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Zhang J, Wu Y, Chen S, Luo Q, Xi H, Li J, Qin X, Peng Y, Ma N, Yang B, Qiu X, Lu W, Chen Y, Jiang Y, Chen P, Liu Y, Zhang C, Zhang Z, Xiong Y, Shen J, Liang H, Ren Y, Ying C, Dong M, Li X, Xu C, Wang H, Zhang D, Xu C, Huang H. Prospective prenatal cell-free DNA screening for genetic conditions of heterogenous etiologies. Nat Med 2024; 30:470-479. [PMID: 38253798 DOI: 10.1038/s41591-023-02774-x] [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: 02/14/2023] [Accepted: 12/18/2023] [Indexed: 01/24/2024]
Abstract
Prenatal cell-free DNA (cfDNA) screening uses extracellular fetal DNA circulating in the peripheral blood of pregnant women to detect prevalent fetal chromosomal anomalies. However, numerous severe conditions with underlying single-gene defects are not included in current prenatal cfDNA screening. In this prospective, multicenter and observational study, pregnant women at elevated risk for fetal genetic conditions were enrolled for a cfDNA screening test based on coordinative allele-aware target enrichment sequencing. This test encompasses the following three of the most frequent pathogenic genetic variations: aneuploidies, microdeletions and monogenic variants. The cfDNA screening results were compared to invasive prenatal or postnatal diagnostic test results for 1,090 qualified participants. The comprehensive cfDNA screening detected a genetic alteration in 135 pregnancies with 98.5% sensitivity and 99.3% specificity relative to standard diagnostics. Of 876 fetuses with suspected structural anomalies on ultrasound examination, comprehensive cfDNA screening identified 55 (56.1%) aneuploidies, 6 (6.1%) microdeletions and 37 (37.8%) single-gene pathogenic variants. The inclusion of targeted monogenic conditions alongside chromosomal aberrations led to a 60.7% increase (from 61 to 98) in the detection rate. Overall, these data provide preliminary evidence that a comprehensive cfDNA screening test can accurately identify fetal pathogenic variants at both the chromosome and single-gene levels in high-risk pregnancies through a noninvasive approach, which has the potential to improve prenatal evaluation of fetal risks for severe genetic conditions arising from heterogenous molecular etiologies. ClinicalTrials.gov registration: ChiCTR2100045739 .
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Affiliation(s)
- Jinglan Zhang
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China.
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China.
- School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
- Beijing BioBiggen Technology Co., Ltd, Beijing, China.
| | - Yanting Wu
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Songchang Chen
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
| | - Qiong Luo
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Women's Reproductive Health of Zhejiang Province, and Zhejiang Provincial Clinical Research Center for Child Health, Zhejiang University School of Medicine, Hangzhou, China
| | - Hui Xi
- National Health Commission (NHC) Key Laboratory of Birth Defect for Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China
| | - Jianli Li
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Xiaomei Qin
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Ying Peng
- National Health Commission (NHC) Key Laboratory of Birth Defect for Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China
| | - Na Ma
- National Health Commission (NHC) Key Laboratory of Birth Defect for Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China
| | - Bingxin Yang
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiang Qiu
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Weiliang Lu
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Yuan Chen
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Women's Reproductive Health of Zhejiang Province, and Zhejiang Provincial Clinical Research Center for Child Health, Zhejiang University School of Medicine, Hangzhou, China
| | - Ying Jiang
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Women's Reproductive Health of Zhejiang Province, and Zhejiang Provincial Clinical Research Center for Child Health, Zhejiang University School of Medicine, Hangzhou, China
| | - Panpan Chen
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Women's Reproductive Health of Zhejiang Province, and Zhejiang Provincial Clinical Research Center for Child Health, Zhejiang University School of Medicine, Hangzhou, China
| | - Yifeng Liu
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Women's Reproductive Health of Zhejiang Province, and Zhejiang Provincial Clinical Research Center for Child Health, Zhejiang University School of Medicine, Hangzhou, China
| | - Chen Zhang
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
| | - Zhiwei Zhang
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Yu Xiong
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Jie Shen
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Huan Liang
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Yunyun Ren
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Chunmei Ying
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Minyue Dong
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Women's Reproductive Health of Zhejiang Province, and Zhejiang Provincial Clinical Research Center for Child Health, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaotian Li
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Congjian Xu
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Hua Wang
- National Health Commission (NHC) Key Laboratory of Birth Defect for Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China.
- NHC Key Laboratory of Birth Defects Research, Prevention and Treatment, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China.
| | - Dan Zhang
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China.
- Key Laboratory of Women's Reproductive Health of Zhejiang Province, and Zhejiang Provincial Clinical Research Center for Child Health, Zhejiang University School of Medicine, Hangzhou, China.
| | - Chenming Xu
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China.
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China.
| | - Hefeng Huang
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China.
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China.
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China.
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
- Research Units of Embryo Original Diseases, Chinese Academy of Medical Sciences, Shanghai, China.
- Shanghai Frontiers Science Research Center of Reproduction and Development, Shanghai, China.
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2
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De Falco L, Vitiello G, Savarese G, Suero T, Ruggiero R, Savarese P, Ianniello M, Petrillo N, Bruno M, Legnante A, Passaretti FF, Ardisia C, Di Spiezio Sardo A, Fico A. A Case Report of a Feto-Placental Mosaicism Involving a Segmental Aneuploidy: A Challenge for Genome Wide Screening by Non-Invasive Prenatal Testing of Cell-Free DNA in Maternal Plasma. Genes (Basel) 2023; 14:668. [PMID: 36980940 PMCID: PMC10048202 DOI: 10.3390/genes14030668] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 02/28/2023] [Accepted: 03/04/2023] [Indexed: 03/11/2023] Open
Abstract
Non-invasive prenatal testing (NIPT) using cell-free DNA can detect fetal chromosomal anomalies with high clinical sensitivity and specificity. In approximately 0.1% of clinical cases, the NIPT result and a subsequent diagnostic karyotype are discordant. Here we report a case of a 32-year-old pregnant patient with a 44.1 Mb duplication on the short arm of chromosome 4 detected by NIPT at 12 weeks' gestation. Amniocentesis was carried out at 18 weeks' gestation, followed by conventional and molecular cytogenetic analysis on cells from the amniotic fluid. SNP array analysis found a de novo deletion of 1.2 Mb at chromosome 4, and this deletion was found to be near the critical region of the Wolf-Hirschhorn syndrome. A normal 46,XY karyotype was identified by G-banding analysis. The patient underwent an elective termination and molecular investigations on tissues from the fetus, and the placenta confirmed the presence of type VI true fetal mosaicism. It is important that a patient receives counselling following a high-risk call on NIPT, with appropriate diagnostic analysis advised before any decisions regarding the pregnancy are taken. This case highlights the importance of genetic counselling following a high-risk call on NIPT, especially in light of the increasing capabilities of NIPT detection of sub-chromosomal deletions and duplications.
