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Abstract
The landscape of genetic testing and screening has changed tremendously since the initial description of the molecular structure of DNA. Given this, it is critical that providers reflect on the goals of prenatal screening and diagnostic testing, and how these tests impact perinatal outcomes. The participants of this workshop were in agreement that the goal of prenatal genetic testing should be focused on improving outcomes for women and families. While prenatal testing has historically focused on the option for pregnancy termination, increasing numbers of prenatal and perinatal treatments are available. As more in utero therapies are developed, the detection of disorders that are amenable to, and would benefit from, prenatal or immediate neonatal targeted therapy will increasingly be a focus of prenatal testing. Prenatal genetic testing must also balance the ethical principles of autonomy and distributive justice. The workshop participants agreed that stakeholders such as medical professionals, professional societies, insurers, commercial laboratories, and the public should consider and come to agreement regarding the appropriate objectives for and use of these tests.
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Affiliation(s)
- Stephanie Dukhovny
- Department of OBGYN, Maternal Fetal Medicine, Oregon Health & Sciences University, 3181 SW Sam Jackson Park Road, Portland OR 97239, United States.
| | - Mary E Norton
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Francisco, 550 16th St, 7th floor, San Francisco CA 94143, United States.
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Chen JK, Liu P, Hu LQ, Xie Q, Huang QF, Liu HL. A foetus with 18p11.32-q21.2 duplication and Xp22.33-p11.1 deletion derived from a maternal reciprocal translocation t(X;18)(q13;q21.3). Mol Cytogenet 2018; 11:37. [PMID: 29946361 PMCID: PMC6001049 DOI: 10.1186/s13039-018-0381-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 04/27/2018] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Non-invasive prenatal testing (NIPT) evaluates circulating cell-free DNA (cfDNA) and has been widely applied, with highly accurate results for detecting foetal trisomies 21, 18 and 13. Recently, increasing attention has been paid to the clinical application of the non-invasive detection of foetal sub-chromosomal duplications and deletions beyond common aneuploidies. CASE PRESENTATION A 32-year-old healthy pregnant woman was referred to the Medical Genetic Centre of Ganzhou Maternal and Child Health Care Hospital. As routine practice, ultrasound examination at a gestational age of 16 weeks showed that the foetus is normal. To avoid invasive prenatal diagnosis procedures, an NIPT was offered to further screen for common foetal chromosomal abnormalities. The result showed that there was an approximately 50.94 Mb duplication in p11.32-q21.2 of chromosome 18 and an approximately 58.46 Mb deletion in p22.33-p11.1 of chromosome X. In addition, the chromosome karyotypes of the parents and foetus were also analysed. Chromosome karyotype analysis results showed that foetal karyotype was 46,X,der(18), the maternal karyotype was 46,XX,t(X;18)(q13;q21.3), and the paternal karyotype revealed no obvious abnormality. CONCLUSION In this case, we successfully detected a healthy pregnant woman with balanced translocation X;18(q13;q21.3) and described the foetal karyotype as 46,X,der(18)t(X;18)(q11;q21.1)mat. Our report illustrated these cases which present complex X;autosome balance translocation and X;autosome unbalance translocation which may contribute to severe clinical phenotypes. In addition, our report also proved that the interruption of genes in the Xq critical region is not only reason of primary infertility. Finally, we prompted that NIPT might play a role in the first trimester screening of sub-chromosomal rearrangement.
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Affiliation(s)
- Jun-Kun Chen
- Medical Genetic Centre of Ganzhou Maternal and Child Health Care Hospital, Ganzhou, 341000 China
| | - Ping Liu
- Medical Genetic Centre of Ganzhou Maternal and Child Health Care Hospital, Ganzhou, 341000 China
| | - Li-Qin Hu
- Medical Genetic Centre of Ganzhou Maternal and Child Health Care Hospital, Ganzhou, 341000 China
| | - Qing Xie
- Medical Genetic Centre of Ganzhou Maternal and Child Health Care Hospital, Ganzhou, 341000 China
| | | | - Hai-Liang Liu
- CapitalBio Genomics Co., Ltd., Dongguan, 532808 China
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Pertile MD, Halks-Miller M, Flowers N, Barbacioru C, Kinnings SL, Vavrek D, Seltzer WK, Bianchi DW. Rare autosomal trisomies, revealed by maternal plasma DNA sequencing, suggest increased risk of feto-placental disease. Sci Transl Med 2018; 9:9/405/eaan1240. [PMID: 28855395 PMCID: PMC10040211 DOI: 10.1126/scitranslmed.aan1240] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 06/22/2017] [Accepted: 08/10/2017] [Indexed: 12/13/2022]
Abstract
Whole-genome sequencing (WGS) of maternal plasma cell-free DNA (cfDNA) can potentially evaluate all 24 chromosomes to identify abnormalities of the placenta, fetus, or pregnant woman. Current bioinformatics algorithms typically only report on chromosomes 21, 18, 13, X, and Y; sequencing results from other chromosomes may be masked. We hypothesized that by systematically analyzing WGS data from all chromosomes, we could identify rare autosomal trisomies (RATs) to improve understanding of feto-placental biology. We analyzed two independent cohorts from clinical laboratories, both of which used a similar quality control parameter, normalized chromosome denominator quality. The entire data set included 89,817 samples. Samples flagged for analysis and classified as abnormal were 328 of 72,932 (0.45%) and 71 of 16,885 (0.42%) in cohorts 1 and 2, respectively. Clinical outcome data were available for 57 of 71 (80%) of abnormal cases in cohort 2. Visual analysis of WGS data demonstrated RATs, copy number variants, and extensive genome-wide imbalances. Trisomies 7, 15, 16, and 22 were the most frequently observed RATs in both cohorts. Cytogenetic or pregnancy outcome data were available in 52 of 60 (87%) of cases with RATs in cohort 2. Cases with RATs detected were associated with miscarriage, true fetal mosaicism, and confirmed or suspected uniparental disomy. Comparing the trisomic fraction with the fetal fraction allowed estimation of possible mosaicism. Analysis and reporting of aneuploidies in all chromosomes can clarify cases in which cfDNA findings on selected "target" chromosomes (21, 18, and 13) are discordant with the fetal karyotype and may identify pregnancies at risk of miscarriage and other complications.
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Affiliation(s)
- Mark D Pertile
- Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, Melbourne, Victoria 3052, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria 3010, Australia
| | | | - Nicola Flowers
- Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, Melbourne, Victoria 3052, Australia
| | | | | | | | | | - Diana W Bianchi
- Tufts Medical Center and Tufts University School of Medicine, Boston, MA 02111, USA. .,National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
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Van Opstal D, van Maarle MC, Lichtenbelt K, Weiss MM, Schuring-Blom H, Bhola SL, Hoffer MJV, Huijsdens-van Amsterdam K, Macville MV, Kooper AJA, Faas BHW, Govaerts L, Tan-Sindhunata GM, den Hollander N, Feenstra I, Galjaard RJH, Oepkes D, Ghesquiere S, Brouwer RWW, Beulen L, Bollen S, Elferink MG, Straver R, Henneman L, Page-Christiaens GC, Sistermans EA. Origin and clinical relevance of chromosomal aberrations other than the common trisomies detected by genome-wide NIPS: results of the TRIDENT study. Genet Med 2018; 20:480-485. [PMID: 29121006 PMCID: PMC5929118 DOI: 10.1038/gim.2017.132] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 06/30/2017] [Indexed: 12/23/2022] Open
Abstract
PurposeNoninvasive prenatal screening (NIPS) using cell-free DNA in maternal blood is highly sensitive for detecting fetal trisomies 21, 18, and 13. Using a genome-wide approach, other chromosome anomalies can also be detected. We report on the origin, frequency, and clinical significance of these other chromosome aberrations found in pregnancies at risk for trisomy 21, 18, or 13.MethodsWhole-genome shallow massively parallel sequencing was used and all autosomes were analyzed.ResultsIn 78 of 2,527 cases (3.1%) NIPS was indicative of trisomy 21, 18, or 13, and in 41 (1.6%) of other chromosome aberrations. The latter were of fetal (n = 10), placental (n = 22), maternal (n = 1) or unknown (n = 7). One case lacked cytogenetic follow-up. Nine of the 10 fetal cases were associated with an abnormal phenotype. Thirteen of the 22 (59%) placental aberrations were associated with fetal congenital anomalies and/or poor fetal growth (
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Affiliation(s)
- Diane Van Opstal
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Merel C van Maarle
- Department of Clinical Genetics, Academic Medical Center, Amsterdam, Amsterdam, The Netherlands
| | - Klaske Lichtenbelt
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Marjan M Weiss
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Heleen Schuring-Blom
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Shama L Bhola
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Mariette J V Hoffer
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Merryn V Macville
- Department of Clinical Genetics, Maastricht UMC+, Maastricht, The Netherlands
| | - Angelique J A Kooper
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Brigitte H W Faas
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Lutgarde Govaerts
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Gita M Tan-Sindhunata
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | | | - Ilse Feenstra
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Dick Oepkes
- Department of Obstetrics, Leiden University Medical Center, Leiden, The Netherlands
| | - Stijn Ghesquiere
- Department of Clinical Genetics, Maastricht UMC+, Maastricht, The Netherlands
| | - Rutger W W Brouwer
- Erasmus Center for Biomics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Lean Beulen
- Department of Obstetrics and Gynaecology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Sander Bollen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Martin G Elferink
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Roy Straver
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Lidewij Henneman
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | | | - Erik A Sistermans
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
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Gray KJ, Wilkins-Haug LE. Have we done our last amniocentesis? Updates on cell-free DNA for Down syndrome screening. Pediatr Radiol 2018; 48:461-470. [PMID: 29550862 PMCID: PMC7088458 DOI: 10.1007/s00247-017-3958-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Revised: 06/11/2017] [Accepted: 07/26/2017] [Indexed: 12/19/2022]
Abstract
Prenatal aneuploidy screening changed significantly in 2012 when cell-free fetal deoxyribonucleic acid (DNA) was introduced as a noninvasive prenatal test. A noninvasive prenatal test detects cell free fragments of fetal DNA from the placenta circulating in maternal blood that coexist with cell-free DNA (cfDNA) of maternal origin. Using next-generation sequencing, the noninvasive prenatal test compares maternal and fetal cfDNA ratios for chromosomes of interest (i.e., 21, 18, 13, X, and Y) to assess chromosomal aneuploidy. Compared to traditional screening using ultrasound and serum markers, the noninvasive prenatal test has superior test characteristics, including a higher detection rate and positive predictive value, and a lower false-positive rate. The noninvasive prenatal test is already used for primary screening in high-risk women and is rapidly expanding to all women. Given its increasing use, understanding the noninvasive prenatal test's limitations is critical. Discordant results (i.e. noninvasive prenatal test is positive for aneuploidy with a normal fetal karyotype) can occur because of biological processes such as aneuploidy confined to the placenta, a vanished twin, maternal aneuploidy or maternal cancer. Use of the noninvasive prenatal test for screening beyond the most common aneuploidies is not recommended. The noninvasive prenatal test is a major advance in prenatal aneuploidy screening but it is not diagnostic and does not replace invasive testing (i.e. chorionic villous sampling or amniocentesis) for confirmation of fetal chromosomal disorders.
