. In our cohort, the ES diagnostic yield for SNHL by manual analysis was 50.19% (132/263) and 50.95% (134/263) by EVIDENCE. EVIDENCE processed ES data 24-fold faster than humans, and the concordant call rate between humans and EVIDENCE was 97.72% (257/263). Additionally, EVIDENCE outperformed human accuracy, especially at discovering causative variants of rare syndromic deafness, whereas flexible interpretations that required predefined specific genotype–phenotype correlations were possible only by manual prioritization. The automated variant prioritization system remarkably facilitated the molecular diagnosis of hearing loss with high accuracy and efficiency, fostering the popularization of molecular genetic diagnosis of SNHL.
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Affiliation(s)
- So Young Kim
- Department of Otorhinolaryngology-Head and Neck Surgery, CHA Bundang Medical Center, CHA University, Seongnam, Republic of Korea
| | - Seungmin Lee
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seongnam, Republic of Korea.,R&D Center, ENCell Co. Ltd, Seoul, Republic of Korea
| | - Go Hun Seo
- 3billion, Inc., Seoul, Republic of Korea
| | - Bong Jik Kim
- Department of Otolaryngology-Head and Neck Surgery, Chungnam National University Sejong Hospital, College of Medicine, Chungnam National University, Daejeon, Republic of Korea
| | - Doo Yi Oh
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Jin Hee Han
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Moo Kyun Park
- Department of Otorhinolaryngology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - So Min Lee
- Department of Otorhinolaryngology-Head and Neck Surgery, CHA Bundang Medical Center, CHA University, Seongnam, Republic of Korea
| | - Bonggi Kim
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Nayoung Yi
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Namju Justin Kim
- Department of Biological Sciences, Vanderbilt University, Nashville, USA
| | - Doo Hyun Koh
- Department of Biomedical Science, The Graduate School, CHA University, Seongnam, Republic of Korea
| | - Sohyun Hwang
- Department of Biomedical Science, The Graduate School, CHA University, Seongnam, Republic of Korea.,Department of Pathology, CHA University, CHA Bundang Medical Center, Seongnam, Republic of Korea
| | | | - Byung Yoon Choi
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seongnam, Republic of Korea.
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26
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Daum H, Ganapathi M, Hirsch Y, Griffin EL, LeDuc CA, Hagen J, Yagel S, Meiner V, Chung WK, Mor-Shaked H. Bi-allelic PAGR1 variants are associated with microcephaly and a severe neurodevelopmental disorder: Genetic evidence from two families. Am J Med Genet A 2021; 188:336-342. [PMID: 34585832 DOI: 10.1002/ajmg.a.62513] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 08/23/2021] [Accepted: 08/26/2021] [Indexed: 11/05/2022]
Abstract
Exome and genome sequencing were used to identify the genetic etiology of a severe neurodevelopmental disorder in two unrelated Ashkenazi Jewish families with three affected individuals. The clinical findings included a prenatal presentation of microcephaly, polyhydramnios and clenched hands while postnatal findings included microcephaly, severe developmental delay, dysmorphism, neurologic deficits, and death in infancy. A shared rare homozygous, missense variant (c.274A > G; p.Ser92Gly, NM_024516.4) was identified in PAGR1, a gene currently not associated with a Mendelian disease. PAGR1 encodes a component of the histone methyltransferase MLL2/MLL3 complex and may function in the DNA damage response pathway. Complete knockout of the murine Pagr1a is embryonic-lethal. Given the available evidence, PAGR1 is a strong candidate gene for a novel autosomal recessive severe syndromic neurodevelopmental disorder.
