1
|
Olayiwola JO, Marhabaie M, Koboldt D, Matthews T, Siemon A, Mouhlas D, Porter T, Kyle G, Myers C, Mei H, Hou YC, Babcock M, Hunter J, Schieffer KM, Akkari Y, Reshmi S, Cottrell C, Mathew MT, Leung ML. Clinically significant findings in a decade-long retrospective study of prenatal chromosomal microarray testing. Mol Genet Genomic Med 2024; 12:e2349. [PMID: 38263869 PMCID: PMC10958178 DOI: 10.1002/mgg3.2349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 01/25/2024] Open
Abstract
BACKGROUND Chromosomal microarray (CMA) is commonly utilized in the obstetrics setting. CMA is recommended when one or more fetal structural abnormalities is identified. CMA is also commonly used to determine genetic etiologies for miscarriages, fetal demise, and confirming positive prenatal cell-free DNA screening results. METHODS In this study, we retrospectively examined 523 prenatal and 319 products-of-conception (POC) CMA cases tested at Nationwide Children's Hospital from 2011 to 2020. We reviewed the referral indications, the diagnostic yield, and the reported copy number variants (CNV) findings. RESULTS In our cohort, the diagnostic yield of clinically significant CNV findings for prenatal testing was 7.8% (n = 41/523) compared to POC testing (16.3%, n = 52/319). Abnormal ultrasound findings were the most common indication present in 81% of prenatal samples. Intrauterine fetal demise was the common indication identified in POC samples. The most common pathogenic finding observed in all samples was isolated trisomy 21, detected in seven samples. CONCLUSION Our CMA study supports the clinical utility of prenatal CMA for clinical management and identifying genetic etiology in POC arrays. In addition, it provides insight to the spectrum of prenatal and POC CMA results as detected in an academic hospital clinical laboratory setting that serves as a reference laboratory.
Collapse
|
2
|
Cai M, Lin N, Chen X, Li Y, Lin M, Fu X, Huang H, He S, Xu L. Non-invasive prenatal testing for the diagnosis of congenital abnormalities: Insights from a large multicenter study in southern China. Braz J Med Biol Res 2023; 56:e12506. [PMID: 37377305 DOI: 10.1590/1414-431x2023e12506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 05/04/2023] [Indexed: 06/29/2023] Open
Abstract
Although non-invasive prenatal testing (NIPT) is widely used to detect fetal abnormalities, the results of NIPT vary by population, and data for the screening efficiency of NIPT positive predictive value (PPV) from different populations is limited. Herein, we retrospectively analyzed the NIPT results in a large multicenter study involving 52,855 pregnant women. Depending on gestational age, amniotic fluid or umbilical cord blood was extracted for karyotype and/or chromosome microarray analysis (CMA) in NIPT-positive patients, and the PPV and follow-up data were evaluated to determine its clinical value. Among the 52,855 cases, 754 were NIPT-positive, with a positivity rate of 1.4%. Karyotype analysis and/or CMA confirmed 323 chromosomal abnormalities, with a PPV of 45.1%. PPV for trisomy 21 (T21), trisomy 18 (T18), trisomy 13 (T13), sex chromosomal aneuploidies (SCAs), and copy number variations (CNVs) were 78.9, 35.3, 22.2, 36.9, and 32.9%, respectively. The PPVs for T21, T18, and T13 increased with age, whereas the PPVs for SCAs and CNVs had little correlation with age. The PPV was significantly higher in patients with advanced age and abnormal ultrasound. The NIPT results are affected by population characteristics. NIPT had a high PPV for T21 and a low PPV for T13 and T18, and screening for SCAs and CNVs showed clinical significance in southern China.
Collapse
Affiliation(s)
- Meiying Cai
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Na Lin
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Xuemei Chen
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Ying Li
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Min Lin
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Xianguo Fu
- Department of Prenatal Diagnosis, Ningde Municipal Hospital, Ningde Normal University, Ningde, China
| | - Hailong Huang
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Shuqiong He
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Liangpu Xu
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| |
Collapse
|
3
|
Sheehan E, Bacon V, Lascurain S, Stone J, Yatsenko S, Aarabi M, Skvarca LB, Clemens M, Saller D. Prenatal and fetal diagnosis of trisomy 18 after low-risk cell-free fetal DNA screening: A report of four cases. Prenat Diagn 2023; 43:36-41. [PMID: 36426655 DOI: 10.1002/pd.6273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 11/15/2022] [Accepted: 11/19/2022] [Indexed: 11/27/2022]
Abstract
INTRODUCTION Non-Invasive Prenatal Screening (NIPS) is a useful screening method for common aneuploidies that can occur in pregnancies. It yields high sensitivities and specificities for the targeted conditions it tests for. Most commonly, these include Trisomies in chromosomes 21, 18, and 13, as well as aneuploidies in chromosomes X and Y. It does not, however, replace diagnostic testing. We review four cases seen by our institutions of patients who had NIPS performed with low-risk results and subsequently had fetuses affected with trisomy 18. METHODS All fetal samples were evaluated by level II anatomic ultrasound and tested on amniocytes or products of conception through karyotype or chromosomal microarray following low-risk NIPS. RESULTS None of the fetuses showed evidence of mosaicism and had features (both on ultrasound and postnatally) consistent with Trisomy 18. Postnatal fluorescence in situ hybridization performed on Formalin-Fixed Paraffin-Embedded tissue from 3 of the affected pregnancies' placentas identified mosaicism of trisomy 18. DISCUSSION We discuss the possible explanations for the discrepancy between NIPS results and fetal karyotype, including, but not limited to placental mosaicism, placental size, and limitations of NIPS as a screening test.
Collapse
Affiliation(s)
- Elizabeth Sheehan
- Center for Medical Genetics, UPMC Magee-Womens Hospital, Pittsburgh, Pennsylvania, USA
| | - Victoria Bacon
- Center for Medical Genetics, UPMC Magee-Womens Hospital, Pittsburgh, Pennsylvania, USA
| | - Seth Lascurain
- Maternal Fetal Medicine Department, UPMC Harrisburg, Harrisburg, Pennsylvania, USA
| | - Julia Stone
- Center for Medical Genetics, UPMC Magee-Womens Hospital, Pittsburgh, Pennsylvania, USA
| | - Svetlana Yatsenko
- Department of Medical Genetics and Genomics Laboratories, UPMC, Pittsburgh, Pennsylvania, USA.,Departments of Pathology and Obstetrics, Gynecology, and Reproductive Sciences, UPMC, Pittsburgh, Pennsylvania, USA
| | - Mahmoud Aarabi
- Department of Medical Genetics and Genomics Laboratories, UPMC, Pittsburgh, Pennsylvania, USA.,Departments of Pathology and Obstetrics, Gynecology, and Reproductive Sciences, UPMC, Pittsburgh, Pennsylvania, USA
| | - Lauren B Skvarca
- Departments of Pathology and Obstetrics, Gynecology, and Reproductive Sciences, UPMC, Pittsburgh, Pennsylvania, USA
| | - Michele Clemens
- Center for Medical Genetics, UPMC Magee-Womens Hospital, Pittsburgh, Pennsylvania, USA
| | - Devereux Saller
- Departments of Pathology and Obstetrics, Gynecology, and Reproductive Sciences, UPMC, Pittsburgh, Pennsylvania, USA
| |
Collapse
|
4
|
Deng C, Liu S. Factors Affecting the Fetal Fraction in Noninvasive Prenatal Screening: A Review. Front Pediatr 2022; 10:812781. [PMID: 35155308 PMCID: PMC8829468 DOI: 10.3389/fped.2022.812781] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 01/03/2022] [Indexed: 12/03/2022] Open
Abstract
A paradigm shift in noninvasive prenatal screening has been made with the discovery of cell-free fetal DNA in maternal plasma. Noninvasive prenatal screening is primarily used to screen for fetal aneuploidies, and has been used globally. Fetal fraction, an important parameter in the analysis of noninvasive prenatal screening results, is the proportion of fetal cell-free DNA present in the total maternal plasma cell-free DNA. It combines biological factors and bioinformatics algorithms to interpret noninvasive prenatal screening results and is an integral part of quality control. Maternal and fetal factors may influence fetal fraction. To date, there is no broad consensus on the factors that affect fetal fraction. There are many different approaches to evaluate this parameter, each with its advantages and disadvantages. Different fetal fraction calculation methods may be used in different testing platforms or laboratories. This review includes numerous publications that focused on the understanding of the significance, influencing factors, and interpretation of fetal fraction to provide a deeper understanding of this parameter.
