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van Vliet MM, Schoenmakers S, Gribnau J, Steegers-Theunissen RP. The one-carbon metabolism as an underlying pathway for placental DNA methylation - a systematic review. Epigenetics 2024; 19:2318516. [PMID: 38484284 PMCID: PMC10950272 DOI: 10.1080/15592294.2024.2318516] [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: 10/25/2023] [Accepted: 02/07/2024] [Indexed: 03/19/2024] Open
Abstract
Epigenetic modifications, including DNA methylation, are proposed mechanisms explaining the impact of parental exposures to foetal development and lifelong health. Micronutrients including folate, choline, and vitamin B12 provide methyl groups for the one-carbon metabolism and subsequent DNA methylation processes. Placental DNA methylation changes in response to one-carbon moieties hold potential targets to improve obstetrical care. We conducted a systematic review on the associations between one-carbon metabolism and human placental DNA methylation. We included 22 studies. Findings from clinical studies with minimal ErasmusAGE quality score 5/10 (n = 15) and in vitro studies (n = 3) are summarized for different one-carbon moieties. Next, results are discussed per study approach: (1) global DNA methylation (n = 9), (2) genome-wide analyses (n = 4), and (3) gene specific (n = 14). Generally, one-carbon moieties were not associated with global methylation, although conflicting outcomes were reported specifically for choline. Using genome-wide approaches, few differentially methylated sites associated with S-adenosylmethionine (SAM), S-adenosylhomocysteine (SAH), or dietary patterns. Most studies taking a gene-specific approach indicated site-specific relationships depending on studied moiety and genomic region, specifically in genes involved in growth and development including LEP, NR3C1, CRH, and PlGF; however, overlap between studies was low. Therefore, we recommend to further investigate the impact of an optimized one-carbon metabolism on DNA methylation and lifelong health.
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Affiliation(s)
- Marjolein M van Vliet
- Department of Obstetrics and Gynaecology, Erasmus MC, Rotterdam, the Netherlands
- Department of Developmental Biology, Erasmus MC, Rotterdam, the Netherlands
| | - Sam Schoenmakers
- Department of Obstetrics and Gynaecology, Erasmus MC, Rotterdam, the Netherlands
| | - Joost Gribnau
- Department of Developmental Biology, Erasmus MC, Rotterdam, the Netherlands
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2
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Integrating chromatin accessibility states in the design of targeted sequencing panels for liquid biopsy. Sci Rep 2022; 12:10447. [PMID: 35729208 PMCID: PMC9213477 DOI: 10.1038/s41598-022-14675-z] [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: 01/01/2022] [Accepted: 06/10/2022] [Indexed: 11/09/2022] Open
Abstract
Dying tumor cells shed DNA fragments into the circulation that are known as circulating tumor DNA (ctDNA). Liquid biopsy tests aim to detect cancer using known markers, including genetic alterations and epigenetic profiles of ctDNA. Despite various advantages, the major limitation remains the low fraction of tumor-originating DNA fragments in a high background of normal blood-cell originating fragments in the cell-free DNA (cfDNA) pool in plasma. Deep targeted sequencing of cfDNA allows for enrichment of fragments in known cancer marker-associated regions of the genome, thus increasing the chances of detecting the low fraction variant harboring fragments. Most targeted sequencing panels are designed to include known recurrent mutations or methylation markers of cancer. Here, we propose the integration of cancer-specific chromatin accessibility states into panel designs for liquid biopsy. Using machine learning approaches, we first identify accessible and inaccessible chromatin regions specific to each major human cancer type. We then introduce a score that quantifies local chromatin accessibility in tumor relative to blood cells and show that this metric can be useful for prioritizing marker regions with higher chances of being detected in cfDNA for inclusion in future panel designs.
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3
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Yan YY, Guo QR, Wang FH, Adhikari R, Zhu ZY, Zhang HY, Zhou WM, Yu H, Li JQ, Zhang JY. Cell-Free DNA: Hope and Potential Application in Cancer. Front Cell Dev Biol 2021; 9:639233. [PMID: 33693004 PMCID: PMC7938321 DOI: 10.3389/fcell.2021.639233] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 01/20/2021] [Indexed: 12/16/2022] Open
Abstract
Cell-free DNA (cfDNA) is easily accessible in peripheral blood and can be used as biomarkers for cancer diagnostics, prognostics, and therapeutics. The applications of cfDNA in various areas of cancer management are attracting attention. In this review article, we discuss the potential relevance of using cfDNA analysis in clinical oncology, particularly in cancer screening, early diagnosis, therapeutic evaluation, monitoring disease progression; and determining disease prognosis.