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Affiliation(s)
- Hagit Daum
- Department of Genetics, Hadassah Medical Organization and Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Mythily Ganapathi
- Department of Pathology & Cell Biology, Columbia University, New York, New York, USA
| | - Yoel Hirsch
- Dor Yeshorim, Committee for Prevention of Jewish Genetic Diseases, Brooklyn, New York, USA
| | - Emily L Griffin
- Department of Pediatrics, Columbia University, New York, New York, USA
| | - Charles A LeDuc
- Department of Pediatrics, Columbia University, New York, New York, USA
| | - Jacob Hagen
- Department of Pediatrics, Columbia University, New York, New York, USA
| | - Simcha Yagel
- Obstetrics and gynecology, Hadassah Medical Organization and Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Vardiella Meiner
- Department of Genetics, Hadassah Medical Organization and Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University, New York, New York, USA
| | - Hagar Mor-Shaked
- Department of Genetics, Hadassah Medical Organization and Faculty of Medicine, Hebrew University of Jerusalem, Israel
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27
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Mor-Shaked H, Paz-Ebstein E, Basal A, Ben-Haim S, Grobe H, Heymann S, Israel Z, Namnah M, Nitzan A, Rosenbluh C, Saada A, Tzur T, Yanovsky-Dagan S, Zaidel-Bar R, Harel T, Arkadir D. Levodopa-responsive dystonia caused by biallelic PRKN exon inversion invisible to exome sequencing. Brain Commun 2021; 3:fcab197. [PMID: 34514401 PMCID: PMC8421701 DOI: 10.1093/braincomms/fcab197] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 06/20/2021] [Accepted: 07/05/2021] [Indexed: 11/23/2022] Open
Abstract
Biallelic pathogenic variants in PRKN (PARK2), encoding the E3 ubiquitin ligase parkin, lead to early-onset Parkinson's disease. Structural variants, including duplications or deletions, are common in PRKN due to their location within the fragile site FRA6E. These variants are readily detectable by copy number variation analysis. We studied four siblings with levodopa-responsive dystonia by exome sequencing followed by genome sequencing. Affected individuals developed juvenile levodopa-responsive dystonia with subsequent appearance of parkinsonism and motor fluctuations that improved by subthalamic stimulation. Exome sequencing and copy number variation analysis were not diagnostic, yet revealed a shared homozygous block including PRKN. Genome sequencing revealed an inversion within PRKN, with intronic breakpoints flanking exon 5. Breakpoint junction analysis implicated non-homologous end joining and possibly replicative mechanisms as the repair pathways involved. Analysis of cDNA indicated skipping of exon 5 (84 bp) that was replaced by 93 bp of retained intronic sequence, preserving the reading frame yet altering a significant number of residues. Balanced copy number inversions in PRKN are associated with a severe phenotype. Such structural variants, undetected by exome analysis and by copy number variation analysis, should be considered in the relevant clinical setting. These findings raise the possibility that PRKN structural variants are more common than currently estimated.
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Affiliation(s)
- Hagar Mor-Shaked
- Department of Genetics, Hadassah Medical Organization, Jerusalem 91120, Israel.,Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Emuna Paz-Ebstein
- Department of Genetics, Hadassah Medical Organization, Jerusalem 91120, Israel.,Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Adily Basal
- Department of Genetics, Hadassah Medical Organization, Jerusalem 91120, Israel
| | - Simona Ben-Haim
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel.,Department of Nuclear Medicine, Hadassah Medical Organization, Jerusalem 91120, Israel.,Institute of Nuclear Medicine, University College London and UCL Hospitals, NHS Trust, London NW1 2BU, UK
| | - Hanna Grobe
- Department of Cell and Developmental Biology, Faculty of Medicine, Tel Aviv University, Tel Aviv-Yafo 69978, Israel
| | - Sami Heymann
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel.,Department of Neurosurgery, Hadassah Medical Organization, Jerusalem 91120, Israel
| | - Zvi Israel
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel.,Department of Neurosurgery, Hadassah Medical Organization, Jerusalem 91120, Israel
| | - Montaser Namnah
- Department of Neurology, Hadassah Medical Organization, Jerusalem 91120, Israel
| | - Anat Nitzan
- Department of Cell and Developmental Biology, Faculty of Medicine, Tel Aviv University, Tel Aviv-Yafo 69978, Israel
| | - Chaggai Rosenbluh
- Department of Genetics, Hadassah Medical Organization, Jerusalem 91120, Israel
| | - Ann Saada
- Department of Genetics, Hadassah Medical Organization, Jerusalem 91120, Israel.,Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Tomer Tzur
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel.,Department of Plastic Surgery, Hadassah Medical Organization, Jerusalem 91120, Israel
| | | | - Ronen Zaidel-Bar
- Department of Cell and Developmental Biology, Faculty of Medicine, Tel Aviv University, Tel Aviv-Yafo 69978, Israel
| | - Tamar Harel
- Department of Genetics, Hadassah Medical Organization, Jerusalem 91120, Israel.,Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - David Arkadir
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel.,Department of Neurology, Hadassah Medical Organization, Jerusalem 91120, Israel
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28
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Nieboer MM, Nguyen L, de Ridder J. Predicting pathogenic non-coding SVs disrupting the 3D genome in 1646 whole cancer genomes using multiple instance learning. Sci Rep 2021; 11:14411. [PMID: 34257393 PMCID: PMC8277903 DOI: 10.1038/s41598-021-93917-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 07/01/2021] [Indexed: 11/21/2022] Open
Abstract
Over the past years, large consortia have been established to fuel the sequencing of whole genomes of many cancer patients. Despite the increased abundance in tools to study the impact of SNVs, non-coding SVs have been largely ignored in these data. Here, we introduce svMIL2, an improved version of our Multiple Instance Learning-based method to study the effect of somatic non-coding SVs disrupting boundaries of TADs and CTCF loops in 1646 cancer genomes. We demonstrate that svMIL2 predicts pathogenic non-coding SVs with an average AUC of 0.86 across 12 cancer types, and identifies non-coding SVs affecting well-known driver genes. The disruption of active (super) enhancers in open chromatin regions appears to be a common mechanism by which non-coding SVs exert their pathogenicity. Finally, our results reveal that the contribution of pathogenic non-coding SVs as opposed to driver SNVs may highly vary between cancers, with notably high numbers of genes being disrupted by pathogenic non-coding SVs in ovarian and pancreatic cancer. Taken together, our machine learning method offers a potent way to prioritize putatively pathogenic non-coding SVs and leverage non-coding SVs to identify driver genes. Moreover, our analysis of 1646 cancer genomes demonstrates the importance of including non-coding SVs in cancer diagnostics.
