1
|
Gao B, Jiang Y, Han M, Ji X, Zhang D, Wu L, Gao X, Huang S, Zhao C, Su Y, Yang S, Zhang X, Liu N, Han L, Wang L, Ren L, Yang J, Wu J, Yuan Y, Dai P. Targeted Linked-Read Sequencing for Direct Haplotype Phasing of Parental GJB2/SLC26A4 Alleles: A Universal and Dependable Noninvasive Prenatal Diagnosis Method Applied to Autosomal Recessive Nonsyndromic Hearing Loss in At-Risk Families. J Mol Diagn 2024; 26:638-651. [PMID: 38663495 DOI: 10.1016/j.jmoldx.2024.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 03/04/2024] [Accepted: 04/10/2024] [Indexed: 05/04/2024] Open
Abstract
Noninvasive prenatal diagnosis (NIPD) for autosomal recessive nonsyndromic hearing loss (ARNSHL) has been rarely reported until recent years. Additionally, the existing method can not be used for challenging genome loci (eg, copy number variations, deletions, inversions, or gene recombinants) or on families without proband genotype. This study assessed the performance of relative haplotype dosage analysis (RHDO)-based NIPD for identifying fetal genotyping in pregnancies at risk of ARNSHL. Fifty couples carrying pathogenic variants associated with ARNSHL in either GJB2 or SLC26A4 were recruited. The RHDO-based targeted linked-read sequencing combined with whole gene coverage probes was used to genotype the fetal cell-free DNA of 49 families who met the quality control standard. Fetal amniocyte samples were genotyped using invasive prenatal diagnosis (IPD) to assess the performance of NIPD. The NIPD results showed 100% (49/49) concordance with those obtained through IPD. Two families with copy number variation and recombination were also successfully identified. Sufficient specific informative single-nucleotide polymorphisms for haplotyping, as well as the fetal cell-free DNA concentration and sequencing depth, are prerequisites for RHDO-based NIPD. This method has the merits of covering the entire genes of GJB2 and SLC26A4, qualifying for copy number variation and recombination analysis with remarkable sensitivity and specificity. Therefore, it has clinical potential as an alternative to traditional IPD for ARNSHL.
Collapse
Affiliation(s)
- Bo Gao
- Senior Department of Otolaryngology Head and Neck Surgery, The 6th Medical Center of Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China; State Key Laboratory of Hearing and Balance Science, Beijing, China; National Clinical Research Center for Otolaryngologic Diseases, Beijing, China; Key Laboratory of Hearing Science, Ministry of Education, Beijing, China; Beijing Key Laboratory of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Yi Jiang
- Department of Otolaryngology-Head and Neck Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Ear Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, China
| | - Mingyu Han
- Senior Department of Otolaryngology Head and Neck Surgery, The 6th Medical Center of Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China; State Key Laboratory of Hearing and Balance Science, Beijing, China; National Clinical Research Center for Otolaryngologic Diseases, Beijing, China; Key Laboratory of Hearing Science, Ministry of Education, Beijing, China; Beijing Key Laboratory of Hearing Impairment Prevention and Treatment, Beijing, China
| | | | - Dejun Zhang
- Senior Department of Otolaryngology Head and Neck Surgery, The 6th Medical Center of Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China; State Key Laboratory of Hearing and Balance Science, Beijing, China; National Clinical Research Center for Otolaryngologic Diseases, Beijing, China; Key Laboratory of Hearing Science, Ministry of Education, Beijing, China; Beijing Key Laboratory of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Lihua Wu
- Department of Otolaryngology, Fujian Medical University ShengLi Clinical College, Fujian Provincial Hospital, Fuzhou, China
| | - Xue Gao
- Department of Otolaryngology, PLA Rocket Force Characteristic Medical Center, Beijing, China