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Affiliation(s)
- Luigia De Falco
- AMES, Centro Polidiagnostico Strumentale, 80013 Naples, Italy
- Fondazione Genetica per la Vita Onlus, Via Cuma, 80132 Naples, Italy
| | - Giuseppina Vitiello
- Department of Molecular Medicine and Medical Biotechnologies, Federico II University Hospital, Via Pansini 5, 80131 Naples, Italy
| | - Giovanni Savarese
- AMES, Centro Polidiagnostico Strumentale, 80013 Naples, Italy
- Fondazione Genetica per la Vita Onlus, Via Cuma, 80132 Naples, Italy
| | - Teresa Suero
- AMES, Centro Polidiagnostico Strumentale, 80013 Naples, Italy
- Fondazione Genetica per la Vita Onlus, Via Cuma, 80132 Naples, Italy
| | - Raffaella Ruggiero
- AMES, Centro Polidiagnostico Strumentale, 80013 Naples, Italy
- Fondazione Genetica per la Vita Onlus, Via Cuma, 80132 Naples, Italy
| | - Pasquale Savarese
- AMES, Centro Polidiagnostico Strumentale, 80013 Naples, Italy
- Fondazione Genetica per la Vita Onlus, Via Cuma, 80132 Naples, Italy
| | - Monica Ianniello
- AMES, Centro Polidiagnostico Strumentale, 80013 Naples, Italy
- Fondazione Genetica per la Vita Onlus, Via Cuma, 80132 Naples, Italy
| | - Nadia Petrillo
- AMES, Centro Polidiagnostico Strumentale, 80013 Naples, Italy
- Fondazione Genetica per la Vita Onlus, Via Cuma, 80132 Naples, Italy
| | - Mariasole Bruno
- AMES, Centro Polidiagnostico Strumentale, 80013 Naples, Italy
- Fondazione Genetica per la Vita Onlus, Via Cuma, 80132 Naples, Italy
| | - Antonietta Legnante
- Department of Public Health, University of Naples “Federico II”, 80145 Naples, Italy
| | - Francesco Fioravanti Passaretti
- Department of Molecular Medicine and Medical Biotechnologies, Federico II University Hospital, Via Pansini 5, 80131 Naples, Italy
| | - Carmela Ardisia
- CRR Genetica Medica, Azienda Ospedaliera s. Maria della Misericordia, 06156 Perugia, Italy
| | | | - Antonio Fico
- AMES, Centro Polidiagnostico Strumentale, 80013 Naples, Italy
- Fondazione Genetica per la Vita Onlus, Via Cuma, 80132 Naples, Italy
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Alyafee Y, Al Tuwaijri A, Umair M, Alharbi M, Haddad S, Ballow M, Alayyar L, Alam Q, Althenayyan S, Al Ghilan N, Al Khaldi A, Faden MS, Al Sufyan H, Alfadhel M. Non-invasive prenatal testing for autosomal recessive disorders: A new promising approach. Front Genet 2022; 13:1047474. [PMID: 36406136 PMCID: PMC9669374 DOI: 10.3389/fgene.2022.1047474] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 10/19/2022] [Indexed: 11/06/2022] Open
Abstract
Background: In pregnant women at risk of autosomal recessive (AR) disorders, prenatal diagnosis of AR disorders primarily involves invasive procedures, such as chorionic villus sampling and amniocentesis. Methods: We collected blood samples from four pregnant women in their first trimester who presented a risk of having a child with an AR disorder. Cell-free DNA (cfDNA) was extracted, amplified, and double-purified to reduce maternal DNA interference. Additionally, whole-genome amplification was performed for traces of residual purified cfDNA for utilization in subsequent applications. Results: Based on our findings, we detected the fetal status with the family corresponding different genes, i.e., LZTR1, DVL2, HBB, RNASEH2B, and MYO7A, as homozygous affected, wild-type, and heterozygous carriers, respectively. Results were subsequently confirmed by prenatal amniocentesis. The results of AmpFLSTR™ Identifiler™ presented a distinct profile from the corresponding mother profile, thereby corroborating the result reflecting the genetic material of the fetus. Conclusion: Herein, we detected AR disease mutations in the first trimester of pregnancy while surmounting limitations associated with maternal genetic material interference. Importantly, such detection strategies would allow the screening of pregnant women for common AR diseases, especially in highly consanguineous marriage populations. This technique would open avenues for the early detection and prevention of recessive diseases among the population.
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Affiliation(s)
- Yusra Alyafee
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Abeer Al Tuwaijri
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
- Clinical Laboratory Sciences Department, College of Applied Medical Sciences, King Saud Bin Abdulaziz University for Health Sciences (KSAU-HS), Riyadh, Saudi Arabia
| | - Muhammad Umair
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Mashael Alharbi
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Shahad Haddad
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Maryam Ballow
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Latifah Alayyar
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Qamre Alam
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Saleh Althenayyan
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Nadia Al Ghilan
- Maternal Fetal Medicine Department, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Aziza Al Khaldi
- Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Majid S. Faden
- Department of Obstetrics and Gynaecology, Maternal Fetal Medicine, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Hamad Al Sufyan
- Assisted Reproductive Technology Laboratories, Thuriah Medical Center, Riyadh, Saudi Arabia
| | - Majid Alfadhel
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
- Genetics and Precision Medicine Department (GPM), King Abdullah Specialized Children’s Hospital, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, MNG-HA, Riyadh, Saudi Arabia
- *Correspondence: Majid Alfadhel,
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4
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Xu C, Li J, Chen S, Cai X, Jing R, Qin X, Pan D, Zhao X, Ma D, Xu X, Liu X, Wang C, Yang B, Zhang L, Li S, Chen Y, Pan N, Tang P, Song J, Liu N, Zhang C, Zhang Z, Qiu X, Lu W, Ying C, Li X, Xu C, Wang Y, Wu Y, Huang HF, Zhang J. Genetic deconvolution of fetal and maternal cell-free DNA in maternal plasma enables next-generation non-invasive prenatal screening. Cell Discov 2022; 8:109. [PMID: 36229437 PMCID: PMC9562363 DOI: 10.1038/s41421-022-00457-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 08/09/2022] [Indexed: 11/09/2022] Open
Abstract
Current non-invasive prenatal screening (NIPS) analyzes circulating fetal cell-free DNA (cfDNA) in maternal peripheral blood for selected aneuploidies or microdeletion/duplication syndromes. Many genetic disorders are refractory to NIPS largely because the maternal genetic material constitutes most of the total cfDNA present in the maternal plasma, which hinders the detection of fetus-specific genetic variants. Here, we developed an innovative sequencing method, termed coordinative allele-aware target enrichment sequencing (COATE-seq), followed by multidimensional genomic analyses of sequencing read depth, allelic fraction, and linked single nucleotide polymorphisms, to accurately separate the fetal genome from the maternal background. Analytical confounders including multiple gestations, maternal copy number variations, and absence of heterozygosity were successfully recognized and precluded for fetal variant analyses. In addition, fetus-specific genomic characteristics, including the cfDNA fragment length, meiotic error origins, meiotic recombination, and recombination breakpoints were identified which reinforced the fetal variant assessment. In 1129 qualified pregnancies tested, 54 fetal aneuploidies, 8 microdeletions/microduplications, and 8 monogenic variants were detected with 100% sensitivity and 99.3% specificity. Using the comprehensive cfDNA genomic analysis tools developed, we found that 60.3% of aneuploidy samples had aberrant meiotic recombination providing important insights into the mechanism underlying meiotic nondisjunctions. Altogether, we show that the genetic deconvolution of the fetal and maternal cfDNA enables thorough and accurate delineation of fetal genome which paves the way for the next-generation prenatal screening of essentially all types of human genetic disorders.
