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Putra M, Idler J, Patek K, Contos G, Walker C, Olson D, Hicks MA, Chaperon J, Korzeniewski SJ, Patwardhan SC, Sokol RJ. The association of HBB-related significant hemoglobinopathies and low fetal fraction on noninvasive prenatal screening for fetal aneuploidy. J Matern Fetal Neonatal Med 2019; 34:3657-3661. [PMID: 31736384 DOI: 10.1080/14767058.2019.1689558] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Objectives: HBB-related significant hemoglobinopathies have been anecdotally associated with low fetal fraction on noninvasive prenatal screening (NIPS). We sought to compare the difference in fetal fraction using NIPS in women with HBB-related significant hemoglobinopathies (HSH) and women with normal hemoglobin.Study design: This is a retrospective case-control study. Cases were women with a diagnosis of HSH using NIPS from a commercial laboratory. The comparison group was women with hemoglobin AA from a tertiary care center database. We tested for differences in median fetal fraction using quantile regression analysis, adjusting for maternal body weight and gestational age.Results: This study includes 35 women with clinically significant HSH and a comparison group of 636 women with hemoglobin AA. Adjusting for gestational age and body weight, the median fetal fraction was 4.1 point lower in the HSH than in the comparison group (β - 4.1; 95% -5.7 to -2.5, p < .05). The rate of no-calls due to low fetal fraction was significantly higher in the clinically significant HSH group than in the comparison group [HSH: n = 9/35, 25.7% versus comparison: n = 32/636, 5.0% (p < .001)].Conclusion: Women with HSH were more likely to have a lower fetal fraction and ultimately a five-fold higher no-call rate. What's already known about this topic?Low fetal fraction is one of the most common causes of no-call result in noninvasive prenatal screeningHigh maternal weight, early gestational age and fetal aneuploidies are associated with low fetal fraction What does this study add?HBB-related significant hemoglobinopathies are associated with low fetal fractionReduction in fetal fraction due to HBB-related significant hemoglobinopathies may also result in higher no-call rate.
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Affiliation(s)
- Manesha Putra
- Department of Reproductive Biology, Division of Maternal-Fetal Medicine, MetroHealth Medical Center, Cleveland, OH, USA.,University Hospitals Cleveland Medical Center, Cleveland, OH, USA.,Case Western Reserve University, Cleveland, OH, USA
| | - Jay Idler
- Detroit Medical Center, Detroit, MI, USA.,Wayne State University School of Medicine, Detroit, MI, USA
| | - Kara Patek
- Detroit Medical Center, Detroit, MI, USA.,Wayne State University School of Medicine, Detroit, MI, USA
| | - George Contos
- Detroit Medical Center, Detroit, MI, USA.,Wayne State University School of Medicine, Detroit, MI, USA
| | - Christopher Walker
- Detroit Medical Center, Detroit, MI, USA.,Wayne State University School of Medicine, Detroit, MI, USA
| | - Danielle Olson
- Department of Reproductive Biology, Division of Maternal-Fetal Medicine, MetroHealth Medical Center, Cleveland, OH, USA.,Case Western Reserve University, Cleveland, OH, USA
| | | | | | | | | | - Robert J Sokol
- Wayne State University School of Medicine, Detroit, MI, USA
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Nicht invasive Pränataldiagnostik mittels molekulargenetischer Tests (NIPT) zur Erkennung der Trisomien 13, 18 und 21. MED GENET-BERLIN 2019. [DOI: 10.1007/s11825-019-00251-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Zusammenfassung
Hintergrund
Molekulargenetische Tests (NIPT) auf Trisomie sind längst Teil der nicht invasiven Pränataldiagnostik (NIPD). In Deutschland wird derzeit geprüft, ob und für wen diese Tests von den gesetzlichen Krankenkassen künftig bezahlt werden sollen.
Fragestellung
(I) Diagnostische Eigenschaften der NIPT zur Entdeckung der Trisomien 13, 18 und 21 und (II) hypothetische Berechnung der möglichen Anwendung der NIPT in verschiedenen Gruppen.
Methoden
(I) Systematische Recherche nach Primärliteratur und systematischen Übersichten in MEDLINE und vier weiteren Datenbanken. Einschlusskriterien: Studien mit schwangeren Frauen, Indextest: NIPT mittels molekulargenetischer Analyse von cffDNA im mütterlichen Blut zur Bestimmung des Trisomie-Risikos; Referenztest: zytogenetische Diagnostik oder postnatale klinische Untersuchung. (II) Orientierende Recherche. Hypothetische Berechnungen für (1) alle schwangeren Frauen nach aktuellem Vorgehen ohne NIPT am Beispiel von Ersttrimesterscreening (ETS), (2) Anwendung bei schwangeren Frauen mit erhöhtem Risiko, z. B. nach vorgeschaltetem auffälligem ETS und (3) NIPT in einer Population mit und ohne erhöhtes Risiko für eine Trisomie.
