1
|
Panchalee T, Poungvarin N, Amornrit W, Yaiyiam C, Wataganara T. The first 2-year prospective audit of prenatal cell-free deoxyribonucleic screening using single nucleotide polymorphisms approach in a single academic laboratory. J Perinat Med 2024:jpm-2024-0339. [PMID: 39468924 DOI: 10.1515/jpm-2024-0339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2024] [Accepted: 10/10/2024] [Indexed: 10/30/2024]
Abstract
OBJECTIVES We reported a performance during an implementation of prenatal cell-free (cf) DNA screening using single nucleotide polymorphism (SNP) approach in our accredited laboratory. METHODS Prospective audit with prompt intervention was set for the processing of 2,502 samples from singleton pregnancy from August 2017 to July 2019. Risks of trisomy 21 (T21), T18, T13, monosomy X (XO), and other sex chromosome aneuploidies (SCAs) were clarified by a proprietary bioinformatics algorithm. RESULTS Laboratory failure occurred in 192 samples (7.7 %) as a result of inadequate sequencing (n=144), fundamental limitation of the testing (n=19), and obvious human error (n=29). Faulty setting of the calibration curve was the most common human error (n=22/29). After a redraw (n=110), 79 (71.8 %) were settled. Overall, 2,389/2,502 samples (95.5 %) were reportable. Thirty-five samples were high-risk for T21 (n=19), T18 (n=5), T13 (n=1), XO (n=3), and other SCAs (n=7), respectively. Positive predictive values calculated from either prenatal confirmatory tests or postnatal findings were 93.8 % (n=16), 100 % (n=4), 50 % (n=2), and 83.3 % (n=6) for T21, T18, XO, and other SCAs, respectively, with high sensitivity and specificity (>99.9 %). Vanishing twin was detected from 1 out of 4 samples with detected additional haplotypes. CONCLUSIONS An overall performance of SNP-based prenatal cf-DNA screening during our initial implementation can be optimized with proactive approach. The technical know-how was a significant limiting factor for adopting the technology. The lessons learnt may be of interest to the academic laboratory considering adopting their own test instead of sending blood to a testing service of a supplier.
Collapse
Affiliation(s)
- Tachjaree Panchalee
- Department of Obstetrics and Gynecology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Naravat Poungvarin
- Department of Clinical Pathology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Warisa Amornrit
- Department of Clinical Pathology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Chutima Yaiyiam
- Department of Obstetrics and Gynecology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Tuangsit Wataganara
- Department of Obstetrics and Gynecology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| |
Collapse
|
2
|
Claudel N, Barrois M, Vivanti AJ, Rosenblatt J, Salomon LJ, Jouannic JM, Picone O, Carbillon L, Vialard F, Launay E, Tsatsaris V, Curis E, El Khattabi L. Non-invasive cell-free DNA prenatal screening for trisomy 21 as part of primary screening strategy in twin pregnancy. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2024; 63:807-814. [PMID: 37470702 DOI: 10.1002/uog.26311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 05/27/2023] [Accepted: 05/31/2023] [Indexed: 07/21/2023]
Abstract
OBJECTIVES The performance of non-invasive prenatal screening using cell-free DNA testing of maternal blood in twin pregnancy is underevaluated, while serum marker-based strategies yield poor results. This study aimed to assess the performance of non-invasive prenatal screening for trisomy 21 in twin pregnancy as a first-tier test. Secondary objectives were to assess its failure rate and factors associated with failure. METHODS This retrospective cohort study included twin pregnancies in which non-invasive prenatal screening using cell-free DNA was performed as the primary screening strategy between May 2017 and October 2019. We used the NIPT VeriSeq® test for in-vitro diagnosis and set a fetal fraction cut-off of 4% for monochorionic pregnancies and 8% for dichorionic ones. Clinical data and pregnancy outcome were collected from physicians or midwives via a questionnaire or were retrieved directly on-site. We calculated the performance of non-invasive cell-free DNA screening for trisomy 21, analyzed its failure rate and assessed potentially associated factors. RESULTS Among 1885 twin pregnancies with follow-up, there were six (0.32%) confirmed cases of trisomy 21. The sensitivity of non-invasive prenatal screening for trisomy 21 was 100% (95% CI, 54.1-100%) and the false-positive rate was 0.23% (95% CI, 0.06-0.59%). The primary failure rate was 4.6%, with 4.0% being due to insufficient fetal fraction. A successful result was obtained for 65.4% of women who underwent a new blood draw, reducing the overall failure rate to 2.8%. Maternal body mass index, gestational age at screening as well as chorionicity were significantly associated with the risk of failure. CONCLUSION This study provides further evidence of the high performance, at an extremely low false-positive rate, of non-invasive prenatal screening in twins as part of a primary screening strategy for trisomy 21. © 2023 The Authors. Ultrasound in Obstetrics & Gynecology published by John Wiley & Sons Ltd on behalf of International Society of Ultrasound in Obstetrics and Gynecology.
Collapse
Affiliation(s)
- N Claudel
- Maternité Port Royal, AP-HP Hôpital Cochin, FHU Prema, Paris, France
- Université Paris Cité, Paris, France
- INSERM UMR_S1139, Paris, France
| | - M Barrois
- Maternité Port Royal, AP-HP Hôpital Cochin, FHU Prema, Paris, France
- Université Paris Cité, Paris, France
- INSERM UMR_S1139, Paris, France
| | - A J Vivanti
- Service de Gynécologie-Obstétrique, DMU Santé des Femmes et des Nouveau-nés, AP-HP Hôpital Antoine Béclère, Clamart, France
- Université Paris-Saclay, Orsay, France
| | - J Rosenblatt
- Service de Gynécologie-Obstétrique, AP-HP Hôpital Universitaire Robert-Debré, Paris, France
| | - L J Salomon
- Université Paris Cité, Paris, France
- Service de Gynécologie-Obstétrique, AP-HP Hôpital Universitaire Necker-Enfants Malades, Paris, France
| | - J-M Jouannic
- Département de Médecine Fœtale, Pôle ORIGYNE.6, AP-HP Hôpital Armand Trousseau, Paris, France
- Université Sorbonne Paris Cité, Paris, France
| | - O Picone
- Service de Gynécologie-Obstétrique, AP-HP Hôpital Louis Mourier, Colombes, France
- Université Paris Diderot, INSERM UMR1137, IAME, Paris, France
| | - L Carbillon
- Service de Gynécologie-Obstétrique, AP-HP Hôpital Jean-Verdier, Bondy, France
- Université Paris 13, Bobigny, France
| | - F Vialard
- Service de Cytogénétique, CHI Poissy-Saint Germain en Laye, Poissy, France
| | - E Launay
- Service de Cytogénétique et Biologie Cellulaire, CHU Rennes, Rennes, France
| | - V Tsatsaris
- UR 7537 BioSTM, UFR de Pharmacie, Faculté de Santé, Université Paris Cité, Paris, France
| | - E Curis
- UR 7537 BioSTM, UFR de Pharmacie, Faculté de Santé, Université Paris Cité, Paris, France
- Laboratoire d'Hématologie, Hôpital Lariboisière, AP-HP.nord, Paris, France
| | - L El Khattabi
- Plateforme de Dépistage Prénatal Non Invasif par Analyse de l'ADN Libre Circulant, AP-HP, Hôpital Cochin and Université Paris Cité, Paris, France
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute (ICM), Inserm, CNRS, Hôpital Pitié Salpêtrière, Paris, France
- Unité de Génomique Chromosomique, Département de Génétique Médicale, APHP, Hôpitaux Armand Trousseau et Pitié-Salpêtrière, Paris Brain Institute - ICM, Sorbonne Université, Paris, France
| |
Collapse
|
3
|
Chen Y, Wu Z, Sutlive J, Wu K, Mao L, Nie J, Zhao XZ, Guo F, Chen Z, Huang Q. Noninvasive prenatal diagnosis targeting fetal nucleated red blood cells. J Nanobiotechnology 2022; 20:546. [PMID: 36585678 PMCID: PMC9805221 DOI: 10.1186/s12951-022-01749-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 12/15/2022] [Indexed: 12/31/2022] Open
Abstract
Noninvasive prenatal diagnosis (NIPD) aims to detect fetal-related genetic disorders before birth by detecting markers in the peripheral blood of pregnant women, holding the potential in reducing the risk of fetal birth defects. Fetal-nucleated red blood cells (fNRBCs) can be used as biomarkers for NIPD, given their remarkable nature of carrying the entire genetic information of the fetus. Here, we review recent advances in NIPD technologies based on the isolation and analysis of fNRBCs. Conventional cell separation methods rely primarily on physical properties and surface antigens of fNRBCs, such as density gradient centrifugation, fluorescence-activated cell sorting, and magnetic-activated cell sorting. Due to the limitations of sensitivity and purity in Conventional methods, separation techniques based on micro-/nanomaterials have been developed as novel methods for isolating and enriching fNRBCs. We also discuss emerging methods based on microfluidic chips and nanostructured substrates for static and dynamic isolation of fNRBCs. Additionally, we introduce the identification techniques of fNRBCs and address the potential clinical diagnostic values of fNRBCs. Finally, we highlight the challenges and the future directions of fNRBCs as treatment guidelines in NIPD.
Collapse
Affiliation(s)
- Yanyu Chen
- grid.207374.50000 0001 2189 3846Academy of Medical Sciences, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450052 China ,grid.49470.3e0000 0001 2331 6153School of Physics and Technology, Wuhan University, Wuhan, 430072 China
| | - Zhuhao Wu
- grid.411377.70000 0001 0790 959XDepartment of Intelligent Systems Engineering, Indiana University, Bloomington, IN 47405 USA
| | - Joseph Sutlive
- grid.38142.3c000000041936754XDivision of Thoracic and Cardiac Surgery, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115 USA
| | - Ke Wu
- grid.49470.3e0000 0001 2331 6153School of Physics and Technology, Wuhan University, Wuhan, 430072 China
| | - Lu Mao
- grid.207374.50000 0001 2189 3846Academy of Medical Sciences, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450052 China
| | - Jiabao Nie
- grid.38142.3c000000041936754XDivision of Thoracic and Cardiac Surgery, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115 USA ,grid.261112.70000 0001 2173 3359Department of Biological Sciences, Northeastern University, Boston, MA 02115 USA
| | - Xing-Zhong Zhao
- grid.49470.3e0000 0001 2331 6153School of Physics and Technology, Wuhan University, Wuhan, 430072 China
| | - Feng Guo
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN, 47405, United States.
| | - Zi Chen
- Division of Thoracic and Cardiac Surgery, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
| | - Qinqin Huang
- The Research and Application Center of Precision Medicine, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450052, China.
| |
Collapse
|
4
|
Clinical, Cytogenetic and Molecular Cytogenetic Outcomes of Cell-Free DNA Testing for Rare Chromosomal Anomalies. Genes (Basel) 2022; 13:genes13122389. [PMID: 36553656 PMCID: PMC9777917 DOI: 10.3390/genes13122389] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 12/13/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
The scope of cell-free DNA (cfDNA) testing was expanded to the genome, which allowed screening for rare chromosome anomalies (RCAs). Since the efficiency of the test for RCAs remains below the common aneuploidies, there is a debate on the usage of expanded tests. This study focuses on the confirmatory and follow-up data of cases with positive cfDNA testing for RCAs and cases with screen-negative results in a series of 912 consecutive cases that underwent invasive testing following cfDNA testing. Chorion villus sampling (CVS), amniocentesis (AS), fetal blood sampling, and term placenta samples were investigated using classical cytogenetic and molecular cytogenetic techniques. Out of 593 screen-positive results, 504 (85%) were for common aneuploidies, 40 (6.7%) for rare autosomal trisomies (RATs), and 49 (8.3%) for structural chromosome anomalies (SAs). Of the screen-positives for RATs, 20 cases were evaluated only in fetal tissue, and confined placental mosaicism (CPM) could not be excluded. Among cases with definitive results (n = 20), the rates of true positives, placental mosaics, and false positives were 35%, 45%, and 10%, respectively. Among screen-positives for SAs, 32.7% were true positives. The confirmation rate was higher for duplications than deletions (58.3% vs. 29.4%). The rate of chromosomal abnormality was 10.9% in the group of 256 screen-negatives with pathological ultrasound findings. This study provides further data to assess the efficiency of expanded cfDNA testing for RATs and SAs. The test efficiency for cfDNA seems to be higher for duplications than for deletions, which is evidence of the role of expert ultrasound in identifying pregnancies at increased risk for chromosome anomalies, even in pregnancies with screen-negatives. Furthermore, we discussed the efficiency of CVS vs. AC in screen-positives for RATs.
Collapse
|
5
|
Yang L, Bu G, Ma Y, Zhao J, Rezak J, La X. Comparison of noninvasive prenatal screening for defined pathogenic microdeletion/microduplication syndromes and nonsyndromic copy number variations: a large multicenter study. J Comp Eff Res 2022; 11:1277-1291. [PMID: 36200453 DOI: 10.2217/cer-2022-0088] [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: 12/26/2022] Open
Abstract
Background: This retrospective study assessed the precision of noninvasive prenatal testing (NIPT) in detecting microdeletion/microduplication syndromes (MMSs) and nonsyndromic copy number variations (CNVs). Methods: The study included 19,086 singleton pregnancies screened on NIPT using high-throughput sequencing. Pregnancies with CNVs on NIPT underwent amniocentesis for karyotyping and CNV sequencing (CNV-seq). We analyzed pathogenic MMSs and nonsyndromic CNVs separately, dividing the CNVs into subgroups based on fragment size and fetal ultrasound findings. Results: A total of 170 abnormalities were detected by NIPT, of which 113 (66.5%) underwent invasive testing. The positive predictive value (PPV) of CNV-seq for all types of CNV detected by NIPT was 35.4%, with PPVs of 61.5 and 27.6% for pathogenic MMSs and nonsyndromic CNVs, respectively. PPVs for NIPT showed different values depending on gestational characteristics, with the highest PPV for NIPT in the group with increased nuchal thickness (66.7%) and for the abnormal ultrasound group (57.1%). CNVs ≤5 Mb with normal ultrasound findings were generally associated with a healthy fetus. Conclusion: NIPT can detect chromosomal aberrations in the first trimester, with high performance for MMSs. However, due to the low PPV for nonsyndromic CNVs, and the good pregnancy outcome in most cases, the introduction of expanded NIPT would cause an increase in unnecessary invasive procedures and inappropriate terminations of pregnancy.