| | - Shasha Huang
- Senior Department of Otolaryngology Head and Neck Surgery, The 6th Medical Center of Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China; State Key Laboratory of Hearing and Balance Science, Beijing, China; National Clinical Research Center for Otolaryngologic Diseases, Beijing, China; Key Laboratory of Hearing Science, Ministry of Education, Beijing, China; Beijing Key Laboratory of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Chaoyue Zhao
- Senior Department of Otolaryngology Head and Neck Surgery, The 6th Medical Center of Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China; State Key Laboratory of Hearing and Balance Science, Beijing, China; National Clinical Research Center for Otolaryngologic Diseases, Beijing, China; Key Laboratory of Hearing Science, Ministry of Education, Beijing, China; Beijing Key Laboratory of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Yu Su
- Senior Department of Otolaryngology Head and Neck Surgery, The 6th Medical Center of Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China; State Key Laboratory of Hearing and Balance Science, Beijing, China; National Clinical Research Center for Otolaryngologic Diseases, Beijing, China; Key Laboratory of Hearing Science, Ministry of Education, Beijing, China; Beijing Key Laboratory of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Suyan Yang
- Senior Department of Otolaryngology Head and Neck Surgery, The 6th Medical Center of Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China; State Key Laboratory of Hearing and Balance Science, Beijing, China; National Clinical Research Center for Otolaryngologic Diseases, Beijing, China; Key Laboratory of Hearing Science, Ministry of Education, Beijing, China; Beijing Key Laboratory of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Xin Zhang
- Senior Department of Otolaryngology Head and Neck Surgery, The 6th Medical Center of Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China; State Key Laboratory of Hearing and Balance Science, Beijing, China; National Clinical Research Center for Otolaryngologic Diseases, Beijing, China; Key Laboratory of Hearing Science, Ministry of Education, Beijing, China; Beijing Key Laboratory of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Na Liu
- MyGenostics Inc., Beijing, China
| | - Lu Han
- MyGenostics Inc., Beijing, China
| | | | - Lina Ren
- MyGenostics Inc., Beijing, China
| | - Jinyuan Yang
- Senior Department of Otolaryngology Head and Neck Surgery, The 6th Medical Center of Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China; State Key Laboratory of Hearing and Balance Science, Beijing, China; National Clinical Research Center for Otolaryngologic Diseases, Beijing, China; Key Laboratory of Hearing Science, Ministry of Education, Beijing, China; Beijing Key Laboratory of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Jian Wu
- MyGenostics Inc., Beijing, China
| | - Yongyi Yuan
- Senior Department of Otolaryngology Head and Neck Surgery, The 6th Medical Center of Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China; State Key Laboratory of Hearing and Balance Science, Beijing, China; National Clinical Research Center for Otolaryngologic Diseases, Beijing, China; Key Laboratory of Hearing Science, Ministry of Education, Beijing, China; Beijing Key Laboratory of Hearing Impairment Prevention and Treatment, Beijing, China.
| | - Pu Dai
- Senior Department of Otolaryngology Head and Neck Surgery, The 6th Medical Center of Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China; State Key Laboratory of Hearing and Balance Science, Beijing, China; National Clinical Research Center for Otolaryngologic Diseases, Beijing, China; Key Laboratory of Hearing Science, Ministry of Education, Beijing, China; Beijing Key Laboratory of Hearing Impairment Prevention and Treatment, Beijing, China.