Collapse
Affiliation(s)
- Cechuan Deng
- Prenatal Diagnostic Center, Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Shanling Liu
- Prenatal Diagnostic Center, Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| |
Collapse
|
5
|
Jin XX, Xu YF, Ying X, Qian YQ, Jin PZ, Dong MY. Clinical Application of Noninvasive Prenatal Testing for Pregnant Women with Assisted Reproductive Pregnancy. Int J Womens Health 2021; 13:1167-1174. [PMID: 34876859 PMCID: PMC8643197 DOI: 10.2147/ijwh.s337249] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 11/18/2021] [Indexed: 11/23/2022] Open
Abstract
Objective This paper analyzes the clinical significance of noninvasive prenatal testing (NIPT) for fetal chromosome aneuploidy in the screening of in vitro fertilization–embryo transfer (IVF) pregnancies. Methods The study subjects consisted of 3163 IVF-pregnant women who underwent NIPT at the Women’s Hospital, School of Medicine, Zhejiang University and Taizhou Hospital, Zhejiang Province from February 2015 to June 2019. Fetal or neonatal karyotype analysis was carried out in high-risk patients, with subsequent follow-up on pregnancy outcomes. Results NIPT results of 3163 pregnant women suggested 20 cases of high-risk fetal chromosome aneuploidy, of which 2185 cases were a single pregnancy. Of the 13 cases of high-risk chromosome aneuploidy in single pregnancies, seven were true positive, and six were false positive according to fetal or newborn chromosomal karyotype diagnosis. Twin pregnancies accounted for 978 cases in which NIPT indicated seven cases of high-risk chromosome aneuploidy; six of these cases were true positive, and one case was false positive according to fetal or newborn chromosomal karyotype diagnosis. The specificity, positive predictive value, and false-positive rate of trisomy 21 syndrome in IVF single embryo NIPT were 99.86%, 62.5%, and 0.14%, respectively. The specificity, positive predictive value, and false-positive rate of trisomy 18 syndrome were 99.95%, 66.67%, and 0.05%, respectively. The specificity of trisomy 13 syndrome was 99.91%, and the false-positive rate was 0.09%. The specificity of trisomy 21 syndrome in IVF twin NIPT was 99.89%, the positive predictive value was 83.33%, and the false-positive rate was 0.11%. The specificity and positive predictive value of fetal trisomy 18 syndrome were 100.00%, and the false-positive rate of it were 0.00%. Sensitivity and false-negative rates were 100% in all cases. Conclusion NIPT is an ideal prenatal test for IVF-pregnant women due to its high sensitivity and specificity in screening for fetal aneuploidy.
Collapse
Affiliation(s)
- Xiao-Xiao Jin
- Prenatal Diagnosis Center of Taizhou Hospital, Wenzhou Medical University, Taizhou, 317000, People's Republic of China.,Key Laboratory of Reproductive Genetics, Ministry of Education, Department of Reproductive Genetics, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, People's Republic of China
| | - Yan-Fei Xu
- Key Laboratory of Reproductive Genetics, Ministry of Education, Department of Reproductive Genetics, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, People's Republic of China
| | - Xiang Ying
- Prenatal Diagnosis Center of Taizhou Hospital, Wenzhou Medical University, Taizhou, 317000, People's Republic of China
| | - Ye-Qing Qian
- Key Laboratory of Reproductive Genetics, Ministry of Education, Department of Reproductive Genetics, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, People's Republic of China
| | - Peng-Zhen Jin
- Key Laboratory of Reproductive Genetics, Ministry of Education, Department of Reproductive Genetics, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, People's Republic of China
| | - Min-Yue Dong
- Key Laboratory of Reproductive Genetics, Ministry of Education, Department of Reproductive Genetics, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, People's Republic of China
| |
Collapse
|
6
|
Rosner M, Kolbe T, Voronin V, Hengstschläger M. Amniotic fluid stem cells and the cell source repertoire for non-invasive prenatal testing. Stem Cell Rev Rep 2021; 18:1366-1371. [PMID: 34383184 PMCID: PMC9033748 DOI: 10.1007/s12015-021-10228-5] [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] [Accepted: 07/26/2021] [Indexed: 12/04/2022]
Abstract
Cell-free fetal DNA (cffDNA)-based non-invasive prenatal testing (NIPT) is considered to be a very promising screening tool for pregnant women with an increased risk of fetal aneuploidy. Already millions of women worldwide underwent NIPT. However, due to the observed false-positive and false-negative results, this screening approach does not fulfil the criteria of a diagnostic test. Accordingly, positive results still require risk-carrying invasive prenatal testing, such as amniocentesis or chorionic villus sampling (CVS), for confirmation. Such hurdles need to be overcome before NIPT could become a diagnostic approach widely used in the general population. Here we discuss new evidence that besides the placenta amniotic fluid stem cells (AFSCs) could also represent an origin of cffDNA in the mother’s blood. A comprehensive picture of the involved cell source repertoire could pave the way to more reliable interpretations of NIPT results and ameliorate counselling of advice-seeking patients.
Collapse
Affiliation(s)
- Margit Rosner
- Institute of Medical Genetics, Center for Pathobiochemistry and Genetics, Medical University of Vienna, Währinger Strasse 10, 1090, 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
| | - Viktor Voronin
- Institute of Medical Genetics, Center for Pathobiochemistry and Genetics, Medical University of Vienna, Währinger Strasse 10, 1090, Vienna, Austria
| | - Markus Hengstschläger
- Institute of Medical Genetics, Center for Pathobiochemistry and Genetics, Medical University of Vienna, Währinger Strasse 10, 1090, Vienna, Austria.
| |
Collapse
|
7
|
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
|
8
|
Li J, Xie M, Wang F, Ma J, Li J, Chen C, Li Z, Wang J, Zhang Y, Li Y. A rare case of NIPT discrepancy caused by the placental mosaicism of three different karyotypes, 47,XXX, 47,XX,+21, and 48,XXX,+21. Mol Genet Genomic Med 2020; 8:e1279. [PMID: 32463164 PMCID: PMC7434741 DOI: 10.1002/mgg3.1279] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 03/24/2020] [Accepted: 03/27/2020] [Indexed: 12/11/2022] Open
Abstract
Background Placental mosaicism is one of the major reasons for noninvasive prenatal testing (NIPT) discrepancy. Herein, we discovered a rare case of placenta with complex karyotypes that caused false‐positive and false‐negative results in noninvasive prenatal testing. Methods Next‐generation sequencing (NGS) and Quantitative fluorescent polymerase chain reaction (QF‐PCR) were performed on the cord blood sample, fetal tissues, and eight placental biopsies. Fluorescent In Situ Hybridization (FISH) and karyotyping were also carried to confirm the fetal genome status. Results The results suggested that the fetal chromosome was 47,XXX and the placenta had three karyotypes of 48,XXX,+21, 47,XX,+21, and 47,XXX. QF‐PCR indicated that the extra chromosome 21 and chromosome X were all from the father. It is speculated that the zygote may have 48,XXX,+21 karyotype and trisomy rescue could be the main mechanism for the development of the homogeneous fetus and complex mosaic placenta. Conclusion Overall, the complicated nature of our case underlines the importance of discussing with parents the possibility of both atypical and discordant results during preconfirmatory amniocentesis counseling and consent.
Collapse
Affiliation(s)
- Jin Li
- Department of Laboratory Medicine, Zhongnan Hospital, Wuhan university, Wuhan, Hubei, P. R. China.,Hubei Clinical Research Center for prenatal Diagnosis and Birth Health, Wuhan, Hubei, P. R. China
| | - Mingshui Xie
- Department of Laboratory Medicine, Suizhou Central People's Hospital, Suizhou, Hubei, P. R. China
| | - Fang Wang
- Hubei Clinical Research Center for prenatal Diagnosis and Birth Health, Wuhan, Hubei, P. R. China.,Department of Obstetrics and gynecology, Zhongnan Hospital, Wuhan University, Wuhan, Hubei, P. R. China
| | - Jianhong Ma
- Hubei Clinical Research Center for prenatal Diagnosis and Birth Health, Wuhan, Hubei, P. R. China.,Department of Obstetrics and gynecology, Zhongnan Hospital, Wuhan University, Wuhan, Hubei, P. R. China
| | - Jiafu Li
- Hubei Clinical Research Center for prenatal Diagnosis and Birth Health, Wuhan, Hubei, P. R. China.,Department of Obstetrics and gynecology, Zhongnan Hospital, Wuhan University, Wuhan, Hubei, P. R. China
| | - Chen Chen
- Zhejiang Annoroad Biotechnology Co., Ltd, Zhejiang, P.R. China.,Annoroad Life Sciences Research Institute, Zhejiang, P.R. China
| | - Zhimin Li
- Annoroad Gene Technology (Beijing) Co., Ltd, Beijing, P.R. China
| | - Juan Wang
- Annoroad Gene Technology (Beijing) Co., Ltd, Beijing, P.R. China
| | - Yuanzhen Zhang
- Hubei Clinical Research Center for prenatal Diagnosis and Birth Health, Wuhan, Hubei, P. R. China.,Department of Obstetrics and gynecology, Zhongnan Hospital, Wuhan University, Wuhan, Hubei, P. R. China
| | - Yirong Li
- Department of Laboratory Medicine, Zhongnan Hospital, Wuhan university, Wuhan, Hubei, P. R. China.,Hubei Clinical Research Center for prenatal Diagnosis and Birth Health, Wuhan, Hubei, P. R. China
| |
Collapse
|
9
|
Hu HJ, Lee MY, Cho DY, Oh M, Kwon YJ, Han YJ, Ryu HM, Kim YN, Won HS. Prospective clinical evaluation of Momguard non-invasive prenatal test in 1011 Korean high-risk pregnant women. J OBSTET GYNAECOL 2019; 40:1090-1095. [PMID: 31826681 DOI: 10.1080/01443615.2019.1680617] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Clinical performance of the Momguard non-invasive prenatal test (NIPT) was evaluated in a cohort of Korean pregnant women. The foetal trisomies 21, 18 and 13 (T21, T18 and T13) were screened by low-coverage massive parallel sequencing in the maternal blood. Among the 1011 confirmed samples, 32 cases (3.2%) had positive NIPT results. Of these positive cases, 20 cases of T21, all cases of T18 and two cases of T13 had concordant karyotype findings. Only one case out of the remaining 979 negative NIPT samples showed a false negative result. The overall sensitivity and specificity of Momguard to detect the three chromosomal aneuploidies were 96.8% and 99.8%, respectively. Momguard is a clinically useful tool for the detection of T21, T18 and T13 in singleton pregnancy. However, as other NIPT tests, it carries the risk of false positive and false negative results. Hence, the genetic counsellors should provide these limitations to the examinees.Impact StatementWhat is already known on this subject? The NIPT approach using massive parallel sequencing (MPS) showed high sensitivity and specificity in various clinical studies. These results are based on analysis systems using their own bioinformatics algorithms.What the results of this study add? When this NIPT technology was introduced in Korea, the first biological specimens collected in Korea were transported overseas for processing in overseas laboratories and analysed by other country's analysis methods. We needed our own NIPT algorithm and developed Momguard NIPT for the first time in Korea. This study attempted to evaluate this Momguard NIPT protocol prospectively in a large number of samples obtained from three Korean hospitals.What the implications are of these findings for clinical practice and/or further research? The overall sensitivity and specificity to identify T13, T18 and T21 were 96.8% and 99.8%, respectively. These accuracy values were comparable to that of other studies. From this study, we found that Momguard is a clinically useful tool for the detection of three chromosomal aneuploidies. However, as other NIPT tests, it carries the risk of false positive and false negative results. Hence, the genetic counsellors should provide these limitations to the examinees.