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Affiliation(s)
- Kathryn J Gray
- Division of Maternal-Fetal Medicine, Brigham & Women's Hospital, 75 Francis St., Boston, MA, 02115, USA
| | - Louise E Wilkins-Haug
- Division of Maternal-Fetal Medicine, Brigham & Women's Hospital, 75 Francis St., Boston, MA, 02115, USA.
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56
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Shaffer BL, Norton ME. Cell-Free DNA Screening for Aneuploidy and Microdeletion Syndromes. Obstet Gynecol Clin North Am 2018; 45:13-26. [DOI: 10.1016/j.ogc.2017.10.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Mosaic maternal 10qter deletions are associated with FRA10B expansions and may cause false-positive noninvasive prenatal screening results. Genet Med 2018; 20:1472-1476. [DOI: 10.1038/gim.2018.32] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 01/26/2018] [Indexed: 12/16/2022] Open
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Brison N, Neofytou M, Dehaspe L, Bayindir B, Van Den Bogaert K, Dardour L, Peeters H, Van Esch H, Van Buggenhout G, Vogels A, de Ravel T, Legius E, Devriendt K, Vermeesch JR. Predicting fetoplacental chromosomal mosaicism during non-invasive prenatal testing. Prenat Diagn 2018; 38:258-266. [PMID: 29388226 DOI: 10.1002/pd.5223] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 01/14/2018] [Accepted: 01/23/2018] [Indexed: 12/16/2022]
Abstract
OBJECTIVE Non-invasive prenatal detection of aneuploidies can be achieved with high accuracy through sequencing of cell-free maternal plasma DNA in the maternal blood plasma. However, false positive and negative non-invasive prenatal testing (NIPT) results remain. Fetoplacental mosaicism is the main cause for false positive and false negative NIPT. We set out to develop a method to detect placental chromosomal mosaicism via genome-wide circulating cell-free maternal plasma DNA screening. METHOD Aneuploidy detection was combined with fetal fraction determination to enable the detection of placental mosaicism. This pipeline was applied to whole genome sequencing data derived from 19 735 plasma samples. Following an abnormal NIPT, test results were validated by conventional invasive prenatal or postnatal genetic testing. RESULTS Respectively 3.2% (5/154), 12.8% (5/39), and 13.3% (2/15) of trisomies 21, 18, and 13 were predicted and confirmed to be mosaic. The incidence of other, rare autosomal trisomies was ~0.3% (58/19,735), 45 of which were predicted to be mosaic. Twin pregnancies with discordant fetal genotypes were predicted and confirmed. CONCLUSION This approach permits the non-invasive detection of fetal autosomal aneuploidies and identifies pregnancies with a high risk of fetoplacental mosaicism. Knowledge about the presence of chromosomal mosaicism in the placenta influences risk estimation, genetic counseling, and improves prenatal management.
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Affiliation(s)
| | | | - Luc Dehaspe
- Centre for Human Genetics, KU Leuven, Leuven, Belgium
| | | | | | - Leila Dardour
- Department of Genetics, Faculty of Medicine "Ibn Al Jazzar", Sousse, Tunisia
| | - Hilde Peeters
- Centre for Human Genetics, KU Leuven, Leuven, Belgium
| | | | | | - Annick Vogels
- Centre for Human Genetics, KU Leuven, Leuven, Belgium
| | | | - Eric Legius
- Centre for Human Genetics, KU Leuven, Leuven, Belgium
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59
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Xie MJ, Liang ZK, He D, Xu WW, Wu YS, Yang XX, Li M. Noninvasive Prenatal Testing of Rare Autosomal Aneuploidies by Semiconductor Sequencing. DNA Cell Biol 2018; 37:174-181. [PMID: 29381401 DOI: 10.1089/dna.2017.4075] [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: 11/13/2022] Open
Abstract
Rare autosomal aneuploidies (RAAs) can cause miscarriage or other pregnancy complications and lead to inconsistent results of noninvasive prenatal testing (NIPT), but many NIPT providers have not yet started to provide related services. Our aim was to develop a semiconductor sequencing platform (SSP)-based method for detecting RAAs when pregnant women performed NIPT. Fifty-three aneuploidy samples with verified karyotyping or array comparative genomic hybridization (aCGH) results were collected and subjected to RAAs detection using an SSP to develop a method by genomic sequencing. Various trisomies on all chromosomes other than chromosomes 17 and 19, four multiple aneusomies, one monosomy and five sex chromosome abnormalities were got by our method which can directly identify RAAs via a z-score. Then, artificial mixtures of 10% and 5% DNA were created by adding fragmented fifty-three tissue samples and used in an NIPT simulation to develop a bioinformatics analysis method which can use in NIPT. And the results were in accordance with those of karyotyping and aCGH. Therefore, our method has potential for use in NIPT. Finally, 23,823 clinical plasma samples were tested to verify the performance of our approach. Karyotyping or aCGH was performed on the positive clinical samples. In total, 188 of 23,823 clinical samples were positive (T2, n = 1; T7, n = 1; T13, n = 15; T18, n = 45; T21, n = 125; and multiple aneusomies, n = 1) and verified by karyotyping or aCGH; no sample was a false negative. Several false positives were detected, one of which showed maternal copy number variation (CNV). One case of multiple aneusomies was caused by a maternal tumor. The method developed enables detection of RAAs without increasing costs.
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Affiliation(s)
- Mei-Juan Xie
- 1 Institute of Antibody Engineering, School of Laboratory Medical and Biotechnology, Southern Medical University , Guangzhou, China
| | - Zhi-Kun Liang
- 2 Clinical Laboratory Center, Guangzhou Darui Biotechnology, Co., Ltd. , Guangzhou, China
| | - Dan He
- 2 Clinical Laboratory Center, Guangzhou Darui Biotechnology, Co., Ltd. , Guangzhou, China
| | - Wei-Wen Xu
- 1 Institute of Antibody Engineering, School of Laboratory Medical and Biotechnology, Southern Medical University , Guangzhou, China
| | - Ying-Song Wu
- 1 Institute of Antibody Engineering, School of Laboratory Medical and Biotechnology, Southern Medical University , Guangzhou, China
| | - Xue-Xi Yang
- 1 Institute of Antibody Engineering, School of Laboratory Medical and Biotechnology, Southern Medical University , Guangzhou, China
| | - Ming Li
- 1 Institute of Antibody Engineering, School of Laboratory Medical and Biotechnology, Southern Medical University , Guangzhou, China
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Bianchi DW. Cherchez la femme: maternal incidental findings can explain discordant prenatal cell-free DNA sequencing results. Genet Med 2017; 20:910-917. [PMID: 29215645 PMCID: PMC10082650 DOI: 10.1038/gim.2017.219] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 10/31/2017] [Indexed: 12/19/2022] Open
Abstract
Circulating DNA fragments in a pregnant woman's plasma derive from three sources: placenta, maternal bone marrow, and fetus. Prenatal sequencing to noninvasively screen for fetal chromosome abnormalities is performed on this mixed sample; results can therefore reflect the maternal as well as the fetoplacental DNA. Although it is recommended that pretest counseling include the possibility of detecting maternal genomic imbalance, this seldom occurs. Maternal abnormalities that can affect a prenatal screening test result include disorders that affect the size and metabolism of DNA, such as B12 deficiency, autoimmune disease, and intrahepatic cholestasis of pregnancy. Similarly, maternal tumors, both benign and malignant, can release DNA fragments that contain duplications or deletions. Bioinformatics algorithms can subsequently interpret the raw sequencing data incorrectly, resulting in false-positive test reports of fetal monosomies or test failures. Maternal sex-chromosome abnormalities, both constitutional and somatic, can generate results that are discordant with fetal ultrasound examination or karyotype. Maternal copy-number variants and mosaicism for autosomal aneuploidies can also skew interpretation. A maternal etiology should therefore be considered in the differential diagnosis of prenatal cell-free DNA test failures, false-positive and false-negative sequencing results. Further study is needed regarding the clinical utility of reporting maternal incidental findings.