| |
Collapse
|
2
|
Liu D, Nong X, Lai F, Nong C, Wang T, Tang Y. Noninvasive Prenatal Diagnosis of SEA-Thalassemia by Combining 1000 Genomes Database and Relative Haplotype Dosage. Hemoglobin 2024:1-8. [PMID: 38632980 DOI: 10.1080/03630269.2024.2327830] [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: 08/25/2023] [Accepted: 02/29/2024] [Indexed: 04/19/2024]
Abstract
To explore a noninvasive method for diagnosis of SEA-thalassemia and to investigate whether the regional factors affect the accuracy of this method. The method involved using a public database and bioinformatics software to construct parental haplotypes for proband and predicting fetal genotypes using relative haplotype dosage. We screened and downloaded sequencing data of couples who were both SEA-thalassemia carriers from the China National Genebank public data platform, and matched the sequencing data format with that of the reference panel using Ubuntu system tools. We then used Beagle software to construct parental haplotypes, predicted fetal haplotypes by relative haplotype dosage. Finally, we used Hidden Markov Model and Viterbi algorithm to determine fetal pathogenic haplotypes. All noninvasive fetal genotype diagnosis results were compared with gold standard gap-PCR electrophoresis results. Our method was successful in diagnosing 13 families with SEA-thalassemia carriers. The best diagnostic results were obtained when Southern Chinese Han was used as the reference panel, and 10 families showed full agreement between our noninvasive diagnostic results and the gap-PCR electrophoresis results. The accuracy of our method was higher when using a Chinese Han as the reference panel for haplotype construction in the Southern Chinese Han region as opposed to Beijing Chinese region. The combined use of public databases and relative haplotype dosage for diagnosing SEA-thalassemia is a feasible approach. Our method produces the best noninvasive diagnostic results when the test samples and population reference panel are closely matched in both ethnicity and geography. When constructing parental haplotypes with our method, it is important to consider the effect of region in addition to population background alone.
Collapse
Affiliation(s)
- Dewen Liu
- Graduate School, Youjiang Medical University for Nationalities, Baise, Guangxi, China
| | - Xuejuan Nong
- Center for Medical Laboratory Science, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi, China
| | - Fengming Lai
- Graduate School, Youjiang Medical University for Nationalities, Baise, Guangxi, China
| | - Chen Nong
- Graduate School, Youjiang Medical University for Nationalities, Baise, Guangxi, China
| | - Taizhong Wang
- School of Medical Laboratory, Youjiang Medical University for Nationalities, Baise, Guangxi, China
| | - Yulian Tang
- School of Medical Laboratory, Youjiang Medical University for Nationalities, Baise, Guangxi, China
| |
Collapse
|
3
|
Suwannakhon N, Hemvuthiphan J, Pangeson T, Mahingsa K, Pingyod A, Bumrungpakdee W, Sanguansermsri T. Non-invasive prenatal screening & diagnosis of β-thalassaemia in an affected foetus. Indian J Med Res 2023; 157:447-452. [PMID: 37322635 PMCID: PMC10443724 DOI: 10.4103/ijmr.ijmr_3226_20] [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: 07/28/2020] [Indexed: 06/17/2023] Open
Abstract
Background & objectives Non-invasive prenatal testing (NIPT) of maternally inherited alleles of β-thalassaemia (MIB) remains to be a challenge. Furthermore, current techniques are not available for use as routine tests. NIPT for β-thalassaemia disease was developed by using a specific droplet digital polymerase chain reaction (ddPCR) assay to analyze the cell-free foetal DNA (cffDNA) derived from maternal plasma. Methods Pregnant women and their spouses who are at risk of bearing an offspring with β-thalassaemia disease from common MIB mutations (CD 41/42-TCTT, CD17A>T, IVS1-1G>T and CD26G>A) were enrolled. The ddPCR assay sets were constructed for each of the four mutations. All cell-free DNA samples were first screened for the paternally inherited β-thalassaemia (PIB) mutation. The PIB-negative samples were considered as non-disease and were not further analyzed. For PIB-positive samples, DNA fragments of 50-300 base pairs in size were isolated and purified, and further analyzed for MIB mutation. The allelic ratio between the mutant and the wild-type was used to determine the presence of MIB in cffDNA. All cases underwent a prenatal diagnosis by amniocentesis for a definite diagnosis. Results Forty two couples at risk were enrolled. Twenty two samples were positive for PIBs. Among these 22 samples, there were 10 cases with allelic ratio >1.0 (MIB positive). All foetuses with over-represented mutant alleles were further diagnosed with β-thalassaemia disease; eight with compound heterozygous and two with homozygous mutations. The 20 PIB-negative and 12 MIB-negative foetuses were non-affected. Interpretation & Conclusions The results of this study suggest that NIPT utilizing the ddPCR assay can be effectively used for the screening and diagnosis of foetal β-thalassaemia in at risk pregnancies.