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Affiliation(s)
- Yan-Yan Yan
- School of Medicine, Shanxi Datong University, Datong, China.,Key Laboratory of Molecular Target and Clinical Pharmacology and the State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences and the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Qiao-Ru Guo
- Key Laboratory of Molecular Target and Clinical Pharmacology and the State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences and the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, China.,The First Affiliated Hospital, Hainan Medical University, Haikou, China
| | - Feng-Hua Wang
- Guangzhou Institute of Pediatrics/Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Rameshwar Adhikari
- Research Centre for Applied Science and Technology, Tribhuvan University, Kirtipur, Nepal
| | - Zhuang-Yan Zhu
- School of Medicine, Shanxi Datong University, Datong, China
| | - Hai-Yan Zhang
- School of Medicine, Shanxi Datong University, Datong, China
| | - Wen-Min Zhou
- Key Laboratory of Molecular Target and Clinical Pharmacology and the State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences and the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Hua Yu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, Avenida da Universidade, Taipa, China
| | - Jing-Quan Li
- The First Affiliated Hospital, Hainan Medical University, Haikou, China
| | - Jian-Ye Zhang
- School of Medicine, Shanxi Datong University, Datong, China.,Key Laboratory of Molecular Target and Clinical Pharmacology and the State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences and the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, China.,The First Affiliated Hospital, Hainan Medical University, Haikou, China
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4
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Chen C, Li R, Sun J, Zhu Y, Jiang L, Li J, Fu F, Wan J, Guo F, An X, Wang Y, Fan L, Sun Y, Guo X, Zhao S, Wang W, Zeng F, Yang Y, Ni P, Ding Y, Xiang B, Peng Z, Liao C. Noninvasive prenatal testing of α-thalassemia and β-thalassemia through population-based parental haplotyping. Genome Med 2021; 13:18. [PMID: 33546747 PMCID: PMC7866698 DOI: 10.1186/s13073-021-00836-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 01/20/2021] [Indexed: 02/07/2023] Open
Abstract
Background Noninvasive prenatal testing (NIPT) of recessive monogenic diseases depends heavily on knowing the correct parental haplotypes. However, the currently used family-based haplotyping method requires pedigrees, and molecular haplotyping is highly challenging due to its high cost, long turnaround time, and complexity. Here, we proposed a new two-step approach, population-based haplotyping-NIPT (PBH-NIPT), using α-thalassemia and β-thalassemia as prototypes. Methods First, we deduced parental haplotypes with Beagle 4.0 with training on a large retrospective carrier screening dataset (4356 thalassemia carrier screening-positive cases). Second, we inferred fetal haplotypes using a parental haplotype-assisted hidden Markov model (HMM) and the Viterbi algorithm. Results With this approach, we enrolled 59 couples at risk of having a fetus with thalassemia and successfully inferred 94.1% (111/118) of fetal alleles. We confirmed these alleles by invasive prenatal diagnosis, with 99.1% (110/111) accuracy (95% CI, 95.1–100%). Conclusions These results demonstrate that PBH-NIPT is a sensitive, fast, and inexpensive strategy for NIPT of thalassemia. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-021-00836-8.
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Affiliation(s)
- Chao Chen
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.,Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Ru Li
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China
| | - Jun Sun
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.,Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Yaping Zhu
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.,Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Lu Jiang
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.,Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Jian Li
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China
| | - Fang Fu
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China
| | - Junhui Wan
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China
| | - Fengyu Guo
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.,Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Xiaoying An
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.,Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Yaoshen Wang
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.,Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Linlin Fan
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.,Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Yan Sun
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.,BGI-Wuhan Clinical Laboratories, BGI-Shenzhen, Wuhan, 490079, China
| | - Xiaosen Guo
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Sumin Zhao
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.,Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Wanyang Wang
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.,Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Fanwei Zeng
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Yun Yang
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.,BGI-Wuhan Clinical Laboratories, BGI-Shenzhen, Wuhan, 490079, China.,Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Peixiang Ni
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.,Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Yi Ding
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.,Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Bixia Xiang
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Zhiyu Peng
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.
| | - Can Liao
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China.
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5
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Noninvasive prenatal test of single-gene disorders by linked-read direct haplotyping: application in various diseases. Eur J Hum Genet 2020; 29:463-470. [PMID: 33235377 DOI: 10.1038/s41431-020-00759-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 08/26/2020] [Accepted: 10/20/2020] [Indexed: 11/08/2022] Open
Abstract
Direct haplotyping enables noninvasive prenatal testing (NIPT) without analyzing proband, which is a promising strategy for pregnancies at risk of an inherited single-gene disorder. Here, we aimed to expand the scope of single-gene disorders that NIPT using linked-read direct haplotyping would be applicable to. Three families at risk of myotonic dystrophy type 1, lipoid congenital adrenal hyperplasia, and Fukuyama congenital muscular dystrophy were recruited. All cases exhibited distinct characteristics that are often encountered as hurdles (i.e., repeat expansion, identical variants in both parents, and novel variants with retrotransposon insertion) in the universal clinical application of NIPT. Direct haplotyping of parental genomes was performed by linked-read sequencing, combined with allele-specific PCR, if necessary. Target DMPK, STAR, and FKTN genes in the maternal plasma DNA were sequenced. Posterior risk calculations and an Anderson-Darling test were performed to deduce the maternal and paternal inheritance, respectively. In all cases, we could predict the inheritance of maternal mutant allele with > 99.9% confidence, while paternal mutant alleles were not predicted to be inherited. Our study indicates that direct haplotyping and posterior risk calculation can be applied with subtle modifications to NIPT for the detection of an expanded range of diseases.