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Affiliation(s)
- Marleen M Nieboer
- Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Luan Nguyen
- Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Jeroen de Ridder
- Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG, Utrecht, The Netherlands.
- Oncode Institute, Utrecht, The Netherlands.
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29
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Han Q, Yang Y, Wu S, Liao Y, Zhang S, Liang H, Cram DS, Zhang Y. Cruxome: a powerful tool for annotating, interpreting and reporting genetic variants. BMC Genomics 2021; 22:407. [PMID: 34082700 PMCID: PMC8173893 DOI: 10.1186/s12864-021-07728-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 05/20/2021] [Indexed: 01/23/2023] Open
Abstract
Background Next-generation sequencing (NGS) is an efficient tool used for identifying pathogenic variants that cause Mendelian disorders. However, the lack of bioinformatics training of researchers makes the interpretation of identified variants a challenge in terms of precision and efficiency. In addition, the non-standardized phenotypic description of human diseases also makes it difficult to establish an integrated analysis pathway for variant annotation and interpretation. Solutions to these bottlenecks are urgently needed. Results We develop a tool named “Cruxome” to automatically annotate and interpret single nucleotide variants (SNVs) and small insertions and deletions (InDels). Our approach greatly simplifies the current burdensome task of clinical geneticists and scientists to identify the causative pathogenic variants and build personal knowledge reference bases. The integrated architecture of Cruxome offers key advantages such as an interactive and user-friendly interface and the assimilation of electronic health records of the patient. By combining a natural language processing algorithm, Cruxome can efficiently process the clinical description of diseases to HPO standardized vocabularies. By using machine learning, in silico predictive algorithms, integrated multiple databases and supplementary tools, Cruxome can automatically process SNVs and InDels variants (trio-family or proband-only cases) and clinical diagnosis records, then annotate, score, identify and interpret pathogenic variants to finally generate a standardized clinical report following American College of Medical Genetics and Genomics/ Association for Molecular Pathology (ACMG/AMP) guidelines. Cruxome also provides supplementary tools to examine and visualize the genes or variations in historical cases, which can help to better understand the genetic basis of the disease. Conclusions Cruxome is an efficient tool for annotation and interpretation of variations and dramatically reduces the workload for clinical geneticists and researchers to interpret NGS results, simplifying their decision-making processes. We present an online version of Cruxome, which is freely available to academics and clinical researchers. The site is accessible at http://114.251.61.49:10024/cruxome/. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07728-6.
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Affiliation(s)
- Qingmei Han
- Berry Genomics Company Limited, Building 5, Courtyard 4, Shengmingyuan Road, ZGC Life Science Park, Changping District, 102200, Beijing, China
| | - Ying Yang
- Xian Children's Hospital, 710003, Xian, China
| | - Shengyang Wu
- Berry Genomics Company Limited, Building 5, Courtyard 4, Shengmingyuan Road, ZGC Life Science Park, Changping District, 102200, Beijing, China
| | - Yingchun Liao
- Berry Genomics Company Limited, Building 5, Courtyard 4, Shengmingyuan Road, ZGC Life Science Park, Changping District, 102200, Beijing, China
| | - Shuang Zhang
- Berry Genomics Company Limited, Building 5, Courtyard 4, Shengmingyuan Road, ZGC Life Science Park, Changping District, 102200, Beijing, China
| | - Hongbin Liang
- Berry Genomics Company Limited, Building 5, Courtyard 4, Shengmingyuan Road, ZGC Life Science Park, Changping District, 102200, Beijing, China
| | - David S Cram
- Berry Genomics Company Limited, Building 5, Courtyard 4, Shengmingyuan Road, ZGC Life Science Park, Changping District, 102200, Beijing, China.
| | - Yu Zhang
- Berry Genomics Company Limited, Building 5, Courtyard 4, Shengmingyuan Road, ZGC Life Science Park, Changping District, 102200, Beijing, China.