Collapse
Affiliation(s)
| | | | - Tanapat Pangeson
- Department of Biochemistry, School of Medical Science, University of Phayao, Phayao, Thailand
| | - Khwanruedee Mahingsa
- Thalassaemia Unit, University of Phayao Hospital, University of Phayao, Phayao, Thailand
| | - Arunee Pingyod
- Thalassaemia Unit, University of Phayao Hospital, University of Phayao, Phayao, Thailand
| | - Wanwipa Bumrungpakdee
- Thalassaemia Unit, University of Phayao Hospital, University of Phayao, Phayao, Thailand
| | - Torpong Sanguansermsri
- Thalassaemia Unit, University of Phayao Hospital, University of Phayao, Phayao, Thailand
| |
Collapse
|
4
|
Afzal M, Naeem MA, Ahmed S, Amin N, Rahim A, Munawar M, Ishaq M, Rathore A, Maria K. Noninvasive prenatal testing of beta-thalassemia for common Pakistani mutations: a comparative study using cell-free fetal DNA from maternal plasma and chorionic villus sampling. Hematology 2022; 27:353-359. [PMID: 35287566 DOI: 10.1080/16078454.2022.2045052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
BACKGROUND The discovery of circulating cell-free fetal DNA (cff-DNA) in maternal plasma has inspired the noninvasive prenatal testing (NIPT) approaches for various genetic fetal screening including rhesus D typing, sex determination, aneuploidies, and single-gene disorders. OBJECTIVE Noninvasive determination of paternally inherited beta-thalassemia mutations in maternal total cell-free DNA (cf-DNA) by using allele-specific amplification refractory mutation system (ARMS) real-time PCR (RT-PCR) in concordance with the conventional invasive method. METHODS An observational study was conducted at the Armed Forces Institute of Blood Transfusion in collaboration with the genetics resource center from March 2021 to August 2021. A total number of 26 couples were selected having a history of previously affected children with beta-thalassemia. A routine chorionic villus sampling (CVS) invasive procedure was carried out, and the mutation analysis was done using conventional PCR. To assess NIPT, a total cf-DNA was also extracted from maternal plasma and analyzed using allele-specific ARMS RT-PCR. RESULTS Based on conventional PCR testing, 13 of 26 couples were found having beta-thalassemia carriers with homozygous mutation, and 13 couples were carriers with heterozygous mutations. Further to assess NIPT, the cf-DNA of 13 pregnant females among the couples with different mutational patterns was analyzed by allele-specific ARMS RT-PCR to detect paternally inherited mutations. In comparison with conventional PCR, 11 cases (84.6%) were matched successfully, while two cases (15.4%) had no concordance with conventional invasive prenatal testing (IPT). CONCLUSION NIPT using maternal cf-DNA by allele-specific ARMS RT-PCR can be feasible to screen paternal inherited mutant alleles to rule out pregnant women from invasive procedures where the test would be negative for paternal inheritance. However, a low amount of fetal DNA in maternal plasma is a limiting factor and required further improvement to enrich fetal cf-DNA for complete concordance with conventional IPT.