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6
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Lee JS, Lee KB, Song H, Sun C, Kim MJ, Cho SI, Lee YK, Park SS, Seong MW. Direct Haplotyping-Based Noninvasive Prenatal Test for Myotonic Dystrophy Type 1 with Large CTG Expansion. Clin Chem 2020; 66:614-615. [PMID: 32167563 DOI: 10.1093/clinchem/hvaa025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/23/2020] [Indexed: 11/12/2022]
Affiliation(s)
- Jee-Soo Lee
- Department of Laboratory Medicine, Hallym University Sacred Heart Hospital, Anyang, Republic of Korea
| | - Kyung Bok Lee
- Department of Statistics, Seoul National University, Seoul, Republic of Korea
| | - Han Song
- Genome Opinion Inc., Seongdong-gu, Seoul, Republic of Korea
| | - ChoongHyun Sun
- Genome Opinion Inc., Seongdong-gu, Seoul, Republic of Korea
| | - Man Jin Kim
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sung Im Cho
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Young Kyung Lee
- Department of Laboratory Medicine, Hallym University Sacred Heart Hospital, Anyang, Republic of Korea
| | - Sung Sup Park
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Moon-Woo Seong
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
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7
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Li H, Du B, Jiang F, Guo Y, Wang Y, Zhang C, Zeng X, Xie Y, Ouyang S, Xian Y, Chen M, Liu W, Sun X. Noninvasive prenatal diagnosis of β-thalassemia by relative haplotype dosage without analyzing proband. Mol Genet Genomic Med 2019; 7:e963. [PMID: 31566929 PMCID: PMC6825866 DOI: 10.1002/mgg3.963] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Revised: 07/30/2019] [Accepted: 08/04/2019] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND β-thalassemia is one of the most common monogenic diseases in the world. Southeast China is a highly infected area affected by four β-thalassemia mutation types (HBB:c.-78A>G, HBB:c.52A>T, HBB:c.126_129delCTTT, and HBB:c.316-197C>T). Relative haplotype dosage (RHDO), a haplotype-based approach, has shown promise as an application for noninvasive prenatal diagnosis (NIPD); however, additional family members (such as the proband) are required for haplotype construction. The abovementioned circumstances make RHDO-based NIPD cost prohibitive; additionally, the genetic information of the proband is not always available. Thus, it is necessary to find a practical method to solve these problems. METHODS Targeted sequencing was applied to sequence parental genomic DNA and cell-free fetal DNA (cffDNA). Parental haplotypes were constructed with the SHAPEIT software based on the 1000 Genomes Project (1000G) Phase 3 v5 Southern Han Chinese (CHS) haplotype dataset. Single-nucleotide polymorphisms (SNPs) in the target region were called and classified, and the fetal mutation inheritance status was deduced using the RHDO method. RESULTS Construction of the parental haplotypes and detection of the inherited parental mutations were successfully achieved in five families, despite a suspected recombination event. The status of the affected fetuses is consistent with the results of traditional reverse dot blot (RDB) diagnosis. CONCLUSION This research introduced SHAPEIT into the classical RHDO workflow and proved that it is applicable to construct parental haplotypes without information from other family members.
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Affiliation(s)
- Haoxian Li
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Bole Du
- GuangZhou JingKe Biotech Co., Ltd, Guangzhou, China
| | - Fuman Jiang
- GuangZhou JingKe Biotech Co., Ltd, Guangzhou, China
| | - Yulai Guo
- GuangZhou JingKe Biotech Co., Ltd, Guangzhou, China
| | - Yang Wang
- GuangZhou JingKe Biotech Co., Ltd, Guangzhou, China
| | | | | | - Yuhuan Xie
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Shuming Ouyang
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yexing Xian
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Min Chen
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Department of Fetal Medicine and Prenatal Diagnosis, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Weiqiang Liu
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xiaofang Sun
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
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8
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Temilola DO, Wium M, Coulidiati TH, Adeola HA, Carbone GM, Catapano CV, Zerbini LF. The Prospect and Challenges to the Flow of Liquid Biopsy in Africa. Cells 2019; 8:E862. [PMID: 31404988 PMCID: PMC6721679 DOI: 10.3390/cells8080862] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 07/30/2019] [Accepted: 08/03/2019] [Indexed: 12/24/2022] Open
Abstract
Liquid biopsy technologies have the potential to transform cancer patient management as it offers non-invasive diagnosis and real-time monitoring of disease progression and treatment responses. The use of liquid biopsy for non-invasive cancer diagnosis can have pivotal importance for the African continent where access to medical infrastructures is limited, as it eliminates the need for surgical biopsies. To apply liquid biopsy technologies in the African setting, the influence of environmental and population genetic factors must be known. In this review, we discuss the use of circulating tumor cells, cell-free nucleic acids, extracellular vesicles, protein, and other biomolecules in liquid biopsy technology for cancer management with special focus on African studies. We discussed the prospect, barriers, and other aspects that pose challenges to the use of liquid biopsy in the African continent.
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Affiliation(s)
- Dada Oluwaseyi Temilola
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town 7925, South Africa
- Integrative Biomedical Sciences Division, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Martha Wium
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town 7925, South Africa
| | - Tangbadioa Herve Coulidiati
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town 7925, South Africa
- Training and Research unit in Sciences and Technology, University Norbert Zongo, P.O. Box 376, Koudougou 376, Burkina Faso
| | - Henry Ademola Adeola
- Division of Dermatology, Department of Medicine, Faculty of Health Sciences and Groote Schuur Hospital, University of Cape Town, Cape Town 7925, South Africa
| | - Giuseppina Maria Carbone
- Institute of Oncology Research, Università della Svizzera Italiana, Via Vincenzo Vela 6, CH-6500 Bellinzona, Switzerland
| | - Carlo Vittorio Catapano
- Institute of Oncology Research, Università della Svizzera Italiana, Via Vincenzo Vela 6, CH-6500 Bellinzona, Switzerland
| | - Luiz Fernando Zerbini
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town 7925, South Africa.