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Affiliation(s)
- Chenming Xu
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China. .,International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Jianli Li
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Songchang Chen
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China.,International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, China
| | - Xiaoqiang Cai
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Ruilin Jing
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Xiaomei Qin
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Dong Pan
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Xin Zhao
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Dongyang Ma
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Xiufeng Xu
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Xiaojun Liu
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Can Wang
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Bingxin Yang
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Lanlan Zhang
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Shuyuan Li
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yiyao Chen
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Nina Pan
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ping Tang
- Jiaxing Maternity and Child Health Care Hospital, Jiaxing, Zhejiang, China
| | - Jieping Song
- Medical Genetics Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, Hubei, China
| | - Nian Liu
- Medical Genetics Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, Hubei, China
| | - Chen Zhang
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China.,International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Zhiwei Zhang
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Xiang Qiu
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Weiliang Lu
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Chunmei Ying
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Xiaotian Li
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Congjian Xu
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Yanlin Wang
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yanting Wu
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China. .,Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China.
| | - He-Feng Huang
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China. .,International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China. .,Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China. .,Research Units of Embryo Original Diseases, Chinese Academy of Medical Sciences, Shanghai, China.
| | - Jinglan Zhang
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China. .,International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China. .,Beijing BioBiggen Technology Co., Ltd, Beijing, China.
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5
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Liehr T. False-positives and false-negatives in non-invasive prenatal testing (NIPT): what can we learn from a meta-analyses on > 750,000 tests? Mol Cytogenet 2022; 15:36. [PMID: 35986330 PMCID: PMC9392255 DOI: 10.1186/s13039-022-00612-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 07/28/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Non-invasive prenatal testing (NIPT) has had an incomparable triumph in prenatal diagnostics in the last decade. Over 1400 research articles have been published, predominantly praising the advantages of this test.
Methods
The present study identified among the 1400 papers 24 original and one review paper, which were suited to re-evaluate the efficacy of > 750,000 published NIPT-results. Special attention was given to false-positive and false-negative result-rates. Those were discussed under different aspects—mainly from a patient-perspective.
Results
A 27: 1 rate of false-positive compared to false-negative NIPT results was found. Besides, according to all reported, real-positive, chromosomally aberrant NIPT cases, 90% of those would have been aborted spontaneously before birth. These findings are here discussed under aspects like (i) How efficient is NIPT compared to first trimester screening? (ii) What are the differences in expectations towards NIPT from specialists and the public? and (iii) There should also be children born suffering from not by NIPT tested chromosomal aberrations; why are those never reported in all available NIPT studies?
Conclusions
Even though much research has been published on NIPT, unbiased figures concerning NIPT and first trimester screening efficacy are yet not available. While false positive rates of different NIPT tests maybe halfway accurate, reported false-negative rates are most likely too low. The latter is as NIPT-cases with negative results for tested conditions are yet not in detail followed up for cases with other genetic or teratogenic caused disorders. This promotes an image in public, that NIPT is suited to replace all invasive tests, and also to solve the problem of inborn errors in humans, if not now then in near future. Overall, it is worth discussing the usefulness of NIPT in practical clinical application. Particularly, asking for unbiased figures concerning the efficacy of first trimester-screening compared to NIPT, and for really comprehensive data on false-positive and false-negative NIPT results.
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6
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Jin S, Huang D, Jin W, Wang Y, Shao H, Gong L, Luo Z, Yang Z, Luan J, Xie D, Ding C. Detection of DNA copy number alterations by matrix-assisted laser desorption/ionization time-of-flight mass spectrometric analysis of single nucleotide polymorphisms. Clin Chem Lab Med 2022; 60:1543-1550. [PMID: 35938948 DOI: 10.1515/cclm-2022-0511] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 07/20/2022] [Indexed: 12/13/2022]
Abstract
OBJECTIVES Copy number alterations (CNAs) are frequently found in malignant tissues. Different approaches have been used for CNA detection. However, it is not easy to detect a large panel of CNA targets in heterogenous tumors. METHODS We have developed a CNAs detection approach through quantitatively analyzed allelic imbalance by allelotyping single nucleotide polymorphisms (SNPs) by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Furthermore, the copy number changes were quantified by real-competitive PCR (rcPCR) to distinguish loss of heterozygosity (LOH) and genomic amplification. The approach was used to validate the CNA regions detected by next generation sequencing (NGS) in early-stage lung carcinoma. RESULTS CNAs were detected in heterogeneous DNA samples where tumor DNA is present at only 10% through the SNP based allelotyping. In addition, two different types of CNAs (loss of heterozygosity and chromosome amplification) were able to be distinguished quantitatively by rcPCR. Validation on a total of 41 SNPs from the selected CNA regions showed that copy number changes did occur, and the tissues from early-stage lung carcinoma were distinguished from normal. CONCLUSIONS CNA detection by MALDI-TOF MS can be used for validating potentially interesting genomic regions identified from next generation sequencing, and for detecting CNAs in tumor tissues consisting of a mixture of neoplastic and normal cells.
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Affiliation(s)
- Shengnan Jin
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China.,Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China
| | - Dan Huang
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China.,Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China
| | - Weijiang Jin
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China.,Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China
| | - Yourong Wang
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China.,Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China
| | - Hengrong Shao
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China.,Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China
| | - Lisha Gong
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China.,Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China
| | - Zhenni Luo
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China.,Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China
| | - Zhengquan Yang
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China.,Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China
| | - Ju Luan
- Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China; and InnoMed Diagnostics Inc., Wenzhou, P.R. China
| | - Deyao Xie
- Department of Thoracic Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China
| | - Chunming Ding
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China.,Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China
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7
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Enrichment of circulating trophoblasts from maternal blood using filtration-based Metacell® technology. PLoS One 2022; 17:e0271226. [PMID: 35834570 PMCID: PMC9282611 DOI: 10.1371/journal.pone.0271226] [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: 11/25/2021] [Accepted: 06/26/2022] [Indexed: 11/23/2022] Open
Abstract
In a cell-based non-invasive prenatal test (cbNIPT), intact circulating trophoblasts (CTs) are isolated from maternal blood for subsequent genetic analysis. Enrichment of these CTs from maternal blood is the most challenging step in the cbNIPT workflow. This study aims to assess the suitability of the filtration-based Metacell® technology to enrich CTs from maternal blood at week 10 to 13 of gestation. The Metacell® technology is a novel size-based enrichment technology that combines blood filtration through 8 μm pores with an in vitro culture method. Three protocols were evaluated. First, 8 mL or 16 mL of maternal blood was filtered and subsequently cultured in vitro on the separation membrane for 3 days in RPMI 1640. In addition, 16 mL of maternal blood was filtered, and immediately processed without further culturing. Y-chromosome-specific qPCR or STR analysis was performed to evaluate the enrichment of CTs. A total of 44 samples from pregnant women, out of which 26 were carrying a male fetus, were processed. Although five enriched male fetus samples show detectable male DNA quantities, it cannot be excluded that the obtained positive signal is caused by cell-free fetal DNA sticking to the Metacell® separation membrane. In conclusion, the Metacell® technology, tested as described, is not suitable for consistent enrichment of CTs.