Collapse
Affiliation(s)
- Li Yang
- Department of Prenatal Diagnosis, Center for Reproductive Medicine, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, 830054, PR China
| | - Guosen Bu
- Department of Neurology, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, 830054, PR China
| | - Yuyu Ma
- State Key Laboratory of Pathogenesis, Prevention & Treatment of High Incidence Diseases in Central Asia, Clinical Laboratory Center, Tumor Hospital Affiliated to Xinjiang Medical University, Urumqi, Xinjiang, 830011, PR China
| | - Jing Zhao
- Department of Prenatal Diagnosis, Center for Reproductive Medicine, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, 830054, PR China
| | - Jiamilla Rezak
- Department of Prenatal Diagnosis, Center for Reproductive Medicine, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, 830054, PR China
| | - Xiaolin La
- Department of Prenatal Diagnosis, Center for Reproductive Medicine, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, 830054, PR China
| |
Collapse
|
6
|
Xue H, Yu A, Lin M, Chen X, Guo Q, Xu L, Huang H. Efficiency of expanded noninvasive prenatal testing in the detection of fetal subchromosomal microdeletion and microduplication in a cohort of 31,256 single pregnancies. Sci Rep 2022; 12:19750. [PMID: 36396840 PMCID: PMC9672043 DOI: 10.1038/s41598-022-24337-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 11/14/2022] [Indexed: 11/18/2022] Open
Abstract
Noninvasive prenatal testing (NIPT) is widely used to screen for common fetal chromosomal aneuploidies. However, the ability of NIPT-Plus to detect copy number variation (CNV) is debatable. Accordingly, we assessed the efficiency of NIPT-Plus to detect clinically significant fetal CNV. We performed a prospective analysis of 31,260 singleton pregnancies, included from June 2017 to December 2020. Cell-free fetal DNA was directly sequenced using the semiconductor sequencing platform for women with high-risk CNV with clinically significant results. Fetal karyotyping and chromosomal microarray analysis (or next-generation sequencing) are recommended for invasive diagnostic procedures. Women at low risk with no other abnormal results continued their pregnancies. We analyzed the expanded NIPT results, diagnostic test results, and follow-up information to evaluate its performance in detecting fetal CNV. Of the 31,260 pregnant women who received NIPT-Plus, 31,256 cases were tested successfully, a high risk of clinically significant CNV was detected in 221 cases (0.71%); 18 women refused further diagnosis; 203 women underwent invasive prenatal diagnosis; and 78 true positive cases and 125 false positive cases, with an overall positive predictive value (PPV) of 38.42% and a false positive rate of 0.40%. For known microdeletion/microduplication syndromes (n = 27), the PPVs were 75% DiGeorge syndrome (DGS), 80% 22q11.22 microduplication, 50% Prader-Willi syndrome, and 50% cri-du-chat. For the remaining clinically significant fetal CNVs (n = 175), the combined PPVs were 46.5% (CNVs > 10 Mb) and 28.57% (CNVs ≤ 10 Mb). NIPT-Plus screening for CNV has certain clinical value. NIPT-Plus yielded relatively high PPVs for 22q11.2 microduplication syndrome and DGS, and low to moderate PPVs for other CNVs.
Collapse
Affiliation(s)
- Huili Xue
- grid.256112.30000 0004 1797 9307Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001 Fujian Province China
| | - Aili Yu
- grid.256112.30000 0004 1797 9307Reproductive Medicine Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001 Fujian Province China
| | - Min Lin
- grid.256112.30000 0004 1797 9307Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001 Fujian Province China
| | - Xuemei Chen
- grid.256112.30000 0004 1797 9307Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001 Fujian Province China
| | - Qun Guo
- grid.256112.30000 0004 1797 9307Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001 Fujian Province China
| | - Liangpu Xu
- grid.256112.30000 0004 1797 9307Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001 Fujian Province China
| | - Hailong Huang
- grid.256112.30000 0004 1797 9307Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001 Fujian Province China
| |
Collapse
|
7
|
Liehr T, Harutyunyan T, Williams H, Weise A. Non-Invasive Prenatal Testing in Germany. Diagnostics (Basel) 2022; 12:2816. [PMID: 36428876 PMCID: PMC9689121 DOI: 10.3390/diagnostics12112816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/09/2022] [Accepted: 11/14/2022] [Indexed: 11/18/2022] Open
Abstract
In the short 10 years following the introduction of non-invasive prenatal testing (NIPT), it has been adapted in many countries around the world as a standard screening test. In this review, this development was analyzed with a special focus on Germany. As a result, it can be stated that all known advantages of NIPT apart from "compensating for having no access to centers offering invasive diagnostics" are valid for Germany. In addition, following a review of the international literature, all documented issues with NIPT are also observed in Germany. However, the German Gene Diagnostics Act (GenDG) addresses a number of these issues, for example, the regulations by GenDG hamper induced abortions, based exclusively on an abnormal NIPT result. At the same time, GenDG has created new problems, as a possible collusion between the "right not to know with regard to parts of the examination result" may occur, or that the sex of the fetus must not be reported to the pregnant woman before the 12th week of gestation. Main conclusions drawn are that appropriate training and the continuing education of the physicians providing NIPT-related counseling are needed, as well as the provision of balanced and comprehensive information for the pregnant woman or the couple that is imperative.
Collapse
Affiliation(s)
- Thomas Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, 07747 Jena, Germany
| | - Tigran Harutyunyan
- Department of Genetics and Cytology, Yerevan State University, Yerevan 0001, Armenia
| | | | - Anja Weise
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, 07747 Jena, Germany
| |
Collapse
|
8
|
Tong X, Yu X, Du Y, Su F, Liu Y, Li H, Liu Y, Mu K, Liu Q, Li H, Zhu J, Xu H, Xiao F, Li Y. Peripheral Blood Microbiome Analysis via Noninvasive Prenatal Testing Reveals the Complexity of Circulating Microbial Cell-Free DNA. Microbiol Spectr 2022; 10:e0041422. [PMID: 35608350 PMCID: PMC9241824 DOI: 10.1128/spectrum.00414-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 05/02/2022] [Indexed: 11/25/2022] Open
Abstract
While circulating cell-free DNA (cfDNA) is becoming a powerful marker for noninvasive identification of infectious pathogens in liquid biopsy specimens, a microbial cfDNA baseline in healthy individuals is urgently needed for the proper interpretation of microbial cfDNA sequencing results in clinical metagenomics. Because noninvasive prenatal testing (NIPT) shares many similarities with the sequencing protocol of metagenomics, we utilized the standard low-pass whole-genome-sequencing-based NIPT to establish a microbial cfDNA baseline in healthy people. Sequencing data from a total of 107,763 peripheral blood samples of healthy pregnant women undergoing NIPT screening were retrospectively collected and reanalyzed for microbiome DNA screening. It was found that more than 95% of exogenous cfDNA was from bacteria, 3% from eukaryotes, and 0.4% from viruses, indicating the gut/environment origins of many microorganisms. Overall and regional abundance patterns were well illustrated, with huge regional diversity and complexity, and unique interspecies and symbiotic relationships were observed for TORCH organisms (Toxoplasma gondii, others [Treponema pallidum {causing syphilis}, hepatitis B virus {HBV}, and human parvovirus B19 {HPV-B19}], rubella virus, cytomegalovirus [CMV], and herpes simplex virus [HSV]) and another common virus, Epstein-Barr virus (EBV). To sum up, our study revealed the complexity of the baseline circulating microbial cfDNA and showed that microbial cfDNA sequencing results need to be interpreted in a more comprehensive manner. IMPORTANCE While circulating cell-free DNA (cfDNA) has been becoming a powerful marker for noninvasive identification of infectious pathogens in liquid biopsy specimens, a baseline for microbial cfDNA in healthy individuals is urgently needed for the proper interpretation of microbial cfDNA sequencing results in clinical metagenomics. Standard low-pass whole-genome-sequencing-based NIPT shares many similarities with the sequencing protocol for metagenomics and could provide a microbial cfDNA baseline in healthy people; thus, a reference cfDNA data set of the human microbiome was established with sequencing data from a total of 107,763 peripheral blood samples of healthy pregnant women undergoing NIPT screening. Our study revealed the complexity of circulating microbial cfDNA and indicated that microbial cfDNA sequencing results need to be interpreted in a more comprehensive manner, especially with regard to geographic patterns and coexistence networks.
Collapse
Affiliation(s)
- Xunliang Tong
- Department of Pulmonary and Critical Care Medicine, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Xiaowei Yu
- Center for Reproductive Medicine, Center for Prenatal Diagnosis, First Hospital, Jilin University, Changchun, Jilin, China
| | - Yang Du
- Annoroad Gene Technology Co., Ltd., Beijing, China
| | - Fei Su
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Ye Liu
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Hexin Li
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Yunshan Liu
- Annoroad Gene Technology Co., Ltd., Beijing, China
| | - Kai Mu
- Department of Medical Genetics, Zibo Women and Children Hospital, Zibo, China
| | - Qingsong Liu
- Chengdu Women’s and Children’s Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Hui Li
- Clinical Laboratory, Maternal and Child Health Hospital of Hubei Province, Wuhan, China
| | - Jiansheng Zhu
- Medical Genetic Center, Maternity and Child Health Hospital of Anhui Province, Hefei, China
| | - Hongtao Xu
- Department of Laboratory Medicine, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Fei Xiao
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
- The Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Yanming Li
- Department of Pulmonary and Critical Care Medicine, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| |
Collapse
|
9
|
Atli EI, Atli E, Inan C, Varol GF, Mail C, Erbilen EA, Yalcintepe S, Demir S, Gurkan H. Prenatal diagnosis and molecular cytogenetic characterization of partial dup (18p)/del (18q) due to a maternal pericentric inversion 18 in a foetus with multiple anomalies. Taiwan J Obstet Gynecol 2022; 61:504-509. [PMID: 35595446 DOI: 10.1016/j.tjog.2022.03.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/19/2021] [Indexed: 10/18/2022] Open
Abstract
OBJECTIVE The 18q terminal deletion with inverted duplication is an extremely rare abnormality, with only three confirmed cases in Europe to date. Here, we report, for the first time, a case of de novo 18q inv-dup-del in a Turkish pregnant woman. CASE REPORT A 30-year-old pregnant woman was referred for genetic analysis at her 25th gestational week due to foetal diaphragmatic hernia and rocker bottom feet. Cytogenetic analysis of the parents revealed a karyotype of 46,XX,inv(18) (p11.3q21.3) of the mother and a normal karyotype of the father. The foetal karyotype was defined as 46,XX,rec(18)del(18q)inv(18) (p11.3q21.3)mat. CONCLUSION To our knowledge, this is the first report of a prenatal diagnosis. Genetic counselling issues for this family, particularly affected individuals, include an increased likelihood of reduced fertility and a risk of recurrence of parental inversion equal to 1/2 in surviving offspring.
Collapse
Affiliation(s)
- Emine Ikbal Atli
- Department of Medical Genetics, Faculty of Medicine, Trakya University, Edirne, Turkey.
| | - Engin Atli
- Department of Medical Genetics, Faculty of Medicine, Trakya University, Edirne, Turkey
| | - Cihan Inan
- Division of Perinatology, Department of Obstetrics & Gynecology, Faculty of Medicine, Trakya University, Edirne, Turkey
| | - Gülizar Fusun Varol
- Division of Perinatology, Department of Obstetrics & Gynecology, Faculty of Medicine, Trakya University, Edirne, Turkey
| | - Cisem Mail
- Department of Medical Genetics, Faculty of Medicine, Trakya University, Edirne, Turkey
| | - Esra Altan Erbilen
- Division of Perinatology, Department of Obstetrics & Gynecology, Faculty of Medicine, Trakya University, Edirne, Turkey
| | - Sinem Yalcintepe
- Department of Medical Genetics, Faculty of Medicine, Trakya University, Edirne, Turkey
| | - Selma Demir
- Department of Medical Genetics, Faculty of Medicine, Trakya University, Edirne, Turkey
| | - Hakan Gurkan
- Department of Medical Genetics, Faculty of Medicine, Trakya University, Edirne, Turkey
| |
Collapse
|
10
|
Li J, Ju J, Zhao Q, Liu W, Yuan Y, Liu Q, Zhou L, Han Y, Yuan W, Huang Y, Xie Y, Li Z, Chen J, Huang S, Chen R, Li W, Tan M, Wang D, Zhou S, Zhang J, Zeng F, Yu N, Su F, Chen M, Ge Y, Huang Y, Jin X. Effective Identification of Maternal Malignancies in Pregnancies Undergoing Noninvasive Prenatal Testing. Front Genet 2022; 13:802865. [PMID: 35265103 PMCID: PMC8900746 DOI: 10.3389/fgene.2022.802865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 01/10/2022] [Indexed: 11/22/2022] Open
Abstract
Background: The existence of maternal malignancy may cause false-positive results or failed tests of NIPT. Though recent studies have shown multiple chromosomal aneuploidies (MCA) are associated with malignancy, there is still no effective solution to identify maternal cancer patients from pregnant women with MCA results using NIPT. We aimed to develop a new method to effectively detect maternal cancer in pregnant women with MCA results using NIPT and a random forest classifier to identify the tissue origin of common maternal cancer types. Methods: For examination, 496 participants with MCA results via NIPT were enrolled from January 2016 to June 2019 at BGI. Cancer and non-cancer participants were confirmed through the clinical follow-up. The cohort comprising 42 maternal cancer cases and 294 non-cancer cases enrolled from January 2016 to December 2017 was utilized to develop a method named mean of the top five chromosome z scores (MTOP5Zscores). The remaining 160 participants enrolled from January 2018 to June 2019 were used to validate the performance of MTOP5Zscores. We established a random forest model to classify three common cancer types using normalized Pearson correlation coefficient (NPCC) values, z scores of 22 chromosomes, and seven plasma tumor markers (PTMs) as predictor variables. Results: 62 maternal cancer cases were confirmed with breast cancer, liver cancer, and lymphoma, the most common cancer types. MTOP5Zscores showed a sensitivity of 85% (95% confidence interval (CI), 62.11–96.79%) and specificity of 80% (95% CI, 72.41–88.28%) in the detection of maternal cancer among pregnant women with MCA results. The sensitivity of the classifier was 93.33, 66.67, and 50%, while specificity was 66.67, 90, and 97.06%, and positive predictive value (PPV) was 60.87, 72.73, and 80% for the prediction of breast cancer, liver cancer, and lymphoma, respectively. Conclusion: This study presents a solution to identify maternal cancer patients from pregnant women with MCA results using NIPT, indicating it as a value-added application of NIPT in the detection of maternal malignancies in addition to screening for fetal aneuploidies with no extra cost.