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9
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Shi J, Zhang R, Li J, Zhang R. Novel perspectives in fetal biomarker implementation for the noninvasive prenatal testing. Crit Rev Clin Lab Sci 2019; 56:374-392. [PMID: 31290367 DOI: 10.1080/10408363.2019.1631749] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Noninvasive prenatal testing (NIPT) utilizes cell-free fetal DNA (cffDNA) present in maternal peripheral blood to detect chromosomal abnormalities. The detection of 21-trisomy, 18-trisomy, and 13-trisomy in the fetus has become a common screening method during pregnancy and has been widely applied in routine clinical testing because of its analytical and clinical validity. Currently, noninvasive prenatal testing involving copy number variations (CNVs) and other frequent single-gene disorders is being widely studied, and it plays an important and indispensable role in prenatal detection. The multiple approaches that have been reported and validated by various laboratories have different merits and limitations. Their clinical validity, utility, and application vary with different diseases. This review summarizes the principles, methods, advantages, and limitations of noninvasive prenatal testing for the detection of aneuploidy, CNVs and single-gene disorders. Before implementation of NIPT into clinical practice, a list of criteria that the application must meet is crucial. Essential parameters such as clinical sensitivity, clinical specificity, positive predictive value (PPV) and negative predictive value (NPV) are required to properly evaluate the clinical validity and utility of NIPT. We then discuss and analyze these clinical parameters and clinical application guidelines, providing physicians and scientists with feasible strategies and the latest research information.
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Affiliation(s)
- Jiping Shi
- Peking University Fifth School of Clinical Medicine, National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital , Beijing , China.,National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital , Beijing , China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital , Beijing , China
| | - Runling Zhang
- National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital , Beijing , China.,Graduate School, Chinese Academy of Medical Sciences, Peking Union Medical College , Beijing , China
| | - Jinming Li
- National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital , Beijing , China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital , Beijing , China
| | - Rui Zhang
- Peking University Fifth School of Clinical Medicine, National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital , Beijing , China.,National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital , Beijing , China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital , Beijing , China
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10
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Epigenetic Biomarkers in Cell-Free DNA and Applications in Liquid Biopsy. Genes (Basel) 2019; 10:genes10010032. [PMID: 30634483 PMCID: PMC6356936 DOI: 10.3390/genes10010032] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 12/20/2018] [Accepted: 01/02/2019] [Indexed: 12/21/2022] Open
Abstract
Cell-free circulating DNA (cfDNA) in plasma has gained global interest as a diagnostic material for noninvasive prenatal testing and cancer diagnosis, or the so-called “liquid biopsy”. Recent studies have discovered a great number of valuable genetic and epigenetic biomarkers for cfDNA-based liquid biopsy. Considering that the genetic biomarkers, e.g., somatic mutations, usually vary from case to case in most cancer patients, epigenetic biomarkers that are generalizable across various samples thus possess certain advantages. In this study, we reviewed the most recent studies and advances on utilizing epigenetic biomarkers for liquid biopsies. We first reviewed more traditional methods of using tissue/cancer-specific DNA methylation biomarkers and digital PCR or sequencing technologies for cancer diagnosis, as well as tumor origin determination. In the second part, we discussed the emerging novel approaches for exploring the biological basis and clinical applications of cfDNA fragmentation patterns. We further provided our comments and points of view on the future directions on epigenetic biomarker development for cfDNA-based liquid biopsies.
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11
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Chen L, Guan J, Wei Q, Yuan Z, Zhang M. Potential role of "omics" technique in prenatal diagnosis of congenital heart defects. Clin Chim Acta 2018; 482:185-190. [PMID: 29649453 DOI: 10.1016/j.cca.2018.04.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 04/04/2018] [Accepted: 04/06/2018] [Indexed: 02/08/2023]
Abstract
Congenital heart defect (CHD) is one of the most common birth defects and is the leading cause of neonatal death. Currently, there are no biomarkers available for prenatal diagnosis of CHD. Clinical strategies to diagnose CHD mostly depend on fetal echocardiography. Recent advances in "omics" techniques have opened up new possibilities for biomarker discoveries. In this review, we discuss recent advances in prenatal detection of CHD using biomarkers obtained by "omics" approaches, including genomics, proteomics, metabolomics, and others. There is great potential in obtaining various kinds of parameters using "omics" studies to facilitate early and accurate diagnosis of CHD.
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Affiliation(s)
- Lizhu Chen
- Department of Ultrasound, Shengjing Hospital, China Medical University, Shenyang 110004, China; Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital, China Medical University, Shenyang 110004, China
| | - Johnny Guan
- Department of Urology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Qiuju Wei
- Department of Obstetrics and Gynecology, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Zhengwei Yuan
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital, China Medical University, Shenyang 110004, China.
| | - Mo Zhang
- Department of Urology, Shengjing Hospital, China Medical University, Shenyang 110004, China..