Collapse
Affiliation(s)
- Hae-Jin Hu
- LabGenomics Clinical Research Institute, LabGenomics, Seongnam, Korea
| | - Mi-Young Lee
- Department of Obstetrics and Gynaecology, University of Ulsan College of Medicine, Asan Medical Centre, Seoul, Korea
| | - Dae-Yeon Cho
- LabGenomics Clinical Research Institute, LabGenomics, Seongnam, Korea
| | - Mijin Oh
- LabGenomics Clinical Research Institute, LabGenomics, Seongnam, Korea
| | - Young-Jun Kwon
- LabGenomics Clinical Research Institute, LabGenomics, Seongnam, Korea
| | - You-Jung Han
- Department of Obstetrics and Gynaecology, CHA Gangnam Medical Centre, CHA University, Seoul, Korea
| | - Hyun Mee Ryu
- Department of Obstetrics and Gynaecology, CHA Bundang Medical Centre, CHA University, Seongnam, Korea
| | - Young Nam Kim
- Busan Paik Hospital, Inje University College of Medicine, Busan, Korea
| | - Hye-Sung Won
- Department of Obstetrics and Gynaecology, University of Ulsan College of Medicine, Asan Medical Centre, Seoul, Korea
| |
Collapse
|
10
|
Abstract
AbstractNon-invasive prenatal testing (NIPT) is a new technology used in prenatal testing (PT) that capitalizes on genomic platforms to transform DNA fragments in the blood of pregnant women into information about the genome of a foetus. Since its market introduction in 2011, it has travelled around the globe with remarkable speed. This article engages with the emergence of NIPT in and around Vienna, the capital city of Austria, to explore why and how this technology could travel so quickly in practice. Based on a qualitative analysis of interviews, documents, and field notes, it argues, first, that NIPT could travel so quickly because it travelled as ‘adaptable boxes’ that added on to different ‘local worlds of prenatal testing (PT)’, without disrupting them. Second, in so doing, NIPT could travel on a moral and material ground, or an ‘imaginary of PT’, built in the past. Third, the article argues that elements of this imaginary were also mobilized by commercial pioneers of NIPT, who ‘infrastructurized’ extant values, practices, and networks among biomedical professionals. Thus, various actors converged in mobilizing moral and material elements of an imaginary, transforming them into an infrastructure that facilitated the travels of NIPT, while also shaping its use.
Collapse
|
11
|
Lee DE, Kim H, Park J, Yun T, Park DY, Kim M, Ryu HM. Clinical Validation of Non-Invasive Prenatal Testing for Fetal Common Aneuploidies in 1,055 Korean Pregnant Women: a Single Center Experience. J Korean Med Sci 2019; 34:e172. [PMID: 31222985 PMCID: PMC6589404 DOI: 10.3346/jkms.2019.34.e172] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 05/28/2019] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Non-invasive prenatal testing (NIPT) using cell-free fetal DNA from maternal plasma for fetal aneuploidy identification is expanding worldwide. The objective of this study was to evaluate the clinical utility of NIPT for the detection of trisomies 21, 18, and 13 of high-risk fetus in a large Korean population. METHODS This study was performed retrospectively, using stored maternal plasma from 1,055 pregnant women with singleton pregnancies who underwent invasive prenatal diagnosis because of a high-risk indication for chromosomal abnormalities. The NIPT results were confirmed by karyotype analysis. RESULTS Among 1,055 cases, 108 cases of fetal aneuploidy, including trisomy 21 (n = 57), trisomy 18 (n = 42), and trisomy 13 (n = 9), were identified by NIPT. In this study, NIPT showed 100% sensitivity and 99.9% specificity for trisomy 21, and 92.9% sensitivity and 100% specificity for trisomy 18, and 100% sensitivity and 99.9% specificity for trisomy 13. The overall positive predictive value (PPV) was 98.1%. PPVs for trisomies 21, 18, and 13 ranged from 90.0% to 100%. CONCLUSION This study demonstrates that our NIPT technology is reliable and accurate when applied to maternal DNA samples collected from pregnant women. Further large prospective studies are needed to adequately assess the performance of NIPT.
Collapse
Affiliation(s)
- Da Eun Lee
- Laboratory of Medical Genetics, Medical Research Institute, Cheil General Hospital and Women's Healthcare Center, Seoul, Korea
| | - Hyunjin Kim
- Laboratory of Medical Genetics, Medical Research Institute, Cheil General Hospital and Women's Healthcare Center, Seoul, Korea
| | | | - Taegyun Yun
- Data Analytics CoE, SK Telecom, Seoul, Korea
| | | | - Minhyoung Kim
- Department of Obstetrics and Gynecology, Cheil General Hospital and Women's Healthcare Center, Dankook University College of Medicine, Seoul, Korea
| | - Hyun Mee Ryu
- Department of Obstetrics and Gynecology, CHA Bundang Medical Center, CHA University, Seongnam, Korea.
| |
Collapse
|
12
|
Xue Y, Zhao G, Li H, Zhang Q, Lu J, Yu B, Wang T. Non-invasive prenatal testing to detect chromosome aneuploidies in 57,204 pregnancies. Mol Cytogenet 2019; 12:29. [PMID: 31249627 PMCID: PMC6584990 DOI: 10.1186/s13039-019-0441-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 06/06/2019] [Indexed: 01/06/2023] Open
Abstract
Background Non-invasive prenatal testing (NIPT) has been widely used to detect common fetal chromosome aneuploidies, such as trisomy 13, 18, and 21 (T13, T18, and T21), and has expanded to sex chromosome aneuploidies (SCAs) during recent years, but few studies have reported NIPT detection of rare fetal chromosome aneuploidies (RCAs). In this study, we evaluated the clinical practical performance of NIPT to analyze all 24 chromosome aneuploidies among 57,204 pregnancies in the Suzhou area of China. Methods This was a retrospective analysis of prospectively collected NIPT data from two next-generation sequencing (NGS) platforms (Illumina and Proton) obtained from The Affiliated Suzhou Hospital of Nanjing Medical University. NIPT results were validated by karyotyping or clinical follow-up. Results NIPT using the Illumina platform identified 586 positive cases; fetal karyotyping and follow-up results validated 178 T21 cases, 49 T18 cases, 4 T13 cases, and 52 SCAs. On the Proton platform, 270 cases were positive during NIPT. Follow-up confirmed 85 T21 cases, 17 T18 cases, 4 T13 cases, 28 SCAs, and 1 fetal chromosome 22 aneuploidy case as true positives. There were 5 false-negative results, including 4 T21 and 1 T18 cases. The NGS platforms showed similar sensitivities and positive predictive values (PPVs) in detecting T21, T18, T13 and SCAs (p > 0.01). However, the Proton platform showed better specificity in detecting 45, X and the Illumina platform had better specificity in detecting T13 (p < 0.01). The major factor contributing to NIPT false-positives on the Illumina platform was false SCAs cases (65.11%). Maternal chromosome aneuploidies, maternal cancers, and confined placental mosaicism caused discordant results between fetal karyotyping and NIPT. Conclusion NIPT with NGS showed good performance for detecting T13, T18, and T21. The Proton platform had better performance for detecting SCAs, but the NIPT accuracy rate for detecting RCAs was insufficient.