Collapse
Affiliation(s)
- Jia Li
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
- Hebei Industrial Technology Research Institute of Genomics in Maternal & Child Health, Shijiazhuang BGI Genomics Co., Ltd., Shijiazhuang, China
| | - Jia Ju
- BGI-Shenzhen, Shenzhen, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | - Qiang Zhao
- Department of Obstetrics and Gynecology, Jiangmen Central Hospital, Jiangmen, China
- Reproductive Medicine Center, Jiangmen Central Hospital, Jiangmen, China
| | - Weiqiang Liu
- Central Lab, Longgang District Maternity & Child Healthcare Hospital of Shenzhen City, Shenzhen, China
| | | | - Qiang Liu
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Lijun Zhou
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Yuan Han
- BGI-Wuhan, BGI-Shenzhen, Wuhan, China
| | - Wen Yuan
- BGI-Wuhan, BGI-Shenzhen, Wuhan, China
| | - Yonghua Huang
- Department of Obstetrics and Gynecology, Jiangmen Central Hospital, Jiangmen, China
| | - Yingjun Xie
- Department of Obstetrics and Gynecology, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zhihua Li
- Department of Prenatal Diagnosis and Fetal Medical, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jingsi Chen
- Department of Prenatal Diagnosis and Fetal Medical, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Shuyu Huang
- The Department of Obstetrics, Foshan First People’s Hospital, Foshan, China
| | - Rufang Chen
- The Department of Obstetrics, Foshan First People’s Hospital, Foshan, China
| | - Wei Li
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Meihua Tan
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | - Danchen Wang
- School of Basic Medicine, Qingdao University, Qingdao, China
| | - Si Zhou
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
- Hebei Industrial Technology Research Institute of Genomics in Maternal & Child Health, Shijiazhuang BGI Genomics Co., Ltd., Shijiazhuang, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jian Zhang
- Department of Prenatal Diagnosis Center, Women and Children’s Hospital, School of Medicine, Xiamen University, Xiamen, Fujian province, China
| | | | - Nan Yu
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | | | - Min Chen
- Department of Prenatal Diagnosis and Fetal Medical, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- *Correspondence: Xin Jin, ; Min Chen, ; Yunsheng Ge, ; Yanming Huang,
| | - Yunsheng Ge
- Department of Prenatal Diagnosis Center, Women and Children’s Hospital, School of Medicine, Xiamen University, Xiamen, Fujian province, China
- *Correspondence: Xin Jin, ; Min Chen, ; Yunsheng Ge, ; Yanming Huang,
| | - Yanming Huang
- Clinical Experimental Center, Jiangmen Central Hospital, Jiangmen, Guangdong province, China
- *Correspondence: Xin Jin, ; Min Chen, ; Yunsheng Ge, ; Yanming Huang,
| | - Xin Jin
- BGI-Shenzhen, Shenzhen, China
- School of Medicine, South China University of Technology, Guangzhou, China
- *Correspondence: Xin Jin, ; Min Chen, ; Yunsheng Ge, ; Yanming Huang,
| |
Collapse
|
11
|
Haidar H, Iskander R. Non-invasive Prenatal Testing for Fetal Whole Genome Sequencing: An Interpretive Critical Review of the Ethical, Legal, Social, and Policy Implications. CANADIAN JOURNAL OF BIOETHICS 2022. [DOI: 10.7202/1087199ar] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
|
12
|
Rosner M, Kolbe T, Hengstschläger M. Fetomaternal microchimerism and genetic diagnosis: On the origins of fetal cells and cell-free fetal DNA in the pregnant woman. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2021; 788:108399. [PMID: 34893150 DOI: 10.1016/j.mrrev.2021.108399] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 11/11/2021] [Accepted: 11/14/2021] [Indexed: 06/14/2023]
Abstract
During pregnancy several types of fetal cells and fetal stem cells, including pregnancy-associated progenitor cells (PAPCs), traffic into the maternal circulation. Whereas they also migrate to various maternal organs and adopt the phenotype of the target tissues to contribute to regenerative processes, fetal cells also play a role in the pathogenesis of maternal diseases. In addition, cell-free fetal DNA (cffDNA) is detectable in the plasma of pregnant women. Together they constitute the well-known phenomenon of fetomaternal microchimerism, which inspired the concept of non-invasive prenatal testing (NIPT) using maternal blood. An in-depth knowledge concerning the origins of these fetal cells and cffDNA allows a more comprehensive understanding of the biological relevance of fetomaternal microchimerism and has implications for the ongoing expansion of resultant clinical applications.
Collapse
Affiliation(s)
- Margit Rosner
- Institute of Medical Genetics, Center for Pathobiochemistry and Genetics, Medical University of Vienna, Vienna, Austria
| | - Thomas Kolbe
- Biomodels Austria, University of Veterinary Medicine Vienna, Vienna, Austria; Department IFA Tulln, University of Natural Resources and Life Sciences, Tulln, Austria
| | - Markus Hengstschläger
- Institute of Medical Genetics, Center for Pathobiochemistry and Genetics, Medical University of Vienna, Vienna, Austria.
| |
Collapse
|
13
|
Direct Assessment of Single-Cell DNA Using Crudely Purified Live Cells: A Proof of Concept for Noninvasive Prenatal Definitive Diagnosis. J Mol Diagn 2021; 22:132-140. [PMID: 32033633 DOI: 10.1016/j.jmoldx.2019.10.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 07/26/2019] [Accepted: 10/16/2019] [Indexed: 11/20/2022] Open
Abstract
Noninvasive testing techniques are often used for fetal diagnosis of genetic abnormalities but are limited by certain characteristics, including noninformative results. Thus, novel methods of noninvasive definitive diagnosis of fetal genetic abnormalities are needed. The aim of this study was to develop a single-cell DNA analysis method with high sensitivity and specificity that enables direct extraction of genetic information from live fetal cells in a crude mixture for simultaneous evaluation. Genomic DNA from circulating fetal CD45-CD14- cells, an extremely rare cell type, extracted from 10-mL samples of maternal peripheral blood, was extracted using a single-cell-based droplet digital (sc-dd) PCR system with a modified amount of polymerase. A hexachloro-6-carboxyfluorescein-labeled RPP30 probe was used as an internal control and a 6-carboxyfluorescein-labeled SRY probe as a target. The results indicated that no droplets generated with samples from pregnant women carrying female fetuses were positive for both probe signals, whereas droplets prepared with samples from pregnant women carrying male fetuses were positive for both probe signals. The latter was considered a direct assessment of genetic information from single circulating male fetal cells. Thus, the modified sc-ddPCR system allows the detection of genetic information from rare target cells in a crudely purified cell population. This research also serves as a proof of concept for noninvasive prenatal definitive diagnosis.
Collapse
|
14
|
Snyder EA, San Roman AK, Piña-Aguilar RE, Steeves MA, McNamara EA, Souter I, Hayes FJ, Levitsky LL, Lin AE. Genetic counseling for women with 45,X/46,XX mosaicism: Towards more personalized management. Eur J Med Genet 2021; 64:104140. [PMID: 33524610 PMCID: PMC11134314 DOI: 10.1016/j.ejmg.2021.104140] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 12/21/2020] [Accepted: 01/08/2021] [Indexed: 01/06/2023]
Abstract
Despite numerous clinical series, consistent karyotype-phenotype correlations for Turner syndrome have not been established, although a lower level of 45,X is generally thought to be associated with a milder phenotype. This limits personalized counseling for women with 45,X/46,XX mosaicism. To better understand the phenotypic spectrum associated with various levels of 45,X/46,XX mosaicism, we compared patients evaluated in the Massachusetts General Hospital Turner Syndrome Clinic to determine if cardiac, renal, and thyroid abnormalities correlated with the percentage of 45,X cells present in a peripheral blood karyotype. of the 118 patients included in the study, 78 (66%) patients had non-mosaic 45,X and 40 (34%) patients had varying levels of 45,X/46,XX mosaicism. Patients with ≤70% 45,X compared with those with >70% 45,X had a significantly lower frequency of cardiac and renal anomalies. The presence of hypothyroidism was somewhat lower for the ≤70% 45,X group, but was not statistically significant. Supplemental tissue testing on another tissue type, typically buccal mucosa, was often useful in counseling patients with 45,X mosaicism. Given the modest sample size of patients with varying levels of mosaicism and the variability of Turner syndrome abnormalities, we hope this preliminary study will inspire a multicenter collaboration, which may lead to modification of clinical guidelines. Because several patients with ≤70% 45,X were ascertained from perinatal care referrals, we still advise women with 45,X mosaicism pursuing pregnancy to receive standard Turner syndrome cardiac surveillance. There is an opportunity to personalize counseling and surveillance for patients based on percentage of 45,X cells on chromosome analysis.
Collapse
Affiliation(s)
- Emma A Snyder
- MassGeneral Hospital for Children, Medical Genetics, Department of Pediatrics, Boston, MA, USA
| | | | | | - Marcie A Steeves
- MassGeneral Hospital for Children, Medical Genetics, Department of Pediatrics, Boston, MA, USA
| | - Erin A McNamara
- MassGeneral Hospital for Children, Medical Genetics, Department of Pediatrics, Boston, MA, USA
| | - Irene Souter
- Massachusetts General Hospital, Reproductive Endocrinology and Infertility, Boston, MA, USA
| | - Frances J Hayes
- Massachusetts General Hospital, Reproductive Endocrine Unit, Boston, MA, USA
| | - Lynne L Levitsky
- MassGeneral Hospital for Children, Pediatric Endocrinology, Boston, MA, USA
| | - Angela E Lin
- MassGeneral Hospital for Children, Medical Genetics, Department of Pediatrics, Boston, MA, USA.
| |
Collapse
|
15
|
Zhu J, Hui F, Mao X, Zhang S, Qi H, Du Y. cfDNA deconvolution via NIPT of a pregnant woman after bone marrow transplant and donor egg IVF. Hum Genomics 2021; 15:14. [PMID: 33622405 PMCID: PMC7901183 DOI: 10.1186/s40246-021-00311-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 02/08/2021] [Indexed: 11/10/2022] Open
Abstract
Cell-free DNA is known to be a mixture of DNA fragments originating from various tissue types and organs of the human body and can be utilized for several clinical applications and potentially more to be created. Non-invasive prenatal testing (NIPT), by high throughput sequencing of cell-free DNA (cfDNA), has been successfully applied in the clinical screening of fetal chromosomal aneuploidies, with more extended coverage under active research.In this study, via a quite unique and rare NIPT sample, who has undergone both bone marrow transplant and donor egg IVF, we investigated the sources of oddness observed in the NIPT result using a combination of molecular genetics and genomic methods and eventually had the case fully resolved. Along the process, we devised a clinically viable process to dissect the sample mixture.Eventually, we used the proposed scheme to evaluate the relatedness of individuals and the demultiplexed sample components following modified population genetics concepts, exemplifying a noninvasive prenatal paternity test prototype. For NIPT specific applicational concern, more thorough and detailed clinical information should therefore be collected prior to cfDNA-based screening procedure like NIPT and systematically reviewed when an abnormal report is obtained to improve genetic counseling and overall patient care.
Collapse
Affiliation(s)
- Jianjiang Zhu
- Prenatal Diagnosis Center, Beijing Haidian Maternal and Child Health Hospital, Beijing, China
| | - Feng Hui
- Annoroad Gene Technology Co., Ltd., Beijing, China
| | - Xuequn Mao
- Prenatal Diagnosis Center, Beijing Haidian Maternal and Child Health Hospital, Beijing, China
| | - Shaoqin Zhang
- Prenatal Diagnosis Center, Beijing Haidian Maternal and Child Health Hospital, Beijing, China
| | - Hong Qi
- Prenatal Diagnosis Center, Beijing Haidian Maternal and Child Health Hospital, Beijing, China.
| | - Yang Du
- Annoroad Gene Technology Co., Ltd., Beijing, China.
| |
Collapse
|
16
|
Dai R, Yu Y, Zhang H, Li L, Jiang Y, Liu R, Zhang H. Analysis of 17,428 pregnant women undergoing non-invasive prenatal testing for fetal chromosome in Northeast China. Medicine (Baltimore) 2021; 100:e24740. [PMID: 33578623 PMCID: PMC10545248 DOI: 10.1097/md.0000000000024740] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 11/13/2020] [Accepted: 01/16/2021] [Indexed: 11/26/2022] Open
Abstract
ABSTRACT Non-invasive prenatal testing (NIPT) is an incomparable prenatal screening technology, but we should undergo amniocentesis to confirm fetal chromosome when pregnancies receive a positive result via NIPT. We aimed to investigate the detection rate and positive predictive value of NIPT results in pregnancies from Northeast China, and to determine the reasons for false positive and false negative NIPT results.This study evaluates 17,428 singleton pregnancies had undergone NIPT detection. 202 samples were NIPT positive with the detection rate was 1.16% (202/17,428). Among all the positive samples, 160 samples (79.21%) were referred for an amniocentesis procedure to investigate the fetal chromosome. The positive predictive value of T21, T18, and T13 was found to be 75% with a 0.07% false positive rate. Positive predictive value from high to low was as follows: trisomy 21 (84.38%), followed by trisomy 18 (61.54%), autosomal abnormalities (52.94%), sex chromosomal abnormalities (38.46%), and trisomy 13 (33.33%). The positive predictive values for sex chromosome abnormalities turned out to be mosaic sex chromosome aneuploidies (83.33%), followed by XYY (57.14%), XXY (37.50%), XXX (36.36%), and Monosomy X (28.95%). Out of the 160 samples had amniocentesis, the true positive cases in trisomy 21 had a higher percentage of Z-scores compared with the false positive cases in trisomy 21 (P < .05). And the true positive cases in trisomy 18 had a significantly higher percentage of Z-scores compared with the false positive cases in trisomy 18 (P < .01).These findings indicate that the positive predictive value of T21, T18, and T13 was found to be 75% with a 0.07% false positive rate. It is worth noting that the positive predictive value of NIPT for autosomes and sex chromosomes. Moreover, if women receive a positive result via NIPT, they should pay attention to the results with undergoing further prenatal diagnosis.