Ergebnisse
Bei 22 eingeschlossenen Studien lagen die Sensitivität und die Spezifität zur Erkennung der Trisomie 21 bei 99,13 % (95 %-KI: [97,39 %; 99,72 %]) und 99,95 % (95 %-KI: [99,88 %; 99,98 %]). Der mögliche Einfluss von Testversagern blieb bei den Berechnungen unberücksichtigt, womit die Sensitivität oder die Spezifität der NIPT möglicherweise überschätzt wurde. Für die Erkennung der Trisomien 13 und 18 konnte jeweils die Sensitivität nicht robust geschätzt werden.
Diskussion
Bei Frauen mit erhöhtem Risiko können NIPT die Zahl der invasiven Tests und damit der testbedingten Fehlgeburten vermutlich verringern.
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Prentice G, Welsh A, Howat A, Ross D, Henry A. Isolated 'soft signs' of fetal choroid plexus cysts or echogenic intracardiac focus - consequences of their continued reporting. Australas J Ultrasound Med 2019; 22:253-264. [PMID: 34760567 DOI: 10.1002/ajum.12180] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Background Choroid plexus cysts (CPC) and echogenic intracardiac focus (EIF) are obsolete soft markers found on morphology ultrasound and not a valid reason for adjusting fetal risk of aneuploidy. Method We conducted a retrospective audit of women referred to genetic counsellor and fetal medicine services at St George Hospital (SGH) and the Royal Hospital for Women (RHW) for CPC and EIF from 1 January 2006 to 31 December 2016 inclusive. Results In total, 208 CPC and/or EIF referrals were identified, 118 (57%) of which were for isolated CPC and/or EIF and 102 (49%) occurring in women low risk for aneuploidy prior to morphology ultrasound. Significantly, more women had undergone combined first-trimester screening in the 2014 to 2016 epoch vs. previous years at both SGH (P = 0.03) and RHW (P = 0.004). However, the number of women referred for CPC and EIF remained relatively constant. No fetus was born with a major structural or chromosomal abnormality in the group of low-risk women with isolated signs. However, 18% of these women were referred to both genetic counselling and fetal medicine services, 7% had NIPT after morphology, 14% had amniocentesis, and 33% had additional ultrasound(s). Conclusion Despite advances in screening technology, low-risk women are still referred to specialist services for these 2 soft signs and undergoing unnecessary follow-up, NIPT and amniocentesis.
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Affiliation(s)
- Grace Prentice
- School of Women's and Children's Health University of New South Wales Sydney New South Wales Australia
| | - Alec Welsh
- School of Women's and Children's Health University of New South Wales Sydney New South Wales Australia
- Department of Maternal-Fetal Medicine Royal Hospital for Women Sydney New South Wales Australia
| | - Amy Howat
- Department of Maternal-Fetal Medicine Royal Hospital for Women Sydney New South Wales Australia
| | - Dominic Ross
- Department of Women's and Children's Health St George Hospital Sydney New South Wales Australia
| | - Amanda Henry
- School of Women's and Children's Health University of New South Wales Sydney New South Wales Australia
- Department of Maternal-Fetal Medicine Royal Hospital for Women Sydney New South Wales Australia
- Department of Women's and Children's Health St George Hospital Sydney New South Wales Australia
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Qiao L, Yu B, Liang Y, Zhang C, Wu X, Xue Y, Shen C, He Q, Lu J, Xiang J, Li H, Zheng Q, Wang T. Sequencing shorter cfDNA fragments improves the fetal DNA fraction in noninvasive prenatal testing. Am J Obstet Gynecol 2019; 221:345.e1-345.e11. [PMID: 31125545 DOI: 10.1016/j.ajog.2019.05.023] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 04/29/2019] [Accepted: 05/15/2019] [Indexed: 01/12/2023]
Abstract
BACKGROUND Sequencing cell-free DNA in maternal plasma is an effective noninvasive prenatal testing technique that has been used in fetal aneuploidy screening worldwide. However, its clinical application is limited by the low fetal fraction (<4%) of cell-free DNA in many singleton pregnancies, which usually results in screen failures or no calls. In addition, dizygotic twin contributions of cell-free DNA into the maternal circulation can vary by 2-fold, complicating the quantitative diagnosis of fetal aneuploidy. OBJECTIVE We performed semiconductor sequencing of shorter fragments (107-145 bp) of circulating cell-free DNA to improve the fetal DNA fraction at lower uniquely mapped reads (1-8.5 MB) to reduce the probability of no calls. STUDY DESIGN We identified 2903 plasma samples from pregnant women, including 86 dizygotic twin pregnancy, that were collected at a single prenatal diagnostic center between October 2015 and July 2018. Size-selection noninvasive prenatal testing for fetal aneuploidy was applied to 2817 plasma samples (1409 male and 1408 female fetuses) and 86 dizygotic twins using noninvasive prenatal testing with and without size selection. Shorter fragment size was the key factor affecting fetal fraction in multivariable linear regression models as well as to validate the accuracy of the size selection for noninvasive prenatal testing. RESULTS Analysis of 1409 male fetuses by multivariable linear regression showed that maternal age, body mass index, number of pregnancies, average cell-free DNA size, maternal plasma cell-free DNA concentration, library