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Petersen AK, Cheung SW, Smith JL, Bi W, Ward PA, Peacock S, Braxton A, Van Den Veyver IB, Breman AM. Positive predictive value estimates for cell-free noninvasive prenatal screening from data of a large referral genetic diagnostic laboratory. Am J Obstet Gynecol 2017; 217:691.e1-691.e6. [PMID: 29032050 DOI: 10.1016/j.ajog.2017.10.005] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Revised: 09/29/2017] [Accepted: 10/03/2017] [Indexed: 02/07/2023]
Abstract
BACKGROUND Since its debut in 2011, cell-free fetal DNA screening has undergone rapid expansion with respect to both utilization and coverage. However, conclusive data regarding the clinical validity and utility of this screening tool, both for the originally included common autosomal and sex-chromosomal aneuploidies as well as the more recently added chromosomal microdeletion syndromes, have lagged behind. Thus, there is a continued need to educate clinicians and patients about the current benefits and limitations of this screening tool to inform pre- and posttest counseling, pre/perinatal decision making, and medical risk assessment/management. OBJECTIVE The objective of this study was to determine the positive predictive value and false-positive rates for different chromosomal abnormalities identified by cell-free fetal DNA screening using a large data set of diagnostic testing results on invasive samples submitted to the laboratory for confirmatory studies. STUDY DESIGN We tested 712 patient samples sent to our laboratory to confirm a cell-free fetal DNA screening result, indicating high risk for a chromosome abnormality. We compiled data from all cases in which the indication for confirmatory testing was a positive cell-free fetal DNA screen, including the common trisomies, sex chromosomal aneuploidies, microdeletion syndromes, and other large genome-wide copy number abnormalities. Testing modalities included fluorescence in situ hybridization, G-banded karyotype, and/or chromosomal microarray analysis performed on chorionic villus samples, amniotic fluid, or postnatally obtained blood samples. Positive predictive values and false-positive rates were calculated from tabulated data. RESULTS The positive predictive values for trisomy 13, 18, and 21 were consistent with previous reports at 45%, 76%, and 84%, respectively. For the microdeletion syndrome regions, positive predictive values ranged from 0% for detection of Cri-du-Chat syndrome and Prader-Willi/Angelman syndrome to 14% for 1p36 deletion syndrome and 21% for 22q11.2 deletion syndrome. Detection of sex chromosomal aneuploidies had positive predictive values of 26% for monosomy X, 50% for 47,XXX, and 86% for 47,XXY. CONCLUSION The positive predictive values for detection of common autosomal and sex chromosomal aneuploidies by cell-free fetal DNA screening were comparable with other studies. Identification of microdeletions was associated with lower positive predictive values and higher false-positive rates, likely because of the low prevalence of the individual targeted microdeletion syndromes in the general population. Although the obtained positive predictive values compare favorably with those seen in traditional screening approaches for common aneuploidies, they highlight the importance of educating clinicians and patients on the limitations of cell-free fetal DNA screening tests. Improvement of the cell-free fetal DNA screening technology and continued monitoring of its performance after introduction into clinical practice will be important to fully establish its clinical utility. Nonetheless, our data provide valuable information that may aid result interpretation, patient counseling, and clinical decision making/management.
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Affiliation(s)
- Andrea K Petersen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Sau Wai Cheung
- Baylor Genetics, Baylor College of Medicine, Houston, TX; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Janice L Smith
- Baylor Genetics, Baylor College of Medicine, Houston, TX; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Weimin Bi
- Baylor Genetics, Baylor College of Medicine, Houston, TX; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Patricia A Ward
- Baylor Genetics, Baylor College of Medicine, Houston, TX; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Sandra Peacock
- Baylor Genetics, Baylor College of Medicine, Houston, TX
| | - Alicia Braxton
- Baylor Genetics, Baylor College of Medicine, Houston, TX; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Ignatia B Van Den Veyver
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX; Texas Children's Hospital, Houston, TX
| | - Amy M Breman
- Baylor Genetics, Baylor College of Medicine, Houston, TX; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX.
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Wald NJ, Huttly WJ, Bestwick JP, Old R, Morris JK, Cheng R, Aquilina J, Peregrine E, Roberts D, Alfirevic Z. Prenatal reflex DNA screening for trisomies 21, 18, and 13. Genet Med 2017; 20:825-830. [DOI: 10.1038/gim.2017.188] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 08/24/2017] [Indexed: 12/11/2022] Open
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Audibert F, De Bie I, Johnson JA, Okun N, Wilson RD, Armour C, Chitayat D, Kim R. N o 348-Directive clinique de la SOGC et du CCGM : mise à jour sur le dépistage prénatal de l’aneuploïdie fœtale, des anomalies fœtales et des issues défavorables de la grossesse. JOURNAL OF OBSTETRICS AND GYNAECOLOGY CANADA 2017; 39:818-832. [DOI: 10.1016/j.jogc.2017.05.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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64
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Maternal iAMP21 acute lymphoblastic leukemia detected on prenatal cell-free DNA genetic screening. Blood Adv 2017; 1:1491-1494. [PMID: 29296790 DOI: 10.1182/bloodadvances.2017008680] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 07/21/2017] [Indexed: 12/18/2022] Open
Abstract
cfDNA sequencing for fetal aneuploidy may detect chromosomal abnormalities representative of maternal malignancy.Maternal malignancy must be considered when abnormal cfDNA sequencing for fetal aneuploidy is associated with normal fetal karyotype.
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Cherry AM, Akkari YM, Barr KM, Kearney HM, Rose NC, South ST, Tepperberg JH, Meck JM. Diagnostic cytogenetic testing following positive noninvasive prenatal screening results: a clinical laboratory practice resource of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2017; 19:845-850. [PMID: 28726804 DOI: 10.1038/gim.2017.91] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 05/11/2017] [Indexed: 01/05/2023] Open
Abstract
Disclaimer: ACMG Clinical Laboratory Practice Resources are developed primarily as an educational tool for clinical laboratory geneticists to help them provide quality clinical laboratory genetic services. Adherence to these practice resources is voluntary and does not necessarily assure a successful medical outcome. This Clinical Laboratory Practice Resource should not be considered inclusive of all proper procedures and tests or exclusive of other procedures and tests that are reasonably directed to obtaining the same results. In determining the propriety of any specific procedure or test, the clinical laboratory geneticist should apply his or her own professional judgment to the specific circumstances presented by the individual patient or specimen. Clinical laboratory geneticists are encouraged to document in the patient's record the rationale for the use of a particular procedure or test, whether or not it is in conformance with this Clinical Laboratory Practice Resource. They also are advised to take notice of the date any particular guideline was adopted, and to consider other relevant medical and scientific information that becomes available after that date. It also would be prudent to consider whether intellectual property interests may restrict the performance of certain tests and other procedures.Noninvasive prenatal screening (NIPS) using cell-free DNA has been rapidly adopted into prenatal care. Since NIPS is a screening test, diagnostic testing is recommended to confirm all cases of screen-positive NIPS results. For cytogenetics laboratories performing confirmatory testing on prenatal diagnostic samples, a standardized testing algorithm is needed to ensure that the appropriate testing takes place. This algorithm includes diagnostic testing by either chorionic villi sampling or amniocentesis samples and encompasses chromosome analysis, fluorescence in situ hybridization, and chromosomal microarray.
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Affiliation(s)
- Athena M Cherry
- Department of Pathology, Stanford University School of Medicine, Stanford Health Care, Stanford, California, USA
| | - Yassmine M Akkari
- Cytogenetics and Molecular Pathology, Legacy Laboratory Sciences, Legacy Health, Portland, Oregon, USA
| | - Kimberly M Barr
- Genetics Department, Kaiser Permanente, San Francisco, California, USA
| | - Hutton M Kearney
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Nancy C Rose
- Department of Obstetrics and Gynecology, University of Utah, Intermountain Healthcare University of Utah, Salt Lake City, Utah, USA
| | | | - James H Tepperberg
- Clinical Cytogenetics Laboratory, Laboratory Corporation of America, Research Triangle Park, North Carolina, USA
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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
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67
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Vermeesch JR, Voet T, Devriendt K. Prenatal and pre-implantation genetic diagnosis. Nat Rev Genet 2017; 17:643-56. [PMID: 27629932 DOI: 10.1038/nrg.2016.97] [Citation(s) in RCA: 117] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The past decade has seen the development of technologies that have revolutionized prenatal genetic testing; that is, genetic testing from conception until birth. Genome-wide single-cell arrays and high-throughput sequencing analyses are dramatically increasing our ability to detect embryonic and fetal genetic lesions, and have substantially improved embryo selection for in vitro fertilization (IVF). Moreover, both invasive and non-invasive mutation scanning of the genome are helping to identify the genetic causes of prenatal developmental disorders. These advances are changing clinical practice and pose novel challenges for genetic counselling and prenatal care.