Collapse
|
17
|
Lu X, Wang C, Sun Y, Tang J, Tong K, Zhu J. Noninvasive prenatal testing for assessing foetal sex chromosome aneuploidy: a retrospective study of 45,773 cases. Mol Cytogenet 2021; 14:1. [PMID: 33407708 PMCID: PMC7786464 DOI: 10.1186/s13039-020-00521-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 12/09/2020] [Indexed: 12/22/2022] Open
Abstract
OBJECTIVE To assess the positive predictive value (PPV) of noninvasive prenatal testing (NIPT) as a screening test for sex chromosome aneuploidy (SCA) with different maternal characteristics and prenatal decisions in positive cases. MATERIALS AND METHODS We retrospectively analysed 45,773 singleton pregnancies with different characteristics that were subjected to NIPT in the Maternity and Child Health Hospital of Anhui Province. The results were validated by karyotyping. Clinical data, diagnostic results, and data on pregnancy outcomes were collected. RESULTS In total, 314 cases were SCA positive by NIPT; among those, 143 underwent invasive prenatal diagnostic testing, and 58 were true-positive. Overall, the PPVs for 45,X, 47,XXX, 47,XXY and 47,XYY were 12.5%, 51.72%, 66.67% and 83.33%, respectively. Interestingly, when only pregnant women of advanced maternal age (AMA) were screened, the PPVs for 45,X, 47,XXX, 47,XXY and 47,XYY were 23.81%, 53.33%, 78.95%, and 66.67%, respectively. The frequency of SCA was significantly higher in the AMA group than in the non-AMA group. The frequencies of 47,XXX and 47,XXY were significantly correlated with maternal age. CONCLUSION NIPT performed better in predicting sex chromosome trisomies than monosomy X, and patients with 45,X positive foetuses were more eager to terminate pregnancy than those with 47,XXX and 47,XYY. AMA may be a risk factor of having a foetus with SCA. Our findings may assist in genetic counselling of AMA pregnant women. Our pre- and posttest counselling are essential for familiarizing pregnant women with the benefits and limitations of NIPT, which may ease their anxiety and enable them to make informed choices for further diagnosis and pregnancy decisions.
Collapse
Affiliation(s)
- Xinran Lu
- Affiliated Maternity and Child Health Hospital of Anhui Medical University, Hefei, China.,Maternity and Child Health Hospital of Anhui Province, Hefei, China
| | - Chaohong Wang
- Maternity and Child Health Hospital of Anhui Province, Hefei, China
| | - Yuxiu Sun
- Maternity and Child Health Hospital of Anhui Province, Hefei, China
| | - Junxiang Tang
- Maternity and Child Health Hospital of Anhui Province, Hefei, China
| | - Keting Tong
- Maternity and Child Health Hospital of Anhui Province, Hefei, China
| | - Jiansheng Zhu
- Affiliated Maternity and Child Health Hospital of Anhui Medical University, Hefei, China. .,Maternity and Child Health Hospital of Anhui Province, Hefei, China.
| |
Collapse
|
18
|
Noninvasive Prenatal Testing for Fetal XXY Aneuploidies Among Pregnancies in Beijing of China. MATERNAL-FETAL MEDICINE 2020. [DOI: 10.1097/fm9.0000000000000056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
|
19
|
Tamaki Y, Katagiri Y, Umemura N, Takeshita N, Morita M. Noninvasive prenatal testing aids identification of tetrasomy 18p: A case report. Case Rep Womens Health 2020; 27:e00236. [PMID: 32642449 PMCID: PMC7334301 DOI: 10.1016/j.crwh.2020.e00236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 06/22/2020] [Accepted: 06/23/2020] [Indexed: 11/01/2022] Open
Abstract
Tetrasomy 18p syndrome (Online Mendelian Inheritance in Man 614290) is a rare chromosomal disorder that is seen in approximately 1 in every 180,000 live births. It is caused by the presence of isochromosome 18p, which is a supernumerary marker composed of two copies of the short arms of chromosome 18. Isochromosome 18p is one of the most commonly observed isochromosomes. We report tetrasomy 18p syndrome diagnosed prenatally after noninvasive prenatal testing (NIPT) was positive for trisomy 18. Tetrasomy 18p was finally diagnosed by G-banding and fluorescence in situ hybridization of chromosome 18p, before invasive confirmatory testing the karyotype findings by NIPT showed an increase in the DNA fragments from chromosome 18p, indicating duplication of chromosome 18p. NIPT can detect not only trisomy 13, 18, and 21, but also structural chromosomal anomalies, such as deletions and duplications. An NIPT report "positive for trisomy 18" indicates the possibility of tetrasomy 18p, and detailed analysis of NIPT data can reveal subchromosomal copy number variations, to a certain extent, before definitive diagnostic testing.
Collapse
Affiliation(s)
- Yuko Tamaki
- Department of Obstetrics and Gynecology, Toho University Omori Medical Center, Japan
| | - Yukiko Katagiri
- Department of Obstetrics and Gynecology, Toho University Omori Medical Center, Japan
| | - Nahomi Umemura
- Department of Obstetrics and Gynecology, Toho University Omori Medical Center, Japan
| | - Naoki Takeshita
- Department of Obstetrics and Gynecology, Toho University Sakura Medical Center, Japan
| | - Mineto Morita
- Department of Obstetrics and Gynecology, Toho University Omori Medical Center, Japan
| |
Collapse
|
20
|
Application of next-generation sequencing for the diagnosis of fetuses with congenital heart defects. Curr Opin Obstet Gynecol 2020; 31:132-138. [PMID: 30608255 DOI: 10.1097/gco.0000000000000520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
PURPOSE OF REVIEW Congenital heart defects (CHDs) are the most common type of birth defects, and are thought to result from genetic-environmental interactions. Currently, karyotype and chromosomal microarray analyses are the primary methods used to detect chromosomal abnormalities and copy number variations in fetuses with CHD. Recently, with the introduction of next-generation sequencing (NGS) in prenatal diagnosis, gene mutations have been identified in cases of CHD. The purpose of this review is to summarize current studies about the genetic cause of fetal CHD, paying particular attention to the application of NGS for fetuses with CHD. RECENT FINDINGS In addition to chromosomal abnormalities, gene mutations are an important genetic cause of fetal CHD. Furthermore, incidences of pathogenic mutations in fetuses with CHD are associated with the presence of other structural anomalies, but are irrelevant to the categories of CHD. SUMMARY Gene mutations are important causes of fetal CHD and NGS should be applied to all fetuses with normal karyotype and copy number variations, regardless of whether the CHD is isolated or syndromic.
Collapse
|
21
|
Wang Y, Li S, Wang W, Dong Y, Zhang M, Wang X, Yin C. Cell-free DNA screening for sex chromosome aneuploidies by non-invasive prenatal testing in maternal plasma. Mol Cytogenet 2020; 13:10. [PMID: 32190123 PMCID: PMC7068885 DOI: 10.1186/s13039-020-0478-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 03/02/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Non-invasive prenatal testing (NIPT) has been confirmed as the most accurate screening test for trisomies 21, 18, and 13. However, reports on NIPT performance in sex chromosome aneuploidies (SCA) based on real clinical data are still limited. METHODS High-throughput massively parallel genomic sequencing (MPS) technique was used to screen for fetal SCAs as part of the research to determine the potential value of NIPT in detecting fetal SCAs in the second trimester. A number of 12,243 consecutive cases from a single center were included in this study. RESULTS The positive predictive value (PPV) of NIPT in the present study was 57.6%, which was divided and categorized by individual SCAs as follows: 21.4% for Turner syndrome (45,X), 75.0% for Triple X syndrome (47,XXX), 90.9% for Klinefelter syndrome (47,XXY), and 75.0% for XYY syndrome (47,XYY). CONCLUSION The NIPT-based SCA test cannot be used as a diagnostic method, and performing an invasive confirmation test on NIPT-based SCA-positive cases is strongly recommended.
Collapse
Affiliation(s)
- Yipeng Wang
- Prenatal Diagnostic Center, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, 100026 China
| | - Shanshan Li
- Prenatal Diagnostic Center, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, 100026 China
| | - Wei Wang
- Prenatal Diagnostic Center, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, 100026 China
| | - Yuan Dong
- Prenatal Diagnostic Center, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, 100026 China
| | - Meng Zhang
- Prenatal Diagnostic Center, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, 100026 China
| | - Xin Wang
- Prenatal Diagnostic Center, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, 100026 China
| | - Chenghong Yin
- Prenatal Diagnostic Center, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, 100026 China
| |
Collapse
|
22
|
Zhang B, Zhou Q, Chen Y, Shi Y, Zheng F, Liu J, Yu B. High false‐positive non‐invasive prenatal screening results for sex chromosome abnormalities: Are maternal factors the culprit? Prenat Diagn 2020; 40:463-469. [PMID: 31318441 DOI: 10.1002/pd.5529] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 07/03/2019] [Accepted: 07/15/2019] [Indexed: 12/24/2022]
Affiliation(s)
- Bin Zhang
- Department of Prenatal Diagnosis CenterChangzhou Maternity and Child Health Care Hospital affiliated to Nanjing Medical University Changzhou China
| | - Qin Zhou
- Department of Prenatal Diagnosis CenterChangzhou Maternity and Child Health Care Hospital affiliated to Nanjing Medical University Changzhou China
| | - Yingping Chen
- Department of Prenatal Diagnosis CenterChangzhou Maternity and Child Health Care Hospital affiliated to Nanjing Medical University Changzhou China
| | - Ye Shi
- Department of Prenatal Diagnosis CenterChangzhou Maternity and Child Health Care Hospital affiliated to Nanjing Medical University Changzhou China
| | - Fangxiu Zheng
- Department of Prenatal Diagnosis CenterChangzhou Maternity and Child Health Care Hospital affiliated to Nanjing Medical University Changzhou China
| | - Jianbing Liu
- Department of Prenatal Diagnosis CenterChangzhou Maternity and Child Health Care Hospital affiliated to Nanjing Medical University Changzhou China
| | - Bin Yu
- Department of Prenatal Diagnosis CenterChangzhou Maternity and Child Health Care Hospital affiliated to Nanjing Medical University Changzhou China
| |
Collapse
|
23
|
Ivashchenko TE, Vashukova ES, Kozyulina PY, Dvoynova NM, Talantova OE, Koroteev AL, Pendina AA, Tikhonov AV, Chiryaeva OG, Petrova LI, Dudkina VS, Efimova OA, Baranov VS, Glotov AS. Noninvasive Prenatal Testing Using Next Generation Sequencing: Pilot Experience of the D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology. RUSS J GENET+ 2019. [DOI: 10.1134/s1022795419100053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
24
|
Audibert F, De Bie I, Johnson JA, Okun N, Wilson RD, Armour C, Chitayat D, Kim R. No. 348-Joint SOGC-CCMG Guideline: Update on Prenatal Screening for Fetal Aneuploidy, Fetal Anomalies, and Adverse Pregnancy Outcomes. JOURNAL OF OBSTETRICS AND GYNAECOLOGY CANADA 2019; 39:805-817. [PMID: 28859766 DOI: 10.1016/j.jogc.2017.01.032] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
OBJECTIVE To review the available prenatal screening options in light of the recent technical advances and to provide an update of previous guidelines in the field of prenatal screening. INTENDED USERS Health care providers involved in prenatal screening, including general practitioners, obstetricians, midwives, maternal fetal medicine specialists, geneticists, and radiologists. TARGET POPULATION All pregnant women receiving counselling and providing informed consent for prenatal screening. EVIDENCE Published literature was retrieved through searches of Medline, PubMed, and the Cochrane Library in and prior to March 2016 using an appropriate controlled vocabulary (prenatal diagnosis, amniocentesis, chorionic villi sampling, non-invasive prenatal screening) and key words (prenatal screening, prenatal genetic counselling). Results were restricted to systematic reviews, randomized control trials/controlled clinical trials, and observational studies written in English and published from January 1985 to May 2016. Searches were updated on a regular basis and incorporated in the guideline. Grey (unpublished) literature was identified through searching the websites of health technology assessment and health technology-related agencies, clinical practice guideline collections, clinical trial registries, and national and international medical speciality societies. GUIDELINE UPDATE Evidence will be reviewed 5 years after publication to determine whether all or part of the guideline should be updated. However, if important new evidence is published prior to the 5-year cycle, the review process may be accelerated for a more rapid update of some recommendations.