concentration, and multiple gestation were negatively correlated with fetal fraction. Conversely, gestational age and uniquely mapped reads were positively correlated with fetal fraction. Compared with ≤120 bp cell-free DNA fragments, mean fetal fraction differences were -3.57% (95% confidence interval, -5.95% to -1.19%), for 121-130 bp, -9.52% (95% confidence interval, -11.89% to -7.14%) for 131-140 bp, and -14.47% (95% confidence interval, -18.37% to -10.58%) for ≥141 bp (Ptrend < .0001). These results were statistically significant after multivariable adjustments in models for fetal fraction. Meanwhile, results from 86 dizygotic twins showed that the size selection increased the fetal fraction by ∼3.2-fold, with 98.8% of samples reaching a fetal fraction >10%. Improved detection accuracy was also achieved. CONCLUSION Sequencing shorter cell-free DNA fragments is a reasonable strategy to reduce the probability of no calls results because of low fetal fraction and should be recommended to pregnant subjects.
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Affiliation(s)
- Longwei Qiao
- Affiliated Suzhou Hospital of Nanjing Medical University; Suzhou affiliated to State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Suzhou, Jiangsu Province
| | - Bin Yu
- Changzhou Woman and Children Health Hospital affiliated to Nanjing Medical University, Changzhou, Jiangsu Province
| | - Yuting Liang
- Department of Laboratory Medicine, Shanghai First People's Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Chunhua Zhang
- Affiliated Suzhou Hospital of Nanjing Medical University; Suzhou affiliated to State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Suzhou, Jiangsu Province
| | - Xiaojuan Wu
- Affiliated Suzhou Hospital of Nanjing Medical University; Suzhou affiliated to State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Suzhou, Jiangsu Province
| | - Ying Xue
- Affiliated Suzhou Hospital of Nanjing Medical University; Suzhou affiliated to State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Suzhou, Jiangsu Province
| | - Cong Shen
- Affiliated Suzhou Hospital of Nanjing Medical University; Suzhou affiliated to State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Suzhou, Jiangsu Province
| | - Quanze He
- Affiliated Suzhou Hospital of Nanjing Medical University; Suzhou affiliated to State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Suzhou, Jiangsu Province
| | - Jiafeng Lu
- Affiliated Suzhou Hospital of Nanjing Medical University; Suzhou affiliated to State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Suzhou, Jiangsu Province
| | - Jingjing Xiang
- Affiliated Suzhou Hospital of Nanjing Medical University; Suzhou affiliated to State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Suzhou, Jiangsu Province
| | - Hong Li
- Affiliated Suzhou Hospital of Nanjing Medical University; Suzhou affiliated to State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Suzhou, Jiangsu Province.
| | - Qiping Zheng
- Department of Hematology and Hematological Laboratory Science, Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China.
| | - Ting Wang
- Affiliated Suzhou Hospital of Nanjing Medical University; Suzhou affiliated to State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Suzhou, Jiangsu Province.
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105
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Du Y, Chen A, Yang R, Zhou T, Zhou Q, Yang L, Wang J, Hong Y, Chen C, Wan Q, Yang L, Chen Y. A proof-of-concept study on the effects of low total cfDNA content and solutions to increase the NIPT trisomy 21 detection rate. J Clin Lab Anal 2019; 34:e23035. [PMID: 31568605 PMCID: PMC7031630 DOI: 10.1002/jcla.23035] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 07/18/2019] [Accepted: 08/12/2019] [Indexed: 11/18/2022] Open
Abstract
Background Non‐invasive prenatal testing (NIPT) is routinely used in clinical practice for fetal trisomy screening, but low total cfDNA content and low fetal fraction (LFF) are two factors that affect the detection rate. Samples with low total cfDNA or LFF usually end up with “no‐call” results, followed by the blood redraw and re‐testing, which is inconvenient for pregnant women and clinicians. Methods We created mock trisomy 21 (T21) samples to investigate the effects of low total cfDNA with low LFF and possible solutions to increase their detection rate. Results Samples with low total cfDNA resulted in the decreased unique reads number and increased duplication rate. Abnormal correlations between library concentration and raw reads number and the coverage fluctuation value, ZsdNorm, were also discovered, suggesting that low total cfDNA could lead to the overestimation of the library concentration. Additionally, a non‐reference‐based derivative value method (DV method) was evaluated and the data demonstrated that the detection sensitivity of trisomy 21 was increased from 33.33% (6/18) to 94.44% (17/18) in samples with 5% fetal fraction comparing with the z‐score approach, whereas for LFF (3.5%) group, the performance was raised from 0% to 35.29% (6/17). Conclusion Low total cfDNA has significant impacts on NIPT performance by altering sequencing quality. The non‐reference‐based DV method could increase the T21 detection rate in samples with limited cfDNA content and 5% fetal fraction, but it was not as effective for those with LFF.