Collapse
Affiliation(s)
- Ying Xue
- 1The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, 215000 Jiangsu Province China.,2Suzhou Municipal Hospital, Suzhou, 215000 Jiangsu China
| | - Guodong Zhao
- 3Zhejiang University Kunshan Biotechnology Laboratory, Zhejiang University Kunshan Innovation Institute, Kunshan, 215300 Jiangsu China
| | - Hong Li
- 1The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, 215000 Jiangsu Province China.,2Suzhou Municipal Hospital, Suzhou, 215000 Jiangsu China
| | - Qin Zhang
- 1The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, 215000 Jiangsu Province China.,2Suzhou Municipal Hospital, Suzhou, 215000 Jiangsu China
| | - Jiafeng Lu
- 1The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, 215000 Jiangsu Province China.,2Suzhou Municipal Hospital, Suzhou, 215000 Jiangsu China
| | - Bin Yu
- 4Changzhou Maternity and Child Health Care Hospital affiliated to Nanjing Medical University, Changzhou, Jiangsu Province, 213003 China
| | - Ting Wang
- 1The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, 215000 Jiangsu Province China.,2Suzhou Municipal Hospital, Suzhou, 215000 Jiangsu China
| |
Collapse
|
13
|
A gradual change of chromosome mosaicism from placenta to fetus leading to T18 false negative result by NIPS. Clin Chim Acta 2019; 495:263-268. [PMID: 30998911 DOI: 10.1016/j.cca.2019.04.064] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 04/06/2019] [Accepted: 04/10/2019] [Indexed: 11/23/2022]
Abstract
BACKGROUND Noninvasive prenatal screening (NIPS) has higher sensitivity and specificity compared to traditional prenatal screening. Nevertheless, the discordant results between the NIPS and prenatal diagnosis were occasionally reported. In current study, we investigated the genetic basis of a T18 fetus with a discordant trisomy 5 (T5) positive and trisomy 18 (T18) negative NIPS result. METHODS NIPS was used to detect fetal DNA in maternal circulating plasma based on semiconductor sequencing platform. The aneuploidies of the fetus and different part of placental tissues were investigated by copy number variation sequencing (CNV-seq) and chromosome microarray analysis (CMA). RESULTS The positive result of T5 was detected for the pregnant woman in NIPS, while T18 was found in the fetal karyotyping analysis after amniocentesis. Furthermore, placental mosaicism of T5 and T18 was found by CNV-seq and CMA, which revealed the mosaic ratio of T5 was gradually increased from umbilical cord to the placenta center, while that of T18 was gradually decreased. CONCLUSION For the reason of cell-free fetal DNA (cff DNA) in the maternal circulation originates from trophoblast cells of placenta, the level of placental mosaicism could cause false negative NIPS result in multiple aneuploidies. The present study proved that a discordant T5 positive and T18 negative NIPS result was caused by placental mosaicism. This study highlights placental mosaicism as a significant risk factor for discordant NIPS results. The result will be helpful for genetic counseling and clinical management of such pregnant woman.
Collapse
|
14
|
Chen YP, He ZQ, Shi Y, Zhou Q, Cai ZM, Yu B, Wang T. Not all chromosome aberrations can be detected by NIPT in women at advanced maternal age: A multicenter retrospective study. Clin Chim Acta 2018; 486:232-236. [PMID: 30114407 DOI: 10.1016/j.cca.2018.08.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 08/13/2018] [Accepted: 08/13/2018] [Indexed: 11/19/2022]
Abstract
OBJECTIVE To discuss the detectability of NIPT for pregnant women at advanced maternal age (AMA), and mainly focused on how many fetal abnormalities will be missed by NIPT. METHODS A total of 4194 women at AMA who accepted cytogenetic prenatal diagnosis were recruited in this study. All the AMA women received amniocentesis at 18-23 weeks. Combined with our detection level of NIPT and literature reports, we evaluated the detectability of NIPT. RESULTS After cell karyotype analysis, a total of 233 (5.56%) fetuses were confirmed to have chromosomal abnormalities, including 91.0% were abnormal chromosome number and 9.0% were abnormal chromosome structure. According to the detectability of NIPT we calculated, 87.6% abnormal results could also be detected by NIPT. However, NIPT would miss 12.4% abnormal results which could be originally found by the karyotype analysis of amniotic fluid cells. The major types of missed fetal abnormalities include structural rearrangement, mosaic and triploidy. Meanwhile, there were no relationship between the detectability of NIPT and the age of AMA pregnant women. CONCLUSIONS About 12.4% of fetal chromosomal abnormalities will be missed if NIPT completely replaces invasive prenatal diagnosis in AMA women. Fortunately, these types of fetal abnormalities missed by NIPT did not increase with the age elevating of pregnant women.
Collapse
Affiliation(s)
- Ying-Ping Chen
- Changzhou Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, No. 16 Bo Ai Road, Changzhou, Jiangsu Province, China
| | - Ze-Quan He
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou 215000, Jiangsu Province, China
| | - Ye Shi
- Changzhou Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, No. 16 Bo Ai Road, Changzhou, Jiangsu Province, China
| | - Qin Zhou
- Changzhou Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, No. 16 Bo Ai Road, Changzhou, Jiangsu Province, China
| | - Zheng-Mao Cai
- Changzhou Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, No. 16 Bo Ai Road, Changzhou, Jiangsu Province, China
| | - Bin Yu
- Changzhou Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, No. 16 Bo Ai Road, Changzhou, Jiangsu Province, China.
| | - Ting Wang
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou 215000, Jiangsu Province, China.
| |
Collapse
|
15
|
Decreased DNA methylation of a CpG site in the HBAP1 gene in plasma DNA from pregnant women. PLoS One 2018; 13:e0198165. [PMID: 29795670 PMCID: PMC5967787 DOI: 10.1371/journal.pone.0198165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 05/15/2018] [Indexed: 12/03/2022] Open
Abstract
Objective The objective of this study is to identify potential CpG site(s) or DNA methylation pattern(s) in the pseudo α-globin 1 gene (HBAP1 gene), the gene which locates in α-thalassemia-1 deletion mutation, to differentiate plasma DNA between pregnant and non-pregnant women. Method DNA methylation profiles of placenta and peripheral blood from the MethBase database were compared to screen differentially methylated regions. This region was confirmed the differential by methylation-sensitive high resolution melt (MS-HRM) analysis. The differential region was used to compare DNA methylation profile of plasma DNA between pregnant and non-pregnant women by bisulfite amplicon sequencing in three levels: overall, individual CpG sites and individual molecules (DNA methylation patterns). Result Using MethBase data, four consecutive CpG sites in the HBAP1 gene were identified as regions of differential DNA methylation between placenta and peripheral blood. The confirmation by MS-HRM showed the differential DNA methylation profile between the placenta and plasma from non-pregnant women. The comparison of DNA methylation profiles between the plasma of pregnant and non-pregnant women showed that, in the overall levels of the four CpG sites, DNA methylation of pregnant women was detected at lower levels than non-pregnant women. In the individual CpG site level, only the second CpG site showed differential DNA methylation between the groups. In the DNA methylation pattern level, there was no strongly significant differences in DNA methylation patterns between the pregnant and non-pregnant groups. Conclusion Our result demonstrated that, in the plasma from pregnant women, only one of the four CpG sites displays a decrease in DNA methylation compared with non-pregnant women. It indicates that this CpG site might be useful for determining the presence or absence of fetal wild-type α-globin gene cluster allele in maternal plasma.
Collapse
|
16
|
Zhang S, Han S, Zhang M, Wang Y. Non-invasive prenatal paternity testing using cell-free fetal DNA from maternal plasma: DNA isolation and genetic marker studies. Leg Med (Tokyo) 2018; 32:98-103. [PMID: 29626747 DOI: 10.1016/j.legalmed.2018.03.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 03/01/2018] [Accepted: 03/31/2018] [Indexed: 12/13/2022]
Abstract
Invasive prenatal paternity tests can result in miscarriage and congenital malformations; therefore, a non-invasive method of testing is preferable. However, little progress could be made in this field until the introduction of cell-free fetal DNA (cffDNA) in 2009. In this review, two aspects regarding the history and development of non-invasive prenatal paternity testing (NIPAT) are summarized: (1) extraction and enrichment of cffDNA and (2) genetic marker-based studies. Although column-based kits are used widely for NIPAT, some researchers have suggested that an automated method, such as magnetic extraction, generally has a higher cffDNA yield than that of manual column-based extraction; therefore, its popularity might increase in the near future. In addition, size- and methylation-based enrichment methods are expected to perform better than formaldehyde-based methods. On the other hand, single nucleotide polymorphism-based techniques have contributed to NIPAT, whereas the application of short tandem repeat testing has so far been restricted to pregnant women bearing male fetuses only. Additional methods and techniques are expected to be innovated to facilitate the forensic practice of NIPAT.
Collapse
Affiliation(s)
- Shanshan Zhang
- Medical Research & Laboratory Diagnostic Center, Jinan Central Hospital Affiliated to Shandong University, No. 105 Jiefang Road, Jinan, Shandong 250013, PR China
| | - Shuyi Han
- Medical Research & Laboratory Diagnostic Center, Jinan Central Hospital Affiliated to Shandong University, No. 105 Jiefang Road, Jinan, Shandong 250013, PR China.
| | - Maoxiu Zhang
- Medical Research & Laboratory Diagnostic Center, Jinan Central Hospital Affiliated to Shandong University, No. 105 Jiefang Road, Jinan, Shandong 250013, PR China
| | - Yunshan Wang
- Medical Research & Laboratory Diagnostic Center, Jinan Central Hospital Affiliated to Shandong University, No. 105 Jiefang Road, Jinan, Shandong 250013, PR China.
| |
Collapse
|
17
|
Pangeson T, Sanguansermsri P, Sanguansermsri T, Seeratanachot T, Suwanakhon N, Srikummool M, Kaewkong W, Mahingsa K. Association of Tissue-Specific DNA Methylation Alterations with α-Thalassemia Southeast Asian Deletion. GENETICS & EPIGENETICS 2017; 9:1179237X17736107. [PMID: 29162979 PMCID: PMC5692129 DOI: 10.1177/1179237x17736107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 03/15/2017] [Indexed: 12/31/2022]
Abstract
In the wild-type allele, DNA methylation levels of 10 consecutive CpG sites adjacent to the upstream 5′-breakpoint of α-thalassemia Southeast Asian (SEA) deletion are not different between placenta and leukocytes. However, no previous study has reported the map of DNA methylation in the SEA allele. This report aims to show that the SEA mutation is associated with DNA methylation changes, resulting in differential methylation between placenta and leukocytes. Methylation-sensitive high-resolution analysis was used to compare DNA methylation among placenta, leukocytes, and unmethylated control DNA. The result indicates that the DNA methylation between placenta and leukocyte DNA is different and shows that the CpG status of both is not fully unmethylated. Mapping of individual CpG sites was performed by targeted bisulfite sequencing. The DNA methylation level of the 10 consecutive CpG sites was different between placenta and leukocyte DNA. When the 10th CpG of the mutation allele was considered as a hallmark for comparing DNA methylation level, it was totally different from the unmethylated 10th CpG of the wild-type allele. Finally, the distinct DNA methylation patterns between both DNA were extracted. In total, 24 patterns were found in leukocyte samples and 9 patterns were found in placenta samples. This report shows that the large deletion is associated with DNA methylation change. In further studies for clinical application, the distinct DNA methylation pattern might be a potential marker for detecting cell-free fetal DNA.