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Zaninović L, Bašković M, Ježek D, Katušić Bojanac A. Validity and Utility of Non-Invasive Prenatal Testing for Copy Number Variations and Microdeletions: A Systematic Review. J Clin Med 2022; 11:jcm11123350. [PMID: 35743413 PMCID: PMC9224664 DOI: 10.3390/jcm11123350] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/31/2022] [Accepted: 06/08/2022] [Indexed: 02/07/2023] Open
Abstract
Valid data on prenatal cell-free DNA-based screening tests for copy number variations and microdeletions are still insufficient. We aimed to compare different methodological approaches concerning the achieved diagnostic accuracy measurements and positive predictive values. For this systematic review, we searched the Scopus and PubMed databases and backward citations for studies published between 2013 and 4 February 2022 and included articles reporting the analytical and clinical performance of cfDNA screening tests for CNVs and microdeletions. Of the 1810 articles identified, 32 met the criteria. The reported sensitivity of the applied tests ranged from 20% to 100%, the specificity from 81.62% to 100%, and the PPV from 3% to 100% for cases with diagnostic or clinical follow-up information. No confirmatory analysis was available in the majority of cases with negative screening results, and, therefore, the NPVs could not be determined. NIPT for CNVs and microdeletions should be used with caution and any developments regarding new technologies should undergo strict evaluation before their implementation into clinical practice. Indications for testing should be in correlation with the application guidelines issued by international organizations in the field of prenatal diagnostics.
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Affiliation(s)
- Luca Zaninović
- Scientific Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Šalata 3, 10 000 Zagreb, Croatia; (L.Z.); (D.J.); (A.K.B.)
- Children’s Hospital Zagreb, Ulica Vjekoslava Klaića 16, 10 000 Zagreb, Croatia
| | - Marko Bašković
- Scientific Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Šalata 3, 10 000 Zagreb, Croatia; (L.Z.); (D.J.); (A.K.B.)
- Children’s Hospital Zagreb, Ulica Vjekoslava Klaića 16, 10 000 Zagreb, Croatia
- Correspondence: ; Tel.: +385-1-3636-379
| | - Davor Ježek
- Scientific Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Šalata 3, 10 000 Zagreb, Croatia; (L.Z.); (D.J.); (A.K.B.)
- Department of Histology and Embryology, School of Medicine, University of Zagreb, Šalata 3, 10 000 Zagreb, Croatia
- Department of Transfusion Medicine and Transplantation Biology, University Hospital Centre Zagreb, Kišpatićeva 12, 10 000 Zagreb, Croatia
| | - Ana Katušić Bojanac
- Scientific Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Šalata 3, 10 000 Zagreb, Croatia; (L.Z.); (D.J.); (A.K.B.)
- Department of Medical Biology, School of Medicine, University of Zagreb, Šalata 3, 10 000 Zagreb, Croatia
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9
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Gug C, Mozos I, Ratiu A, Tudor A, Gorduza EV, Caba L, Gug M, Cojocariu C, Furau C, Furau G, Vaida MA, Stoicanescu D. Genetic Counseling and Management: The First Study to Report NIPT Findings in a Romanian Population. MEDICINA (KAUNAS, LITHUANIA) 2022; 58:medicina58010079. [PMID: 35056387 PMCID: PMC8777823 DOI: 10.3390/medicina58010079] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 12/18/2021] [Accepted: 12/30/2021] [Indexed: 04/25/2023]
Abstract
Background and Objectives: Non-invasive prenatal testing (NIPT) has been confirmed as the most accurate screening test for trisomies 21, 18, 13, sex chromosomes aneuploidies and several microdeletions. This study aimed to assess the accuracy of cell free DNA testing based on low-level whole-genome sequencing to screen for these chromosomal abnormalities and to evaluate the clinical performance of NIPT. Materials and Methods: 380 consecutive cases from a single genetic center, from Western Romania were included in this retrospective study. Cell-free nucleic acid extraction from maternal blood, DNA sequencing and analysis of sequenced regions were performed by BGI Hong Kong and Invitae USA to determine the risk of specific fetal chromosomal abnormalities. In high-risk cases the results were checked by direct analysis of fetal cells obtained by invasive methods: 6 chorionic villus sampling and 10 amniocenteses followed by combinations of QF-PCR, karyotyping and aCGH. Results: NIPT results indicated low risk in 95.76% of cases and high risk in 4.23%. Seven aneuploidies and one microdeletion were confirmed, the other results were found to be a false-positive. A gestational age of up to 22 weeks had no influence on fetal fraction. There were no significant differences in fetal fraction across the high and low risk groups. Conclusions: This is the first study in Romania to report the NIPT results. The confirmation rate was higher for autosomal aneuploidies compared to sex chromosome aneuploidies and microdeletions. All cases at risk for trisomy 21 were confirmed. Only one large fetal microdeletion detected by NIPT has been confirmed. False positive NIPT results, not confirmed by invasive methods, led to the decision to continue the pregnancy. The main limitation of the study is the small number of patients included. NIPT can be used as a screening method for all pregnancies, but in high-risk cases, an invasive confirmation test was performed.