Collapse
|
25
|
Shi J, Zhang R, Li J, Zhang R. Novel perspectives in fetal biomarker implementation for the noninvasive prenatal testing. Crit Rev Clin Lab Sci 2019; 56:374-392. [PMID: 31290367 DOI: 10.1080/10408363.2019.1631749] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Noninvasive prenatal testing (NIPT) utilizes cell-free fetal DNA (cffDNA) present in maternal peripheral blood to detect chromosomal abnormalities. The detection of 21-trisomy, 18-trisomy, and 13-trisomy in the fetus has become a common screening method during pregnancy and has been widely applied in routine clinical testing because of its analytical and clinical validity. Currently, noninvasive prenatal testing involving copy number variations (CNVs) and other frequent single-gene disorders is being widely studied, and it plays an important and indispensable role in prenatal detection. The multiple approaches that have been reported and validated by various laboratories have different merits and limitations. Their clinical validity, utility, and application vary with different diseases. This review summarizes the principles, methods, advantages, and limitations of noninvasive prenatal testing for the detection of aneuploidy, CNVs and single-gene disorders. Before implementation of NIPT into clinical practice, a list of criteria that the application must meet is crucial. Essential parameters such as clinical sensitivity, clinical specificity, positive predictive value (PPV) and negative predictive value (NPV) are required to properly evaluate the clinical validity and utility of NIPT. We then discuss and analyze these clinical parameters and clinical application guidelines, providing physicians and scientists with feasible strategies and the latest research information.
Collapse
Affiliation(s)
- Jiping Shi
- Peking University Fifth School of Clinical Medicine, National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital , Beijing , China.,National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital , Beijing , China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital , Beijing , China
| | - Runling Zhang
- National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital , Beijing , China.,Graduate School, Chinese Academy of Medical Sciences, Peking Union Medical College , Beijing , China
| | - Jinming Li
- National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital , Beijing , China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital , Beijing , China
| | - Rui Zhang
- Peking University Fifth School of Clinical Medicine, National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital , Beijing , China.,National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital , Beijing , China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital , Beijing , China
| |
Collapse
|
26
|
Ji X, Li J, Huang Y, Sung PL, Yuan Y, Liu Q, Chen Y, Ju J, Zhou Y, Huang S, Chen F, Han Y, Yuan W, Fan C, Zhao Q, Wu H, Feng S, Liu W, Li Z, Chen J, Chen M, Yao H, Zeng L, Ma T, Fan S, Zhang J, Yuen KY, Cheng SH, Chik IWS, Liu NT, Zhu J, Lin S, Cao J, Tong S, Shan Z, Li W, Hekmat MR, Garshasbi M, Suela J, Torres Y, Cigudosa JC, Ruiz FJP, Rodríguez L, García M, Bernik J, Traven E, Reš U, Tul N, Tseng CF, Zhao D, Sun L, Pan Q, Shen L, Dai M, Wang Y, Wang J, Yang H, Yin Y, Duan T, Zhu B, Choolani M, Jin X, Chen Y, Mao M. Identifying occult maternal malignancies from 1.93 million pregnant women undergoing noninvasive prenatal screening tests. Genet Med 2019; 21:2293-2302. [PMID: 30976098 DOI: 10.1038/s41436-019-0510-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 03/25/2019] [Indexed: 12/28/2022] Open
Abstract
PURPOSE Multiple chromosomal aneuploidies may be associated with maternal malignancies and can cause failure of noninvasive prenatal screening (NIPS) tests. However, multiple chromosomal aneuploidies show poor specificity and selectivity for diagnosing maternal malignancies. METHODS This multicenter retrospective analysis evaluated 639 pregnant women who tested positive for multiple chromosomal aneuploidies on initial NIPS test between January 2016 and December 2017. Women were assessed using genome profiling of copy-number variations, which was translated to cancer risk using a novel bioinformatics algorithm called the cancer detection pipeline (CDP). Sensitivity, specificity, and positive predictive value (PPV) of diagnosing maternal malignancies were compared for multiple chromosomal aneuploidies, the CDP model, and the combination of CDP and plasma tumor markers. RESULTS Of the 639 subjects, 41 maternal malignant cancer cases were diagnosed. Multiple chromosomal aneuploidies predicted maternal malignancies with a PPV of 7.6%. Application of the CDP algorithm to women with multiple chromosomal aneuploidies allowed 34 of the 41 (83%) cancer cases to be identified, while excluding 422 of 501 (84.2%) of the false positive cases. Combining the CDP with plasma tumor marker testing gave PPV of 75.0%. CONCLUSION The CDP algorithm can diagnose occult maternal malignancies with a reasonable PPV in multiple chromosomal aneuploidies-positive pregnant women in NIPS tests. This performance can be further improved by incorporating findings for plasma tumor markers.
Collapse
Affiliation(s)
- Xing Ji
- Center for Clinical Genetics, Xin Hua Hospital Affiliated to Shanghai Jiao Tong University, School of Medicine, Shanghai, China.,Department of Genetics, Shanghai Institute for Pediatric Research, Shanghai, China
| | - Jia Li
- BGI Genomics, BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Yonghua Huang
- Department of Obstetrics and Gynecology, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-Sen University, Jiangmen, Guangdong, China
| | - Pi-Lin Sung
- Department of Obstetrics and Gynecology, Taipei Veterans General Hospital, Taipei, Taiwan.,Department of Obstetrics and Gynecology, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Yuying Yuan
- BGI Genomics, BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Qiang Liu
- BGI Genomics, BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Yan Chen
- BGI Genomics, BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Jia Ju
- BGI Genomics, BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Yafeng Zhou
- BGI Genomics, BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Shujia Huang
- BGI Genomics, BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Fang Chen
- BGI Genomics, BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Yuan Han
- BGI-Wuhan, BGI-Shenzhen, Wuhan, Guangdong, China
| | - Wen Yuan
- BGI-Wuhan, BGI-Shenzhen, Wuhan, Guangdong, China
| | - Cheng Fan
- BGI Genomics, BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Qiang Zhao
- Department of Obstetrics and Gynecology, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-Sen University, Jiangmen, Guangdong, China
| | - Haitao Wu
- Reproductive Medicine Center, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-Sen University, Jiangmen, Guangdong, China
| | - Suihua Feng
- Department of Obstetrics and Gynecology, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-Sen University, Jiangmen, Guangdong, China
| | - Weiqiang Liu
- Key Laboratory for Major Obstetric Diseases of Guangdong, Key Laboratory for Reproduction and Genetics of Guangdong Higher Education Institutes, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Zhihua Li
- Department of Prenatal Diagnosis and Fetal Medicine, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jingsi Chen
- Department of Prenatal Diagnosis and Fetal Medicine, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Min Chen
- Department of Prenatal Diagnosis and Fetal Medicine, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Hong Yao
- Prenatal Diagnosis Center, Southwest Hospital, Chongqing, China
| | - Li Zeng
- Department of Obstetrics and Gynecology, Bazhong Central Hospital, Bazhong, Sichuan, China
| | - Tao Ma
- Department of Obstetrics and Gynecology, Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
| | - Shushu Fan
- Genetic Diagnosis Center and Reproductive Center, Yue Bei People's Hospital, Shaoguan, Guangdong, China
| | - Jinman Zhang
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, Yunnan, China.,Genetic Diagnosis Center, First People's Hospital of Yunnan, Kunming, Yunnan, China
| | | | | | | | | | - Jianyu Zhu
- BGI Genomics, BGI-Shenzhen, Shenzhen, Guangdong, China
| | | | | | | | | | - Wenyan Li
- BGI Genomics, BGI-Shenzhen, Shenzhen, Guangdong, China
| | | | - Masoud Garshasbi
- Department of Medical Genetics, DeNA laboratory, Tehran, Iran.,Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | | | | | | | - F J Pérez Ruiz
- Servicio de Ginecología y Obstetricia, Hospital General San Jorge, Huesca, Spain
| | - Laura Rodríguez
- Laboratorio de Genética Molecular AbaCid, Hospitales HM, Madrid, Spain
| | - Mónica García
- Laboratorio de Genética Molecular AbaCid, Hospitales HM, Madrid, Spain
| | | | | | - Uršula Reš
- Dravlje Health Center-IVF, Ljubljana, Slovenia
| | - Nataša Tul
- Division of Obstetrics and Gynecology, Department of Perinatology, University Medical Centre, Ljubljana, Slovenia
| | | | - Depeng Zhao
- Department of Prenatal Diagnosis and Fetal Medicine, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Luming Sun
- Department of Prenatal Diagnosis and Fetal Medicine, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Qiong Pan
- Laboratory of Clinical Genetics, Huai'an Maternity and Child Health Care Hospital of Jiangsu Province, Yangzhou University, Huai'an, Jiangsu, China
| | - Li Shen
- Department of Pathology, Shanghai Pu Nan Hospital, Shanghai, China
| | - Mengyao Dai
- Center for Clinical Genetics, Xin Hua Hospital Affiliated to Shanghai Jiao Tong University, School of Medicine, Shanghai, China.,Department of Genetics, Shanghai Institute for Pediatric Research, Shanghai, China
| | - Yuying Wang
- BGI Genomics, BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Jian Wang
- BGI Genomics, BGI-Shenzhen, Shenzhen, Guangdong, China.,James D. Watson Institute of Genome Sciences, Hangzhou, Zhejiang, China
| | - Huanming Yang
- BGI Genomics, BGI-Shenzhen, Shenzhen, Guangdong, China.,James D. Watson Institute of Genome Sciences, Hangzhou, Zhejiang, China
| | - Ye Yin
- BGI Genomics, BGI-Shenzhen, Shenzhen, Guangdong, China.,Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Tao Duan
- Department of Prenatal Diagnosis and Fetal Medicine, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Baosheng Zhu
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, Yunnan, China.,Genetic Diagnosis Center, First People's Hospital of Yunnan, Kunming, Yunnan, China
| | - Mahesh Choolani
- Division of Maternal Fetal Medicine, Department of Obstetrics and Gynecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Xin Jin
- BGI Genomics, BGI-Shenzhen, Shenzhen, Guangdong, China. .,School of Medicine, South China University of Technology, Guangzhou, Guangdong, China. .,BGI-Guangzhou Medical Laboratory, BGI-Shenzhen, Guangzhou, Guangdong, China.
| | - Yingwei Chen
- Center for Clinical Genetics, Xin Hua Hospital Affiliated to Shanghai Jiao Tong University, School of Medicine, Shanghai, China.
| | - Mao Mao
- BGI Genomics, BGI-Shenzhen, Shenzhen, Guangdong, China.
| |
Collapse
|
27
|
Abstract
Single-cell omics studies provide unique information regarding cellular heterogeneity at various levels of the molecular biology central dogma. This knowledge facilitates a deeper understanding of how underlying molecular and architectural changes alter cell behavior, development, and disease processes. The emerging microchip-based tools for single-cell omics analysis are enabling the evaluation of cellular omics with high throughput, improved sensitivity, and reduced cost. We review state-of-the-art microchip platforms for profiling genomics, epigenomics, transcriptomics, proteomics, metabolomics, and multi-omics at single-cell resolution. We also discuss the background of and challenges in the analysis of each molecular layer and integration of multiple levels of omics data, as well as how microchip-based methodologies benefit these fields. Additionally, we examine the advantages and limitations of these approaches. Looking forward, we describe additional challenges and future opportunities that will facilitate the improvement and broad adoption of single-cell omics in life science and medicine.
Collapse
Affiliation(s)
- Yanxiang Deng
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut 06511, USA; , ,
| | - Amanda Finck
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut 06511, USA; , ,
| | - Rong Fan
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut 06511, USA; , ,
| |
Collapse
|
28
|
Li Y, Wu Y, Ma L, Guo Z, Xiao W, Yuan Y. Loss of heterozygosity by SCRaMbLEing. SCIENCE CHINA-LIFE SCIENCES 2019; 62:381-393. [PMID: 30900161 DOI: 10.1007/s11427-019-9504-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 02/19/2019] [Indexed: 02/06/2023]
Abstract
Genetic variation drives phenotypic evolution within populations. Genetic variation can be divided into different forms according to the size of genomic changes. However, study of large-scale genomic variation such as structural variation and aneuploidy is still limited and mainly based on the static, predetermined feature of individual genomes. Here, using SCRaMbLE, different levels of loss of heterozygosity (LOH) events including short-range LOH, long-range LOH and whole chromosome LOH were detected in evolved strains. By contrast, using rapid adaptive evolution, aneuploidy was detected in the adaptive strains. It was further found that deletion of gene GLN3, long-range LOH in the left arm of synthetic chromosome X, whole chromosome LOH of synthetic chromosome X, and duplication of chromosome VIII (trisomy) lead to increased rapamycin resistance in synthetic yeast. Comparative analysis of genome stability of evolved strains indicates that the aneuploid strain has a higher frequency of degeneration than the SCRaMbLEd strain. These findings enrich our understanding of genetic mechanism of rapamycin resistance in yeast, and provide valuable insights into yeast genome architecture and function.
Collapse
Affiliation(s)
- Yunxiang Li
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Yi Wu
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Lu Ma
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Zhou Guo
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Wenhai Xiao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Yingjin Yuan
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China. .,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
| |
Collapse
|
29
|
Ji X, Chen F, Zhou Y, Li J, Yuan Y, Mo Y, Liu Q, Tseng JY, Shih-Chieh Lin D, Shen SH, Liu Y, Ye W, Cheung YN, Yuen KY, Lin S, Fu M, Zhang H, Liu N, Wang J, Yang H, Wang Y, Li S, Fan S, Jin X, Mao M, Sung PL. Copy number variation profile in noninvasive prenatal testing (NIPT) can identify co-existing maternal malignancies: Case reports and a literature review. Taiwan J Obstet Gynecol 2019; 57:871-877. [PMID: 30545544 DOI: 10.1016/j.tjog.2018.10.032] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/20/2018] [Indexed: 10/27/2022] Open
Abstract
OBJECTIVE The coexistence of maternal malignancy and pregnancy has received increasing attention in Noninvasive prenatal testing (NIPT) studies. Malignancy in pregnant women potentially affects the copy number variation (CNV) profile in NIPT results. Only one case of hematologic cancer has been reported in a Hong-Kong pregnant women, and solid tumors have never been reported in pregnant Chinese women. CASE REPORT The patients with dysgerminoma and cervical cancer showed aberrant chromosomal aneuploidies in NIPT and concordant patterns of genome disruption in tumor tissues. The genomic aberrations in the gastric cancer patient had similar copy number variation pattern of gastric cancer. CONCLUSION The findings in this study and the literature review further validate the effect of maternal malignancy on the copy number variation profile in NIPT data and strengthen the possibility of detecting malignant tumors with NIPT in the future.