Collapse
Affiliation(s)
- Tanapat Pangeson
- Department of Biochemistry, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand.,Department of Biochemistry, School of Medical Sciences, University of Phayao, Phayao, Thailand.,Thalassemia Research Unit, Institute of Human Genetics, University of Phayao, Phayao, Thailand
| | - Phanchana Sanguansermsri
- Department of Biochemistry, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand
| | - Torpong Sanguansermsri
- Thalassemia Research Unit, Institute of Human Genetics, University of Phayao, Phayao, Thailand
| | - Teerapat Seeratanachot
- Department of Biochemistry, School of Medical Sciences, University of Phayao, Phayao, Thailand.,Thalassemia Research Unit, Institute of Human Genetics, University of Phayao, Phayao, Thailand
| | - Narutchala Suwanakhon
- Thalassemia Research Unit, Institute of Human Genetics, University of Phayao, Phayao, Thailand.,Department of Biology, School of Science, University of Phayao, Phayao, Thailand
| | - Metawee Srikummool
- Department of Biochemistry, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand
| | - Worasak Kaewkong
- Department of Biochemistry, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand
| | - Khwanruedee Mahingsa
- Thalassemia Research Unit, Institute of Human Genetics, University of Phayao, Phayao, Thailand
| |
Collapse
|
18
|
Grati FR, Malvestiti F, Branca L, Agrati C, Maggi F, Simoni G. Chromosomal mosaicism in the fetoplacental unit. Best Pract Res Clin Obstet Gynaecol 2017; 42:39-52. [DOI: 10.1016/j.bpobgyn.2017.02.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 01/20/2017] [Accepted: 02/04/2017] [Indexed: 01/12/2023]
|
19
|
Hartwig TS, Ambye L, Sørensen S, Jørgensen FS. Discordant non-invasive prenatal testing (NIPT) - a systematic review. Prenat Diagn 2017; 37:527-539. [DOI: 10.1002/pd.5049] [Citation(s) in RCA: 127] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 03/28/2017] [Accepted: 03/31/2017] [Indexed: 12/22/2022]
Affiliation(s)
- Tanja Schlaikjaer Hartwig
- Fetal Medicine Unit, Department of Obstetrics and Gynecology; Copenhagen University Hospital; Hvidovre Denmark
| | - Louise Ambye
- Department of Clinical Biochemistry; Copenhagen University Hospital; Hvidovre Denmark
| | - Steen Sørensen
- Department of Clinical Biochemistry; Copenhagen University Hospital; Hvidovre Denmark
| | - Finn Stener Jørgensen
- Fetal Medicine Unit, Department of Obstetrics and Gynecology; Copenhagen University Hospital; Hvidovre Denmark
| |
Collapse
|
20
|
Massively Parallel Sequencing (MPS) of Cell-Free Fetal DNA (cffDNA)
for Trisomies 21, 18, and 13 in Twin Pregnancies. Twin Res Hum Genet 2017; 20:242-249. [DOI: 10.1017/thg.2017.23] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Massively parallel sequencing (MPS) technology has become increasingly available
and has been widely used to screen for trisomies 21, 18, and 13 in singleton
pregnancies. This study assessed the performance of MPS testing of cell-free
fetal DNA (cffDNA) from maternal plasma for trisomies 21, 18, and 13 in twin
pregnancies. Ninety-two women with twin pregnancies were recruited. The results
were identified through karyotypes of amniocentesis or clinical examination and
follow-up of the neonates. Fluorescent in-situ hybridization was used to examine
the placentas postnatally in cases of false-positive results. The fetuses with
autosomal trisomy 21 (n = 2) and trisomy 15 (n
= 1) were successfully detected via MPS testing of cffDNA. There was one
false-positive for trisomy 13 (n = 1), and fluorescence in-situ
hybridization (FISH) identified confined placental mosaicism in this case. For
twin pregnancies undergoing second-trimester screening for trisomy, MPS testing
of cffDNA is feasible and can enhance the diagnostic spectrum of non-invasive
prenatal testing, which could effectively reduce invasive prenatal diagnostic
methods. In addition to screening for trisomy 21, 18, and 13 by cffDNA, MPS can
detect fetal additional autosomal trisomy. False-positive results cannot
completely exclude confined placental mosaicism.
Collapse
|
21
|
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
|
22
|
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
|
23
|
NIPTRIC: an online tool for clinical interpretation of non-invasive prenatal testing (NIPT) results. Sci Rep 2016; 6:38359. [PMID: 27917919 PMCID: PMC5137038 DOI: 10.1038/srep38359] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 11/09/2016] [Indexed: 12/31/2022] Open
Abstract
To properly interpret the result of a pregnant woman’s non-invasive prenatal test (NIPT), her a priori risk must be taken into account in order to obtain her personalised a posteriori risk (PPR), which more accurately expresses her true likelihood of carrying a foetus with trisomy. Our aim was to develop a tool for laboratories and clinicians to calculate easily the PPR for genome-wide NIPT results, using diploid samples as a control group. The tool takes the a priori risk and Z-score into account. Foetal DNA percentage and coefficient of variation can be given default settings, but actual values should be used if known. We tested the tool on 209 samples from pregnant women undergoing NIPT. For Z-scores < 5, the PPR is considerably higher at a high a priori risk than at a low a priori risk, for NIPT results with the same Z-score, foetal DNA percentage and coefficient of variation. However, the PPR is effectively independent under all conditions for Z-scores above 6. A high PPR for low a priori risks can only be reached at Z-scores > 5. Our online tool can assist clinicians in understanding NIPT results and conveying their true clinical implication to pregnant women, because the PPR is crucial for individual counselling and decision-making.
Collapse
|
24
|
Grati FR. Implications of fetoplacental mosaicism on cell-free DNA testing: a review of a common biological phenomenon. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2016; 48:415-423. [PMID: 27240559 DOI: 10.1002/uog.15975] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 05/16/2016] [Accepted: 05/24/2016] [Indexed: 06/05/2023]
Affiliation(s)
- F R Grati
- Research and Development, Cytogenetics and Medical Genetics Unit, TOMA Advanced Biomedical Assays S.p.A., Busto Arsizio, Varese, Italy .
| |
Collapse
|
25
|
Mardy A, Wapner RJ. Confined placental mosaicism and its impact on confirmation of NIPT results. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2016; 172:118-22. [PMID: 27184347 DOI: 10.1002/ajmg.c.31505] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Non-invasive prenatal testing (NIPT) has been widely used to screen for common aneuploidies since 2011. While NIPT is highly sensitive and specific, false positive results can occur. One important cause of false positive results is confined placental mosaicism (CPM). This can occur through a mitotic nondisjunction event or through aneuploidy rescue. CPM is usually associated with normal fetal outcomes, but has been associated with intrauterine growth restriction, pregnancy loss, or perinatal death in some cases. CPM may also be a marker for uniparental disomy. Given that NIPT can result in false positives, positive results should be confirmed with invasive testing before any irreversible procedure is performed. Whether to perform CVS or amniocentesis to confirm a positive NIPT result is controversial. While CVS can be performed earlier than amniocentesis, CPM can also cause false positive results. Our practice is to proceed with CVS, and to examine all cell lines using both an uncultured sample using fluorescence in situ hybridization (FISH) or short-term culture, as well as long-term culture of the sample. If the results all show aneuploidy, the results are reported to the patient. Otherwise, if the results are also mosaic, amniocentesis is recommended and analyzed by both FISH and karyotype. © 2016 Wiley Periodicals, Inc.
Collapse
|
26
|
Poot M. To NIPT or Not to NIPT. Mol Syndromol 2015; 6:153-5. [PMID: 26648830 DOI: 10.1159/000439237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/01/2015] [Indexed: 11/19/2022] Open
|
27
|
Crooks K, Edwardsen G, O'Connor S, Powell C, Vargo D, Vora N, Kaiser-Rogers K. Cell-free DNA testing in a trisomy 21 pregnancy with confined placental mosaicism for a cell line with trisomy for both chromosomes 18 and 21. Clin Case Rep 2015; 4:19-22. [PMID: 26783428 PMCID: PMC4706389 DOI: 10.1002/ccr3.421] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 08/27/2015] [Indexed: 11/19/2022] Open
Abstract
NIPT (noninvasive prenatal testing) detected trisomy for two chromosomes. One trisomy reflected the fetal karyotype, and the other resulted from CPM (confined placental mosaicism). This case illustrates that extensive cytogenetic analysis can be required to identify CPM, and that patients should be counseled regarding the possibility of discordant NIPT results.