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12
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Rodda AE, Parker BJ, Spencer A, Corrie SR. Extending Circulating Tumor DNA Analysis to Ultralow Abundance Mutations: Techniques and Challenges. ACS Sens 2018; 3:540-560. [PMID: 29441780 DOI: 10.1021/acssensors.7b00953] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Liquid biopsies that analyze circulating tumor DNA (ctDNA) hold great promise in the guidance of clinical treatment for various cancers. However, the innate characteristics of ctDNA make it a difficult target: ctDNA is highly fragmented, and found at very low concentrations, both in absolute terms and relative to wildtype species. Clinically relevant target sequences often differ from the wildtype species by a single DNA base pair. These characteristics make analyzing mutant ctDNA a uniquely difficult process. Despite this, techniques have recently emerged for analyzing ctDNA, and have been used in pilot studies that showed promising results. These techniques each have various drawbacks, either in their analytical capabilities or in practical considerations, which restrict their application to many clinical situations. Many of the most promising potential applications of ctDNA require assay characteristics that are not currently available, and new techniques with these properties could have benefits in companion diagnostics, monitoring response to treatment and early detection. Here we review the current state of the art in ctDNA detection, with critical comparison of the analytical techniques themselves. We also examine the improvements required to expand ctDNA diagnostics to more advanced applications and discuss the most likely pathways for these improvements.
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Affiliation(s)
| | | | - Andrew Spencer
- Myeloma Research Group, Australian Center for Blood Diseases, Monash University, Melbourne, Victoria 3004, Australia
- Malignant Haematology & Stem Cell Transplantation Service, Alfred Hospital, Melbourne, Victoria 3004, Australia
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13
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Sun K, Lun FMF, Leung TY, Chiu RWK, Lo YMD, Sun H. Noninvasive reconstruction of placental methylome from maternal plasma DNA: Potential for prenatal testing and monitoring. Prenat Diagn 2018; 38:196-203. [PMID: 29334402 DOI: 10.1002/pd.5214] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 01/05/2018] [Accepted: 01/05/2018] [Indexed: 12/15/2022]
Abstract
OBJECTIVE During human pregnancy, the DNA methylation of placental tissue is highly relevant to the normal growth and development of the fetus; therefore, methylomic analysis of the placental tissue possesses high research and clinical value in prenatal testing and monitoring. Thus, our aim is to develop an approach for reconstruction of the placental methylome, which should be completely noninvasive and achieve high accuracy and resolution. RESULTS We propose a novel size-based algorithm, FEtal MEthylome Reconstructor (FEMER), to noninvasively reconstruct the placental methylome by genomewide bisulfite sequencing and size-based analysis of maternal plasma DNA. By applying FEMER on a real clinical dataset, we demonstrate that FEMER achieves both high accuracy and resolution, thus provides a high-quality view of the placental methylome from maternal plasma DNA. FEtal MEthylome Reconstructor could also predict the DNA methylation profile of CpG islands with high accuracy, thus shows potential in monitoring of key genes involved in placental/fetal development. Source code and testing datasets for FEMER are available at http://sunlab.cpy.cuhk.edu.hk/FEMER/. CONCLUSION FEtal MEthylome Reconstructor could enhance the noninvasive fetal/placental methylomic analysis and facilitate its application in prenatal testing and monitoring.
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Affiliation(s)
- Kun Sun
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong.,Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Fiona M F Lun
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong.,Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Tak Y Leung
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Rossa W K Chiu
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong.,Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Y M Dennis Lo
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong.,Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Hao Sun
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong.,Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, Hong Kong
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Andersen GB, Tost J. A Summary of the Biological Processes, Disease-Associated Changes, and Clinical Applications of DNA Methylation. Methods Mol Biol 2018; 1708:3-30. [PMID: 29224136 DOI: 10.1007/978-1-4939-7481-8_1] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
DNA methylation at cytosines followed by guanines, CpGs, forms one of the multiple layers of epigenetic mechanisms controlling and modulating gene expression through chromatin structure. It closely interacts with histone modifications and chromatin remodeling complexes to form the local genomic and higher-order chromatin landscape. DNA methylation is essential for proper mammalian development, crucial for imprinting and plays a role in maintaining genomic stability. DNA methylation patterns are susceptible to change in response to environmental stimuli such as diet or toxins, whereby the epigenome seems to be most vulnerable during early life. Changes of DNA methylation levels and patterns have been widely studied in several diseases, especially cancer, where interest has focused on biomarkers for early detection of cancer development, accurate diagnosis, and response to treatment, but have also been shown to occur in many other complex diseases. Recent advances in epigenome engineering technologies allow now for the large-scale assessment of the functional relevance of DNA methylation. As a stable nucleic acid-based modification that is technically easy to handle and which can be analyzed with great reproducibility and accuracy by different laboratories, DNA methylation is a promising biomarker for many applications.
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Affiliation(s)
- Gitte Brinch Andersen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Laboratory for Epigenetics & Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie Francois Jacob, Bâtiment G2, 2 rue Gaston Crémieux, 91000, Evry, France
| | - Jörg Tost
- Laboratory for Epigenetics & Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie Francois Jacob, Bâtiment G2, 2 rue Gaston Crémieux, 91000, Evry, France.