Collapse
Affiliation(s)
- Xing Ji
- Department of Prenatal Diagnosis, Xin Hua Hospital Affiliated to Shanghai Jiaotong University, School of Medicine, Shanghai, China; Department of Genetics, Shanghai Institute for Pediatric Research, Shanghai, China
| | - Fang Chen
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | | | - Jia Li
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | | | - Yu Mo
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Qiang Liu
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Jen-Yu Tseng
- Department of Obstetrics and Gynecology, Taipei Veterans General Hospital, Taipei, Taiwan; Department of Obstetrics and Gynecology, National Yang-Ming University School of Medicine, Taipei, Taiwan
| | - Diego Shih-Chieh Lin
- Department of Obstetrics and Gynecology, National Yang-Ming University School of Medicine, Taipei, Taiwan; Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Shu-Huei Shen
- Department of Obstetrics and Gynecology, National Yang-Ming University School of Medicine, Taipei, Taiwan; Department of Radiology, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Yu Liu
- Department of Prenatal Diagnosis, Xin Hua Hospital Affiliated to Shanghai Jiaotong University, School of Medicine, Shanghai, China; Department of Genetics, Shanghai Institute for Pediatric Research, Shanghai, China
| | - Weiping Ye
- Department of Obstetrics, Xin Hua Hospital Affiliated with Shanghai Jiaotong University, School of Medicine, Shanghai, China
| | | | - Ka Yiu Yuen
- BGI Health Company Limited, Hong Kong SAR, China
| | - Siyuan Lin
- BGI Health Company Limited, Hong Kong SAR, China
| | - Meili Fu
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | | | - Na Liu
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen, Guangdong, China; James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, Guangdong, China; James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
| | | | - Shen Li
- Department of Pathology, Shanghai Punan Hospital, Shanghai, China.
| | - Shushu Fan
- The Genetic Diagnosis Center and Reproductive Center, Yue Bei People's Hospital, Shao Guan, Guangdong, China.
| | - Xin Jin
- BGI-Shenzhen, Shenzhen, Guangdong, China; School of Medicine, South China University of Technology, Guangzhou, China.
| | - Mao Mao
- BGI-Shenzhen, Shenzhen, Guangdong, China.
| | - Pi-Lin Sung
- Department of Obstetrics and Gynecology, Taipei Veterans General Hospital, Taipei, Taiwan; Department of Obstetrics and Gynecology, National Yang-Ming University School of Medicine, Taipei, Taiwan; Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan.
| |
Collapse
|
30
|
Wilkins-Haug L, Zhang C, Cerveira E, Ryan M, Mil-Homens A, Zhu Q, Reddi H, Lee C, Bianchi DW. Biological explanations for discordant noninvasive prenatal test results: Preliminary data and lessons learned. Prenat Diagn 2019; 38:445-458. [PMID: 29633279 DOI: 10.1002/pd.5260] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 03/25/2018] [Accepted: 03/29/2018] [Indexed: 12/14/2022]
Abstract
OBJECTIVE Maternal plasma cell-free DNA (cfDNA) analysis is a powerful screening tool for Down syndrome. In a pilot series, we examined biologic causes of discordance between the cfDNA test results and the fetal karyotype. We also explored the feasibility of obtaining trio biospecimens by using parental engagement. METHODS A convenience sample of women with discordant cfDNA results were recruited by their care providers. We provided shipping materials and instructions for biospecimen collection. Maternal, newborn, and placental samples were examined with droplet digital PCR. RESULTS Thirteen of 15 women successfully had biospecimens obtained remotely. High-quality DNA was extracted in 12 of 13 women. Presumed biologic etiologies for discordance were identified in 7 of 12 women: 3 cases from additional clinical review (male renal transplant, vanishing twin, and colon cancer) and 4 cases from additional laboratory investigation using droplet digital PCR (3 with confined placental mosaicism and 1 with true fetal mosaicism). CONCLUSIONS Understanding the biology behind cfDNA-fetal karyotype discordancy is useful for follow-up clinical care. Our study suggests that most cases could be resolved by using a trio biospecimen protocol and parental involvement. To improve accuracy, additional sequencing of biospecimens will be required.
Collapse
Affiliation(s)
- Louise Wilkins-Haug
- Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Eliza Cerveira
- Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Mallory Ryan
- Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Adam Mil-Homens
- Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Qihui Zhu
- Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Honey Reddi
- Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Charles Lee
- Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Diana W Bianchi
- Mother Infant Research Institute, Tufts Medical Center, Boston, MA, USA.,Prenatal Genomics and Therapy Section, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| |
Collapse
|
31
|
Genome-wide detection of additional fetal chromosomal abnormalities by cell-free DNA testing of 15,626 consecutive pregnant women. SCIENCE CHINA-LIFE SCIENCES 2018; 62:215-224. [PMID: 30076564 DOI: 10.1007/s11427-017-9344-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 06/21/2018] [Indexed: 12/18/2022]
Abstract
Cell-free DNA (cfDNA) testing for common fetal trisomies (T21, T18, T13) is highly effective. However, the usefulness of cfDNA testing in detecting other chromosomal abnormalities is unclear. We evaluated the performance of cfDNA testing for genome-wide abnormalities, and analyzed the incremental yield by reporting extra abnormalities. We performed genome-wide cfDNA testing in 15,626 consecutive pregnancies prospectively enrolled in this study. cfDNA testing results were reported and counseling was given depending on the presence of extra chromosomal abnormalities. cfDNA testing identified 190 cases (1.2%) of chromosomal abnormalities including 100 common trisomies and 90 additional abnormalities. By expanding the cfDNA reporting range to genome-wide abnormalities, the false positive rate increased to 0.39% (P<0.001) and positive predictive value (PPV) was reduced to 65.58% (P=0.42). However, the detection yield increased from 0.44% to 0.65% (P=0.014), and cfDNA testing detected 38.61% (39/101) additional abnormalities with no ultrasound and biochemical screening findings. cfDNA testing outperformed biochemical screening by showing 60 times higher true positive rate and fewer false negative results. Genome-wide cfDNA testing significantly increased the diagnostic yield by detecting extra abnormalities, especially those without diagnostic indications. Genome-wide cfDNA testing has fewer false positive and false negative results compared with biochemical screening.
Collapse
|
32
|
Chen CP, Ko TM, Chen YY, Chern SR, Wu PS, Chen SW, Lai ST, Chuang TY, Yang CW, Pan CW, Wang W. Prenatal diagnosis and molecular cytogenetic characterization of low-level mosaicism for tetrasomy 18p at amniocentesis in a pregnancy with a favorable outcome. Taiwan J Obstet Gynecol 2018; 56:836-839. [PMID: 29241930 DOI: 10.1016/j.tjog.2017.10.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/17/2017] [Indexed: 10/18/2022] Open
Abstract
OBJECTIVE We present prenatal diagnosis of low-level mosaicism for tetrasomy 18p at amniocentesis in a pregnancy with a favorable outcome. CASE REPORT A 40-year-old woman underwent amniocentesis at 17 weeks of gestation because of advanced maternal age. Amniocentesis revealed a de novo supernumerary isochromosome 18p in eight of 39 colonies of cultured amniocytes. The karyotype was 47,XX,+i(18)(p10)[8]/46,XX[31]. Array comparative genomic hybridization (aCGH) analysis using uncultured amniocytes revealed arr 18p11.32p11.21 [hg 19] (148,963-14,081,887) × 2-3. Repeat amniocentesis was performed at 20 weeks of gestation. Interphase fluorescence in situ hybridization (FISH) analysis showed four 18p11.22-specific probe (RP11-918F20) signals in 11.7% (12/103 cells) of uncultured amniocytes. aCGH analysis on uncultured amniocytes did not detect genomic imbalance in chromosome 18. The parental karyotypes were normal. Polymorphic DNA marker analysis excluded uniparental disomy 18. Cytogenetic analysis of cultured amniocytes at repeat amniocentesis revealed a karyotype of 47,XX,+i(18)(p10)[2]/46,XX[12]. Prenatal ultrasound was unremarkable. The pregnancy was carried to 38 weeks of gestation, and a 2742-g phenotypically normal female baby was delivered with a cord blood karyotype of 46,XX. When examined at 8 months of age, the infant was normal in growth and psychomotor development. Interphase FISH analysis on 21 uncultured urinary cells revealed normal signals in all cells and no mosaic tetrasomy 18p. CONCLUSION Low-level mosaic tetrasomy 18p at amniocentesis without ultrasound abnormalities can be associated with a favorable outcome.
Collapse
Affiliation(s)
- Chih-Ping Chen
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan; Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan; Department of Biotechnology, Asia University, Taichung, Taiwan; School of Chinese Medicine, College of Chinese Medicine, China Medical University, Taichung, Taiwan; Institute of Clinical and Community Health Nursing, National Yang-Ming University, Taipei, Taiwan; Department of Obstetrics and Gynecology, School of Medicine, National Yang-Ming University, Taipei, Taiwan.
| | - Tsang-Ming Ko
- Genephile Bioscience Laboratory, Ko's Obstetrics and Gynecology, Taipei, Taiwan
| | - Yi-Yung Chen
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Schu-Rern Chern
- Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan
| | | | - Shin-Wen Chen
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Shih-Ting Lai
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Tzu-Yun Chuang
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Chien-Wen Yang
- Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan
| | - Chen-Wen Pan
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Wayseen Wang
- Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan; Department of Bioengineering, Tatung University, Taipei, Taiwan
| |
Collapse
|
33
|
Noninvasive Prenatal Testing: Comparison of Two Mappers and Influence in the Diagnostic Yield. BIOMED RESEARCH INTERNATIONAL 2018; 2018:9498140. [PMID: 29977923 PMCID: PMC6011118 DOI: 10.1155/2018/9498140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 04/16/2018] [Accepted: 05/07/2018] [Indexed: 11/18/2022]
Abstract
Objective The aim of this study was to determine if the use of different mappers for NIPT may vary the results considerably. Methods Peripheral blood was collected from 217 pregnant women, 58 pathological (34 pregnancies with trisomy 21, 18 with trisomy 18, and 6 with trisomy 13) and 159 euploid. MPS was performed following a manufacturer's modified protocol of semiconductor sequencing. Obtained reads were mapped with two different software programs: TMAP and HPG-Aligner, comparing the results. Results Using TMAP, 57 pathological samples were correctly detected (sensitivity 98.28%, specificity 93.08%): 33 samples as trisomy 21 (sensitivity 97.06%, specificity 99.45%), 16 as trisomy 18 (sensibility 88.89%, specificity 93.97%), and 6 as trisomy 13 (sensibility 100%, specificity 100%). 11 false positives, 1 false negative, and 2 samples incorrectly identified were obtained. Using HPG-Aligner, all the 58 pathological samples were correctly identified (sensibility 100%, specificity 96.86%): 34 as trisomy 21 (sensibility 100%, specificity 98.91%), 18 as trisomy 18 (sensibility 100%, specificity 98.99%), and 6 as trisomy 13 (sensibility 100%, specificity 99.53%). 5 false positives were obtained. Conclusion Different mappers use slightly different algorithms, so the use of one mapper or another with the same batch file can provide different results.
Collapse
|
34
|
Gray KJ, Wilkins-Haug LE. Have we done our last amniocentesis? Updates on cell-free DNA for Down syndrome screening. Pediatr Radiol 2018; 48:461-470. [PMID: 29550862 PMCID: PMC7088458 DOI: 10.1007/s00247-017-3958-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Revised: 06/11/2017] [Accepted: 07/26/2017] [Indexed: 12/19/2022]
Abstract
Prenatal aneuploidy screening changed significantly in 2012 when cell-free fetal deoxyribonucleic acid (DNA) was introduced as a noninvasive prenatal test. A noninvasive prenatal test detects cell free fragments of fetal DNA from the placenta circulating in maternal blood that coexist with cell-free DNA (cfDNA) of maternal origin. Using next-generation sequencing, the noninvasive prenatal test compares maternal and fetal cfDNA ratios for chromosomes of interest (i.e., 21, 18, 13, X, and Y) to assess chromosomal aneuploidy. Compared to traditional screening using ultrasound and serum markers, the noninvasive prenatal test has superior test characteristics, including a higher detection rate and positive predictive value, and a lower false-positive rate. The noninvasive prenatal test is already used for primary screening in high-risk women and is rapidly expanding to all women. Given its increasing use, understanding the noninvasive prenatal test's limitations is critical. Discordant results (i.e. noninvasive prenatal test is positive for aneuploidy with a normal fetal karyotype) can occur because of biological processes such as aneuploidy confined to the placenta, a vanished twin, maternal aneuploidy or maternal cancer. Use of the noninvasive prenatal test for screening beyond the most common aneuploidies is not recommended. The noninvasive prenatal test is a major advance in prenatal aneuploidy screening but it is not diagnostic and does not replace invasive testing (i.e. chorionic villous sampling or amniocentesis) for confirmation of fetal chromosomal disorders.