Collapse
Affiliation(s)
- Kristy Crooks
- Department of Pathology and Laboratory Medicine University of North Carolina at Chapel Hill School of Medicine Chapel Hill North Carolina
| | - Ginger Edwardsen
- Department of Obstetrics and Gynecology University of North Carolina at Chapel Hill School of Medicine Chapel Hill North Carolina
| | - Siobhan O'Connor
- Department of Pathology and Laboratory Medicine University of North Carolina at Chapel Hill School of Medicine Chapel Hill North Carolina
| | - Cynthia Powell
- Department of Pediatrics University of North Carolina at Chapel Hill School of Medicine Chapel Hill North Carolina; Department of Genetics University of North Carolina at Chapel Hill School of Medicine Chapel Hill North Carolina
| | - Diane Vargo
- Department of Obstetrics and Gynecology University of North Carolina at Chapel Hill School of Medicine Chapel Hill North Carolina
| | - Neeta Vora
- Department of Obstetrics and Gynecology University of North Carolina at Chapel Hill School of Medicine Chapel Hill North Carolina
| | - Kathleen Kaiser-Rogers
- Department of Pathology and Laboratory Medicine University of North Carolina at Chapel Hill School of Medicine Chapel Hill North Carolina; Department of Pediatrics University of North Carolina at Chapel Hill School of Medicine Chapel Hill North Carolina; Department of Genetics University of North Carolina at Chapel Hill School of Medicine Chapel Hill North Carolina
| |
Collapse
|
28
|
Zhang H, Zhao YY, Song J, Zhu QY, Yang H, Zheng ML, Xuan ZL, Wei Y, Chen Y, Yuan PB, Yu Y, Li DW, Liang JB, Fan L, Chen CJ, Qiao J. Statistical Approach to Decreasing the Error Rate of Noninvasive Prenatal Aneuploid Detection caused by Maternal Copy Number Variation. Sci Rep 2015; 5:16106. [PMID: 26534864 PMCID: PMC4632076 DOI: 10.1038/srep16106] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 09/29/2015] [Indexed: 12/18/2022] Open
Abstract
Analyses of cell-free fetal DNA (cff-DNA) from maternal plasma using massively parallel sequencing enable the noninvasive detection of feto-placental chromosome aneuploidy; this technique has been widely used in clinics worldwide. Noninvasive prenatal tests (NIPT) based on cff-DNA have achieved very high accuracy; however, they suffer from maternal copy-number variations (CNV) that may cause false positives and false negatives. In this study, we developed an algorithm to exclude the effect of maternal CNV and refined the Z-score that is used to determine fetal aneuploidy. The simulation results showed that the algorithm is robust against variations of fetal concentration and maternal CNV size. We also introduced a method based on the discrepancy between feto-placental concentrations to help reduce the false-positive ratio. A total of 6615 pregnant women were enrolled in a prospective study to validate the accuracy of our method. All 106 fetuses with T21, 20 with T18, and three with T13 were tested using our method, with sensitivity of 100% and specificity of 99.97%. In the results, two cases with maternal duplications in chromosome 21, which were falsely predicted as T21 by the previous NIPT method, were correctly classified as normal by our algorithm, which demonstrated the effectiveness of our approach.
Collapse
Affiliation(s)
- Han Zhang
- Annoroad Gene Technology Co., Ltd, Beijing, China
| | - Yang-Yu Zhao
- Department of Gynecology and Obstetrics, Peking University Third Hospital, Beijing, China
| | - Jing Song
- Department of Obstetrics, Beijing Obsterics and Gynecology Hospital, Capital Medical University, Beijing, China
| | - Qi-Ying Zhu
- The Obstetric Department of First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Hua Yang
- Department of Obstetrics and Gynecology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Mei-Ling Zheng
- Department of Obstetrics and Gynecology, First Hospital of Shanxi Medical University, Shanxi, China
| | | | - Yuan Wei
- Department of Gynecology and Obstetrics, Peking University Third Hospital, Beijing, China
| | - Yang Chen
- Annoroad Gene Technology Co., Ltd, Beijing, China
| | - Peng-Bo Yuan
- Department of Gynecology and Obstetrics, Peking University Third Hospital, Beijing, China
| | - Yang Yu
- Department of Gynecology and Obstetrics, Peking University Third Hospital, Beijing, China
| | - Da-Wei Li
- Annoroad Gene Technology Co., Ltd, Beijing, China
| | | | - Ling Fan
- Department of Obstetrics, Beijing Obsterics and Gynecology Hospital, Capital Medical University, Beijing, China
| | | | - Jie Qiao
- Department of Gynecology and Obstetrics, Peking University Third Hospital, Beijing, China
| |
Collapse
|
29
|
Liu S, Song L, Cram DS, Xiong L, Wang K, Wu R, Liu J, Deng K, Jia B, Zhong M, Yang F. Traditional karyotyping vs copy number variation sequencing for detection of chromosomal abnormalities associated with spontaneous miscarriage. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2015; 46:472-477. [PMID: 25767059 DOI: 10.1002/uog.14849] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2014] [Revised: 02/19/2015] [Accepted: 03/10/2015] [Indexed: 06/04/2023]
Abstract
OBJECTIVES To compare the performance of traditional G-banding karyotyping with that of copy number variation sequencing (CNV-Seq) for detection of chromosomal abnormalities associated with miscarriage. METHODS Products of conception (POC) were collected from spontaneous miscarriages. Chromosomal abnormalities were detected using high-resolution G-banding karyotyping and CNV sequencing. Quantitative fluorescent polymerase chain reaction analysis of maternal and POC DNA for short tandem repeat (STR) markers was used to both monitor maternal cell contamination and confirm the chromosomal status and sex of the miscarriage tissue. RESULTS A total of 64 samples of POC, comprising 16 with an abnormal and 48 with a normal karyotype, were selected and coded for analysis by CNV-Seq. CNV-Seq results were concordant for 14 (87.5%) of the 16 gross chromosomal abnormalities identified by karyotyping, including 11 autosomal trisomies and three sex chromosomal aneuploidies (45,X). Of the two discordant results, a 69,XXX polyploidy was missed by CNV-Seq, although supporting STR marker analysis confirmed the triploidy. In contrast, CNV-Seq identified a sample with 45,X karyotype as a 45,X/46,XY mosaic. In the remaining 48 samples of POC with a normal karyotype, CNV-Seq detected a 2.58-Mb 22q deletion associated with DiGeorge syndrome and nine different smaller CNVs of no apparent clinical significance. CONCLUSIONS CNV-Seq used in parallel with STR profiling is a reliable and accurate alternative to karyotyping for identifying chromosome copy number abnormalities associated with spontaneous miscarriage.
Collapse
Affiliation(s)
- S Liu
- Southern Medical University, Nanfang Hospital, Department of Obstetrics and Gynecology, Technology Center of Prenatal Diagnosis and Genetic Diseases Diagnosis, Guangzhou, Guangdong, China
| | - L Song
- Southern Medical University, Nanfang Hospital, Department of Obstetrics and Gynecology, Technology Center of Prenatal Diagnosis and Genetic Diseases Diagnosis, Guangzhou, Guangdong, China
| | - D S Cram
- Berry Genomics, Chaoyang District, Beijing, China
| | - L Xiong
- Southern Medical University, Nanfang Hospital, Department of Obstetrics and Gynecology, Technology Center of Prenatal Diagnosis and Genetic Diseases Diagnosis, Guangzhou, Guangdong, China
| | - K Wang
- Southern Medical University, Nanfang Hospital, Department of Obstetrics and Gynecology, Technology Center of Prenatal Diagnosis and Genetic Diseases Diagnosis, Guangzhou, Guangdong, China
| | - R Wu
- Southern Medical University, Nanfang Hospital, Department of Obstetrics and Gynecology, Technology Center of Prenatal Diagnosis and Genetic Diseases Diagnosis, Guangzhou, Guangdong, China
| | - J Liu
- Southern Medical University, Nanfang Hospital, Department of Obstetrics and Gynecology, Guangzhou, Guangdong, China
| | - K Deng
- Southern Medical University, Nanfang Hospital, Department of Obstetrics and Gynecology, Technology Center of Prenatal Diagnosis and Genetic Diseases Diagnosis, Guangzhou, Guangdong, China
| | - B Jia
- Southern Medical University, Nanfang Hospital, Department of Obstetrics and Gynecology, Technology Center of Prenatal Diagnosis and Genetic Diseases Diagnosis, Guangzhou, Guangdong, China
| | - M Zhong
- Southern Medical University, Nanfang Hospital, Department of Obstetrics and Gynecology, Technology Center of Prenatal Diagnosis and Genetic Diseases Diagnosis, Guangzhou, Guangdong, China
| | - F Yang
- Southern Medical University, Nanfang Hospital, Department of Obstetrics and Gynecology, Technology Center of Prenatal Diagnosis and Genetic Diseases Diagnosis, Guangzhou, Guangdong, China
| |
Collapse
|
30
|
Grati FR, Bajaj K, Malvestiti F, Agrati C, Grimi B, Malvestiti B, Pompilii E, Maggi F, Gross S, Simoni G, Ferreira JCP. The type of feto-placental aneuploidy detected by cfDNA testing may influence the choice of confirmatory diagnostic procedure. Prenat Diagn 2015. [PMID: 26211640 DOI: 10.1002/pd.4659] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
OBJECTIVES Cell-free DNA (cfDNA) screening can provide false positive/negative results because the fetal fraction originates primarily from trophoblast. Consequently, invasive diagnostic testing is recommended to confirm a high-risk result. Currently, there is debate about the most appropriate invasive method. We sought to estimate the frequency in which a chorionic villus sampling (CVS) performed after a high-risk cfDNA result would require a follow-up amniocentesis due to placental mosaicism. METHODS Analyses of the frequencies of the different types of mosaicism involving cytotrophoblasts, for trisomies 21 (T21), 18 (T18), 13 (T13) and monosomy X (MX) among 52,673 CVS karyotypes obtained from cytotrophoblast, mesenchyme and confirmatory amniocentesis. RESULTS After a high-risk cfDNA result for T21, 18, 13 and MX, the likelihood of finding CVS mosaicism and need for amniocentesis is, respectively, 2%, 4%, 22% and 59%. When mosaicism is detected by CVS, the likelihood of fetal confirmation by amniocentesis is, respectively, 44%, 14%, 4% and 26%. CONCLUSIONS In cases of high-risk cfDNA results for T21/T18, CVS (combining cytotrophoblast and mesenchyme analysis) can be considered, but with the caveat of 2-4% risk of an inconclusive result requiring further testing. In high-risk results for MX/T13, amniocentesis would appear to be the most appropriate follow-up diagnostic test, especially in the absence of sonographic findings.