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30
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Li WH, Han JR, Ren PP, Xie Y, Jiang DY. Exploration of the mechanism of Zisheng Shenqi decoction against gout arthritis using network pharmacology. Comput Biol Chem 2020; 90:107358. [PMID: 33243703 DOI: 10.1016/j.compbiolchem.2020.107358] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 07/14/2020] [Accepted: 08/05/2020] [Indexed: 12/29/2022]
Abstract
BACKGROUND In this study, the network pharmacological methods were used to predict the target of effective components of compounds in Zisheng Shenqi Decoction (ZSD, or Nourishing Kidney Qi Decoction) in the treatment of gouty arthritis (GA). METHOD The main effective components and corresponding key targets of herbs in the ZSD were discerned through the Traditional Chinese Medicine Systems Pharmacology Database and Analysis (TCMSP), Bioinformatics Analysis Tool for Molecular mechanism of Traditional Chinese Medicine (BATMAN-TCM) database. UniProt database and Swiss Target Prediction (STP) database was used to rectify and unify the target names and supply the target information. The targets related to GA were obtained by using GeneCards database. After we discovered the potential common targets between ZSD and GA, the interaction network diagram of "ZSD-component-GA-target" was constructed by Cytoscape software (Version 3.7.1). Subsequently, the Protein-protein interaction (PPI) network of ZSD effective components-targets and GA-related targets was constructed by Search Tool for the Retrieval of Interacting Genes Database (STRING). Bioconductor package "org.Hs.eg.db" and "cluster profiler" package were installed in R software (Version 3.6.0) which used for Gene Ontology analysis and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment analysis. RESULTS 146 components and 613 targets of 11 herbal medicines in the ZSD were got from TCMSP database and BATMAN-TCM database. 987 targets of GA were obtained from GeneCards database. After intersected and removed duplications, 132 common targets between ZSD and GA were screened out by Cytoscape software (Version 3.7.1). These common targets derived from 81 effective components of 146 components, such as quercetin, stigmasterol and kaempferol. They were closely related to anti-inflammatory, analgesic and anti oxidative stress and the principal targets comprised of Purinergic receptor P2X, ligand-gated ion channel 7 (P2x7R), Nod-like receptor protein 3 (NLRP3) and IL-1β. GO enrichment analysis and KEGG pathway enrichment analysis by R software (Version 3.6.0) showed that the key target genes had close relationship with oxidative stress, reactive oxygen species (ROS) metabolic process and leukocyte migration in aspects of biological process, cell components and molecular function. It also indicated that ZSD could decrease inflammatory reaction, alleviate ROS accumulation and attenuate pain by regulating P2 × 7R and NOD like receptor signaling pathway of inflammatory reaction. CONCLUSION A total of 81 effective components and 132 common target genes between ZSD and GA were screened by network pharmacology. The PPI network, GO enrichment analysis and KEGG pathway enrichment analysis suggested that ZSD can exerte anti-inflammatory and analgesic effects on the treatment of GA by reducing decreasing inflammatory reaction, alleviating ROS accumulation, and attenuating pain. The possible molecular mechanism of it mainly involved multiple components, multiple targets and multiple signaling pathways, which provided a comprehensive understanding for further study. In general, the network pharmacological method applied in this study provides an alternative strategy for the mechanism of ZSD in the treatment of GA.
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Affiliation(s)
- Wen-Hao Li
- Department of Synopsis of The Golden Chamber, School of Basic Medical Sciences, Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang, 150040, China.
| | - Jie-Ru Han
- Department of Synopsis of The Golden Chamber, School of Basic Medical Sciences, Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang, 150040, China.
| | - Peng-Peng Ren
- Department of Integrated Chinese and Western medicine, First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, 150001, China.
| | - Ying Xie
- Department of Synopsis of The Golden Chamber, School of Basic Medical Sciences, Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang, 150040, China.
| | - De-You Jiang
- Department of Synopsis of The Golden Chamber, School of Basic Medical Sciences, Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang, 150040, China.
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