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Tran DC, Phan MN, Dao HTT, Nguyen HDL, Nguyen DA, Le QT, Hoang DTT, Tran NT, Thi Ha TM, Dinh TL, Nguyen CC, Thi Doan KP, Thi Luong LA, Vo TS, Nhat Trinh TH, Nguyen VT, Vo PAN, Nguyen YN, Dinh MA, Doan PL, Do TTT, Nguyen QTT, Truong DK, Nguyen HN, Phan MD, Tang HS, Giang H. The genetic landscape of chromosomal aberrations in 3776 Vietnamese fetuses with clinical anomalies during pregnancy. Per Med 2024. [PMID: 38573622 DOI: 10.2217/pme-2023-0113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
Background: Copy number variation sequencing (CNV-seq) is a powerful tool to discover structural genomic variation, but limitations associated with its retrospective study design and inadequate diversity of participants can be impractical for clinical application. Aim: This study aims to use CNV-seq to assess chromosomal aberrations in pregnant Vietnamese women. Materials & methods: A large-scale study was conducted on 3776 pregnant Vietnamese women with abnormal ultrasound findings. Results: Chromosomal aberrations were found in 448 (11.86%) women. Of these, 274 (7.26%) had chromosomal aneuploidies and 174 (4.61%) carried pathogenic/likely pathogenic CNVs. Correlations were established between chromosomal aberrations and various phenotypic markers. Conclusion: This comprehensive clinical study illuminates the pivotal role of CNV-seq in prenatal diagnosis for pregnancies featuring fetal ultrasound anomalies.
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Affiliation(s)
- Danh-Cuong Tran
- National Hospital of Obstetrics & Gynecology, Ha Noi, Vietnam
| | - Minh Ngoc Phan
- Gene Solutions, Ho Chi Minh, Vietnam
- Medical Genetics Institutes, Ho Chi Minh, Vietnam
| | - Hong-Thuy Thi Dao
- Gene Solutions, Ho Chi Minh, Vietnam
- Medical Genetics Institutes, Ho Chi Minh, Vietnam
| | - Hong-Dang Luu Nguyen
- Gene Solutions, Ho Chi Minh, Vietnam
- Medical Genetics Institutes, Ho Chi Minh, Vietnam
| | | | | | | | - Nhat Thang Tran
- University Medical Center, Ho Chi Minh, Vietnam
- University of Medicine & Pharmacy at Ho Chi Minh City, Vietnam
| | | | | | | | | | | | | | | | | | - Phuong-Anh Ngoc Vo
- Gene Solutions, Ho Chi Minh, Vietnam
- Medical Genetics Institutes, Ho Chi Minh, Vietnam
| | - Yen-Nhi Nguyen
- Gene Solutions, Ho Chi Minh, Vietnam
- Medical Genetics Institutes, Ho Chi Minh, Vietnam
| | - My-An Dinh
- Gene Solutions, Ho Chi Minh, Vietnam
- Medical Genetics Institutes, Ho Chi Minh, Vietnam
| | - Phuoc-Loc Doan
- Gene Solutions, Ho Chi Minh, Vietnam
- Medical Genetics Institutes, Ho Chi Minh, Vietnam
| | | | | | | | - Hoai-Nghia Nguyen
- Medical Genetics Institutes, Ho Chi Minh, Vietnam
- University of Medicine & Pharmacy at Ho Chi Minh City, Vietnam
| | - Minh-Duy Phan
- Gene Solutions, Ho Chi Minh, Vietnam
- Medical Genetics Institutes, Ho Chi Minh, Vietnam
| | - Hung-Sang Tang
- Gene Solutions, Ho Chi Minh, Vietnam
- Medical Genetics Institutes, Ho Chi Minh, Vietnam
| | - Hoa Giang
- Gene Solutions, Ho Chi Minh, Vietnam
- Medical Genetics Institutes, Ho Chi Minh, Vietnam
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Nguyen VTC, Nguyen TH, Doan NNT, Pham TMQ, Nguyen GTH, Nguyen TD, Tran TTT, Vo DL, Phan TH, Jasmine TX, Nguyen VC, Nguyen HT, Nguyen TV, Nguyen THH, Huynh LAK, Tran TH, Dang QT, Doan TN, Tran AM, Nguyen VH, Nguyen VTA, Ho LMQ, Tran QD, Pham TTT, Ho TD, Nguyen BT, Nguyen TNV, Nguyen TD, Phu DTB, Phan BHH, Vo TL, Nai THT, Tran TT, Truong MH, Tran NC, Le TK, Tran THT, Duong ML, Bach HPT, Kim VV, Pham TA, Tran DH, Le TNA, Pham TVN, Le MT, Vo DH, Tran TMT, Nguyen MN, Van TTV, Nguyen AN, Tran TT, Tran VU, Le MP, Do TT, Phan TV, Nguyen HDL, Nguyen DS, Cao VT, Do TTT, Truong DK, Tang HS, Giang H, Nguyen HN, Phan MD, Tran LS. Multimodal analysis of methylomics and fragmentomics in plasma cell-free DNA for multi-cancer early detection and localization. eLife 2023; 12:RP89083. [PMID: 37819044 PMCID: PMC10567114 DOI: 10.7554/elife.89083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023] Open