Collapse
Affiliation(s)
| | - Komal Bajaj
- Department of Obstetrics, Gynecology and Women's Health at Albert Einstein College of Medicine, Bronx, NY, USA
| | | | - Cristina Agrati
- Toma Advanced Biomedical Assays, Busto Arsizio, Varese, Italy
| | - Beatrice Grimi
- Toma Advanced Biomedical Assays, Busto Arsizio, Varese, Italy
| | | | - Eva Pompilii
- Toma Advanced Biomedical Assays, Busto Arsizio, Varese, Italy
| | - Federico Maggi
- Toma Advanced Biomedical Assays, Busto Arsizio, Varese, Italy
| | - Susan Gross
- Department of Obstetrics, Gynecology and Women's Health at Albert Einstein College of Medicine, Bronx, NY, USA.,Natera, San Carlos, CA, USA
| | - Giuseppe Simoni
- Toma Advanced Biomedical Assays, Busto Arsizio, Varese, Italy
| | - Jose Carlos P Ferreira
- Department of Obstetrics, Gynecology and Women's Health at Albert Einstein College of Medicine, Bronx, NY, USA.,1st Department of Obstetrics and Gynecology, Medical University of Warsaw, 02-015, Warsaw, Poland
| |
Collapse
|
31
|
Zeevi DA, Altarescu G, Weinberg-Shukron A, Zahdeh F, Dinur T, Chicco G, Herskovitz Y, Renbaum P, Elstein D, Levy-Lahad E, Rolfs A, Zimran A. Proof-of-principle rapid noninvasive prenatal diagnosis of autosomal recessive founder mutations. J Clin Invest 2015; 125:3757-65. [PMID: 26426075 DOI: 10.1172/jci79322] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 07/23/2015] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Noninvasive prenatal testing can be used to accurately detect chromosomal aneuploidies in circulating fetal DNA; however, the necessity of parental haplotype construction is a primary drawback to noninvasive prenatal diagnosis (NIPD) of monogenic disease. Family-specific haplotype assembly is essential for accurate diagnosis of minuscule amounts of circulating cell-free fetal DNA; however, current haplotyping techniques are too time-consuming and laborious to be carried out within the limited time constraints of prenatal testing, hampering practical application of NIPD in the clinic. Here, we have addressed this pitfall and devised a universal strategy for rapid NIPD of a prevalent mutation in the Ashkenazi Jewish (AJ) population. METHODS Pregnant AJ couples, carrying mutation(s) in GBA, which encodes acid β-glucosidase, were recruited at the SZMC Gaucher Clinic. Targeted next-generation sequencing of GBA-flanking SNPs was performed on peripheral blood samples from each couple, relevant mutation carrier family members, and unrelated individuals who are homozygotes for an AJ founder mutation. Allele-specific haplotypes were constructed based on linkage, and a consensus Gaucher disease-associated founder mutation-flanking haplotype was fine mapped. Together, these haplotypes were used for NIPD. All test results were validated by conventional prenatal or postnatal diagnostic methods. RESULTS Ten parental alleles in eight unrelated fetuses were diagnosed successfully based on the noninvasive method developed in this study. The consensus mutation-flanking haplotype aided diagnosis for 6 of 9 founder mutation alleles. CONCLUSIONS The founder NIPD method developed and described here is rapid, economical, and readily adaptable for prenatal testing of prevalent autosomal recessive disease-causing mutations in an assortment of worldwide populations. FUNDING SZMC, Protalix Biotherapeutics Inc., and Centogene AG.
Collapse
|
32
|
Peterson JF, Mikulec K, Grignon JW, Behmaram B, Cruz MO, van Tuinen P. Elucidating discrepant results in a prenatal diagnosis of 48,XXY,+18 (Edwards and Klinefelter syndromes). Am J Med Genet A 2015; 167A:2855-7. [PMID: 26227211 DOI: 10.1002/ajmg.a.37250] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 06/26/2015] [Indexed: 01/21/2023]
Affiliation(s)
- Jess F Peterson
- Department of Pathology, Medical College of Wisconsin, Milwaukee, Wisconsin.,Wisconsin Diagnostic Laboratories, Milwaukee, Wisconsin
| | - Kendra Mikulec
- Department of Obstetrics and Gynecology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | | | - Behnaz Behmaram
- Department of Pathology, Medical College of Wisconsin, Milwaukee, Wisconsin.,Wisconsin Diagnostic Laboratories, Milwaukee, Wisconsin
| | - Meredith O Cruz
- Department of Obstetrics and Gynecology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Peter van Tuinen
- Department of Pathology, Medical College of Wisconsin, Milwaukee, Wisconsin.,Wisconsin Diagnostic Laboratories, Milwaukee, Wisconsin
| |
Collapse
|
33
|
Unexplained False Negative Results in Noninvasive Prenatal Testing: Two Cases Involving Trisomies 13 and 18. Case Rep Genet 2015; 2015:926545. [PMID: 26137330 PMCID: PMC4475527 DOI: 10.1155/2015/926545] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 05/26/2015] [Indexed: 12/27/2022] Open
Abstract
Noninvasive prenatal testing (NIPT) validation studies show high sensitivity and specificity for detection of trisomies 13, 18, and 21. False negative cases have rarely been reported. We describe a false negative case of trisomy 13 and another of trisomy 18 in which NIPT was commercially marketed directly to the clinician. Both cases came to our attention because a fetal anatomy scan at 20 weeks of gestation revealed multiple anomalies. Karyotyping of cultured amniocytes showed nonmosaic trisomies 13 and 18, respectively. Cytogenetic investigation of cytotrophoblast cells from multiple placental biopsies showed a low proportion of nontrisomic cells in each case, but this was considered too small for explaining the false negative NIPT result. The discordant results also could not be explained by early gestational age, elevated maternal weight, a vanishing twin, or suboptimal storage or transport of samples. The root cause of the discrepancies could, therefore, not be identified. The couples involved experienced difficulties in accepting the unexpected and late-adverse outcome of their pregnancy. We recommend that all parties involved in caring for couples who choose NIPT should collaborate to clarify false negative results in order to unravel possible biological causes and to improve the process of patient care from initial counseling to communication of the result.
Collapse
|
34
|
Neufeld-Kaiser WA, Cheng EY, Liu YJ. Positive predictive value of non-invasive prenatal screening for fetal chromosome disorders using cell-free DNA in maternal serum: independent clinical experience of a tertiary referral center. BMC Med 2015; 13:129. [PMID: 26033224 PMCID: PMC4480508 DOI: 10.1186/s12916-015-0374-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 05/18/2015] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Non-invasive prenatal screening (NIPS) for fetal chromosome abnormalities using cell-free deoxyribonucleic acid (cfDNA) in maternal serum has significantly influenced prenatal diagnosis of fetal aneuploidies since becoming clinically available in the fall of 2011. High sensitivity and specificity have been reported in multiple publications, nearly all of which have been sponsored by the commercial performing laboratories. Once results are returned, positive and negative predictive values (PPVs, NPVs) are the performance metrics most relevant to clinical management. The purpose of this report is to present independent data on the PPVs of NIPS in actual clinical practice. METHODS Charts were retrospectively reviewed for patients who had NIPS and were seen March 2012 to December 2013 in a tertiary academic referral center. NIPS results were compared to diagnostic genetic test results, fetal ultrasound results, and clinical phenotype/outcomes. The PPV was calculated using standard epidemiological methods. Correlation between screen results and both maternal age at delivery and gestational age at time of screening was assessed using Wilcoxon's rank sum test. RESULTS Of 632 patients undergoing NIPS, 92 % of tests were performed in one of the four major commercial laboratories offering testing. However, all four laboratories are represented in both the normal and abnormal results groups. There were 55 abnormal NIPS results. Forty-one of 55 abnormal NIPS results were concordant with abnormal fetal outcomes, 12 were discordant, and 2 were undetermined. The PPV for all conditions included in the screen was 77.4 % (95 % CI, 63.4 - 87.3). Of 578 patients with normal NIPS results, normal pregnancy outcome was confirmed for 156 (27 %) patients. This incomplete follow-up of normal NIPS results does not affect PPV calculations, but it did preclude calculations of sensitivity, specificity, and NPV. Maternal age at delivery was significantly lower for patients with abnormal discordant results, compared to patients with abnormal concordant results (P = 0.034). Gestational age at time of screening was not associated with concordance of screen results (P = 0.722). CONCLUSIONS The experience of using NIPS in clinical practice confirms that abnormal results cannot be considered diagnostic. Pre-test counseling should emphasize this. Diagnostic genetic testing should always be offered following abnormal NIPS results.