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Affiliation(s)
- Joris Robert Vermeesch
- Centre for Human Genetics, Department of Human Genetics, University of Leuven, 49 Herestraat, Leuven 3000, Belgium
| | - Thierry Voet
- Centre for Human Genetics, Department of Human Genetics, University of Leuven, 49 Herestraat, Leuven 3000, Belgium
| | - Koenraad Devriendt
- Centre for Human Genetics, Department of Human Genetics, University of Leuven, 49 Herestraat, Leuven 3000, Belgium
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68
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Dervan AP, Deverka PA, Trosman JR, Weldon CB, Douglas MP, Phillips KA. Payer decision making for next-generation sequencing-based genetic tests: insights from cell-free DNA prenatal screening. Genet Med 2017; 19:559-567. [PMID: 27657682 PMCID: PMC5362360 DOI: 10.1038/gim.2016.145] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 08/09/2016] [Indexed: 12/20/2022] Open
Abstract
PURPOSE Cell-free DNA (cfDNA) prenatal screening tests have been rapidly adopted into clinical practice, due in part to positive insurance coverage. We evaluated the framework payers used in making coverage decisions to describe a process that should be informative for other sequencing tests. METHODS We analyzed coverage policies from the 19 largest US private payers with publicly available policies through February 2016, building from the University of California San Francisco TRANSPERS Payer Coverage Policy Registry. RESULTS All payers studied cover cfDNA screening for detection of trisomies 21, 18, and 13 in high-risk, singleton pregnancies, based on robust clinical validity (CV) studies and modeled evidence of clinical utility (CU). Payers typically evaluated the evidence for each chromosomal abnormality separately, although results are offered as part of a panel. Starting in August 2015, 8 of the 19 payers also began covering cfDNA screening in average-risk pregnancies, citing recent CV studies and updated professional guidelines. Most payers attempted, but were unable, to independently assess analytic validity (AV). CONCLUSION Payers utilized the standard evidentiary framework (AV/CV/CU) when evaluating cfDNA screening but varied in their interpretation of the sufficiency of the evidence. Professional guidelines, large CV studies, and decision analytic models regarding health outcomes appeared highly influential in coverage decisions.Genet Med advance online publication 22 September 2016.
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Affiliation(s)
- Andrew P Dervan
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Patricia A Deverka
- American Institutes for Health Research and Innovation, Chapel Hill, North Carolina, USA
- Eshelman School of Pharmacy, Center for Pharmacogenomics and Individualized Therapy, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Julia R Trosman
- Department of Clinical Pharmacy, Center for Translational and Policy Research on Personalized Medicine (TRANSPERS), University of California San Francisco, San Francisco, California, USA
- Center for Business Models in Healthcare, Chicago, Illinois, USA
- Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Christine B Weldon
- Department of Clinical Pharmacy, Center for Translational and Policy Research on Personalized Medicine (TRANSPERS), University of California San Francisco, San Francisco, California, USA
- Center for Business Models in Healthcare, Chicago, Illinois, USA
- Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Michael P Douglas
- Department of Clinical Pharmacy, Center for Translational and Policy Research on Personalized Medicine (TRANSPERS), University of California San Francisco, San Francisco, California, USA
| | - Kathryn A Phillips
- Department of Clinical Pharmacy, Center for Translational and Policy Research on Personalized Medicine (TRANSPERS), University of California San Francisco, San Francisco, California, USA
- Philip R. Lee Institute for Health Policy, University of California San Francisco, San Francisco, California, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA
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69
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Liehr T, Lauten A, Schneider U, Schleussner E, Weise A. Noninvasive Prenatal Testing - When Is It Advantageous to Apply. Biomed Hub 2017; 2:1-11. [PMID: 31988902 PMCID: PMC6945944 DOI: 10.1159/000458432] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 01/27/2017] [Indexed: 12/23/2022] Open
Abstract
Nowadays it is common sense in obstetrics that an increased risk for pregnancy loss due to invasive testing does not exist. Nonetheless, noninvasive prenatal testing (NIPT) is a hot topic, even though this approach does not provide a reduction of unintentionally induced abortions. NIPT has a number of shortcuts which are highlighted in this review, including: (1) in NIPT placental rather than fetal DNA is studied, (2) NIPT fails in 2–6% of cases, and (3) trisomy 21 accounts for only ∼50% of existing chromosomal aberrations. Thus, we agree with the literature that NIPT is a fascinating possibility to gain information on unborn life from minimal amounts of DNA. However, it remains a pure risk estimation test directed towards the detection of specific chromosomal abnormalities from peripheral blood of the pregnant woman. It is important to highlight that families buying this test, and getting a normal result, may be provided with a false sense of security. Thus, careful and comprehensive genetic counselling should be performed before the test is offered, and should include a clear explanation of the advantages and disadvantages, as well as limitations, compared to other methods.
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Affiliation(s)
- Thomas Liehr
- Institute of Human Genetics, Friedrich Schiller University, Jena, Germany
| | - Angela Lauten
- Institute of Clinic for Obstetrics and Gynecology, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Uwe Schneider
- Institute of Clinic for Obstetrics and Gynecology, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Ekkehard Schleussner
- Institute of Clinic for Obstetrics and Gynecology, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Anja Weise
- Institute of Human Genetics, Friedrich Schiller University, Jena, Germany
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Strom CM, Anderson B, Tsao D, Zhang K, Liu Y, Livingston K, Elzinga C, Evans M, Nguyen Q, Wolfson D, Rowland C, Kolacki P, Maxwell M, Wang JC, Rabin D, Catanese J, Owen R, Braastad C, Sun W. Improving the Positive Predictive Value of Non-Invasive Prenatal Screening (NIPS). PLoS One 2017; 12:e0167130. [PMID: 28248967 PMCID: PMC5382935 DOI: 10.1371/journal.pone.0167130] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 11/04/2016] [Indexed: 11/18/2022] Open
Abstract
We evaluated performance characteristics of a laboratory-developed, non-invasive prenatal screening (NIPS) assay for fetal aneuploidies. This assay employs massively parallel shotgun sequencing with full automation. GC sequencing bias correction and statistical smoothing were performed to enhance discrimination of affected and unaffected pregnancies. Maternal plasma samples from pregnancies with known aneuploidy status were used for assay development, verification, and validation. Assay verification studies using 2,085 known samples (1873 unaffected, 69 trisomy 21, 20 trisomy 18, 17 trisomy 13) demonstrated complete discrimination between autosomal trisomy (Z scores >8) and unaffected (Z scores <4) singleton pregnancies. A validation study using 552 known samples (21 trisomy 21, 10 trisomy 18, 1 trisomy 13) confirmed complete discrimination. Twin pregnancies showed similar results. Follow-up of abnormal results from the first 10,000 clinical samples demonstrated PPVs of 98% (41/42) for trisomy 21, 92% (23/25) for trisomy 18, and 69% (9/13) for trisomy 13. Adjustment for causes of false-positive results identified during clinical testing (eg, maternal duplications) improved PPVs to 100% for trisomy 21 and 96% for trisomy 18. This NIPS test demonstrates excellent discrimination between trisomic and unaffected pregnancies. The PPVs obtained in initial clinical testing are substantially higher than previously reported NIPS methods.
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Affiliation(s)
- Charles M. Strom
- Quest Diagnostics Nichols Institute, San Juan Capistrano, California, United States of America
- * E-mail:
| | - Ben Anderson
- Quest Diagnostics Nichols Institute, San Juan Capistrano, California, United States of America
| | - David Tsao
- Quest Diagnostics Nichols Institute, San Juan Capistrano, California, United States of America
| | - Ke Zhang
- Quest Diagnostics Nichols Institute, San Juan Capistrano, California, United States of America
| | - Yan Liu
- Quest Diagnostics Nichols Institute, San Juan Capistrano, California, United States of America
| | - Kayla Livingston
- Quest Diagnostics Nichols Institute, San Juan Capistrano, California, United States of America
| | | | - Matthew Evans
- Athena Diagnostics, Marlborough, Massachusetts, United States of America
| | - Quoclinh Nguyen
- Quest Diagnostics Nichols Institute, San Juan Capistrano, California, United States of America
| | - David Wolfson
- Celera Diagnostics, Alameda, California, United States of America
| | - Charles Rowland
- Celera Diagnostics, Alameda, California, United States of America
| | - Paula Kolacki
- Quest Diagnostics Nichols Institute, San Juan Capistrano, California, United States of America
| | - Megan Maxwell
- Quest Diagnostics Nichols Institute, San Juan Capistrano, California, United States of America
| | - Jia-Chi Wang
- Quest Diagnostics Nichols Institute, San Juan Capistrano, California, United States of America
| | - Douglas Rabin
- Quest Diagnostics Nichols Institute, San Juan Capistrano, California, United States of America
| | - Joseph Catanese
- Quest Diagnostics Nichols Institute, San Juan Capistrano, California, United States of America
| | - Renius Owen
- Quest Diagnostics Nichols Institute, San Juan Capistrano, California, United States of America
| | - Corey Braastad
- Athena Diagnostics, Marlborough, Massachusetts, United States of America
| | - Weimin Sun
- Quest Diagnostics Nichols Institute, San Juan Capistrano, California, United States of America
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Abstract
Screening for fetal aneuploidy in pregnant women using cell-free DNA has increased dramatically since the technology became commercially available in 2011. Since that time, numerous trials have demonstrated high sensitivity and specificity to screen for common aneuploidies in high-risk populations. Studies assessing the performance of these tests in low-risk populations have also demonstrated improved detection rates compared with traditional, serum-based screening strategies. Concurrent with the increased use of this technology has been a decrease in invasive procedures (amniocentesis and chorionic villus sampling). As the technology becomes more widely understood, available, and utilized, challenges regarding its clinical implementation have become apparent. Some of these challenges include test failures, false-positive and false-negative results, limitations in positive predictive value in low-prevalence populations, and potential maternal health implications of abnormal results. In addition, commercial laboratories are expanding screening beyond common aneuploidies to include microdeletion screening and whole genome screening. This review article is intended to provide the practicing obstetrician with a summary of the complexities of cell-free DNA screening and the challenges of implementing it in the clinical setting.