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Affiliation(s)
- Yang Du
- Annoroad Gene Technology Co., Ltd, Beijing, China
| | - Ailing Chen
- Central Lab, Wuxi Maternity and Child Health Care Hospital, Affiliated Wuxi Maternity and Child Health Care Hospital of Nanjing Medical University, Wuxi, Jiangsu, China
| | - Rui Yang
- Central Lab, Wuxi Maternity and Child Health Care Hospital, Affiliated Wuxi Maternity and Child Health Care Hospital of Nanjing Medical University, Wuxi, Jiangsu, China
| | - Tao Zhou
- Central Lab, Wuxi Maternity and Child Health Care Hospital, Affiliated Wuxi Maternity and Child Health Care Hospital of Nanjing Medical University, Wuxi, Jiangsu, China
| | - Qin Zhou
- Neonatal Department, Wuxi Maternity and Child Health Care Hospital, Affiliated Wuxi Maternity and Child Health Care Hospital of Nanjing Medical University, Wuxi, China
| | - Lan Yang
- Central Lab, Wuxi Maternity and Child Health Care Hospital, Affiliated Wuxi Maternity and Child Health Care Hospital of Nanjing Medical University, Wuxi, Jiangsu, China
| | - Juan Wang
- Annoroad Gene Technology Co., Ltd, Beijing, China
| | - Yan Hong
- Annoroad Gene Technology Co., Ltd, Beijing, China
| | - Chen Chen
- Annoroad Gene Technology Co., Ltd, Beijing, China
| | - Qian Wan
- Annoroad Gene Technology Co., Ltd, Beijing, China
| | - Lin Yang
- Annoroad Gene Technology Co., Ltd, Beijing, China
| | - Ying Chen
- Central Lab, Wuxi Maternity and Child Health Care Hospital, Affiliated Wuxi Maternity and Child Health Care Hospital of Nanjing Medical University, Wuxi, Jiangsu, China
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Factors Associated With Informative Redraw After an Initial No Result in Noninvasive Prenatal Testing. Obstet Gynecol 2019; 132:428-435. [PMID: 29995728 DOI: 10.1097/aog.0000000000002728] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE Noninvasive prenatal testing (NIPT) sometimes fails to provide a test result, usually as a result of low cell-free DNA fetal fraction. We investigated how initial fetal fraction, maternal weight, gestational age, and time between blood sampling contribute to obtaining an informative result when a redraw is performed. METHODS We performed a retrospective data review of NIPT samples received between January and October 2016 by a commercial laboratory, where the initial blood draw did not yield a result and a second sample was drawn between 5 and 28 days after the initial sampling. We included cases with fetal fraction less than 2.8% (the threshold for "no result" in this laboratory) and those with higher fetal fraction but where the NIPT results could not be interpreted with high confidence. RESULTS For 4,018 cases in which a redraw was recommended, a result was obtained for the second sample in 2,835 cases (70.6%) (95% CI 69.1-72.0%). For the 2,959 cases with insufficient fetal fraction, there was a result for the second sample in 1,861 cases (62.9%) (95% CI 61.1-64.6%). For this subset, the average increase in fetal fraction was 1.2% with an average interval between draws of 14 days. Informative redraw rate was strongly dependent on maternal weight and fetal fraction measured at the first draw. Gestational age was not an important determinant. Informative redraw rate increased rapidly over the first 8 days after the initial draw and more slowly thereafter. CONCLUSION Based on fetal fraction in the initial sample, maternal weight, and interval between blood draws, women can be provided with a personalized estimate of their likelihood of a result on redraw. This should aid in the counseling of women faced with the choice of reattempting NIPT, conventional screening, or an invasive diagnostic test.