Abstract
Despite their promise, circulating tumor DNA (ctDNA)-based assays for multi-cancer early detection face challenges in test performance, due mostly to the limited abundance of ctDNA and its inherent variability. To address these challenges, published assays to date demanded a very high-depth sequencing, resulting in an elevated price of test. Herein, we developed a multimodal assay called SPOT-MAS (screening for the presence of tumor by methylation and size) to simultaneously profile methylomics, fragmentomics, copy number, and end motifs in a single workflow using targeted and shallow genome-wide sequencing (~0.55×) of cell-free DNA. We applied SPOT-MAS to 738 non-metastatic patients with breast, colorectal, gastric, lung, and liver cancer, and 1550 healthy controls. We then employed machine learning to extract multiple cancer and tissue-specific signatures for detecting and locating cancer. SPOT-MAS successfully detected the five cancer types with a sensitivity of 72.4% at 97.0% specificity. The sensitivities for detecting early-stage cancers were 73.9% and 62.3% for stages I and II, respectively, increasing to 88.3% for non-metastatic stage IIIA. For tumor-of-origin, our assay achieved an accuracy of 0.7. Our study demonstrates comparable performance to other ctDNA-based assays while requiring significantly lower sequencing depth, making it economically feasible for population-wide screening.
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Tran VT, Nguyen ST, Pham XD, Phan TH, Nguyen VC, Nguyen HT, Nguyen HP, Doan PTT, Le TA, Nguyen BT, Jasmine TX, Nguyen DS, Nguyen HDL, Nguyen NM, Do DX, Tran VU, Nguyen HHT, Le MP, Nguyen YN, Do TTT, Truong DK, Tang HS, Phan MD, Nguyen HN, Giang H, Tu LN. Pathogenic Variant Profile of Hereditary Cancer Syndromes in a Vietnamese Cohort. Front Oncol 2022; 11:789659. [PMID: 35070997 PMCID: PMC8767154 DOI: 10.3389/fonc.2021.789659] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 12/09/2021] [Indexed: 12/30/2022] Open
Abstract
Background Hereditary cancer syndromes (HCS) are responsible for 5-10% of cancer cases. Genetic testing to identify pathogenic variants associated with cancer predisposition has not been routinely available in Vietnam. Consequently, the prevalence and genetic landscape of HCS remain unknown. Methods 1165 Vietnamese individuals enrolled in genetic testing at our laboratory in 2020. We performed analysis of germline mutations in 17 high- and moderate- penetrance genes associated with HCS by next generation sequencing. Results A total of 41 pathogenic variants in 11 genes were detected in 3.2% individuals. The carrier frequency was 4.2% in people with family or personal history of cancer and 2.6% in those without history. The percentage of mutation carriers for hereditary colorectal cancer syndromes was 1.3% and for hereditary breast and ovarian cancer syndrome was 1.6%. BRCA1 and BRCA2 mutations were the most prevalent with the positive rate of 1.3% in the general cohort and 5.1% in breast or ovarian cancer patients. Most of BRCA1 mutations located at the BRCA C-terminus domains and the top recurrent mutation was NM_007294.3:c.5251C>T (p.Arg1751Ter). One novel variant NM_000038.6(APC):c.6665C>A (p.Pro2222His) was found in a breast cancer patient with a strong family history of cancer. A case study of hereditary cancer syndrome was illustrated to highlight the importance of genetic testing. Conclusion This is the first largest analysis of carrier frequency and mutation spectrum of HCS in Vietnam. The findings demonstrate the clinical significance of multigene panel testing to identify carriers and their at-risk relatives for better cancer surveillance and management strategies.