Collapse
Affiliation(s)
- Muhammad Afzal
- Biochemistry, Riphah International University Islamabad, Rawalpindi, Pakistan
| | | | - Suhaib Ahmed
- Biochemistry, Riphah International University Islamabad, Rawalpindi, Pakistan
| | - Nayyar Amin
- Hematology, Armed Forces Institute of Transfusion, Rawalpindi, Pakistan
| | - Amena Rahim
- Biochemistry, Riphah International University Islamabad, Rawalpindi, Pakistan
| | - Manazza Munawar
- Biochemistry, Riphah International University Islamabad, Rawalpindi, Pakistan
| | - Mansoor Ishaq
- Hematology, Armed Forces Institute of Transfusion, Rawalpindi, Pakistan
| | - Ali Rathore
- Hematology, Armed Forces Institute of Transfusion, Rawalpindi, Pakistan
| | - K Maria
- Hematology, Armed Forces Institute of Transfusion, Rawalpindi, Pakistan
| |
Collapse
|
5
|
Maskoen AM, Rahayu NS, Laksono B, Fibriani A, Soewondo W, Mose JC, Sahiratmadja E, Panigoro R. Cell-free fetal DNA as a non-invasive method using pyrosequencing in detecting beta-globin gene mutation: A pilot study from area with limited facilities in Indonesia. Front Pediatr 2022; 10:902879. [PMID: 35990000 PMCID: PMC9386223 DOI: 10.3389/fped.2022.902879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 07/07/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Thalassemia is a monogenic, autosomal recessive, inherited disorder of the red blood cells caused by mutations or deletions in the globin gene. Approximately 6-10% of the Indonesian population carries the β-globin gene mutation; however, premarital screening is rarely conducted, and antenatal screening is optional. We explored the use of cell-free fetal DNA (cffDNA) as a potential non-invasive method of detecting the fetal β-globin gene mutation prenatally in pregnant women. MATERIALS AND METHODS Pregnant mothers (n = 10), who were known carriers of thalassemia and who had a history of having borne a baby with thalassemia major, and their carrier husbands (n = 4) were recruited after providing consent. EDTA blood was drawn, and maternal DNA, including cffDNA, and paternal DNA were isolated. Maternal contamination tests were conducted using the variable number tandem repeat test for ApoB and D1S80 loci. Allele quantification was performed by pyrosequencing. Known mutations from the bio-archived DNA of patients with thalassemia major (n = 16) were run alongside as a control. RESULTS In total, 7 out of 10 cffDNA successfully passed the maternal contamination test. The results of the allele quantification showed that six fetuses were predictive carriers of IVS1nt5 and one was predictive normal, in line with the allele quantification for the bio-archived DNA from patients with thalassemia major. The minimum threshold percentage for mutant A allele at cd26 was 32%, mutant T allele at IVS1nt1 was 23%, and mutant C allele at IVS1nt5 was 39%. CONCLUSION Taking cffDNA from the mother's blood proved useful as a non-invasive means of detecting the β-globin gene mutation using pyrosequencing allele quantification. This non-invasive method is of great interest for prenatal diagnosis in settings with limited facilities, as it minimizes the risk of abortion. Further study of other mutations of the β-globin gene is needed.
Collapse
Affiliation(s)
- Ani Melani Maskoen
- Department of Oral Biology, Faculty of Dentistry, Universitas Padjadjaran, Bandung, Indonesia.,Department of Biomedical Sciences, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
| | - Nurul Setia Rahayu
- Laboratory of Molecular Genetics, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
| | - Bremmy Laksono
- Department of Oral Biology, Faculty of Dentistry, Universitas Padjadjaran, Bandung, Indonesia.,Department of Biomedical Sciences, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
| | - Azzania Fibriani
- Department of Biology, School of Life Sciences and Technology, Institut Teknologi Bandung, Bandung, Indonesia
| | - Willyanti Soewondo
- Department of Pediatric Dentistry, Faculty of Dentistry, Universitas Padjadjaran, Bandung, Indonesia
| | - Johanes C Mose
- Department of Obstetrics and Gynecology, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
| | - Edhyana Sahiratmadja
- Department of Biomedical Sciences, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
| | - Ramdan Panigoro
- Department of Biomedical Sciences, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
| |
Collapse
|
6
|
Suwannakhon N, Pangeson T, Seeratanachot T, Mahingsa K, Pingyod A, Bumrungpakdee W, Sanguansermsri T. Noninvasive prenatal screening test for compound heterozygous beta thalassemia using an amplification refractory mutation system real-time polymerase chain reaction technique. Hematol Rep 2019; 11:8124. [PMID: 31579144 PMCID: PMC6761473 DOI: 10.4081/hr.2019.8124] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 07/05/2019] [Indexed: 11/23/2022] Open
Abstract
We propose using a modified amplification refractory mutation system real-time polymerase chain reaction (ARMS RTPCR) technique to exclude the invasive prenatal diagnosis for a non-paternally inherited beta thalassemia mutation in couples atrisk for having a baby with CHBT. The ARMS RT-PCR method was performed for 36 at-risk couples by using isolated fetal cell-free DNA from maternal plasma. The modified ARMS RT-PCR primers targeted one of the following paternally inherited beta thalassemia mutation: -28 A→G, CD17 A→T, CD 26 G→A, IVS1-1 G→T and CD 41-42 -CTTT. The method could be successfully employed for NIPST starting with the 7th week of gestation. The results showed that 19 pregnant women were negative for PIBTM (53%). After an on-track and on-time of one year, including postnatal thalassemia blood tests, none of the babies showed symptoms or signs of beta thalassemia disease. We concluded that the modified ARMS RT-PCR method was an accurate, cost-effective and feasible method for use as a NIPST for at-risk couples with the potential of having a baby with CHBT.