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72
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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
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73
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Non-invasive prenatal diagnosis of thalassemias using maternal plasma cell free DNA. Best Pract Res Clin Obstet Gynaecol 2017; 39:63-73. [DOI: 10.1016/j.bpobgyn.2016.10.016] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 09/23/2016] [Accepted: 10/14/2016] [Indexed: 01/09/2023]
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Abstract
Noninvasive prenatal DNA testing is the vanguard of genomic medicine. In only four years, this screening test has revolutionized prenatal care globally and opened up new prospects for personalized medicine for the fetus. There are widespread implications for increasing the scope of human genetic variation that can be detected before birth, and for discovering more about maternofetal and placental biology. These include an urgent need to develop pretest education for all pregnant women and consistent post-test management recommendations for those with discordant test results. The reduction in invasive testing has had downstream effects on specialist training and caused many countries to re-examine their national approaches to prenatal screening. Finally, the accumulating datasets of genomic information on pregnant women and their fetuses raise ethical issues regarding consent for future data mining and intellectual property.
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Affiliation(s)
- Lisa Hui
- Department of Perinatal Medicine, Mercy Hospital for Women, Heidelberg, Victoria 3084, Australia;
- Translational Obstetrics Group, University of Melbourne, Heidelberg, Victoria 3084, Australia
- Public Health Genetics Group, Murdoch Childrens Research Institute, Parkville, Victoria 3052, Australia
| | - Diana W. Bianchi
- Mother Infant Research Institute, Tufts Medical Center, Boston, Massachusetts 02111;
- Division of Genetics, Department of Pediatrics, Floating Hospital for Children, Boston, Massachusetts 02111
- Tufts University School of Medicine, Boston, Massachusetts 02111
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75
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Strom CM, Maxwell MD, Owen R. Improving the Accuracy of Prenatal Screening with DNA Copy-Number Analysis. N Engl J Med 2017; 376:188-189. [PMID: 28076705 DOI: 10.1056/nejmc1604205] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Charles M Strom
- Quest Diagnostics Nichols Institute, San Juan Capistrano, CA
| | - Megan D Maxwell
- Quest Diagnostics Nichols Institute, San Juan Capistrano, CA
| | - Renius Owen
- Quest Diagnostics Nichols Institute, San Juan Capistrano, CA
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76
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Yu SCY, Jiang P, Chan KCA, Faas BHW, Choy KW, Leung WC, Leung TY, Lo YMD, Chiu RWK. Combined Count- and Size-Based Analysis of Maternal Plasma DNA for Noninvasive Prenatal Detection of Fetal Subchromosomal Aberrations Facilitates Elucidation of the Fetal and/or Maternal Origin of the Aberrations. Clin Chem 2016; 63:495-502. [PMID: 27974386 DOI: 10.1373/clinchem.2016.254813] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 10/10/2016] [Indexed: 12/22/2022]
Abstract
BACKGROUND Noninvasive prenatal detection of fetal subchromosomal copy number aberrations (CNAs) can be achieved through massively parallel sequencing of maternal plasma DNA. However, when a mother herself is a carrier of a CNA, one cannot discern if her fetus has inherited the CNA. In addition, false-positive results would become more prevalent when more subchromosomal regions are analyzed. METHODS We used a strategy that combined count- and size-based analyses of maternal plasma DNA for the detection of fetal subchromosomal CNAs in 7 target regions for 10 test cases. RESULTS For the 5 cases in which CNAs were present only in the fetus, the size-based approach confirmed the aberrations detected by the count-based approach. For the 5 cases in which the mother herself carried an aberration, we successfully deduced that 3 of the fetuses had inherited the aberrations and that the other 2 fetuses had not inherited the aberrations. No false positives were observed in this cohort. CONCLUSIONS Combined count- and size-based analysis of maternal plasma DNA permits the noninvasive elucidation of whether a fetus has inherited a CNA from its mother who herself is a carrier of the CNA. This strategy has the potential to improve the diagnostic specificity of noninvasive prenatal testing.
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Affiliation(s)
- Stephanie C Y Yu
- Centre for Research into Circulating Fetal Nucleic Acids, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Peiyong Jiang
- Centre for Research into Circulating Fetal Nucleic Acids, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - K C Allen Chan
- Centre for Research into Circulating Fetal Nucleic Acids, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Brigitte H W Faas
- Radboud University Nijmegen Medical Center, Department of Human Genetics, Nijmegen, The Netherlands
| | - Kwong W Choy
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Wing C Leung
- Kwong Wah Hospital, Kowloon, Hong Kong SAR, China
| | - Tak Y Leung
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Y M Dennis Lo
- Centre for Research into Circulating Fetal Nucleic Acids, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Rossa W K Chiu
- Centre for Research into Circulating Fetal Nucleic Acids, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China; .,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
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77
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He Z, Guo F, Feng C, Cai B, Lata JP, He R, Huang Q, Yu X, Rao L, Liu H, Guo S, Liu W, Zhang Y, Huang TJ, Zhao X. Fetal nucleated red blood cell analysis for non-invasive prenatal diagnostics using a nanostructure microchip. J Mater Chem B 2016; 5:226-235. [PMID: 32263541 DOI: 10.1039/c6tb02558g] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Cell-free DNA has been widely used in non-invasive prenatal diagnostics (NIPD) nowadays. Compared to these incomplete and multi-source DNA fragments, fetal nucleated red blood cells (fNRBCs), once as an aided biomarker to monitor potential fetal pathological conditions, have re-attracted research interest in NIPD because of their definite fetal source and the total genetic information contained in the nuclei. Isolating these fetal cells from maternal peripheral blood and subsequent cell-based bio-analysis make maximal genetic diagnosis possible, while causing minimal harm to the fetus or its mother. In this paper, an affinity microchip is reported which uses hydroxyapatite/chitosan nanoparticles as well as immuno-agent anti-CD147 to effectively isolate fNRBCs from maternal peripheral blood, and on-chip biomedical analysis was demonstrated as a proof of concept for NIPD based on fNRBCs. Tens of fNRBCs can be isolated from 1 mL of peripheral blood (almost 25 mL-1 in average) from normal pregnant women (from the 10th to 30th gestational week). The diagnostic application of fNRBCs for fetal chromosome disorders (Trisomy 13 and 21) was also demonstrated. Our method offers effective isolation and accurate analysis of fNRBCs to implement comprehensive NIPD and to enhance insights into fetal cell development.
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Affiliation(s)
- Zhaobo He
- Key Laboratory of Artificial Micro- and Nano-Structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, 430072, Hubei, P. R. China.
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78
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Hui L. Noninvasive prenatal testing for aneuploidy using cell-free DNA - New implications for maternal health. Obstet Med 2016; 9:148-152. [PMID: 27829872 PMCID: PMC5089342 DOI: 10.1177/1753495x16652007] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 05/06/2016] [Indexed: 01/20/2023] Open
Abstract
The rapid global uptake of noninvasive prenatal testing for Down syndrome based on maternal plasma cell-free DNA has provided new data on the interrelationship between cell-free DNA and maternal health. Specific maternal conditions that can affect the performance of noninvasive prenatal testing include obesity, active autoimmune disease and low molecular weight heparin treatment. There is also a growing appreciation of the implications of discordant noninvasive prenatal testing results for maternal health, including unexpected diagnoses of maternal chromosomal conditions, or rarely, occult cancer. The interrelatedness of noninvasive prenatal testing and maternal health mean that the longstanding principles underpinning prenatal screening - voluntary testing, informed decision making, availability of specialist genetic counselling and well-defined clinical pathways - are more important than ever before.
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Affiliation(s)
- Lisa Hui
- Department of Perinatal Medicine, The Mercy Hospital for Women, Heidelberg, Australia
- Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, Australia
- Public Health Genetics, Murdoch Childrens Research Institute, Parkville, Australia
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79
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Calabrese G, Fantasia D, Alfonsi M, Morizio E, Celentano C, Guanciali Franchi P, Sabbatinelli G, Palka C, Benn P, Sitar G. Aneuploidy screening using circulating fetal cells in maternal blood by dual-probe FISH protocol: a prospective feasibility study on a series of 172 pregnant women. Mol Genet Genomic Med 2016; 4:634-640. [PMID: 27896286 PMCID: PMC5118208 DOI: 10.1002/mgg3.249] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 08/25/2016] [Accepted: 08/29/2016] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND A long sought goal in medical genetics has been the replacement of invasive procedures for the detection of chromosomal aneuploidies by isolating and analyzing fetal cells or free fetal DNA from maternal blood, avoiding risk to the fetus. However, a rapid, simple, consistent, and low-cost procedure suitable for routine clinical practice has not yet been achieved. The purpose of this study was to assess the feasibility of predicting fetal aneuploidy by applying our recently established dual-probe FISH protocol to fetal cells isolated and enriched from maternal blood. METHODS A total of 172 pregnant women underwent prospective testing for fetal aneuploidy by FISH analysis of fetal cells isolated from maternal blood. Results were compared with the karyotype determined through invasive procedures or at birth. RESULTS Seven of the samples exhibited fetal aneuploidy, which was confirmed by invasive prenatal diagnosis procedures. After enrichment for fetal cells, the frequency of trisomic cells was at least double in samples from aneuploid pregnancies (range 0.38-0.90%) compared to samples from normal pregnancies (≤0.18%). One false negative result was also obtained. CONCLUSIONS Noninvasive prenatal aneuploidy screening using fetal cells isolated from maternal blood is feasible and could substantially reduce the need for invasive procedures.