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Affiliation(s)
- Cristina Gug
- Department of Microscopic Morphology, “Victor Babeş” University of Medicine and Pharmacy, 300041 Timisoara, Romania; (C.G.); (D.S.)
| | - Ioana Mozos
- Department of Functional Sciences, Discipline of Pathophysiology, “Victor Babes” University of Medicine and Pharmacy, 300173 Timisoara, Romania
- Center for Translational Research and Systems Medicine, “Victor Babes” University of Medicine and Pharmacy, 300173 Timisoara, Romania
- Correspondence: ; Tel.: +40-745610004
| | - Adrian Ratiu
- Department of Obstetrics and Gynecology II, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania;
- Obstetrics-Gynecology Clinic IV, Municipal Emergency Clinical Hospital, 300231 Timisoara, Romania
| | - Anca Tudor
- Department of Functional Sciences, Discipline of Medical Informatics and Biostatistics, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania;
| | - Eusebiu Vlad Gorduza
- Department of Medical Genetics, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania; (E.V.G.); (L.C.)
| | - Lavinia Caba
- Department of Medical Genetics, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania; (E.V.G.); (L.C.)
| | - Miruna Gug
- Faculty of Medicine, “Victor Babeş” University of Medicine and Pharmacy, 300041 Timisoara, Romania; (M.G.); (C.C.)
| | - Catalina Cojocariu
- Faculty of Medicine, “Victor Babeş” University of Medicine and Pharmacy, 300041 Timisoara, Romania; (M.G.); (C.C.)
| | - Cristian Furau
- Life Sciences Department, Faculty of Medicine, “Vasile Goldis“ Western University of Arad, 310414 Arad, Romania;
| | - Gheorghe Furau
- General Medicine Department, Faculty of Medicine, “Vasile Goldis“ Western University of Arad, 310414 Arad, Romania;
| | - Monica Adriana Vaida
- Department of Anatomy and Embryology, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania;
| | - Dorina Stoicanescu
- Department of Microscopic Morphology, “Victor Babeş” University of Medicine and Pharmacy, 300041 Timisoara, Romania; (C.G.); (D.S.)
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10
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Bevilacqua E, Jani JC, Chaoui R, Suk EA, Palma‐Dias R, Ko T, Warsof S, Stokowski R, Jones KJ, Grati FR, Schmid M. Performance of a targeted cell-free DNA prenatal test for 22q11.2 deletion in a large clinical cohort. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2021; 58:597-602. [PMID: 34090308 PMCID: PMC8518527 DOI: 10.1002/uog.23699] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 05/10/2021] [Accepted: 05/21/2021] [Indexed: 05/17/2023]
Abstract
OBJECTIVE 22q11.2 deletion is more common than trisomies 18 and 13 combined, yet no routine approach to prenatal screening for this microdeletion has been established. This study evaluated the clinical sensitivity and specificity of a targeted cell-free DNA (cfDNA) test to screen for fetal 22q11.2 deletion in a large cohort, using blinded analysis of prospectively enrolled pregnancies and stored clinical samples. METHODS In order to ensure that the analysis included a meaningful number of cases with fetal 22q11.2 deletion, maternal plasma samples were obtained by prospective, multicenter enrolment of pregnancies with a fetal cardiac abnormality and from stored clinical samples from a research sample bank. Fetal genetic status, as evaluated by microarray analysis, karyotyping with fluorescence in-situ hybridization or a comparable test, was available for all cases. Samples were processed as described previously for the Harmony prenatal test, with the addition of DANSR (Digital Analysis of Selected Regions) assays targeting the 3.0-Mb region of 22q11.2 associated with 22q11.2 deletion syndrome. Operators were blinded to fetal genetic status. Sensitivity and specificity of the cfDNA test for 22q11.2 deletion were calculated based on concordance between the cfDNA result and fetal genotype. RESULTS The final study group consisted of 735 clinical samples, including 358 from prospectively enrolled pregnancies and 377 stored clinical samples. Of 46 maternal plasma samples from pregnancies with a 22q11.2 deletion, ranging in size from 1.25 to 3.25 Mb, 32 had a cfDNA result indicating a high probability of 22q11.2 deletion (sensitivity, 69.6% (95% CI, 55.2-80.9%)). All 689 maternal plasma samples without a 22q11.2 deletion were classified correctly by the cfDNA test as having no evidence of a 22q11.2 deletion (specificity, 100% (95% CI, 99.5-100%)). CONCLUSIONS The results of this large-scale prospective clinical evaluation of the sensitivity and specificity of a targeted cfDNA test for fetal 22q11.2 deletion demonstrate that this test can detect the common and smaller, nested 22q11.2 deletions with a low (0-0.5%) false-positive rate. Although the positive predictive value (PPV) observed in this study population was 100%, the expected PPV in the general pregnant population is estimated to be 12.2% at 99.5% specificity and 41.1% at 99.9% specificity. The use of this cfDNA test to screen for 22q11.2 deletion could enhance identification of pregnancies at risk for 22q11.2 deletion syndrome without significantly increasing the likelihood of maternal anxiety and unnecessary invasive procedures related to a false-positive result. © 2021 The Authors. Ultrasound in Obstetrics & Gynecology published by John Wiley & Sons Ltd on behalf of International Society of Ultrasound in Obstetrics and Gynecology.
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Affiliation(s)
- E. Bevilacqua
- Department of Obstetrics and Gynecology, University Hospital BrugmannUniversité Libre de BruxellesBrusselsBelgium
| | - J. C. Jani
- Department of Obstetrics and Gynecology, University Hospital BrugmannUniversité Libre de BruxellesBrusselsBelgium
| | - R. Chaoui
- Prenatal Diagnosis and Human GeneticsBerlinGermany
| | - E.‐K. A. Suk
- Prenatal Diagnosis and Human GeneticsBerlinGermany
| | - R. Palma‐Dias
- The Royal Women's HospitalUniversity of MelbourneParkvilleVICAustralia
| | - T.‐M. Ko
- Genephile Bioscience Laboratory, Ko's Obstetrics & Gynecology ClinicTaipei CityTaiwan
| | - S. Warsof
- Eastern Virginia Medical SchoolNorfolkVAUSA
| | | | - K. J. Jones
- Roche Sequencing Solutions, Inc.San JoseCAUSA
| | - F. R. Grati
- TOMA Advanced Biomedical Assays S.p.A, Impact Lab.Busto ArsizioItaly
| | - M. Schmid
- Roche Sequencing Solutions, Inc.San JoseCAUSA
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11
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Srebniak MI, Jehee FS, Joosten M, Boter M, de Valk WG, van der Helm R, Sistermans EA, Voorhoeve E, Bhola S, Hoffer MJV, den Hollander N, Macville MVE, Van Opstal D. Non-invasive prenatal diagnosis for translocation carriers-YES please or NO go? Acta Obstet Gynecol Scand 2021; 100:2036-2043. [PMID: 34472080 DOI: 10.1111/aogs.14256] [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: 05/04/2021] [Revised: 08/10/2021] [Accepted: 08/16/2021] [Indexed: 11/28/2022]
Abstract
INTRODUCTION The presence of an unbalanced familial translocation can be reliably assessed in the cytotrophoblast of chorionic villi. However, carriers of a balanced translocation often decline invasive testing. This study aimed to investigate whether an unbalanced translocation can also be diagnosed in cell free DNA by whole-genome non-invasive prenatal screening (NIPS). MATERIAL AND METHODS Pregnant women carrying a fetus with an unbalanced familial translocation, for whom NIPS as well as microarray data were available, were included in this retrospective assessment. NIPS was performed in the course of the TRIDENT study. RESULTS In 12 cases, both NIPS and microarray data were available. In 10 of 12 cases the unbalanced translocation was correctly identified by NIPS without prior knowledge on parental translocation. One was missed because the fetal fraction was too low. One was missed because of technical restrictions in calling 16p gains. CONCLUSIONS This study supports the hypothesis that routine NIPS may be used for prenatal diagnosis of unbalanced inheritance of familial translocations, especially with prior knowledge of the translocation allowing focused examination of the involved chromosomal regions. Our study showed that routine shallow sequencing designed for aneuploidy detection in cell free DNA may be sufficient for higher resolution NIPS, if specialized copy number software is used and if sufficient fetal fraction is present.