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107
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Influence of Body Mass Index on Fetal Fraction Increase With Gestation and Cell-Free DNA Test Failure. Obstet Gynecol 2019; 132:436-443. [PMID: 29995742 DOI: 10.1097/aog.0000000000002752] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
OBJECTIVE To assess the influence of body mass index (BMI) on fetal fraction increase with gestational age and on the rates of test failure. METHODS We performed a cross-sectional study of consecutive singleton pregnancies in which cell-free DNA screening for fetal aneuploidies was performed from 10 weeks of gestation, between May 2013 and January 2018, at two fetal medicine clinics in Australia using one of two different platforms. Maternal characteristics, fetal fraction, and failure after a first attempt ("no-call") and after resampling ("test failure") were recorded. Body mass index was classified as normal (BMI less than 25.0), overweight (BMI 25.0-29.9), obesity class I (BMI 30.0-34.9), and obesity classes II and III (BMI 35.0 or greater). Fetal fraction and proportions of no-call results and test failure were compared between the groups. RESULTS Of 14,223 singleton pregnancies included, 8,583 (60.3%) were screened with platform A and 5,640 (39.7%) with platform B. Median fetal fraction values were lower, and no-call and failure rates were higher in increased BMI groups across both platforms (P<.001 in both). When compared with women with normal BMIs, women with BMIs of 35 or greater had a significantly smaller increase in fetal fraction (0.1 vs 0.3 units/wk, P<.001, in both platforms). In this subgroup, when compared with women with normal BMIs, the odds ratios for a no-call result were 22.0 (95% CI 13.8-35.3, 16.6% vs 0.9%) and 8.0 (95% CI 4.1-15.6, 7.8% vs 1.0%) and for a failed test were 25.0 (95% CI 11.2-55.7, 6.4% vs 0.3%) and 5.8 (95% CI 2.0-17.3, 2.7% vs 0.5%) using platforms A and B, respectively. CONCLUSION The increase in fetal fraction throughout gestation in women with BMIs of 35 or above is minimal. Postponing the test is unlikely to reduce test failure rates in this population.
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108
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Filoche S, Lawton B, Beard A, Dowell A, Stone P. New screen on the block: non-invasive prenatal testing for fetal chromosomal abnormalities. J Prim Health Care 2019. [PMID: 29530134 DOI: 10.1071/hc16055] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Non-invasive prenatal testing (NIPT) is a new screen for fetal chromosomal abnormalities. It is a screening test based on technology that involves the analysis of feto-placental DNA that is present in maternal blood. This DNA is then analysed for abnormalities of specific chromosomes (eg 13, 18, 21, X, Y). NIPT has a much higher screening capability for chromosomal abnormalities than current combined first trimester screening, with ~99% sensitivity for trisomy 21 (Down syndrome) and at least a 10-fold higher positive predictive value. The low false-positive rate (1-3%) is one of the most advertised advantages of NIPT. In practice, this could lead to a significant reduction in the number of false-positive tests and the need for invasive diagnostic procedures. NIPT is now suitable for singleton and twin pregnancies and can be performed from ~10 weeks in a pregnancy. NIPT is not currently publicly funded in most countries. However, the increasing availability of NIPT commercially will likely lead to an increase in demand for this as a screening option. Given the high numbers of women who visit a general practitioner (GP) in their first trimester, GPs are well-placed to also offer NIPT as a screening option. A GP's role in facilitating access to this service will likely be crucial in ensuring equity in access to this technology, and it is important to ensure that they are well supported to do so.
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Affiliation(s)
- Sara Filoche
- Women's Health Research Centre, Department of Obstetrics and Gynaecology, University of Otago Wellington, Wellington, New Zealand
| | - Beverley Lawton
- Women's Health Research Centre, Department of Obstetrics and Gynaecology, University of Otago Wellington, Wellington, New Zealand
| | - Angela Beard
- Christchurch Obstetric Associates, Christchurch, New Zealand
| | - Anthony Dowell
- Department of Obstetrics and Gynaecology, University of Otago Wellington, Wellington, New Zealand
| | - Peter Stone
- School of Medicine, The University of Auckland, Auckland, New Zealand
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Abstract
BACKGROUND The number of citations a published article receives can be used to demonstrate its impact on a field of study. The objective of this study was to identify and characterize the 100 most-cited research articles (T100) published on prenatal diagnosis. METHODS The Web of Science (WOS) database was searched for papers on prenatal diagnosis published between 1900 and 2018. The 100 most-cited original articles and reviews were recorded. Each eligible paper was reviewed for authors, journal name, year of publication, country, institution, total citations, citation density, H-index, research field, article type, and keywords. RESULTS The T100 were published between 1972 and 2015 with a mean of 332.7 citations per paper (range: 196-1254). Most of the T100 were published between 1990 and 2005, in 35 journals led by New England Journal of Medicine (n = 14) followed by Lancet (n = 10), and Proceedings of The National Academy of Sciences of the United States of America (n = 8). Studies on method application, which promotes field development, were the majority article type. The team of Lo YM featured prominently in the field, and the United States of America, United Kingdom, and Hong Kong, China were the leading countries/regions. Frequency of cooperation was also highest among these 3 regions. Hierarchical cluster analysis produced 4 groups of keywords. CONCLUSION Our analysis provides a historical perspective on scientific progress in prenatal diagnosis and may assist clinicians and researchers in assessing the quality of research over the past 50 years. It also provides concise information to guide future research.