Collapse
Affiliation(s)
- Whitney A Neufeld-Kaiser
- Department of Pathology, Cytogenetics and Genomics Laboratory, University of Washington School of Medicine, Box 357470, HSB H474B, 1959 NE Pacific Street, Seattle, WA, 98195-7470, USA.
| | - Edith Y Cheng
- Maternal Fetal Medicine and Medical Genetics, Departments of Obstetrics and Gyencology and Internal Medicine, University of Washington School of Medicine, Seattle, WA, USA.
| | - Yajuan J Liu
- Department of Pathology, Cytogenetics and Genomics Laboratory, University of Washington School of Medicine, Box 357470, HSB H474B, 1959 NE Pacific Street, Seattle, WA, 98195-7470, USA.
| |
Collapse
|
35
|
Hochstenbach R, Nikkels PGJ, Elferink MG, Oudijk MA, van Oppen C, van Zon P, van Harssel J, Schuring-Blom H, Page-Christiaens GCML. Cell-free fetal DNA in the maternal circulation originates from the cytotrophoblast: proof from an unique case. Clin Case Rep 2015; 3:489-91. [PMID: 26185654 PMCID: PMC4498868 DOI: 10.1002/ccr3.285] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 03/24/2015] [Indexed: 11/12/2022] Open
Abstract
Noninvasive prenatal testing (NIPT) and direct karyotyping of cytotrophoblast were normal for a male fetus, but cultured chorionic villus mesenchymal cells and umbilical cord fibroblasts showed nonmosaic trisomy 18. This observation provides direct evidence for the cytotrophoblastic origin of cell-free fetal DNA and yields a biological explanation for falsely reassuring NIPT results.
Collapse
Affiliation(s)
- Ron Hochstenbach
- Department of Medical Genetics, University Medical Center Utrecht, The Netherlands
| | - Peter G J Nikkels
- Department of Pathology, University Medical Center Utrecht, The Netherlands
| | - Martin G Elferink
- Department of Medical Genetics, University Medical Center Utrecht, The Netherlands
| | - Martijn A Oudijk
- Department of Obstetrics and Gynecology, University Medical Center Utrecht, The Netherlands
| | - Carla van Oppen
- Department of Obstetrics and Gynecology, University Medical Center Utrecht, The Netherlands
| | - Patrick van Zon
- Department of Medical Genetics, University Medical Center Utrecht, The Netherlands
| | - Jeske van Harssel
- Department of Medical Genetics, University Medical Center Utrecht, The Netherlands
| | - Heleen Schuring-Blom
- Department of Medical Genetics, University Medical Center Utrecht, The Netherlands
| | | |
Collapse
|
36
|
Snyder MW, Simmons LE, Kitzman JO, Coe BP, Henson JM, Daza RM, Eichler EE, Shendure J, Gammill HS. Copy-number variation and false positive prenatal aneuploidy screening results. N Engl J Med 2015; 372:1639-45. [PMID: 25830323 PMCID: PMC4411081 DOI: 10.1056/nejmoa1408408] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Investigations of noninvasive prenatal screening for aneuploidy by analysis of circulating cell-free DNA (cfDNA) have shown high sensitivity and specificity in both high-risk and low-risk cohorts. However, the overall low incidence of aneuploidy limits the positive predictive value of these tests. Currently, the causes of false positive results are poorly understood. We investigated four pregnancies with discordant prenatal test results and found in two cases that maternal duplications on chromosome 18 were the likely cause of the discordant results. Modeling based on population-level copy-number variation supports the possibility that some false positive results of noninvasive prenatal screening may be attributable to large maternal copy-number variants. (Funded by the National Institutes of Health and others.).
Collapse
Affiliation(s)
- Matthew W Snyder
- From the Department of Genome Sciences (M.W.S., J.O.K., B.P.C., R.M.D., E.E.E., J.S.), Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology (L.E.S., J.M.H., H.S.G.), and Howard Hughes Medical Institute (E.E.E.), University of Washington, and the Clinical Research Division, Fred Hutchinson Cancer Research Center (H.S.G.) - both in Seattle
| | | | | | | | | | | | | | | | | |
Collapse
|
37
|
Bayindir B, Dehaspe L, Brison N, Brady P, Ardui S, Kammoun M, Van der Veken L, Lichtenbelt K, Van den Bogaert K, Van Houdt J, Peeters H, Van Esch H, de Ravel T, Legius E, Devriendt K, Vermeesch JR. Noninvasive prenatal testing using a novel analysis pipeline to screen for all autosomal fetal aneuploidies improves pregnancy management. Eur J Hum Genet 2015; 23:1286-93. [PMID: 25585704 DOI: 10.1038/ejhg.2014.282] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 11/18/2014] [Accepted: 11/26/2014] [Indexed: 12/15/2022] Open
Abstract
Noninvasive prenatal testing by massive parallel sequencing of maternal plasma DNA has rapidly been adopted as a mainstream method for detection of fetal trisomy 21, 18 and 13. Despite the relative high accuracy of current NIPT testing, a substantial number of false-positive and false-negative test results remain. Here, we present an analysis pipeline, which addresses some of the technical as well as the biologically derived causes of error. Most importantly, it differentiates high z-scores due to fetal trisomies from those due to local maternal CNVs causing false positives. This pipeline was retrospectively validated for trisomy 18 and 21 detection on 296 samples demonstrating a sensitivity and specificity of 100%, and applied prospectively to 1350 pregnant women in the clinical diagnostic setting with a result reported in 99.9% of cases. In addition, values indicative for trisomy were observed two times for chromosome 7 and once each for chromosomes 15 and 16, and once for a segmental trisomy 18. Two of the trisomies were confirmed to be mosaic, one of which contained a uniparental disomy cell line. As placental trisomies pose a risk for low-grade fetal mosaicism as well as uniparental disomy, genome-wide noninvasive aneuploidy detection is improving prenatal management.
Collapse
Affiliation(s)
- Baran Bayindir
- Centre for Human Genetics, University Hospital Leuven, KU Leuven, Leuven, Belgium.,Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Luc Dehaspe
- Centre for Human Genetics, University Hospital Leuven, KU Leuven, Leuven, Belgium
| | - Nathalie Brison
- Centre for Human Genetics, University Hospital Leuven, KU Leuven, Leuven, Belgium
| | - Paul Brady
- Centre for Human Genetics, University Hospital Leuven, KU Leuven, Leuven, Belgium
| | - Simon Ardui
- Centre for Human Genetics, University Hospital Leuven, KU Leuven, Leuven, Belgium
| | - Molka Kammoun
- Centre for Human Genetics, University Hospital Leuven, KU Leuven, Leuven, Belgium
| | - Lars Van der Veken
- Department of Medical Genetics, University Medical Center Utrecht, AB Utrecht, The Netherlands
| | - Klaske Lichtenbelt
- Department of Medical Genetics, University Medical Center Utrecht, AB Utrecht, The Netherlands
| | - Kris Van den Bogaert
- Centre for Human Genetics, University Hospital Leuven, KU Leuven, Leuven, Belgium
| | - Jeroen Van Houdt
- Centre for Human Genetics, University Hospital Leuven, KU Leuven, Leuven, Belgium
| | - Hilde Peeters
- Centre for Human Genetics, University Hospital Leuven, KU Leuven, Leuven, Belgium
| | - Hilde Van Esch
- Centre for Human Genetics, University Hospital Leuven, KU Leuven, Leuven, Belgium
| | - Thomy de Ravel
- Centre for Human Genetics, University Hospital Leuven, KU Leuven, Leuven, Belgium
| | - Eric Legius
- Centre for Human Genetics, University Hospital Leuven, KU Leuven, Leuven, Belgium
| | - Koen Devriendt
- Centre for Human Genetics, University Hospital Leuven, KU Leuven, Leuven, Belgium
| | - Joris R Vermeesch
- Centre for Human Genetics, University Hospital Leuven, KU Leuven, Leuven, Belgium
| |
Collapse
|
38
|
Abstract
PURPOSE OF REVIEW Prenatal diagnostic and screening tests are routinely offered to all women in pregnancy. Advances in technology have led to an expansion in available testing. As technology improves, women are facing increasingly complex decisions regarding the quantity and quality of information they wish to have regarding their fetus. RECENT FINDINGS Professional guidelines support the use of chromosomal microarray analysis as a first-tier test in place of standard karyotype for the evaluation of fetal chromosomes when one or more anomaly is detected by ultrasound. These same guidelines indicate that either chromosomal microarray analysis or standard karyotype can be offered for prenatal diagnosis with a phenotypically normal fetus. Additionally, recent work continues to validate the use of noninvasive prenatal testing for the detection of aneuploidy in the high-risk population. This testing utilizes cell-free DNA in the maternal circulation to predict fetal karyotype with greater sensitivity and specificity than maternal serum screening or first trimester screening. Data continue to accumulate supporting noninvasive prenatal testing use in an all-risk or low-risk population. Additionally, noninvasive prenatal testing is clinically available to screen for a select number of microdeletion syndromes, broadening the scope of population-based screening to include conditions not previously evaluated, although there are limited data available regarding this application. SUMMARY As prenatal diagnosis becomes increasingly complex, there is a need for the education of both patients and providers regarding the benefits and limitations of the testing strategies available to them.
Collapse
|
39
|
Liang D, Peng Y, Lv W, Deng L, Zhang Y, Li H, Yang P, Zhang J, Song Z, Xu G, Cram DS, Wu L. Copy Number Variation Sequencing for Comprehensive Diagnosis of Chromosome Disease Syndromes. J Mol Diagn 2014; 16:519-526. [DOI: 10.1016/j.jmoldx.2014.05.002] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 04/18/2014] [Accepted: 05/16/2014] [Indexed: 10/25/2022] Open
|
40
|
Wang L, Cram DS, Shen J, Wang X, Zhang J, Song Z, Xu G, Li N, Fan J, Wang S, Luo Y, Wang J, Yu L, Liu J, Yao Y. Validation of Copy Number Variation Sequencing for Detecting Chromosome Imbalances in Human Preimplantation Embryos1. Biol Reprod 2014; 91:37. [DOI: 10.1095/biolreprod.114.120576] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
|