Collapse
|
7
|
Breveglieri G, D'Aversa E, Finotti A, Borgatti M. Non-invasive Prenatal Testing Using Fetal DNA. Mol Diagn Ther 2019; 23:291-299. [PMID: 30712216 DOI: 10.1007/s40291-019-00385-2] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Non-invasive prenatal diagnosis (NIPD) is based on fetal DNA analysis starting from a simple peripheral blood sample, thus avoiding risks associated with conventional invasive techniques. During pregnancy, the fetal DNA increases to approximately 3-13% of the total circulating free DNA in maternal plasma. The very low amount of circulating cell-free fetal DNA (ccffDNA) in maternal plasma is a crucial issue, and requires specific and optimized techniques for ccffDNA purification from maternal plasma. In addition, highly sensitive detection approaches are required. In recent years, advanced ccffDNA investigation approaches have allowed the application of non-invasive prenatal testing (NIPT) to determine fetal sex, fetal rhesus D (RhD) genotyping, aneuploidies, micro-deletions and the detection of paternally inherited monogenic disorders. Finally, complex and innovative technologies such as digital polymerase chain reaction (dPCR) and next-generation sequencing (NGS) (exhibiting higher sensitivity and/or the capability to read the entire fetal genome from maternal plasma DNA) are expected to allow the detection, in the near future, of maternally inherited mutations that cause genetic diseases. The aim of this review is to introduce the principal ccffDNA characteristics and their applications as the basis of current and novel NIPT.
Collapse
Affiliation(s)
- Giulia Breveglieri
- Department of Life Sciences and Biotechnology, University of Ferrara, Via Fossato di Mortara 74, 44121, Ferrara, Italy
| | - Elisabetta D'Aversa
- Department of Life Sciences and Biotechnology, University of Ferrara, Via Fossato di Mortara 74, 44121, Ferrara, Italy
| | - Alessia Finotti
- Department of Life Sciences and Biotechnology, University of Ferrara, Via Fossato di Mortara 74, 44121, Ferrara, Italy.,Interuniversity Consortium for Biotechnologies (CIB), Trieste, Italy
| | - Monica Borgatti
- Department of Life Sciences and Biotechnology, University of Ferrara, Via Fossato di Mortara 74, 44121, Ferrara, Italy. .,Biotechnology Center, University of Ferrara, Via Fossato di Mortara 64, 44121, Ferrara, Italy.