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Affiliation(s)
- Meilian Zhang
- Department of Ultrasound, Fujian Provincial Maternity and Children's Hospital Affiliated Hospital of Fujian Medical University
| | - Yu Zhou
- Department of Clinical Pharmacy and Pharmacy Administration, School of Pharmacy, Fujian Medical University
| | - Yanfang Lu
- Clinical Laboratory, Fujian Provincial Maternity and Children's Hospital Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Suhui He
- Department of Ultrasound, Fujian Provincial Maternity and Children's Hospital Affiliated Hospital of Fujian Medical University
| | - Min Liu
- Department of Ultrasound, Fujian Provincial Maternity and Children's Hospital Affiliated Hospital of Fujian Medical University
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Li J, Zhen L, Pan M, Li DZ. First prenatal case of 48,XXYY syndrome detected by maternal cell-free DNA testing. J OBSTET GYNAECOL 2019; 40:270-272. [PMID: 31339398 DOI: 10.1080/01443615.2019.1607268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Jian Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Li Zhen
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Min Pan
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Dong-Zhi Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, China
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Audibert F, De Bie I, Johnson JA, Okun N, Wilson RD, Armour C, Chitayat D, Kim R. No. 348-Joint SOGC-CCMG Guideline: Update on Prenatal Screening for Fetal Aneuploidy, Fetal Anomalies, and Adverse Pregnancy Outcomes. JOURNAL OF OBSTETRICS AND GYNAECOLOGY CANADA 2019; 39:805-817. [PMID: 28859766 DOI: 10.1016/j.jogc.2017.01.032] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
OBJECTIVE To review the available prenatal screening options in light of the recent technical advances and to provide an update of previous guidelines in the field of prenatal screening. INTENDED USERS Health care providers involved in prenatal screening, including general practitioners, obstetricians, midwives, maternal fetal medicine specialists, geneticists, and radiologists. TARGET POPULATION All pregnant women receiving counselling and providing informed consent for prenatal screening. EVIDENCE Published literature was retrieved through searches of Medline, PubMed, and the Cochrane Library in and prior to March 2016 using an appropriate controlled vocabulary (prenatal diagnosis, amniocentesis, chorionic villi sampling, non-invasive prenatal screening) and key words (prenatal screening, prenatal genetic counselling). Results were restricted to systematic reviews, randomized control trials/controlled clinical trials, and observational studies written in English and published from January 1985 to May 2016. Searches were updated on a regular basis and incorporated in the guideline. Grey (unpublished) literature was identified through searching the websites of health technology assessment and health technology-related agencies, clinical practice guideline collections, clinical trial registries, and national and international medical speciality societies. GUIDELINE UPDATE Evidence will be reviewed 5 years after publication to determine whether all or part of the guideline should be updated. However, if important new evidence is published prior to the 5-year cycle, the review process may be accelerated for a more rapid update of some recommendations.
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Kypri E, Ioannides M, Touvana E, Neophytou I, Mina P, Velissariou V, Vittas S, Santana A, Alexidis F, Tsangaras K, Achilleos A, Patsalis P, Koumbaris G. Non-invasive prenatal testing of fetal chromosomal aneuploidies: validation and clinical performance of the veracity test. Mol Cytogenet 2019; 12:34. [PMID: 31338126 PMCID: PMC6628499 DOI: 10.1186/s13039-019-0446-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 06/30/2019] [Indexed: 02/05/2023] Open
Abstract