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15
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Chan N, Smet M, Sandow R, Silva Costa F, McLennan A. Implications of failure to achieve a result from prenatal maternal serum cell‐free
DNA
testing: a historical cohort study. BJOG 2017; 125:848-855. [DOI: 10.1111/1471-0528.15006] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/23/2017] [Indexed: 12/17/2022]
Affiliation(s)
- N Chan
- Sydney Medical School University of Sydney Sydney NSW Australia
| | - M‐E Smet
- Sydney Ultrasound for Women Sydney NSW Australia
| | - R Sandow
- Sydney Ultrasound for Women Sydney NSW Australia
| | - F Silva Costa
- Monash Ultrasound for Women Melbourne VIC Australia
- Department of Obstetrics and Gynaecology Monash University Melbourne VICAustralia
| | - A McLennan
- Sydney Ultrasound for Women Sydney NSW Australia
- Discipline of Obstetrics, Gynaecology and Neonatology Faculty of Medicine University of Sydney Sydney NSW Australia
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16
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Filoche S, Cram F, Lawton B, Beard A, Stone P. Implementing non-invasive prenatal testing into publicly funded antenatal screening services for Down syndrome and other conditions in Aotearoa New Zealand. BMC Pregnancy Childbirth 2017; 17:344. [PMID: 28978305 PMCID: PMC5628435 DOI: 10.1186/s12884-017-1535-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 09/25/2017] [Indexed: 11/28/2022] Open
Abstract
Background Non-invasive prenatal testing (NIPT) is a relatively new screen for congenital conditions – specifically, common fetal aneuploidies including Down Syndrome. The test is based on isolating freely circulating fragments of fetal-placental DNA that is present in the mother’s blood. NIPT has a superior clinical performance compared to current screening, and has been available privately in Aotearoa New Zealand for the last 4 years. Main issue The proposed implementation of NIPT as a publicly funded service may widen the inequity in access to optional antenatal screening that already exists in this country. Conclusion This paper discusses precautions that can be taken at the health system, organisation, and personnel levels to ensure that access to NIPT is equitable, that services are culturally responsive, and women’s informed choice is promoted and protected. The adoption of NIPT into publicly funded services is an example of how genetic screening is becoming mainstreamed into health services; as such our approach may also have relevance around the introduction of other genetic and genomic screening initiatives.
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Affiliation(s)
- Sara Filoche
- Women's Health Research Centre, Department of Obstetrics and Gynaecology, University of Otago, Wellington, New Zealand.
| | | | - Bev Lawton
- Women's Health Research Centre, Department of Obstetrics and Gynaecology, University of Otago, Wellington, New Zealand
| | - Angela Beard
- Christchurch Obstetric Associates, Christchurch, New Zealand
| | - Peter Stone
- Department of Obstetrics and Gynaecology, Faculty of Medicine and Health Sciences, The University of Auckland, Auckland, New Zealand
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17
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Vermeesch JR, Voet T, Devriendt K. Prenatal and pre-implantation genetic diagnosis. Nat Rev Genet 2017; 17:643-56. [PMID: 27629932 DOI: 10.1038/nrg.2016.97] [Citation(s) in RCA: 117] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The past decade has seen the development of technologies that have revolutionized prenatal genetic testing; that is, genetic testing from conception until birth. Genome-wide single-cell arrays and high-throughput sequencing analyses are dramatically increasing our ability to detect embryonic and fetal genetic lesions, and have substantially improved embryo selection for in vitro fertilization (IVF). Moreover, both invasive and non-invasive mutation scanning of the genome are helping to identify the genetic causes of prenatal developmental disorders. These advances are changing clinical practice and pose novel challenges for genetic counselling and prenatal care.
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Affiliation(s)
- Joris Robert Vermeesch
- Centre for Human Genetics, Department of Human Genetics, University of Leuven, 49 Herestraat, Leuven 3000, Belgium
| | - Thierry Voet
- Centre for Human Genetics, Department of Human Genetics, University of Leuven, 49 Herestraat, Leuven 3000, Belgium
| | - Koenraad Devriendt
- Centre for Human Genetics, Department of Human Genetics, University of Leuven, 49 Herestraat, Leuven 3000, Belgium
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18
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Non-invasive prenatal diagnosis of beta-thalassemia by semiconductor sequencing: a feasibility study in the sardinian population. Eur J Hum Genet 2017; 25:600-607. [PMID: 28272531 DOI: 10.1038/ejhg.2017.26] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 01/18/2017] [Accepted: 01/22/2017] [Indexed: 01/31/2023] Open
Abstract
β-Thalassemia is the most common autosomal recessive single-gene disorder in Sardinia, where approximately 10.3% of the population is a carrier. Prenatal diagnosis is carried out at 12 weeks of gestation via villocentesis and is commonly aimed at ascertaining the presence or absence of the HBB variant c.118C>T, which is the most common in Sardinia. In this study, we describe for the first time the application of semiconductor sequencing to the non-invasive prenatal diagnosis of β-thalassemia in 37 couples at risk for this variant. In particular, by using a haplotyping-based approach with a hidden Markov model (HMM) and a dedicated pipeline, the two parental haplotypes most likely inherited by the foetus could be established in 30 out of 37 cffDNA samples. Specifically, the paternally inherited haplotype was correctly determined in all 30 of the samples, while the maternal haplotype was incorrectly predicted in six of the 30 genotyped samples. The lack of informative SNPs hampered the inference of both parental haplotypes in the remaining seven samples. As shown in previous studies, we have confirmed that the haplotyping-based approach represents a valuable resource, as it improves the detection of both parental haplotypes inherited by the foetus. In general, our results are encouraging, as we have proven that NIPD is also feasible in couples who are at risk for a monogenic disorder and share the same variant.