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Affiliation(s)
| | | | - Melissa Alfonsi
- Genetica Medica Università Chieti-Pescara Chieti Scalo Italy
| | - Elisena Morizio
- Genetica Medica Università Chieti-Pescara Chieti Scalo Italy
| | | | | | | | - Chiara Palka
- Genetica Medica Università Chieti-Pescara Chieti Scalo Italy
| | - Peter Benn
- University of Connecticut Health Center Farmington Connecticut
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Chudova DI, Sehnert AJ, Bianchi DW. Copy-Number Variation and False Positive Prenatal Screening Results. N Engl J Med 2016; 375:97-8. [PMID: 27406371 DOI: 10.1056/nejmc1509813] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Dheedene A, Sante T, De Smet M, Vanbellinghen JF, Grisart B, Vergult S, Janssens S, Menten B. Implementation of non-invasive prenatal testing by semiconductor sequencing in a genetic laboratory. Prenat Diagn 2016; 36:699-707. [PMID: 27176606 PMCID: PMC5108441 DOI: 10.1002/pd.4841] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Revised: 04/15/2016] [Accepted: 05/10/2016] [Indexed: 12/16/2022]
Abstract
OBJECTIVES To implement non-invasive prenatal testing (NIPT) for fetal aneuploidies with semiconductor sequencing in an academic cytogenomic laboratory and to evaluate the first 15-month experience on clinical samples. METHODS We validated a NIPT protocol for cell-free fetal DNA sequencing from maternal plasma for the detection of trisomy 13, 18 and 21 on a semiconductor sequencing instrument. Fetal DNA fraction calculation for all samples and several quality parameters were implemented in the workflow. One thousand eighty-one clinical NIPT samples were analysed, following the described protocol. RESULTS Non-invasive prenatal testing was successfully implemented and validated on 201 normal and 74 aneuploid samples. From 1081 clinical samples, 17 samples showed an abnormal result: 14 trisomy 21 samples, one trisomy 18 and one trisomy 16 were detected. Also a maternal copy number variation on chromosome 13 was observed, which could potentially lead to a false positive trisomy 13 result. One sex discordant result was reported, possibly attributable to a vanishing twin. Moreover, our combined fetal fraction calculation enabled a more reliable risk estimate for trisomy 13, 18 and 21. CONCLUSIONS Non-invasive prenatal testing for trisomy 21, 18 and 13 has a very high specificity and sensitivity. Because of several biological phenomena, diagnostic invasive confirmation of abnormal results remains required. © 2016 The Authors. Prenatal Diagnosis published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Annelies Dheedene
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Tom Sante
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Matthias De Smet
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Jean-François Vanbellinghen
- Plateforme de Biologie Moléculaire, Département des Laboratoires, Cliniques Universitaires Saint-Luc, Bruxelles, Belgium
| | - Bernard Grisart
- Centre de Génétique Humaine, Institut de Pathologie et Génétique, Charleroi, Belgium
| | - Sarah Vergult
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Sandra Janssens
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Björn Menten
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium
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Cell-free DNA testing of an extended range of chromosomal anomalies: clinical experience with 6,388 consecutive cases. Genet Med 2016; 19:169-175. [PMID: 27362910 PMCID: PMC5303761 DOI: 10.1038/gim.2016.72] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2015] [Accepted: 04/25/2016] [Indexed: 01/01/2023] Open
Abstract
Purpose: Cell-free DNA (cfDNA) testing for fetal aneuploidies was broadly implemented for common trisomies and sex-chromosome anomalies (SCAs). However, such an approach identifies only 75 to 85% of clinically relevant aneuploidies. Methods: We present a consecutive series of 6,388 cases, thus uncovering a broader array of aneuploidies, including the rare autosomal trisomies (RATs) and the maternally inherited deletion and duplication copy-number variations (CNVs), with complete and stratified follow-up by amniocentesis. Combined measurements of z-scores and the fetal fraction, in conjunction with fetal cfDNA enrichment, were used to stratify the likelihood of true and false results. Results: We obtained an incremental diagnostic yield of 50%; RATs and CNVs were found to be significant causes of fetal pathology. Scrutinizing z-scores and the fetal fraction made it possible to distinguish the sources of false-negative results; predict the likelihood of false-positive results for major trisomies and SCAs; classify maternal mosaic SCAs and CNVs, preventing false-positive results; and robustly identify maternally inherited CNVs and detect recurrent genomic disorders as a standardized function of the fetal fraction. Conclusion: With the clinical pertinence of this broader detection scheme confirmed, we offer recommendations for its implementation. Genet Med19 2, 169–175.
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Koumbaris G, Kypri E, Tsangaras K, Achilleos A, Mina P, Neofytou M, Velissariou V, Christopoulou G, Kallikas I, González-Liñán A, Benusiene E, Latos-Bielenska A, Marek P, Santana A, Nagy N, Széll M, Laudanski P, Papageorgiou EA, Ioannides M, Patsalis PC. Cell-Free DNA Analysis of Targeted Genomic Regions in Maternal Plasma for Non-Invasive Prenatal Testing of Trisomy 21, Trisomy 18, Trisomy 13, and Fetal Sex. Clin Chem 2016; 62:848-55. [DOI: 10.1373/clinchem.2015.252502] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 03/21/2016] [Indexed: 12/19/2022]
Abstract
Abstract
BACKGROUND
There is great need for the development of highly accurate cost effective technologies that could facilitate the widespread adoption of noninvasive prenatal testing (NIPT).
METHODS
We developed an assay based on the targeted analysis of cell-free DNA for the detection of fetal aneuploidies of chromosomes 21, 18, and 13. This method enabled the capture and analysis of selected genomic regions of interest. An advanced fetal fraction estimation and aneuploidy determination algorithm was also developed. This assay allowed for accurate counting and assessment of chromosomal regions of interest. The analytical performance of the assay was evaluated in a blind study of 631 samples derived from pregnancies of at least 10 weeks of gestation that had also undergone invasive testing.
RESULTS
Our blind study exhibited 100% diagnostic sensitivity and specificity and correctly classified 52/52 (95% CI, 93.2%–100%) cases of trisomy 21, 16/16 (95% CI, 79.4%–100%) cases of trisomy 18, 5/5 (95% CI, 47.8%–100%) cases of trisomy 13, and 538/538 (95% CI, 99.3%–100%) normal cases. The test also correctly identified fetal sex in all cases (95% CI, 99.4%–100%). One sample failed prespecified assay quality control criteria, and 19 samples were nonreportable because of low fetal fraction.
CONCLUSIONS
The extent to which free fetal DNA testing can be applied as a universal screening tool for trisomy 21, 18, and 13 depends mainly on assay accuracy and cost. Cell-free DNA analysis of targeted genomic regions in maternal plasma enables accurate and cost-effective noninvasive fetal aneuploidy detection, which is critical for widespread adoption of NIPT.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Egle Benusiene
- Department of Human and Medical Genetics, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | | | - Pietryga Marek
- Gynecology and Obstetrics, Poznan University of Medical Sciences, Poland
| | - Alfredo Santana
- Clinical Genetics, Childhood Hospital Materno-Infantil, Las Palmas GC, Canary Islands, Spain
| | - Nikoletta Nagy
- Department of Medical Genetics, University of Szeged, Szeged, Hungary
| | - Márta Széll
- Department of Medical Genetics, University of Szeged, Szeged, Hungary
| | - Piotr Laudanski
- Department of Perinatology and Obstetrics Medical University of Bialystok, Poland
| | | | | | - Philippos C Patsalis
- NIPD Genetics, Ltd, Nicosia, Cyprus
- The Cyprus Institute of Neurology and Genetics
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84
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Iltis AS. Prenatal screening and prenatal diagnosis: contemporary practices in light of the past. JOURNAL OF MEDICAL ETHICS 2016; 42:334-339. [PMID: 27161556 DOI: 10.1136/medethics-2016-103623] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 04/18/2016] [Indexed: 06/05/2023]
Abstract
The 20th century eugenics movement in the USA and contemporary practices involving prenatal screening (PNS), prenatal diagnosis (PND), abortion and preimplantation genetic diagnosis (PGD) share important morally relevant similarities. I summarise some features of the 20th century eugenics movement; describe the contemporary standard of care in the USA regarding PNS, PND, abortion and PGD; and demonstrate that the 'old eugenics' the contemporary standard of care share the underlying view that social resources should be invested to prevent the birth of people with certain characteristics. This comparison makes evident the difficulty of crafting moral arguments that treat some uses of PNS, PND, abortion and PGD as licit and others as illicit.
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85
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Mather CA, Qi Z, Wiita AP. False positive cell free DNA screening for microdeletions due to non-pathogenic copy number variants. Prenat Diagn 2016; 36:584-6. [DOI: 10.1002/pd.4823] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 04/01/2016] [Accepted: 04/05/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Cheryl A. Mather
- Department of Laboratory Medicine; University of California San Francisco; San Francisco CA USA
- Department of Pathology; University of California San Francisco; San Francisco CA USA
| | - Zhongxia Qi
- Department of Laboratory Medicine; University of California San Francisco; San Francisco CA USA
| | - Arun P. Wiita
- Department of Laboratory Medicine; University of California San Francisco; San Francisco CA USA
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86
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Snyder HL, Curnow KJ, Bhatt S, Bianchi DW. Follow-up of multiple aneuploidies and single monosomies detected by noninvasive prenatal testing: implications for management and counseling. Prenat Diagn 2016; 36:203-9. [PMID: 26785403 PMCID: PMC5067681 DOI: 10.1002/pd.4778] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 01/12/2016] [Accepted: 01/15/2016] [Indexed: 12/17/2022]
Abstract
Objectives To determine the underlying biological basis for noninvasive prenatal testing (NIPT) results of multiple aneuploidies or autosomal monosomies. Methods Retrospective analysis of 113,415 tests to determine the study cohort, consisting of 138 (0.12%) cases reported as a single autosomal monosomy (n = 65), single trisomy with a sex chromosome aneuploidy (n = 36), or with multiple aneuploidies (n = 37). Clinical outcome information was reviewed and stratified into eight categories according to whether the karyotype or sonographic information agreed or disagreed with sequencing results. Results Of 67 cases with fetal or neonatal karyotypes available, 16 (24%) were partially or fully concordant with the NIPT result, 4 (6%) had aneuploidy on a reference chromosome, and 47 (70%) had normal fetal chromosomes, in which 5/47 had maternal malignancies reported. One case of maternal mosaic trisomy 8 was also detected. Of cases with no fetal karyotype information, ten had an abnormal clinical outcome, one was a normal live birth, and one reported maternal malignancy. Conclusions Noninvasive prenatal test results of autosomal monosomy or multiple aneuploidies are rare but have a diversity of underlying biologic causes. Some reflect the fetal karyotype; some reflect the presence of other maternal or fetal chromosome abnormalities, and a small number are linked to maternal disease. © 2016 Illumina. Prenatal Diagnosis published by John Wiley & Sons, Ltd. What's already known about this topic?Noninvasive prenatal testing (NIPT) has been validated for common autosomal trisomies (trisomy 21, 18, and 13), sex chromosome aneuploidies, and a selection of microdeletion syndromes. NIPT findings that are discordant with the fetal karyotype can be because of biological reasons, such as confined placental mosaicism, maternal chromosome abnormalities, and other maternal conditions such as occult malignancy.