Collapse
Affiliation(s)
- Kathryn J Gray
- Division of Maternal-Fetal Medicine, Brigham & Women's Hospital, 75 Francis St., Boston, MA, 02115, USA
| | - Louise E Wilkins-Haug
- Division of Maternal-Fetal Medicine, Brigham & Women's Hospital, 75 Francis St., Boston, MA, 02115, USA.
| |
Collapse
|
35
|
Petersen AK, Cheung SW, Smith JL, Bi W, Ward PA, Peacock S, Braxton A, Van Den Veyver IB, Breman AM. Positive predictive value estimates for cell-free noninvasive prenatal screening from data of a large referral genetic diagnostic laboratory. Am J Obstet Gynecol 2017; 217:691.e1-691.e6. [PMID: 29032050 DOI: 10.1016/j.ajog.2017.10.005] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Revised: 09/29/2017] [Accepted: 10/03/2017] [Indexed: 02/07/2023]
Abstract
BACKGROUND Since its debut in 2011, cell-free fetal DNA screening has undergone rapid expansion with respect to both utilization and coverage. However, conclusive data regarding the clinical validity and utility of this screening tool, both for the originally included common autosomal and sex-chromosomal aneuploidies as well as the more recently added chromosomal microdeletion syndromes, have lagged behind. Thus, there is a continued need to educate clinicians and patients about the current benefits and limitations of this screening tool to inform pre- and posttest counseling, pre/perinatal decision making, and medical risk assessment/management. OBJECTIVE The objective of this study was to determine the positive predictive value and false-positive rates for different chromosomal abnormalities identified by cell-free fetal DNA screening using a large data set of diagnostic testing results on invasive samples submitted to the laboratory for confirmatory studies. STUDY DESIGN We tested 712 patient samples sent to our laboratory to confirm a cell-free fetal DNA screening result, indicating high risk for a chromosome abnormality. We compiled data from all cases in which the indication for confirmatory testing was a positive cell-free fetal DNA screen, including the common trisomies, sex chromosomal aneuploidies, microdeletion syndromes, and other large genome-wide copy number abnormalities. Testing modalities included fluorescence in situ hybridization, G-banded karyotype, and/or chromosomal microarray analysis performed on chorionic villus samples, amniotic fluid, or postnatally obtained blood samples. Positive predictive values and false-positive rates were calculated from tabulated data. RESULTS The positive predictive values for trisomy 13, 18, and 21 were consistent with previous reports at 45%, 76%, and 84%, respectively. For the microdeletion syndrome regions, positive predictive values ranged from 0% for detection of Cri-du-Chat syndrome and Prader-Willi/Angelman syndrome to 14% for 1p36 deletion syndrome and 21% for 22q11.2 deletion syndrome. Detection of sex chromosomal aneuploidies had positive predictive values of 26% for monosomy X, 50% for 47,XXX, and 86% for 47,XXY. CONCLUSION The positive predictive values for detection of common autosomal and sex chromosomal aneuploidies by cell-free fetal DNA screening were comparable with other studies. Identification of microdeletions was associated with lower positive predictive values and higher false-positive rates, likely because of the low prevalence of the individual targeted microdeletion syndromes in the general population. Although the obtained positive predictive values compare favorably with those seen in traditional screening approaches for common aneuploidies, they highlight the importance of educating clinicians and patients on the limitations of cell-free fetal DNA screening tests. Improvement of the cell-free fetal DNA screening technology and continued monitoring of its performance after introduction into clinical practice will be important to fully establish its clinical utility. Nonetheless, our data provide valuable information that may aid result interpretation, patient counseling, and clinical decision making/management.
Collapse
Affiliation(s)
- Andrea K Petersen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Sau Wai Cheung
- Baylor Genetics, Baylor College of Medicine, Houston, TX; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Janice L Smith
- Baylor Genetics, Baylor College of Medicine, Houston, TX; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Weimin Bi
- Baylor Genetics, Baylor College of Medicine, Houston, TX; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Patricia A Ward
- Baylor Genetics, Baylor College of Medicine, Houston, TX; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Sandra Peacock
- Baylor Genetics, Baylor College of Medicine, Houston, TX
| | - Alicia Braxton
- Baylor Genetics, Baylor College of Medicine, Houston, TX; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Ignatia B Van Den Veyver
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX; Texas Children's Hospital, Houston, TX
| | - Amy M Breman
- Baylor Genetics, Baylor College of Medicine, Houston, TX; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX.
| |
Collapse
|
36
|
Wald NJ, Huttly WJ, Bestwick JP, Old R, Morris JK, Cheng R, Aquilina J, Peregrine E, Roberts D, Alfirevic Z. Prenatal reflex DNA screening for trisomies 21, 18, and 13. Genet Med 2017; 20:825-830. [DOI: 10.1038/gim.2017.188] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 08/24/2017] [Indexed: 12/11/2022] Open
|
37
|
Advani HV, Barrett AN, Evans MI, Choolani M. Challenges in non-invasive prenatal screening for sub-chromosomal copy number variations using cell-free DNA. Prenat Diagn 2017; 37:1067-1075. [PMID: 28950403 DOI: 10.1002/pd.5161] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Revised: 08/23/2017] [Accepted: 09/16/2017] [Indexed: 12/14/2022]
Abstract
Non-invasive prenatal screening (NIPS) has revolutionized the approach to prenatal fetal aneuploidy screening. Many commercial providers now offer analyses for sub-chromosomal copy number variations (CNVs). Here, we review the use of NIPS in the context of screening for microdeletions and microduplications, issues surrounding the choice of disorders tested for, and the advantages and disadvantages associated with the inclusion of microdeletions to current NIPS. Several studies have claimed benefits; however, we suggest that microdeletions have not demonstrated a low enough false positive rate to be deemed practical or ethically acceptable, especially considering their low positive predictive values. Because a positive NIPS result should be confirmed using diagnostic techniques, and false positive rates are as high as 90% for some microdeletions, diagnostic testing seems preferable when the goal is to maximize the detection of microdeletion or microduplication syndromes.
Collapse
Affiliation(s)
- Henna V Advani
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Angela N Barrett
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Mark I Evans
- Department of Obstetrics and Gynecology, Mt. Sinai School of Medicine, New York, NY, USA.,Comprehensive Genetics and Fetal Medicine Foundation of America, New York, NY, USA
| | - Mahesh Choolani
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| |
Collapse
|
38
|
Fiorentino F, Bono S, Pizzuti F, Duca S, Polverari A, Faieta M, Baldi M, Diano L, Spinella F. Author's reply to Grati and Benn. Prenat Diagn 2017; 37:1053-1054. [DOI: 10.1002/pd.5136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 08/02/2017] [Indexed: 11/09/2022]
Affiliation(s)
| | - Sara Bono
- GENOMA - Molecular Genetics Laboratories; Rome Italy
| | | | - Sara Duca
- GENOMA - Molecular Genetics Laboratories; Rome Italy
| | | | - Monica Faieta
- GENOMA - Molecular Genetics Laboratories; Rome Italy
| | - Marina Baldi
- GENOMA - Molecular Genetics Laboratories; Rome Italy
| | - Laura Diano
- GENOMA - Molecular Genetics Laboratories; Rome Italy
| | | |
Collapse
|
39
|
Chen M, Fu XY, Luo YQ, Qian YQ, Pan L, Wang LY, Dong MY. Detection of fetal duplication 16p11.2q12.1 by next-generation sequencing of maternal plasma and invasive diagnosis. J Matern Fetal Neonatal Med 2017; 32:38-45. [PMID: 28882078 DOI: 10.1080/14767058.2017.1369947] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
OBJECTIVE The objective of study is to report the feasibility of non-invasive prenatal screening (NIPS) combined with invasive detection by chromosomal analysis in identifying fetal duplication, providing clinical performance of NIPS on copy number variations (CNVs) detection. MATERIAL AND METHODS NIPS was offered to a 35-year-old pregnant woman. Amniocentesis was performed to confirm the positive screening result. Fetal sample was detected by karyotyping, fluorescence in situ hybridization (FISH), and chromosomal microarray (CMA). Parental karyotyping was also conducted. RESULTS NIPS result was positive for chromosome 16, indicating an extra copy of chromosome 16. FISH and chromosomal karyotyping revealed that the fetus had a marker chromosome derived from chromosome 16. CMA further demonstrated an approximately 19-Mb duplication in chromosome 16. The final fetal karyotype was 47,XY,+mar. ish der (16)(D16Z3+).arr 16p11.2q12.1 (30 624 186-49 696 337 × 3). Ultrasound scan and MRI showed some structure malformations. CONCLUSIONS A protocol for CNVs detection by combining a series of genetic methods was presented in this study and a novel marker duplication 16p11.2q12.1 was reported. With the ability to identify subchromosomal deletions and duplications in fetus, NIPS could reduce the possibility of invasive diagnosis. The followed confirmation test for positive sample is necessary and ensures the accuracy of the diagnosis.
Collapse
Affiliation(s)
- Min Chen
- a Women's Hospital, School of Medicine, Zhejiang University , Hangzhou , China.,b Key Laboratory of Reproductive Genetics , Zhejiang University, Ministry of Education , Hangzhou , China.,c Key Laboratory of Women's Reproductive Health of Zhejiang Province , Hangzhou , China
| | - Xiao-Ying Fu
- a Women's Hospital, School of Medicine, Zhejiang University , Hangzhou , China.,b Key Laboratory of Reproductive Genetics , Zhejiang University, Ministry of Education , Hangzhou , China.,c Key Laboratory of Women's Reproductive Health of Zhejiang Province , Hangzhou , China
| | - Yu-Qin Luo
- a Women's Hospital, School of Medicine, Zhejiang University , Hangzhou , China.,b Key Laboratory of Reproductive Genetics , Zhejiang University, Ministry of Education , Hangzhou , China.,c Key Laboratory of Women's Reproductive Health of Zhejiang Province , Hangzhou , China
| | - Ye-Qing Qian
- a Women's Hospital, School of Medicine, Zhejiang University , Hangzhou , China.,b Key Laboratory of Reproductive Genetics , Zhejiang University, Ministry of Education , Hangzhou , China.,c Key Laboratory of Women's Reproductive Health of Zhejiang Province , Hangzhou , China
| | - Ling Pan
- a Women's Hospital, School of Medicine, Zhejiang University , Hangzhou , China.,b Key Laboratory of Reproductive Genetics , Zhejiang University, Ministry of Education , Hangzhou , China.,c Key Laboratory of Women's Reproductive Health of Zhejiang Province , Hangzhou , China
| | - Li-Ya Wang
- a Women's Hospital, School of Medicine, Zhejiang University , Hangzhou , China.,b Key Laboratory of Reproductive Genetics , Zhejiang University, Ministry of Education , Hangzhou , China.,c Key Laboratory of Women's Reproductive Health of Zhejiang Province , Hangzhou , China
| | - Min-Yue Dong
- a Women's Hospital, School of Medicine, Zhejiang University , Hangzhou , China.,b Key Laboratory of Reproductive Genetics , Zhejiang University, Ministry of Education , Hangzhou , China.,c Key Laboratory of Women's Reproductive Health of Zhejiang Province , Hangzhou , China
| |
Collapse
|
40
|
Audibert F, De Bie I, Johnson JA, Okun N, Wilson RD, Armour C, Chitayat D, Kim R. N o 348-Directive clinique de la SOGC et du CCGM : mise à jour sur le dépistage prénatal de l’aneuploïdie fœtale, des anomalies fœtales et des issues défavorables de la grossesse. JOURNAL OF OBSTETRICS AND GYNAECOLOGY CANADA 2017; 39:818-832. [DOI: 10.1016/j.jogc.2017.05.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
41
|
Maternal iAMP21 acute lymphoblastic leukemia detected on prenatal cell-free DNA genetic screening. Blood Adv 2017; 1:1491-1494. [PMID: 29296790 DOI: 10.1182/bloodadvances.2017008680] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 07/21/2017] [Indexed: 12/18/2022] Open
Abstract
cfDNA sequencing for fetal aneuploidy may detect chromosomal abnormalities representative of maternal malignancy.Maternal malignancy must be considered when abnormal cfDNA sequencing for fetal aneuploidy is associated with normal fetal karyotype.
Collapse
|
42
|
Vermeesch JR, Voet T, Devriendt K. Prenatal and pre-implantation genetic diagnosis. Nat Rev Genet 2017; 17:643-56. [PMID: 27629932 DOI: 10.1038/nrg.2016.97] [Citation(s) in RCA: 117] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The past decade has seen the development of technologies that have revolutionized prenatal genetic testing; that is, genetic testing from conception until birth. Genome-wide single-cell arrays and high-throughput sequencing analyses are dramatically increasing our ability to detect embryonic and fetal genetic lesions, and have substantially improved embryo selection for in vitro fertilization (IVF). Moreover, both invasive and non-invasive mutation scanning of the genome are helping to identify the genetic causes of prenatal developmental disorders. These advances are changing clinical practice and pose novel challenges for genetic counselling and prenatal care.
Collapse
Affiliation(s)
- Joris Robert Vermeesch
- Centre for Human Genetics, Department of Human Genetics, University of Leuven, 49 Herestraat, Leuven 3000, Belgium
| | - Thierry Voet
- Centre for Human Genetics, Department of Human Genetics, University of Leuven, 49 Herestraat, Leuven 3000, Belgium
| | - Koenraad Devriendt
- Centre for Human Genetics, Department of Human Genetics, University of Leuven, 49 Herestraat, Leuven 3000, Belgium
| |
Collapse
|
43
|
Qiang R, Cai N, Wang X, Wang L, Cui K, Wang W, Wang X, Li X. Detection of trisomies 13, 18 and 21 using non-invasive prenatal testing. Exp Ther Med 2017; 13:2304-2310. [PMID: 28565842 PMCID: PMC5443185 DOI: 10.3892/etm.2017.4272] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 12/20/2016] [Indexed: 11/12/2022] Open
Abstract
The clinical performance of non-invasive prenatal testing (NIPT) in the Down's syndrome screening based on 1,901 pregnant women in a Chinese hospital was investigated. This was a retrospective analysis of NIPT study in singleton pregnancy (n=1,901). The NIPT test is offered routinely as a prenatal screening test for common fetal aneuploidies, including trisomy 13 (T13), T18 and T21 to pregnant women with risk factors of one or more anomalies. Maternal peripheral blood (5 ml) was collected in an ethylenediaminetetraacetic acid (EDTA) tube at a gestational age of 12+0 to 32+6 weeks. The samples were delivered at -80°C to the certified Shenzhen BGI Clinical Laboratory Center. Sequencing data were analyzed using a proprietary algorithm. Women with positive NIPT results were recommended to receive karyotype analysis and amniotic fluid puncture for further validation. The cases were followed up for 56 days after delivery. All the patients underwent ultrasound examination, and the majority of patients (91.16%) showed normal findings. In contrast, 136 (7.15%) showed ultrasound anomalies. The most common anomaly was echogenic heart focus (n=80), accounting for 4.21% of the patients. Twenty-two cases were classified by the NIPT to be positive for the T21 (n=15), T18 (n=5) and T13 (n=2), respectively, while the others (n=1,879) were classified to be NIPT negative cases. Among these cases, the fetal outcome data were obtained in 1,483 cases, while 396 were lost to follow-up. The majority of cases (75.47%) were normal at birth. Neonatal death was observed in 1 case. Five pregnant women decided termination of pregnancy despite the presence of NIPT negativity. In conclusion, NIPT technique is feasible for the prenatal screening of T18 and T21 with higher sensitivity and specificity compared with conventional methods.