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Affiliation(s)
| | - Fernanda S Jehee
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Marieke Joosten
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Marjan Boter
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Walter G de Valk
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Robert van der Helm
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Erik A Sistermans
- Department of Clinical Genetics and Amsterdam Reproduction and Development Research Institute, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Els Voorhoeve
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Shama Bhola
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Mariette J V Hoffer
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Merryn V E Macville
- Department of Clinical Genetics, GROW School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Diane Van Opstal
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
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12
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Zhytnik L, Peters M, Tilk K, Simm K, Tõnisson N, Reimand T, Maasalu K, Acharya G, Krjutškov K, Salumets A. From late fatherhood to prenatal screening of monogenic disorders: evidence and ethical concerns. Hum Reprod Update 2021; 27:1056-1085. [PMID: 34329448 DOI: 10.1093/humupd/dmab023] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 06/27/2021] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND With the help of ART, an advanced parental age is not considered to be a serious obstacle for reproduction anymore. However, significant health risks for future offspring hide behind the success of reproductive medicine for the treatment of reduced fertility associated with late parenthood. Although an advanced maternal age is a well-known risk factor for poor reproductive outcomes, understanding the impact of an advanced paternal age on offspring is yet to be elucidated. De novo monogenic disorders (MDs) are highly associated with late fatherhood. MDs are one of the major sources of paediatric morbidity and mortality, causing significant socioeconomic and psychological burdens to society. Although individually rare, the combined prevalence of these disorders is as high as that of chromosomal aneuploidies, indicating the increasing need for prenatal screening. With the help of advanced reproductive technologies, families with late paternity have the option of non-invasive prenatal testing (NIPT) for multiple MDs (MD-NIPT), which has a sensitivity and specificity of almost 100%. OBJECTIVE AND RATIONALE The main aims of the current review were to examine the effect of late paternity on the origin and nature of MDs, to highlight the role of NIPT for the detection of a variety of paternal age-associated MDs, to describe clinical experiences and to reflect on the ethical concerns surrounding the topic of late paternity and MD-NIPT. SEARCH METHODS An extensive search of peer-reviewed publications (1980-2021) in English from the PubMed and Google Scholar databases was based on key words in different combinations: late paternity, paternal age, spermatogenesis, selfish spermatogonial selection, paternal age effect, de novo mutations (DNMs), MDs, NIPT, ethics of late fatherhood, prenatal testing and paternal rights. OUTCOMES An advanced paternal age provokes the accumulation of DNMs, which arise in continuously dividing germline cells. A subset of DNMs, owing to their effect on the rat sarcoma virus protein-mitogen-activated protein kinase signalling pathway, becomes beneficial for spermatogonia, causing selfish spermatogonial selection and outgrowth, and in some rare cases may lead to spermatocytic seminoma later in life. In the offspring, these selfish DNMs cause paternal age effect (PAE) disorders with a severe and even life-threatening phenotype. The increasing tendency for late paternity and the subsequent high risk of PAE disorders indicate an increased need for a safe and reliable detection procedure, such as MD-NIPT. The MD-NIPT approach has the capacity to provide safe screening for pregnancies at risk of PAE disorders and MDs, which constitute up to 20% of all pregnancies. The primary risks include pregnancies with a paternal age over 40 years, a previous history of an affected pregnancy/child, and/or congenital anomalies detected by routine ultrasonography. The implementation of NIPT-based screening would support the early diagnosis and management needed in cases of affected pregnancy. However, the benefits of MD-NIPT need to be balanced with the ethical challenges associated with the introduction of such an approach into routine clinical practice, namely concerns regarding reproductive autonomy, informed consent, potential disability discrimination, paternal rights and PAE-associated issues, equity and justice in accessing services, and counselling. WIDER IMPLICATIONS Considering the increasing parental age and risks of MDs, combined NIPT for chromosomal aneuploidies and microdeletion syndromes as well as tests for MDs might become a part of routine pregnancy management in the near future. Moreover, the ethical challenges associated with the introduction of MD-NIPT into routine clinical practice need to be carefully evaluated. Furthermore, more focus and attention should be directed towards the ethics of late paternity, paternal rights and paternal genetic guilt associated with pregnancies affected with PAE MDs.
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Affiliation(s)
- Lidiia Zhytnik
- Competence Centre on Health Technologies, Tartu, Estonia
| | - Maire Peters
- Competence Centre on Health Technologies, Tartu, Estonia.,Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Kadi Tilk
- Competence Centre on Health Technologies, Tartu, Estonia
| | - Kadri Simm
- Institute of Philosophy and Semiotics, Faculty of Arts and Humanities, University of Tartu, Tartu, Estonia.,Centre of Ethics, University of Tartu, Tartu, Estonia
| | - Neeme Tõnisson
- Institute of Genomics, University of Tartu, Tartu, Estonia.,Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia.,Department of Reproductive Medicine, West Tallinn Central Hospital, Tallinn, Estonia
| | - Tiia Reimand
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia.,Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Katre Maasalu
- Clinic of Traumatology and Orthopaedics, Tartu University Hospital, Tartu, Estonia.,Department of Traumatology and Orthopaedics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Ganesh Acharya
- Division of Obstetrics and Gynaecology, Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet, Stockholm, Sweden
| | - Kaarel Krjutškov
- Competence Centre on Health Technologies, Tartu, Estonia.,Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Andres Salumets
- Competence Centre on Health Technologies, Tartu, Estonia.,Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia.,Institute of Genomics, University of Tartu, Tartu, Estonia.,Division of Obstetrics and Gynaecology, Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet, Stockholm, Sweden
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13
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Bianco K, Sherwin EB, Konigshofer Y, Girsen AI, Sylvester KG, Garlick RK. Novel Approaches to Develop Critical Reference Materials for Noninvasive Prenatal Testing: A Pilot Study. J Appl Lab Med 2021; 6:1492-1504. [PMID: 34080621 DOI: 10.1093/jalm/jfab037] [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: 01/04/2021] [Accepted: 03/29/2021] [Indexed: 11/13/2022]
Abstract
BACKGROUND Highly characterized reference materials are required to expand noninvasive prenatal testing (NIPT) for low incidence aneuploidies and microdeletions. The goal of this study was to develop reference materials for the development of next generation circulating cell-free DNA (ccfDNA) assays. METHODS This was a prospective study of pregnancies complicated by positive prenatal genetic screening. ccfDNA was isolated from maternal plasma and amplified. Lymphoblastoid cell lines were prepared from maternal peripheral blood mononuclear cells and fetal cord blood cells. Cells were Epstein-Barr virus immortalized and expanded. Amplified DNA and to a limited extent formulated lymphoblastoid-derived ccfDNA was tested in SNP-based and chromosome counting (CC) based massively parallel sequencing assays. RESULTS Enrolled cases included fetuses with: T21 (2), T18 (1), T18-XXX (1), XYY (1), microdeletions (1), and euploid (2). Three lymphoblastoid cells lines were prepared. Genomic DNA was extracted from cell lines and fragmented to simulate ccfDNA. ccfDNA isolation yielded about 2000 usable genome equivalents of DNA for each case for amplification. Although the sonicated genomic DNA derived from lymphoblastoid cell lines did not yield results compatible with NIPT assays, when blinded, NIPT platforms correctly identified the amplified ccfDNA isolated from blood in the majority of cases. CONCLUSIONS This study showed that maternal blood samples from pregnancies complicated by common chromosomal abnormalities can be used to generate materials for the development and evaluation of NIPT assays.