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19
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Than NG, Papp Z. Ethical issues in genetic counseling. Best Pract Res Clin Obstet Gynaecol 2017; 43:32-49. [PMID: 28259715 DOI: 10.1016/j.bpobgyn.2017.01.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Revised: 12/19/2016] [Accepted: 01/18/2017] [Indexed: 11/19/2022]
Abstract
Genetics has made great progress in the past decades, and prenatal diagnosis, predictive genetic testing, and genetic counseling have drawn the limelight of public attention. Because the subject of genetic counseling is of crucial consequence for both the short and long term, its ethical aspects are paramount. The question is whether mankind is mature enough to use this extraordinary knowledge in the right way for the benefit of the society. In the center of ethical questions is the comprehensiveness of information provided to the couples or patients and counseling them about results and making informed educated decisions. In addition, it is crucial how sensitive personal information is treated and whether and how it should be made public.
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Affiliation(s)
- Nandor Gabor Than
- Maternity Private Department of Obstetrics, Gynaecology and Clinical Genetics, Kutvolgyi Clinical Block, Semmelweis University, Budapest, Hungary; Systems Biology of Reproduction Lendulet Research Group, Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary; First Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Zoltan Papp
- Maternity Private Department of Obstetrics, Gynaecology and Clinical Genetics, Kutvolgyi Clinical Block, Semmelweis University, Budapest, Hungary.
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20
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Eggermann T, Brioude F, Russo S, Lombardi MP, Bliek J, Maher ER, Larizza L, Prawitt D, Netchine I, Gonzales M, Grønskov K, Tümer Z, Monk D, Mannens M, Chrzanowska K, Walasek MK, Begemann M, Soellner L, Eggermann K, Tenorio J, Nevado J, Moore GE, Mackay DJG, Temple K, Gillessen-Kaesbach G, Ogata T, Weksberg R, Algar E, Lapunzina P. Prenatal molecular testing for Beckwith-Wiedemann and Silver-Russell syndromes: a challenge for molecular analysis and genetic counseling. Eur J Hum Genet 2016; 24:784-93. [PMID: 26508573 PMCID: PMC4867462 DOI: 10.1038/ejhg.2015.224] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 09/03/2015] [Accepted: 09/11/2015] [Indexed: 12/22/2022] Open
Abstract
Beckwith-Wiedemann and Silver-Russell syndromes (BWS/SRS) are two imprinting disorders (IDs) associated with disturbances of the 11p15.5 chromosomal region. In BWS, epimutations and genomic alterations within 11p15.5 are observed in >70% of patients, whereas in SRS they are observed in about 60% of the cases. In addition, 10% of the SRS patients carry a maternal uniparental disomy of chromosome 7 11p15.5. There is an increasing demand for prenatal testing of these disorders owing to family history, indicative prenatal ultrasound findings or aberrations involving chromosomes 7 and 11. The complex molecular findings underlying these disorders are a challenge not only for laboratories offering these tests but also for geneticists counseling affected families. The scope of counseling must consider the range of detectable disturbances and their origin, the lack of precise quantitative knowledge concerning the inheritance and recurrence risks for the epigenetic abnormalities, which are hallmarks of these developmental disorders. In this paper, experts in the field of BWS and SRS, including members of the European network of congenital IDs (EUCID.net; www.imprinting-disorders.eu), put together their experience and work in the field of 11p15.5-associated IDs with a focus on prenatal testing. Altogether, prenatal tests of 160 fetuses (122 referred for BWS, 38 for SRS testing) from 5 centers were analyzed and reviewed. We summarize the current knowledge on BWS and SRS with respect to diagnostic testing, the consequences for prenatal genetic testing and counseling and our cumulative experience in dealing with these disorders.