Collapse
Affiliation(s)
- Rong Qiang
- Genetic Medical Center, Northwest Women and Children's Hospital, Xi'an, Shaanxi 710003, P.R. China
- Center for Translational Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Na Cai
- Genetic Medical Center, Northwest Women and Children's Hospital, Xi'an, Shaanxi 710003, P.R. China
| | - Xiaobin Wang
- Genetic Medical Center, Northwest Women and Children's Hospital, Xi'an, Shaanxi 710003, P.R. China
| | - Lin Wang
- Genetic Medical Center, Northwest Women and Children's Hospital, Xi'an, Shaanxi 710003, P.R. China
| | - Ke Cui
- Genetic Medical Center, Northwest Women and Children's Hospital, Xi'an, Shaanxi 710003, P.R. China
| | - Wei Wang
- Shenzhen BGI Clinical Laboratory Center, Shenzhen, Guangdong 518083, P.R. China
| | - Xiang Wang
- Genetics and Department of Gynecology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Xu Li
- Center for Translational Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| |
Collapse
|
44
|
Liehr T, Lauten A, Schneider U, Schleussner E, Weise A. Noninvasive Prenatal Testing - When Is It Advantageous to Apply. Biomed Hub 2017; 2:1-11. [PMID: 31988902 PMCID: PMC6945944 DOI: 10.1159/000458432] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 01/27/2017] [Indexed: 12/23/2022] Open
Abstract
Nowadays it is common sense in obstetrics that an increased risk for pregnancy loss due to invasive testing does not exist. Nonetheless, noninvasive prenatal testing (NIPT) is a hot topic, even though this approach does not provide a reduction of unintentionally induced abortions. NIPT has a number of shortcuts which are highlighted in this review, including: (1) in NIPT placental rather than fetal DNA is studied, (2) NIPT fails in 2–6% of cases, and (3) trisomy 21 accounts for only ∼50% of existing chromosomal aberrations. Thus, we agree with the literature that NIPT is a fascinating possibility to gain information on unborn life from minimal amounts of DNA. However, it remains a pure risk estimation test directed towards the detection of specific chromosomal abnormalities from peripheral blood of the pregnant woman. It is important to highlight that families buying this test, and getting a normal result, may be provided with a false sense of security. Thus, careful and comprehensive genetic counselling should be performed before the test is offered, and should include a clear explanation of the advantages and disadvantages, as well as limitations, compared to other methods.
Collapse
Affiliation(s)
- Thomas Liehr
- Institute of Human Genetics, Friedrich Schiller University, Jena, Germany
| | - Angela Lauten
- Institute of Clinic for Obstetrics and Gynecology, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Uwe Schneider
- Institute of Clinic for Obstetrics and Gynecology, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Ekkehard Schleussner
- Institute of Clinic for Obstetrics and Gynecology, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Anja Weise
- Institute of Human Genetics, Friedrich Schiller University, Jena, Germany
| |
Collapse
|
45
|
Zhou X, Sui L, Xu Y, Song Y, Qi Q, Zhang J, Zhu H, Sun H, Tian F, Xu M, Cram DS, Liu J. Contribution of maternal copy number variations to false-positive fetal trisomies detected by noninvasive prenatal testing. Prenat Diagn 2017; 37:318-322. [PMID: 28152582 DOI: 10.1002/pd.5014] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 01/11/2017] [Accepted: 01/29/2017] [Indexed: 12/19/2022]
Affiliation(s)
- Xiya Zhou
- Department of Obstetrics and Gynecology; Peking Union Medical College Hospital; Beijing China
| | - Lili Sui
- Department of Obstetrics and Gynecology; Peking Union Medical College Hospital; Beijing China
| | - Yalan Xu
- Department of Obstetrics and Gynecology; Peking Union Medical College Hospital; Beijing China
| | - Yijun Song
- Department of Obstetrics and Gynecology; Peking Union Medical College Hospital; Beijing China
| | - Qingwei Qi
- Department of Obstetrics and Gynecology; Peking Union Medical College Hospital; Beijing China
| | | | | | - Huaiyu Sun
- Berry Genomics Corporation; Beijing China
| | - Feng Tian
- Berry Genomics Corporation; Beijing China
| | - Mengnan Xu
- Berry Genomics Corporation; Beijing China
| | | | - Juntao Liu
- Department of Obstetrics and Gynecology; Peking Union Medical College Hospital; Beijing China
| |
Collapse
|
46
|
Yu SCY, Jiang P, Chan KCA, Faas BHW, Choy KW, Leung WC, Leung TY, Lo YMD, Chiu RWK. Combined Count- and Size-Based Analysis of Maternal Plasma DNA for Noninvasive Prenatal Detection of Fetal Subchromosomal Aberrations Facilitates Elucidation of the Fetal and/or Maternal Origin of the Aberrations. Clin Chem 2016; 63:495-502. [PMID: 27974386 DOI: 10.1373/clinchem.2016.254813] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 10/10/2016] [Indexed: 12/22/2022]
Abstract
BACKGROUND Noninvasive prenatal detection of fetal subchromosomal copy number aberrations (CNAs) can be achieved through massively parallel sequencing of maternal plasma DNA. However, when a mother herself is a carrier of a CNA, one cannot discern if her fetus has inherited the CNA. In addition, false-positive results would become more prevalent when more subchromosomal regions are analyzed. METHODS We used a strategy that combined count- and size-based analyses of maternal plasma DNA for the detection of fetal subchromosomal CNAs in 7 target regions for 10 test cases. RESULTS For the 5 cases in which CNAs were present only in the fetus, the size-based approach confirmed the aberrations detected by the count-based approach. For the 5 cases in which the mother herself carried an aberration, we successfully deduced that 3 of the fetuses had inherited the aberrations and that the other 2 fetuses had not inherited the aberrations. No false positives were observed in this cohort. CONCLUSIONS Combined count- and size-based analysis of maternal plasma DNA permits the noninvasive elucidation of whether a fetus has inherited a CNA from its mother who herself is a carrier of the CNA. This strategy has the potential to improve the diagnostic specificity of noninvasive prenatal testing.
Collapse
Affiliation(s)
- Stephanie C Y Yu
- Centre for Research into Circulating Fetal Nucleic Acids, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Peiyong Jiang
- Centre for Research into Circulating Fetal Nucleic Acids, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - K C Allen Chan
- Centre for Research into Circulating Fetal Nucleic Acids, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Brigitte H W Faas
- Radboud University Nijmegen Medical Center, Department of Human Genetics, Nijmegen, The Netherlands
| | - Kwong W Choy
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Wing C Leung
- Kwong Wah Hospital, Kowloon, Hong Kong SAR, China
| | - Tak Y Leung
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Y M Dennis Lo
- Centre for Research into Circulating Fetal Nucleic Acids, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Rossa W K Chiu
- Centre for Research into Circulating Fetal Nucleic Acids, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China; .,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| |
Collapse
|
47
|
Accuracy and clinical value of maternal incidental findings during noninvasive prenatal testing for fetal aneuploidies. Genet Med 2016; 19:306-313. [PMID: 27584908 DOI: 10.1038/gim.2016.113] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Accepted: 06/16/2016] [Indexed: 01/16/2023] Open
Abstract
PURPOSE Genome-wide sequencing of cell-free (cf)DNA of pregnant women aims to detect fetal chromosomal imbalances. Because the largest fraction of cfDNA consists of maternal rather than fetal DNA fragments, maternally derived copy-number variants (CNVs) are also measured. Despite their potential clinical relevance, current analyses do not interpret maternal CNVs. Here, we explore the accuracy and clinical value of maternal CNV analysis. METHODS Noninvasive prenatal testing was performed by whole-genome shotgun sequencing on plasma samples. Following mapping of the sequencing reads, the landscape of maternal CNVs was charted for 9,882 women using SeqCBS analysis. Recurrent CNVs were validated retrospectively by comparing their incidence with published reports. Nonrecurrent CNVs were prospectively confirmed by array comparative genomic hybridization or fluorescent in situ hybridization analysis on maternal lymphocytes. RESULTS Consistent with population estimates, 10% nonrecurrent and 0.4% susceptibility CNVs for low-penetrant genomic disorders were identified. Five clinically actionable variants were reported to the pregnant women, including haploinsufficiency of RUNX1, a mosaicism for segmental chromosome 13 deletion, an unbalanced translocation, and two interstitial chromosome X deletions. CONCLUSION Shotgun sequencing of cfDNA not only enables the detection of fetal aneuploidies but also reveals the presence of maternal CNVs. Some of those variants are clinically actionable or could potentially be harmful for the fetus. Interrogating the maternal CNV landscape can improve overall pregnancy management, and we propose reporting those variants if clinically relevant. The identification and reporting of such CNVs pose novel counseling dilemmas that warrant further discussions and development of societal guidelines.Genet Med 19 3, 306-313.
Collapse
|
48
|
Benn P. Expanding non-invasive prenatal testing beyond chromosomes 21, 18, 13, X and Y. Clin Genet 2016; 90:477-485. [PMID: 27283893 DOI: 10.1111/cge.12818] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 06/05/2016] [Accepted: 06/07/2016] [Indexed: 12/16/2022]
Abstract
Non-invasive prenatal testing (NIPT) based on cell-free DNA in maternal plasma is being expanded to include additional chromosome abnormalities beyond those involving chromosomes 21, 18, 13, X and Y. Review of population cytogenetic data provides insight into the likely number of additional abnormalities detectable. Additional clinically significant and cytogenetically recognizable abnormalities are present in less than 0.1% of newborns but clinically significant, or potentially significant, sub-microscopic imbalances are expected to be present in 1.7%. Cytogenetic studies on chorionic villus samples suggests that after excluding abnormalities involving chromosomes 21, 18, 13, X and Y, approximately 0.6% of NIPT results may be positive for an unbalanced abnormality attributable to mosaicism but most of these will not be confirmed at amniocentesis or in newborns. NIPT has also been developed for specific microdeletion syndromes and initial experience is now available. Laboratory procedures such as deeper sequencing and additional data analytics are rapidly evolving but even with existing protocols, it is already clear that NIPT does not necessarily need to be limited to trisomies 21, 18, 13 and the sex-chromosome abnormalities. Patient educational materials and genetic counseling services need to be available for women offered expanded NIPT.
Collapse
Affiliation(s)
- P Benn
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT, USA
| |
Collapse
|
49
|
Dheedene A, Sante T, De Smet M, Vanbellinghen JF, Grisart B, Vergult S, Janssens S, Menten B. Implementation of non-invasive prenatal testing by semiconductor sequencing in a genetic laboratory. Prenat Diagn 2016; 36:699-707. [PMID: 27176606 PMCID: PMC5108441 DOI: 10.1002/pd.4841] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Revised: 04/15/2016] [Accepted: 05/10/2016] [Indexed: 12/16/2022]
Abstract
OBJECTIVES To implement non-invasive prenatal testing (NIPT) for fetal aneuploidies with semiconductor sequencing in an academic cytogenomic laboratory and to evaluate the first 15-month experience on clinical samples. METHODS We validated a NIPT protocol for cell-free fetal DNA sequencing from maternal plasma for the detection of trisomy 13, 18 and 21 on a semiconductor sequencing instrument. Fetal DNA fraction calculation for all samples and several quality parameters were implemented in the workflow. One thousand eighty-one clinical NIPT samples were analysed, following the described protocol. RESULTS Non-invasive prenatal testing was successfully implemented and validated on 201 normal and 74 aneuploid samples. From 1081 clinical samples, 17 samples showed an abnormal result: 14 trisomy 21 samples, one trisomy 18 and one trisomy 16 were detected. Also a maternal copy number variation on chromosome 13 was observed, which could potentially lead to a false positive trisomy 13 result. One sex discordant result was reported, possibly attributable to a vanishing twin. Moreover, our combined fetal fraction calculation enabled a more reliable risk estimate for trisomy 13, 18 and 21. CONCLUSIONS Non-invasive prenatal testing for trisomy 21, 18 and 13 has a very high specificity and sensitivity. Because of several biological phenomena, diagnostic invasive confirmation of abnormal results remains required. © 2016 The Authors. Prenatal Diagnosis published by John Wiley & Sons, Ltd.
Collapse
Affiliation(s)
- Annelies Dheedene
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Tom Sante
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Matthias De Smet
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Jean-François Vanbellinghen
- Plateforme de Biologie Moléculaire, Département des Laboratoires, Cliniques Universitaires Saint-Luc, Bruxelles, Belgium
| | - Bernard Grisart
- Centre de Génétique Humaine, Institut de Pathologie et Génétique, Charleroi, Belgium
| | - Sarah Vergult
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Sandra Janssens
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Björn Menten
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium
| |
Collapse
|
50
|
Van Opstal D, Srebniak MI. Cytogenetic confirmation of a positive NIPT result: evidence-based choice between chorionic villus sampling and amniocentesis depending on chromosome aberration. Expert Rev Mol Diagn 2016; 16:513-20. [DOI: 10.1586/14737159.2016.1152890] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Diane Van Opstal
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, the Netherlands
| | | |
Collapse
|