| |
Collapse
|
8
|
Yang X, Zhou Q, Zhou W, Zhong M, Guo X, Wang X, Fan X, Yan S, Li L, Lai Y, Wang Y, Huang J, Ye Y, Zeng H, Chuan J, Du Y, Ma C, Li P, Song Z, Xu X. A Cell-free DNA Barcode-Enabled Single-Molecule Test for Noninvasive Prenatal Diagnosis of Monogenic Disorders: Application to β-Thalassemia. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2019; 6:1802332. [PMID: 31179213 PMCID: PMC6548944 DOI: 10.1002/advs.201802332] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 02/14/2019] [Indexed: 05/13/2023]
Abstract
Noninvasive prenatal testing of common aneuploidies has become routine over the past decade, but testing of monogenic disorders remains a challenge in clinical implementation. Most recent studies have inherent limitations, such as complicated procedures, a lack of versatility, and the need for prior knowledge of parental genotypes or haplotypes. To overcome these limitations, a robust and versatile next-generation sequencing-based cell-free DNA (cfDNA) allelic molecule counting system termed cfDNA barcode-enabled single-molecule test (cfBEST) is developed for the noninvasive prenatal diagnosis (NIPD) of monogenic disorders. The accuracy of cfBEST is found to be comparable to that of droplet digital polymerase chain reaction (ddPCR) in detecting low-abundance mutations in cfDNA. The analytical validity of cfBEST is evidenced by a β-thalassemia assay, in which a blind validation study of 143 at-risk pregnancies reveals a sensitivity of 99.19% and a specificity of 99.92% on allele detection. Because the validated cfBEST method can be used to detect maternal-fetal genotype combinations in cfDNA precisely and quantitatively, it holds the potential for the NIPD of human monogenic disorders.
Collapse
Affiliation(s)
- Xingkun Yang
- Department of Medical GeneticsSchool of Basic Medical SciencesSouthern Medical UniversityGuangzhouGuangdong510515China
- Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic DiseasesGuangzhouGuangdong510515China
- Affiliated Foshan Maternity & Child Healthcare HospitalSouthern Medical UniversityFoshanGuangdong528000China
- Guangdong Key Laboratory of Biological ChipGuangzhouGuangdong510515China
| | - Qinghua Zhou
- The Center for Precision Medicine of First Affiliated HospitalBiomedical Translational Research InstituteSchool of PharmacyJinan UniversityGuangzhouGuangdong510632China
- Hunan Research Center for Big Data Application in GenomicsGenetalks Inc.ChangshaHunan410152China
| | - Wanjun Zhou
- Department of Medical GeneticsSchool of Basic Medical SciencesSouthern Medical UniversityGuangzhouGuangdong510515China
- Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic DiseasesGuangzhouGuangdong510515China
- Guangdong Key Laboratory of Biological ChipGuangzhouGuangdong510515China
| | - Mei Zhong
- Nanfang HospitalSouthern Medical UniversityGuangzhouGuangdong510515China
| | - Xiaoling Guo
- Affiliated Foshan Maternity & Child Healthcare HospitalSouthern Medical UniversityFoshanGuangdong528000China
| | - Xiaofeng Wang
- Hunan Research Center for Big Data Application in GenomicsGenetalks Inc.ChangshaHunan410152China
| | - Xin Fan
- Guangxi Zhuang Autonomous Region Women and Children Care HospitalNanningGuangxi530000China
| | - Shanhuo Yan
- Qinzhou Maternity & Child Healthcare HospitalQinzhouGuangxi535000China
| | - Liyan Li
- Nanfang HospitalSouthern Medical UniversityGuangzhouGuangdong510515China
| | - Yunli Lai
- Guangxi Zhuang Autonomous Region Women and Children Care HospitalNanningGuangxi530000China
| | - Yongli Wang
- Hunan Research Center for Big Data Application in GenomicsGenetalks Inc.ChangshaHunan410152China
| | - Jin Huang
- Department of Medical GeneticsSchool of Basic Medical SciencesSouthern Medical UniversityGuangzhouGuangdong510515China
- Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic DiseasesGuangzhouGuangdong510515China
- Guangdong Key Laboratory of Biological ChipGuangzhouGuangdong510515China
| | - Yuhua Ye
- Department of Medical GeneticsSchool of Basic Medical SciencesSouthern Medical UniversityGuangzhouGuangdong510515China
- Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic DiseasesGuangzhouGuangdong510515China
- Guangdong Key Laboratory of Biological ChipGuangzhouGuangdong510515China
| | - Huaping Zeng
- Hunan Research Center for Big Data Application in GenomicsGenetalks Inc.ChangshaHunan410152China
| | - Jun Chuan
- Hunan Research Center for Big Data Application in GenomicsGenetalks Inc.ChangshaHunan410152China
| | - Yuanping Du
- Hunan Research Center for Big Data Application in GenomicsGenetalks Inc.ChangshaHunan410152China
| | - Chouxian Ma
- Hunan Research Center for Big Data Application in GenomicsGenetalks Inc.ChangshaHunan410152China
| | - Peining Li
- Department of GeneticsYale UniversityNew HavenCT06520USA
| | - Zhuo Song
- Hunan Research Center for Big Data Application in GenomicsGenetalks Inc.ChangshaHunan410152China
| | - Xiangmin Xu
- Department of Medical GeneticsSchool of Basic Medical SciencesSouthern Medical UniversityGuangzhouGuangdong510515China
- Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic DiseasesGuangzhouGuangdong510515China
- Guangdong Key Laboratory of Biological ChipGuangzhouGuangdong510515China
| |
Collapse
|
9
|
Lee YK, Kim HJ, Lee K, Park SH, Song SH, Seong MW, Kim M, Han JY. Recent progress in laboratory diagnosis of thalassemia and hemoglobinopathy: a study by the Korean Red Blood Cell Disorder Working Party of the Korean Society of Hematology. Blood Res 2019; 54:17-22. [PMID: 30956959 PMCID: PMC6439293 DOI: 10.5045/br.2019.54.1.17] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 01/03/2019] [Indexed: 12/21/2022] Open
Abstract
Genetic hemoglobin disorders are caused by mutations and/or deletions in the α-globin or β-globin genes. Thalassemia is caused by quantitative defects and hemoglobinopathies by structural defect of hemoglobin. The incidence of thalassemia and hemoglobinopathy is increased in Korea with rapid influx of people from endemic areas. Thus, the awareness of the disease is needed. α-thalassemias are caused by deletions in α-globin gene, while β-thalassemias are associated with decreased synthesis of β-globin due to β-globin gene mutations. Hemoglobinopathies involve structural defects in hemoglobin due to altered amino acid sequence in the α- or β-globin chains. When the patient is suspected with thalassemia/hemoglobinopathy from abnormal complete blood count findings and/or family history, the next step is detecting hemoglobin abnormality using electrophoresis methods including high performance liquid chromatography and mass spectrometry. The development of novel molecular genetic technologies, such as massively parallel sequencing, facilitates a more precise molecular diagnosis of thalassemia/hemoglobinopathy. Moreover, prenatal diagnosis using genetic testing enables the prevention of thalassemia birth and pregnancy complications. We aimed to review the spectrum and classification of thalassemia/hemoglobinopathy diseases and the diagnostic strategies including screening tests, molecular genetic tests, and prenatal diagnosis.
Collapse
Affiliation(s)
- Young Kyung Lee
- Department of Laboratory Medicine, Hallym University College of Medicine, Anyang, Korea
| | - Hee-Jin Kim
- Department of Laboratory Medicine & Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Kyunghoon Lee
- Department of Laboratory Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Sang Hyuk Park
- Department of Laboratory Medicine, University of Ulsan College of Medicine, Ulsan University Hospital, Ulsan, Korea
| | - Sang Hoon Song
- Department of Laboratory Medicine, Seoul National University Hospital and College of Medicine, Seoul, Korea
| | - Moon-Woo Seong
- Department of Laboratory Medicine, Seoul National University Hospital and College of Medicine, Seoul, Korea
| | - Myungshin Kim
- Department of Laboratory Medicine, Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Jin Yeong Han
- Department of Laboratory Medicine, Dong-A University College of Medicine, Busan, Korea
| |
Collapse
|