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Affiliation(s)
- Katherine Bianco
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Stanford University School of Medicine, Stanford, CA, USA
| | - Elizabeth B Sherwin
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Anna I Girsen
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Stanford University School of Medicine, Stanford, CA, USA
| | - Karl G Sylvester
- Division of Pediatric Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA
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14
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Qi QG, Tuo Y, Liu LX, Yu CX, Wu AN. Amniocentesis and Next Generation Sequencing (NGS)-Based Noninvasive Prenatal DNA Testing (NIPT) for Prenatal Diagnosis of Fetal Chromosomal Disorders. Int J Gen Med 2021; 14:1811-1817. [PMID: 34025125 PMCID: PMC8132573 DOI: 10.2147/ijgm.s297585] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 04/15/2021] [Indexed: 11/23/2022] Open
Abstract
Objective The present study aimed to evaluate and analyze the results of karyotyping by amniocentesis and next generation sequencing (NGS)-based noninvasive prenatal DNA testing (NIPT) for the prenatal diagnosis of fetal chromosomal disorders. Methods A total of 2267 high-risk pregnant females with the indications for prenatal diagnosis who met the enrollment criteria between January 2015 and May 2019 at the Affiliated Hospital of Inner Mongolia Medical University were included and underwent NGS-based NIPT in the present study. Amniocentesis, chromosome karyotyping by cell culture, and follow-up of the pregnancy outcomes were also conducted in the NIPT-positive pregnant females to assess the consistency between NIPT and results of karyotyping by amniocentesis. Results Among the 2267 cases, 29 cases were positive for NIPT, including 10 cases with a high risk of trisomy 21, 2 cases with a high risk of trisomy 18, 2 cases with a high risk of chromosome 13, and 20 cases with sex chromosome abnormalities. All the above NIPT-positive cases underwent amniocentesis, and 20 cases were eventually diagnosed. The sensitivity and specificity of NIPT for the diagnosis of trisomy 21, trisomy 13, and trisomy 18 were 100%, 99.96%, 100%, and 99.96%, 100%, 100%, respectively, and the positive predictive values were 91.67%, 66.67%, and 100%, respectively. Conclusion NGS of the fetal free DNA from the peripheral blood of pregnant females was an important complement to the prenatal diagnosis of chromosomal disorders represented by fetal chromosome aneuploidy with high sensitivity and specificity. In combination with the traditional karyotyping by amniocentesis, it could improve the diagnostic efficacy for fetal chromosomal disorders.
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Affiliation(s)
- Qi-Ge Qi
- Department of Clinical Laboratory and Pathology, The 969th Hospital of P.L.A., Hohhot, Inner Mongolia, 010051, People's Republic of China
| | - Ya Tuo
- Department of Obstetrics and Gynecology, The Affiliated Hospital of Inner Mongolia Medical University, Inner Mongolia University, Hohhot, Inner Mongolia, 010050, People's Republic of China
| | - Li-Xue Liu
- Department of Obstetrics and Gynecology, The Affiliated Hospital of Inner Mongolia Medical University, Inner Mongolia University, Hohhot, Inner Mongolia, 010050, People's Republic of China
| | - Cong-Xiang Yu
- Department of Obstetrics and Gynecology, The Affiliated Hospital of Inner Mongolia Medical University, Inner Mongolia University, Hohhot, Inner Mongolia, 010050, People's Republic of China
| | - Ai-Ning Wu
- Department of Obstetrics and Gynecology, The Affiliated Hospital of Inner Mongolia Medical University, Inner Mongolia University, Hohhot, Inner Mongolia, 010050, People's Republic of China
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15
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Yang L, Wu Y, Hu Z, Zhang H, Pu D, Yan H, Zhang S, Jiang H, Liu Q, Yuan Y, Zhang Y, Chen F, Lu Y, Pan S, Lin L, Gao Y. Simultaneous detection of fetal aneuploidy, de novo FGFR3 mutations and paternally derived β-thalassemia by a novel method of noninvasive prenatal testing. Prenat Diagn 2021; 41:440-448. [PMID: 33340121 PMCID: PMC8048498 DOI: 10.1002/pd.5879] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 11/09/2020] [Accepted: 12/02/2020] [Indexed: 11/08/2022]
Abstract
OBJECTIVE The aim is to develop a novel noninvasive prenatal testing (NIPT) method that simultaneously performs fetal aneuploidy screening and the detection of de novo and paternally derived mutations. METHODS A total of 68 pregnancies, including 26 normal pregnancies, 7 cases with fetal aneuploidies, 7 cases with fetal achondroplasia or thanatophoric dysplasia, 18 cases with fetal skeletal abnormalities, and 10 cases with β-thalassemia high risk were recruited. Plasma cell-free DNA was amplified by Targeted And Genome-wide simultaneous sequencing (TAGs-seq) to generate around 99% of total reads covering the whole-genome region and around 1% covering the target genes. The reads on the whole-genome region were analyzed for fetal aneuploidy using a binary hypothesis T-score and the reads on target genes were analyzed for point mutations by calculating the minor allelic frequency of loci on FGFR3 and HBB. TAGs-seq results were compared with conventional NIPT and diagnostic results. RESULTS In each sample, TAGs-seq generated 44.7-54 million sequencing reads covering the whole-genome region of 0.1-3× and the target genes of >1000×depth. All cases of fetal aneuploidy and de novo mutations of achondroplasia/thanatophoric dysplasia were identified with high sensitivities and specificities except for one false-negative paternal mutation of β-thalassemia. CONCLUSIONS TAGs-seq is a novel NIPT method that combines the fetal aneuploidy screening and the detection of de novo FGFR3 mutations and paternal HBB mutations.