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Affiliation(s)
| | - Sao Trung Nguyen
- University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | | | | | | | - Huu Thinh Nguyen
- University Medical Center Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Huu Phuc Nguyen
- University Medical Center Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Phuong Thao Thi Doan
- University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | | | | | | | - Duy Sinh Nguyen
- Department of Oncology, Faculty of Medicine, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
| | - Hong-Dang Luu Nguyen
- Medical Genetics Institute, Ho Chi Minh City, Vietnam.,Gene Solutions, Ho Chi Minh City, Vietnam
| | - Ngoc Mai Nguyen
- Medical Genetics Institute, Ho Chi Minh City, Vietnam.,Gene Solutions, Ho Chi Minh City, Vietnam
| | - Duy Xuan Do
- Medical Genetics Institute, Ho Chi Minh City, Vietnam.,Gene Solutions, Ho Chi Minh City, Vietnam
| | - Vu Uyen Tran
- Medical Genetics Institute, Ho Chi Minh City, Vietnam.,Gene Solutions, Ho Chi Minh City, Vietnam
| | - Hue Hanh Thi Nguyen
- Medical Genetics Institute, Ho Chi Minh City, Vietnam.,Gene Solutions, Ho Chi Minh City, Vietnam
| | - Minh Phong Le
- Medical Genetics Institute, Ho Chi Minh City, Vietnam.,Gene Solutions, Ho Chi Minh City, Vietnam
| | - Yen Nhi Nguyen
- Medical Genetics Institute, Ho Chi Minh City, Vietnam.,Gene Solutions, Ho Chi Minh City, Vietnam
| | | | | | - Hung Sang Tang
- Medical Genetics Institute, Ho Chi Minh City, Vietnam.,Gene Solutions, Ho Chi Minh City, Vietnam
| | - Minh-Duy Phan
- Medical Genetics Institute, Ho Chi Minh City, Vietnam.,Gene Solutions, Ho Chi Minh City, Vietnam
| | - Hoai-Nghia Nguyen
- University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Hoa Giang
- Medical Genetics Institute, Ho Chi Minh City, Vietnam.,Gene Solutions, Ho Chi Minh City, Vietnam
| | - Lan N Tu
- Medical Genetics Institute, Ho Chi Minh City, Vietnam.,Gene Solutions, Ho Chi Minh City, Vietnam
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Tran NH, Nguyen Thi TH, Tang HS, Hoang LP, Nguyen THL, Tran NT, Trinh THN, Nguyen VT, Nguyen BHH, Nguyen HT, Doan LP, Phan NM, Nguyen KHT, Nguyen HDL, Quach MTT, Nguyen TPT, Tran VU, Tran DV, Nguyen QTT, Do TTT, Lam NV, Cao Thi Ngoc P, Truong DK, Nguyen HN, Phan MD, Giang H. Genetic landscape of recessive diseases in the Vietnamese population from large-scale clinical exome sequencing. Hum Mutat 2021; 42:1229-1238. [PMID: 34233069 DOI: 10.1002/humu.24253] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 05/08/2021] [Accepted: 06/13/2021] [Indexed: 11/10/2022]
Abstract
Accurate profiling of population-specific recessive diseases is essential for the design of cost-effective carrier screening programs. However, minority populations and ethnic groups, including Vietnamese, are still underrepresented in existing genetic studies. Here, we reported the first comprehensive study of recessive diseases in the Vietnamese population. Clinical exome sequencing data of 4503 disease-associated genes obtained from a cohort of 985 Vietnamese individuals was analyzed to identify pathogenic variants, associated diseases and their carrier frequencies in the population. A total of 118 recessive diseases associated with 164 pathogenic or likely pathogenic variants were identified, among which 28 diseases had carrier frequencies of at least 1% (1 in 100 individuals). Three diseases were prevalent in the Vietnamese population with carrier frequencies of 2-12 times higher than in the world populations, including beta-thalassemia (1 in 23), citrin deficiency (1 in 31), and phenylketonuria (1 in 40). Seven novel pathogenic and two likely pathogenic variants associated with nine recessive diseases were discovered. The comprehensive profile of recessive diseases identified in this study enables the design of cost-effective carrier screening programs specific to the Vietnamese population.
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Affiliation(s)
- Ngoc Hieu Tran
- Gene Solutions, Ho Chi Minh City, Vietnam.,David R. Cheriton School of Computer Science, University of Waterloo, Waterloo, Ontario, Canada
| | | | - Hung-Sang Tang
- Gene Solutions, Ho Chi Minh City, Vietnam.,Medical Genetics Institute, Ho Chi Minh City, Vietnam
| | | | - Trung-Hieu Le Nguyen
- Department of Neurology, Children Hospital 2, Ho Chi Minh City, Vietnam.,University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | | | | | | | | | | | | | - Ngoc-Minh Phan
- Gene Solutions, Ho Chi Minh City, Vietnam.,Medical Genetics Institute, Ho Chi Minh City, Vietnam
| | - Kim-Huong Thi Nguyen
- Gene Solutions, Ho Chi Minh City, Vietnam.,Medical Genetics Institute, Ho Chi Minh City, Vietnam
| | - Hong-Dang Luu Nguyen
- Gene Solutions, Ho Chi Minh City, Vietnam.,Medical Genetics Institute, Ho Chi Minh City, Vietnam
| | - Minh-Tam Thi Quach
- Gene Solutions, Ho Chi Minh City, Vietnam.,Medical Genetics Institute, Ho Chi Minh City, Vietnam
| | - Thanh-Phuong Thi Nguyen
- Gene Solutions, Ho Chi Minh City, Vietnam.,Medical Genetics Institute, Ho Chi Minh City, Vietnam
| | | | - Dinh-Vinh Tran
- Da Nang Hospital for Women and Children, Da Nang, Vietnam
| | | | | | - Nien Vinh Lam
- University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | | | | | - Hoai-Nghia Nguyen
- University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | | | - Hoa Giang
- Gene Solutions, Ho Chi Minh City, Vietnam.,Medical Genetics Institute, Ho Chi Minh City, Vietnam
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