What does this study add?Clinical and karyotype outcome information for cases that received an NIPT result indicating an autosomal monosomy or multiple aneuploidies. Some autosomal monosomy and multiple aneuploidy results reflect the true fetal karyotype, and some are explained by other factors, such as other fetal or maternal chromosomal abnormalities or maternal disease. This information will help providers with post‐test counseling for these rare and unusual results.
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Affiliation(s)
| | | | | | - Diana W Bianchi
- Mother Infant Research Institute, Tufts Medical Center, Boston, MA, USA
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87
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Deprest J, Ghidini A, Van Mieghem T, Bianchi DW, Faas B, Chitty LS. In case you missed it: the Prenatal Diagnosis
editors bring you the most significant advances of 2015. Prenat Diagn 2016; 36:3-9. [DOI: 10.1002/pd.4758] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Jan Deprest
- Department of Obstetrics and Gynecology; University Hospitals Leuven; Leuven Belgium
- Academic Department Development and Regeneration, Biomedical Sciences; KU Leuven; Leuven Belgium
| | - Alessandro Ghidini
- Department of Obstetrics and Gynecology; Georgetown University Hospital; Washington DC USA
| | - Tim Van Mieghem
- Department of Obstetrics and Gynecology; University Hospitals Leuven; Leuven Belgium
- Academic Department Development and Regeneration, Biomedical Sciences; KU Leuven; Leuven Belgium
| | - Diana W. Bianchi
- Mother Infant Research Institute, Tufts Medical Center; Boston MA
- Floating Hospital for Children; Boston MA USA
| | - Brigitte Faas
- Department of Human Genetics; Radboud University Medical Centre; Nijmegen the Netherlands
| | - Lyn S. Chitty
- UCL Institute of Child Health; Great Ormond Street Hospital for Children and NHS Foundation Trust; London UK
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88
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Affiliation(s)
- Felix C.K. Wong
- Centre for Research into Circulating Fetal Nucleic Acids, Li Ka Shing Institute of Health Sciences, and
- Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China; ,
| | - Y.M. Dennis Lo
- Centre for Research into Circulating Fetal Nucleic Acids, Li Ka Shing Institute of Health Sciences, and
- Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China; ,
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89
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Wang T, Duan C, Shen C, Xiang J, He Q, Ding J, Wen P, Zhang Q, Wang W, Liu M, Li H, Li H, Zhang L. Detection of complex deletions in chromosomes 13 and 21 in a fetus by noninvasive prenatal testing. Mol Cytogenet 2016; 9:3. [PMID: 26759606 PMCID: PMC4709980 DOI: 10.1186/s13039-016-0213-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 12/30/2015] [Indexed: 01/03/2023] Open
Abstract
Background To detect complex fetal subchromosomal abnormalities by noninvasive prenatal testing (NIPT). Case presentation After routine prenatal serum screening, the plasma of high-risk pregnant women were tested via NIPT, and the NIPT results were further validated by fetal karyotype analysis and array-based comparative genomic hybridization (aCGH) through amniocentesis. In addition, the chromosome karyotypes of the parents were also analyzed. NIPT results indicated subchromosomal abnormalities in chromosomes 13 and 21; aCGH results showed 22 Mb and 16 Mb deletions in 13 q31.3 - q34 and 21q11.1 - q21.3, respectively; and the fetal karyotype was 45,XX, der(13),-21. The maternal karyotype 46,XX,inv(9)(p12q13),t(13;21)(q31.3;q21.3) was abnormal, while the paternal karyotype showed no obvious abnormality. Conclusion In this study, we successfully detected complex deletions in chromosomes 13 and 21 in a fetus using NIPT, and NIPT can provide effective genetic information for the detection of fetal subchromosomal abnormalities.
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Affiliation(s)
- Ting Wang
- Center for Reproduction and Genetics, Nanjing Medical University Affiliated Suzhou Hospital, Suzhou, Jiangsu 215002 China
| | - Chengying Duan
- Center for Reproduction and Genetics, Nanjing Medical University Affiliated Suzhou Hospital, Suzhou, Jiangsu 215002 China
| | - Cong Shen
- Center for Reproduction and Genetics, Nanjing Medical University Affiliated Suzhou Hospital, Suzhou, Jiangsu 215002 China
| | - Jingjing Xiang
- Center for Reproduction and Genetics, Nanjing Medical University Affiliated Suzhou Hospital, Suzhou, Jiangsu 215002 China
| | - Quanze He
- Center for Reproduction and Genetics, Nanjing Medical University Affiliated Suzhou Hospital, Suzhou, Jiangsu 215002 China
| | - Jie Ding
- Center for Reproduction and Genetics, Nanjing Medical University Affiliated Suzhou Hospital, Suzhou, Jiangsu 215002 China
| | - Ping Wen
- Center for Reproduction and Genetics, Nanjing Medical University Affiliated Suzhou Hospital, Suzhou, Jiangsu 215002 China
| | - Qin Zhang
- Center for Reproduction and Genetics, Nanjing Medical University Affiliated Suzhou Hospital, Suzhou, Jiangsu 215002 China
| | - Wei Wang
- Center for Reproduction and Genetics, Nanjing Medical University Affiliated Suzhou Hospital, Suzhou, Jiangsu 215002 China
| | - Minjuan Liu
- Center for Reproduction and Genetics, Nanjing Medical University Affiliated Suzhou Hospital, Suzhou, Jiangsu 215002 China
| | - Hong Li
- Center for Reproduction and Genetics, Nanjing Medical University Affiliated Suzhou Hospital, Suzhou, Jiangsu 215002 China
| | - Haibo Li
- Center for Reproduction and Genetics, Nanjing Medical University Affiliated Suzhou Hospital, Suzhou, Jiangsu 215002 China
| | - Lili Zhang
- Center for Medical Ultrasound, Nanjing Medical University Affiliated Suzhou Hospital, Suzhou, Jiangsu China
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Abstract
Cell-free DNA (cfDNA) testing has recently become indispensable in diagnostic testing and screening. In the prenatal setting, this type of testing is often called noninvasive prenatal testing (NIPT). With a number of techniques, using either next-generation sequencing or single nucleotide polymorphism-based approaches, fetal cfDNA in maternal plasma can be analyzed to screen for rhesus D genotype, common chromosomal aneuploidies, and increasingly for testing other conditions, including monogenic disorders. With regard to screening for common aneuploidies, challenges arise when implementing NIPT in current prenatal settings. Depending on the method used (targeted or nontargeted), chromosomal anomalies other than trisomy 21, 18, or 13 can be detected, either of fetal or maternal origin, also referred to as unsolicited or incidental findings. For various biological reasons, there is a small chance of having either a false-positive or false-negative NIPT result, or no result, also referred to as a "no-call." Both pre- and posttest counseling for NIPT should include discussing potential discrepancies. Since NIPT remains a screening test, a positive NIPT result should be confirmed by invasive diagnostic testing (either by chorionic villus biopsy or by amniocentesis). As the scope of NIPT is widening, professional guidelines need to discuss the ethics of what to offer and how to offer. In this review, we discuss the current biochemical, clinical, and ethical challenges of cfDNA testing in the prenatal setting and its future perspectives including novel applications that target RNA instead of DNA.
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91
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Zhang R, Zhang H, Li Y, Han Y, Xie J, Li J. External Quality Assessment for Detection of Fetal Trisomy 21, 18, and 13 by Massively Parallel Sequencing in Clinical Laboratories. J Mol Diagn 2015; 18:244-52. [PMID: 26747585 DOI: 10.1016/j.jmoldx.2015.10.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Revised: 09/24/2015] [Accepted: 10/21/2015] [Indexed: 01/24/2023] Open
Abstract
An external quality assessment for detection of trisomy 21, 18, and 13 by massively parallel sequencing was implemented by the National Center for Clinical Laboratories of People's Republic of China in 2014. Simulated samples were prepared by mixing fragmented abnormal DNA with plasma from non-pregnant women. The external quality assessment panel, comprising 5 samples from pregnant healthy women, 2 samples with sex chromosome aneuploidies, and 13 samples with different concentrations of fetal fractions positive for trisomy 21, 18, and 13, was then distributed to participating laboratories. In total, 55.6% (47 of 84) of respondents correctly identified each of the samples in the panel. Seventeen false-negative and 87 gray zone results were reported, most [102 of 104 (98.1%)] of which were derived from for trisomy samples with effective fetal fractions <4%. No laboratories generated false-positive results. In addition, we observed varied diagnostic capabilities of different assays, with the assay on the basis of NextSeq CN500 performing better than others, whereas Z values generated by BGISEQ-100 fluctuated greatly. There were no significant correlations between the numbers of unique sequence reads and Z values from any trisomy sample generated by BGISEQ-100. Overall, most clinical laboratories detected samples containing effective fetal fractions >4%. Our study shows need for further laboratory training in the management of samples with low fetal fractions. For some assays, precision of Z values needs to be improved.