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Affiliation(s)
- Lin Yang
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China.,School of Future Technology, University of Chinese Academy of Sciences, Beijing, China
| | - Yujing Wu
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China
| | - Zhiyang Hu
- Department of Obstetrics, Shenzhen People's Hospital, The Second Clinical Medical School of Jinan University, Shenzhen, China
| | | | | | | | | | | | - Qiang Liu
- Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen, China
| | - Yuying Yuan
- Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen, China
| | | | | | - Yanping Lu
- Department of Obstetrics and Gynecology, Chinese PLA General Hospital, Beijing, China
| | - Silin Pan
- Qingdao Women and Children's Hospital, Qingdao University, Qingdao, China
| | - Linhua Lin
- Department of Obstetrics, Shenzhen People's Hospital, The Second Clinical Medical School of Jinan University, Shenzhen, China
| | - Ya Gao
- BGI-Shenzhen, Shenzhen, China.,Shenzhen Engineering Laboratory for Birth Defects Screening, Shenzhen, China
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16
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Kiani AK, Paolacci S, Scanzano P, Michelini S, Capodicasa N, D'Agruma L, Notarangelo A, Tonini G, Piccinelli D, Farshid KR, Petralia P, Fulcheri E, Buffelli F, Chiurazzi P, Terranova C, Plotti F, Angioli R, Castori M, Pös O, Szemes T, Bertelli M. Prenatal genetic diagnosis: Fetal therapy as a possible solution to a positive test. ACTA BIO-MEDICA : ATENEI PARMENSIS 2020; 91:e2020021. [PMID: 33170180 PMCID: PMC8023142 DOI: 10.23750/abm.v91i13-s.10534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 09/17/2020] [Indexed: 11/23/2022]
Abstract
BACKGROUND Fetal abnormalities cause 20% of perinatal deaths. Advances in prenatal genetic and other types of screening offer great opportunities for identifying high risk pregnancies. METHODS Through a literature search, here we summarise what are the prenatal diagnostic technique that are being used and how those techniques may allow for prenatal interventions. RESULTS Next generation sequencing and non-invasive prenatal testing are fundamental for clinical diagnostics because of their sensitivity and accuracy in identifying point mutations, aneuploidies, and microdeletions, respectively. Timely identification of genetic disorders and other fetal abnormalities enables early intervention, such as in-utero gene therapy, fetal drug therapy and prenatal surgery. CONCLUSION Prenatal intervention is mainly focused on conditions that may cause death or lifelong disabilities, like spina bifida, congenital diaphragm hernia and sacrococcygeal teratoma; and may be an alternative therapeutic option to termination of pregnancy. However, it is not yet widely available, due to lack of specialized centers.
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Affiliation(s)
| | | | | | - Sandro Michelini
- Department of Rehabilitation, San Giovanni Battista Hospital, Rome, Italy.
| | | | - Leonardo D'Agruma
- Division of Medical Genetics, Fondazione IRCCS-Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy.
| | - Angelantonio Notarangelo
- Division of Medical Genetics, Fondazione IRCCS-Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy.
| | - Gerolamo Tonini
- Surgical Department, Unit of Urology, Poliambulanza Foundation, Brescia, Italy.
| | - Daniela Piccinelli
- Department of Mother and Child Health, Unit of Obstetrics and Gynecology, Poliambulanza Foundation, Brescia, Italy.
| | | | | | - Ezio Fulcheri
- UOSD Fetal and Perinatal Pathology, Department of Translational Research, Laboratory Medicine, Diagnostics and Services, IRCCS Giannina Gaslini Institute, Genoa, Italy.
| | - Francesca Buffelli
- UOSD Fetal and Perinatal Pathology, Department of Translational Research, Laboratory Medicine, Diagnostics and Services, IRCCS Giannina Gaslini Institute, Genoa, Italy.
| | - Pietro Chiurazzi
- Istituto di Medicina Genomica, Università Cattolica del Sacro Cuore, Rome, Italy; UOC Genetica Medica, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome Italy.
| | - Corrado Terranova
- University Campus Bio Medico of Rome, Department of Obstetrics and Gynecology, Rome, Italy.
| | - Francesco Plotti
- University Campus Bio Medico of Rome, Department of Obstetrics and Gynecology, Rome, Italy.
| | - Roberto Angioli
- University Campus Bio Medico of Rome, Department of Obstetrics and Gynecology, Rome, Italy.
| | - Marco Castori
- Division of Medical Genetics, Fondazione IRCCS-Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy.
| | - Ondrej Pös
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia; Geneton Ltd., Bratislava, Slovakia.
| | - Tomas Szemes
- 14 Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia; Geneton Ltd., Bratislava, Slovakia; Comenius University Science Park, Bratislava, Slovakia.
| | - Matteo Bertelli
- MAGI EUREGIO, Bolzano, Italy; MAGI'S LAB, Rovereto (TN), Italy; EBTNA-LAB, Rovereto (TN), Italy.
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17
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A Novel Graphic-Aided Algorithm (gNIPT) Improves the Accuracy of Noninvasive Prenatal Testing. BIOMED RESEARCH INTERNATIONAL 2020; 2020:4712657. [PMID: 32775425 PMCID: PMC7397410 DOI: 10.1155/2020/4712657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 06/24/2020] [Accepted: 06/30/2020] [Indexed: 11/18/2022]
Abstract
Noninvasive Prenatal Testing (NIPT) has advanced the detection of fetal chromosomal aneuploidy by analyzing cell-free DNA in peripheral maternal blood. The statistic Z-test that it utilizes, which measures the deviation of each chromosome dosage from its negative control, is now widely accepted in clinical practice. However, when a chromosome has loss and gain regions which offset each other in the z-score calculation, merely using the Z-test for the result tends to be erroneous. To improve the performance of NIPT in this aspect, a novel graphic-aided algorithm (gNIPT) that requires no extra experiment procedures is reported in this study. In addition to the Z-test, this method provides a detailed analysis of each chromosome by dividing each chromosome into multiple 2 Mb size windows, calculating the z-score and copy number variation of each window, and visualizing the z-scores for each chromosome in a line chart. Data from 13537 singleton pregnancy women were analyzed and compared using both the normal NIPT (nNIPT) analysis and the gNIPT method. The gNIPT method had significantly improved the overall positive predictive value (PPV) of nNIPT (88.14% vs. 68.00%, p = 0.0041) and the PPV for trisomy 21 (T21) detection (93.02% vs. 71.43%, p = 0.0037). There were no significant differences between gNIPT and nNIPT in PPV for trisomy 18 (T18) detection (88.89% vs. 63.64%, p = 0.1974) and in PPV for trisomy 13 (T13) detection (57.14% vs. 50.00%, p = 0.8004). One false-negative T18 case in nNIPT was detected by gNIPT, which demonstrates the potency of gNIPT in discerning chromosomes that have variation in multiple regions with an offsetting effect in z-score calculation. The gNIPT was also able to detect copy number variation (CNV) in chromosomes, and one case with pathogenic CNV was detected during the study. With no additional test requirement, gNIPT presents a reasonable solution in improving the accuracy of normal NIPT.
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