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Affiliation(s)
- Thomas Eggermann
- Institut für Humangenetik, RWTH University Aachen, Aachen, Germany
| | - Frédéric Brioude
- INSERM, UMR_S 938, Paris, France
- Sorbonne Universities, UPMC Univ Paris 06, Paris, France
- Armand Trousseau Hospital, Pediatric Endocrinology, Paris, France
| | - Silvia Russo
- Laboratory of Cytogenetics and Molecular Genetics Istituto Auxologico Italiano IRCCS, Milano, Italy
| | - Maria P Lombardi
- Department of Clinical Genetics, Academic Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Jet Bliek
- Department of Clinical Genetics, Academic Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Eamonn R Maher
- Department of Medical Genetics, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Lidia Larizza
- Laboratory of Cytogenetics and Molecular Genetics Istituto Auxologico Italiano IRCCS, Milano, Italy
| | - Dirk Prawitt
- Center for Pediatrics and Adolescent Medicine, University Medical Center, Mainz, Germany
| | - Irène Netchine
- INSERM, UMR_S 938, Paris, France
- Sorbonne Universities, UPMC Univ Paris 06, Paris, France
- Armand Trousseau Hospital, Pediatric Endocrinology, Paris, France
| | - Marie Gonzales
- Department of Medical Genetics, Armand Trousseau Hospital, AP-HP, Paris, France
- Sorbonne Universitie, UPMC Univ Paris 06, Paris, France
| | - Karen Grønskov
- Clinical Genetic Unit, Kennedy Center, Rigshospitalet, Copenhagen University Hospital, Glostrup, Denmark
| | - Zeynep Tümer
- Clinical Genetic Unit, Kennedy Center, Rigshospitalet, Copenhagen University Hospital, Glostrup, Denmark
| | - David Monk
- Imprinting and Cancer Group, Cancer Epigenetic and Biology Program (PEBC), Institut d'Investigació Biomedica de Bellvitge (IDIBELL), Barcelona, Spain
| | - Marcel Mannens
- Department of Clinical Genetics, Academic Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Krystyna Chrzanowska
- Department of Medical Genetics, The Children's Memorial Health Insitute, Warsaw, Poland
| | - Malgorzata K Walasek
- Department of Medical Genetics, The Children's Memorial Health Insitute, Warsaw, Poland
| | | | - Lukas Soellner
- Institut für Humangenetik, RWTH University Aachen, Aachen, Germany
| | - Katja Eggermann
- Institut für Humangenetik, RWTH University Aachen, Aachen, Germany
| | - Jair Tenorio
- Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain
| | - Julián Nevado
- Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain
| | - Gudrun E Moore
- Fetal Growth and Developmental group, Genetics and Genomic Medicine Programme, UCL-ICH, London, UK
| | - Deborah JG Mackay
- Human Genetics and Genomic Medicine, Faculty of Medicine University of Southampto; Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, UK
| | - Karen Temple
- Human Genetics and Genomic Medicine, Faculty of Medicine University of Southampto; Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, UK
| | | | - Tsutomu Ogata
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamastu, Japan
| | - Rosanna Weksberg
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
- Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Elizabeth Algar
- Genetics and Molecular Pathology Laboratory, Monash Health and Hudson Institute, Clayton, Victoria, Australia
| | - Pablo Lapunzina
- Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain
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21
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Jiang P, Lo YD. The Long and Short of Circulating Cell-Free DNA and the Ins and Outs of Molecular Diagnostics. Trends Genet 2016; 32:360-371. [DOI: 10.1016/j.tig.2016.03.009] [Citation(s) in RCA: 158] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 03/30/2016] [Indexed: 12/25/2022]
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22
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Lee SY, Shim SH, Youn JP, Kim SJ, Kim JH, Jung SA, Choi HJ, Oh MJ, Lee KR, Cha DH, Hwang SY. New application methods for chromosomal abnormalities screening test using digital PCR. BIOCHIP JOURNAL 2015. [DOI: 10.1007/s13206-015-9410-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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23
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Christensen KD, Dukhovny D, Siebert U, Green RC. Assessing the Costs and Cost-Effectiveness of Genomic Sequencing. J Pers Med 2015; 5:470-86. [PMID: 26690481 PMCID: PMC4695866 DOI: 10.3390/jpm5040470] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 12/01/2015] [Accepted: 12/04/2015] [Indexed: 11/17/2022] Open
Abstract
Despite dramatic drops in DNA sequencing costs, concerns are great that the integration of genomic sequencing into clinical settings will drastically increase health care expenditures. This commentary presents an overview of what is known about the costs and cost-effectiveness of genomic sequencing. We discuss the cost of germline genomic sequencing, addressing factors that have facilitated the decrease in sequencing costs to date and anticipating the factors that will drive sequencing costs in the future. We then address the cost-effectiveness of diagnostic and pharmacogenomic applications of genomic sequencing, with an emphasis on the implications for secondary findings disclosure and the integration of genomic sequencing into general patient care. Throughout, we ground the discussion by describing efforts in the MedSeq Project, an ongoing randomized controlled clinical trial, to understand the costs and cost-effectiveness of integrating whole genome sequencing into cardiology and primary care settings.
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Affiliation(s)
- Kurt D Christensen
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
| | - Dmitry Dukhovny
- Department of Pediatrics, Oregon Health and Science University, Portland, OR 97239, USA.
| | - Uwe Siebert
- Department of Public Health, Medical Decision Making and Health Technology Assessment, University for Health Sciences, Medical Informatics and Technology, Hall in Tirol 6060, Austria.
- Department of Health Policy and Management, Harvard School of Public Health, Boston, MA 02115, USA.
- Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
| | - Robert C Green
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Partners Personalized Medicine, Boston, MA 02115, USA.
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Soellner L, Monk D, Rezwan FI, Begemann M, Mackay D, Eggermann T. Congenital imprinting disorders: Application of multilocus and high throughput methods to decipher new pathomechanisms and improve their management. Mol Cell Probes 2015; 29:282-90. [DOI: 10.1016/j.mcp.2015.05.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 05/02/2015] [Accepted: 05/05/2015] [Indexed: 12/17/2022]
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25
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Advancing Horizons in Fetal Medicine. JOURNAL OF FETAL MEDICINE 2015. [DOI: 10.1007/s40556-015-0045-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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