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Affiliation(s)
- Rui Zhang
- National Center for Clinical Laboratories, Beijing Hospital, Beijing, People's Republic of China
| | - Hongyun Zhang
- BGI Clinical Laboratories-Shenzhen, Shenzhen, People's Republic of China
| | - Yulong Li
- Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, National Center for Clinical Laboratories, Beijing Hospital, Beijing, People's Republic of China
| | - Yanxi Han
- National Center for Clinical Laboratories, Beijing Hospital, Beijing, People's Republic of China
| | - Jiehong Xie
- National Center for Clinical Laboratories, Beijing Hospital, Beijing, People's Republic of China
| | - Jinming Li
- National Center for Clinical Laboratories, Beijing Hospital, Beijing, People's Republic of China.
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92
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Affiliation(s)
| | - Hilary S. Gammill
- University of Washington, Department of Obstetrics and Gynecology
- Fred Hutchinson Cancer Research Center, Clinical Research Division
| | - Jay Shendure
- University of Washington, Department of Genome Sciences
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93
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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
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94
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Digital Karyotyping with Whole Genomic Sequencing for Complex Congenital Disorder. J Genet Genomics 2015; 42:651-655. [PMID: 26674382 DOI: 10.1016/j.jgg.2015.06.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 06/17/2015] [Accepted: 06/25/2015] [Indexed: 11/20/2022]
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95
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Noninvasive detection of fetal subchromosomal abnormalities by semiconductor sequencing of maternal plasma DNA. Proc Natl Acad Sci U S A 2015; 112:14670-5. [PMID: 26554006 DOI: 10.1073/pnas.1518151112] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Noninvasive prenatal testing (NIPT) using sequencing of fetal cell-free DNA from maternal plasma has enabled accurate prenatal diagnosis of aneuploidy and become increasingly accepted in clinical practice. We investigated whether NIPT using semiconductor sequencing platform (SSP) could reliably detect subchromosomal deletions/duplications in women carrying high-risk fetuses. We first showed that increasing concentration of abnormal DNA and sequencing depth improved detection. Subsequently, we analyzed plasma from 1,456 pregnant women to develop a method for estimating fetal DNA concentration based on the size distribution of DNA fragments. Finally, we collected plasma from 1,476 pregnant women with fetal structural abnormalities detected on ultrasound who also underwent an invasive diagnostic procedure. We used SSP of maternal plasma DNA to detect subchromosomal abnormalities and validated our results with array comparative genomic hybridization (aCGH). With 3.5 million reads, SSP detected 56 of 78 (71.8%) subchromosomal abnormalities detected by aCGH. With increased sequencing depth up to 10 million reads and restriction of the size of abnormalities to more than 1 Mb, sensitivity improved to 69 of 73 (94.5%). Of 55 false-positive samples, 35 were caused by deletions/duplications present in maternal DNA, indicating the necessity of a validation test to exclude maternal karyotype abnormalities. This study shows that detection of fetal subchromosomal abnormalities is a viable extension of NIPT based on SSP. Although we focused on the application of cell-free DNA sequencing for NIPT, we believe that this method has broader applications for genetic diagnosis, such as analysis of circulating tumor DNA for detection of cancer.
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96
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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.
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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
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97
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Sachs A, Blanchard L, Buchanan A, Norwitz E, Bianchi DW. Recommended pre-test counseling points for noninvasive prenatal testing using cell-free DNA: a 2015 perspective. Prenat Diagn 2015; 35:968-71. [PMID: 26245889 DOI: 10.1002/pd.4666] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 07/29/2015] [Accepted: 08/03/2015] [Indexed: 12/15/2022]
Abstract
Noninvasive prenatal testing (NIPT) using cell-free DNA is being offered to an increasing number of women. Comprehensive pre-test counseling is complicated by emerging information about the benefits and limitations of testing, as well as the potential to detect incidental findings. Genetic counselors are trained to facilitate informed decision-making; however, not all centers have access to these professionals. To aid in the informed consent process, we have summarized key points to be included in discussions with patients who are considering NIPT.
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Affiliation(s)
- Amy Sachs
- Department of Obstetrics and Gynecology, Tufts Medical Center, Boston, MA, USA.,Tufts University School of Medicine, Boston, MA, USA
| | - Leah Blanchard
- Department of Obstetrics and Gynecology, Tufts Medical Center, Boston, MA, USA.,Tufts University School of Medicine, Boston, MA, USA
| | - Amanda Buchanan
- Department of Obstetrics and Gynecology, Tufts Medical Center, Boston, MA, USA
| | - Errol Norwitz
- Department of Obstetrics and Gynecology, Tufts Medical Center, Boston, MA, USA.,Tufts University School of Medicine, Boston, MA, USA.,Mother Infant Research Institute, Tufts Medical Center, Boston, MA, USA
| | - Diana W Bianchi
- Department of Obstetrics and Gynecology, Tufts Medical Center, Boston, MA, USA.,Tufts University School of Medicine, Boston, MA, USA.,Mother Infant Research Institute, Tufts Medical Center, Boston, MA, USA
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98
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Non-invasive Prenatal Screening for Fetal Aneuploidy: Comparison with Cytogenetic Results. CURRENT GENETIC MEDICINE REPORTS 2015. [DOI: 10.1007/s40142-015-0072-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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99
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Helgeson J, Wardrop J, Boomer T, Almasri E, Paxton WB, Saldivar JS, Dharajiya N, Monroe TJ, Farkas DH, Grosu DS, McCullough RM. Clinical outcome of subchromosomal events detected by whole-genome noninvasive prenatal testing. Prenat Diagn 2015; 35:999-1004. [PMID: 26088833 PMCID: PMC5034801 DOI: 10.1002/pd.4640] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 06/14/2015] [Accepted: 06/14/2015] [Indexed: 12/17/2022]
Abstract
Objective A novel algorithm to identify fetal microdeletion events in maternal plasma has been developed and used in clinical laboratory‐based noninvasive prenatal testing. We used this approach to identify the subchromosomal events 5pdel, 22q11del, 15qdel, 1p36del, 4pdel, 11qdel, and 8qdel in routine testing. We describe the clinical outcomes of those samples identified with these subchromosomal events. Methods Blood samples from high‐risk pregnant women submitted for noninvasive prenatal testing were analyzed using low coverage whole genome massively parallel sequencing. Sequencing data were analyzed using a novel algorithm to detect trisomies and microdeletions. Results In testing 175 393 samples, 55 subchromosomal deletions were reported. The overall positive predictive value for each subchromosomal aberration ranged from 60% to 100% for cases with diagnostic and clinical follow‐up information. The total false positive rate was 0.0017% for confirmed false positives results; false negative rate and sensitivity were not conclusively determined. Conclusion Noninvasive testing can be expanded into the detection of subchromosomal copy number variations, while maintaining overall high test specificity. In the current setting, our results demonstrate high positive predictive values for testing of rare subchromosomal deletions. © 2015 The Authors. Prenatal Diagnosis published by John Wiley & Sons Ltd. What's already known about this topic?Circulating cell free DNA is a powerful clinical tool that can detect whole chromosomal aneuploidies in a fetus as early as 10 weeks with high specificity and high sensitivity. Subchromosomal events in the fetus have been shown to be detected via ccfDNA via whole genome sequencing.
What does this study add?This study shows that ccfDNA whole genome analysis for fetal subchromosomal aneuploidies including clinically significant microdeletions can be tested clinically with high specificity and high positive predictive value (PPV).
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Affiliation(s)
- J Helgeson
- Sequenom Laboratories, San Diego, CA, USA
| | - J Wardrop
- Sequenom Laboratories, San Diego, CA, USA
| | - T Boomer
- Sequenom Laboratories, San Diego, CA, USA
| | - E Almasri
- Sequenom Laboratories, San Diego, CA, USA
| | - W B Paxton
- Sequenom Laboratories, San Diego, CA, USA
| | | | | | - T J Monroe
- Sequenom Laboratories, Morrisville, NC, USA
| | - D H Farkas
- Sequenom Laboratories, Grand Rapids, MI, USA.,Department of Obstetrics, Gynecology and Reproductive Medicine, Michigan State University, East Lansing, MI, USA
| | - D S Grosu
- Sequenom Laboratories, San Diego, CA, USA
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100
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Flowers N, Kelley J, Sigurjonsson S, Bruno DL, Pertile MD. Maternal mosaicism for a large segmental duplication of 18q as a secondary finding following non-invasive prenatal testing and implications for test accuracy. Prenat Diagn 2015; 35:986-9. [DOI: 10.1002/pd.4636] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 05/31/2015] [Accepted: 06/11/2015] [Indexed: 02/04/2023]
Affiliation(s)
- Nicola Flowers
- Victorian Clinical Genetics Services Cytogenetics Laboratory; Murdoch Childrens Research Institute; Melbourne Australia
| | - Joanne Kelley
- Genetics Clinic; Mercy Hospital for Women; Melbourne Australia
| | | | - Damien L. Bruno
- Victorian Clinical Genetics Services Cytogenetics Laboratory; Murdoch Childrens Research Institute; Melbourne Australia
| | - Mark D. Pertile
- Victorian Clinical Genetics Services Cytogenetics Laboratory; Murdoch Childrens Research Institute; Melbourne Australia
- Department of Paediatrics; University of Melbourne; Melbourne Australia
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