Introduction Non-Invasive Prenatal Testing (NIPT) for fetal aneuploidies using cell-free DNA (cfDNA) has been widely adopted in clinical practice due to its improved accuracy. A number of NIPT tests have been developed and validated. The purpose of this study is to evaluate the performance of the Veracity NIPT test for sex chromosome aneuploidy (SCA) detection in singleton pregnancies, autosomal aneuploidy detection in twin pregnancies and evaluation of Veracity clinical performance under routine NIPT conditions in a diverse cohort. Methods Blinded retrospective study in singleton pregnancies (n = 305); blinded retrospective and prospective study in twin pregnancies (n = 306) and prospective evaluation of clinical performance in singleton and twin pregnancies (n = 10564). Results Validation study results for the detection of SCAs in singleton pregnancies exhibited 100% sensitivity and specificity and correctly classified 7 (45,X), 4 (47,XXY), 2 (47,XXX) and 1 (47,XYY) cases. Validation study results for autosomal aneuploidy detection in twin pregnancies exhibited 100% sensitivity and specificity and correctly classified 3 trisomy 21, 1 trisomy 18 and 1 trisomy 13 samples. Clinical performance evaluation of Veracity was performed in 10564 pregnancies with median gestational age of 13 weeks, median maternal age 35 years and median gestational weight of 64 kg. Based on confirmation feedback the PPV for trisomies 21, 18 and 13 was estimated at 100% (95% CI, 92–100%), 100% (95% CI, 69–100%) and 71% (95% CI, 29–96%), respectively. Estimated PPV for Monosomy X was 57% (95%CI, 18–90%), while the NPV for SCA detection was estimated at 100% (95% CI, 99.94–100%). Conclusion Veracity NIPT test is based on a very powerful, highly accurate methodology that can be safely applied in the clinical setting. Electronic supplementary material The online version of this article (10.1186/s13039-019-0446-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elena Kypri
- NIPD Genetics Public Company Ltd, Neas Engomis 31, Engomi, 2409 Nicosia, Cyprus
| | - Marios Ioannides
- NIPD Genetics Public Company Ltd, Neas Engomis 31, Engomi, 2409 Nicosia, Cyprus
| | - Evi Touvana
- NIPD Genetics Public Company Ltd, Neas Engomis 31, Engomi, 2409 Nicosia, Cyprus
| | - Ioanna Neophytou
- NIPD Genetics Public Company Ltd, Neas Engomis 31, Engomi, 2409 Nicosia, Cyprus
| | - Petros Mina
- NIPD Genetics Public Company Ltd, Neas Engomis 31, Engomi, 2409 Nicosia, Cyprus
| | - Voula Velissariou
- NIPD Genetics Public Company Ltd, Neas Engomis 31, Engomi, 2409 Nicosia, Cyprus.,DNA Diagnosis N Analysis, Adrianoupoleos 1, 55133 Kalamaria, Thessaloniki, Greece
| | - Spiros Vittas
- DNA Diagnosis N Analysis, Adrianoupoleos 1, 55133 Kalamaria, Thessaloniki, Greece
| | - Alfredo Santana
- Clinical Genetics Unit, Childhood Hospital Materno-Infantil, Childhood Hospital Materno-Infantil, Las Palmas, GC, Canary Islands Spain
| | - Filippos Alexidis
- Eurogenetica, Adrianoupoleos 7, 55133 Kalamaria, Thessaloniki, Greece
| | - Kyriakos Tsangaras
- NIPD Genetics Public Company Ltd, Neas Engomis 31, Engomi, 2409 Nicosia, Cyprus
| | - Achilleas Achilleos
- NIPD Genetics Public Company Ltd, Neas Engomis 31, Engomi, 2409 Nicosia, Cyprus
| | - Philippos Patsalis
- NIPD Genetics Public Company Ltd, Neas Engomis 31, Engomi, 2409 Nicosia, Cyprus
| | - George Koumbaris
- NIPD Genetics Public Company Ltd, Neas Engomis 31, Engomi, 2409 Nicosia, Cyprus
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113
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Shi J, Zhang R, Li J, Zhang R. Novel perspectives in fetal biomarker implementation for the noninvasive prenatal testing. Crit Rev Clin Lab Sci 2019; 56:374-392. [PMID: 31290367 DOI: 10.1080/10408363.2019.1631749] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Noninvasive prenatal testing (NIPT) utilizes cell-free fetal DNA (cffDNA) present in maternal peripheral blood to detect chromosomal abnormalities. The detection of 21-trisomy, 18-trisomy, and 13-trisomy in the fetus has become a common screening method during pregnancy and has been widely applied in routine clinical testing because of its analytical and clinical validity. Currently, noninvasive prenatal testing involving copy number variations (CNVs) and other frequent single-gene disorders is being widely studied, and it plays an important and indispensable role in prenatal detection. The multiple approaches that have been reported and validated by various laboratories have different merits and limitations. Their clinical validity, utility, and application vary with different diseases. This review summarizes the principles, methods, advantages, and limitations of noninvasive prenatal testing for the detection of aneuploidy, CNVs and single-gene disorders. Before implementation of NIPT into clinical practice, a list of criteria that the application must meet is crucial. Essential parameters such as clinical sensitivity, clinical specificity, positive predictive value (PPV) and negative predictive value (NPV) are required to properly evaluate the clinical validity and utility of NIPT. We then discuss and analyze these clinical parameters and clinical application guidelines, providing physicians and scientists with feasible strategies and the latest research information.
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Affiliation(s)
- Jiping Shi
- Peking University Fifth School of Clinical Medicine, National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital , Beijing , China.,National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital , Beijing , China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital , Beijing , China
| | - Runling Zhang
- National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital , Beijing , China.,Graduate School, Chinese Academy of Medical Sciences, Peking Union Medical College , Beijing , China
| | - Jinming Li
- National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital , Beijing , China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital , Beijing , China
| | - Rui Zhang
- Peking University Fifth School of Clinical Medicine, National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital , Beijing , China.,National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital , Beijing , China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital , Beijing , China
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114
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Teder H, Paluoja P, Rekker K, Salumets A, Krjutškov K, Palta P. Computational framework for targeted high-coverage sequencing based NIPT. PLoS One 2019; 14:e0209139. [PMID: 31283802 PMCID: PMC6613673 DOI: 10.1371/journal.pone.0209139] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 06/20/2019] [Indexed: 12/16/2022] Open
Abstract
Non-invasive prenatal testing (NIPT) enables accurate detection of fetal chromosomal trisomies. The majority of publicly available computational methods for sequencing-based NIPT analyses rely on low-coverage whole-genome sequencing (WGS) data and are not applicable for targeted high-coverage sequencing data from cell-free DNA samples. Here, we present a novel computational framework for a targeted high-coverage sequencing-based NIPT analysis. The developed framework uses a hidden Markov model (HMM) in conjunction with a supplemental machine learning model, such as decision tree (DT) or support vector machine (SVM), to detect fetal trisomy and parental origin of additional fetal chromosomes. These models were developed using simulated datasets covering a wide range of biologically relevant scenarios with various chromosomal quantities, parental origins of extra chromosomes, fetal DNA fractions, and sequencing read depths. Developed models were tested on simulated and experimental targeted sequencing datasets. Consequently, we determined the functional feasibility and limitations of each proposed approach and demonstrated that read count-based HMM achieved the best overall classification accuracy of 0.89 for detecting fetal euploidies and trisomies on simulated dataset. Furthermore, we show that by using the DT and SVM on the HMM classification results, it was possible to increase the final trisomy classification accuracy to 0.98 and 0.99, respectively. We demonstrate that read count and allelic ratio-based models can achieve a high accuracy (up to 0.98) for detecting fetal trisomy even if the fetal fraction is as low as 2%. Currently, existing commercial NIPT analysis requires at least 4% of fetal fraction, which can be possibly a challenge in case of early gestational age (<10 weeks) or high maternal body mass index (>35 kg/m2). More accurate detection can be achieved at higher sequencing depth using HMM in conjunction with supplemental models, which significantly improve the trisomy detection especially in borderline scenarios (e.g., very low fetal fraction) and enables to perform NIPT even earlier than 10 weeks of pregnancy.
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Affiliation(s)
- Hindrek Teder
- Competence Centre on Health Technologies, Tartu, Estonia.,Institute of Biomedicine and Translational Medicine, Department of Biomedicine, University of Tartu, Tartu, Estonia
| | - Priit Paluoja
- Competence Centre on Health Technologies, Tartu, Estonia.,Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Kadri Rekker
- Competence Centre on Health Technologies, Tartu, Estonia.,Institute of Clinical Medicine, Department of Obstetrics and Gynecology, University of Tartu, Tartu, Estonia
| | - Andres Salumets
- Competence Centre on Health Technologies, Tartu, Estonia.,Institute of Biomedicine and Translational Medicine, Department of Biomedicine, University of Tartu, Tartu, Estonia.,Institute of Clinical Medicine, Department of Obstetrics and Gynecology, University of Tartu, Tartu, Estonia.,Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Kaarel Krjutškov
- Competence Centre on Health Technologies, Tartu, Estonia.,Research Program of Molecular Neurology, Research Programs Unit, University of Helsinki and Folkhälsan Institute of Genetics, Helsinki, Finland
| | - Priit Palta
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia.,Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
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115
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Rajs B, Pasternok M, Nocuń A, Matyszkiewicz A, Ziętek D, Rozmus-Warcholińska W, Zalewski S, Migda M, Mavrikis J, Wiecheć M. Clinical article: screening for trisomy 13 using traditional combined screening versus an ultrasound-based protocol. J Matern Fetal Neonatal Med 2019; 34:1048-1054. [PMID: 31122094 DOI: 10.1080/14767058.2019.1623779] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
AIMS To compare the screening capability of ultrasonography in detecting trisomy 13 (T13) using a multiparameter sonographic protocol (NT+) with a classical combined screening test (CST) protocol. METHODS The project was a prospective, multicenter study based on a nonselected mixed-risk population of women referred for a first-trimester screening examination. Each subject was offered a choice between either the gold standard, traditional combined screening test (CSG arm) or the ultrasound-based screening protocol (USG arm). General and MA-based screening performances were checked. RESULTS The study population comprised 20,887 pregnancies: 12,933 in the CSG arm, including 27 cases of T13, and 7954 in the USG arm, including 30 cases of T13. The DR for T13 was higher in the CSG arm than in the USG arm for all tested cutoff points: 1/50 (88.5 versus 63.3%, respectively), 1/100 (88.5 versus 70%, respectively) and 1/300 (92.3 versus 83.3%, respectively). Using the ROC curves for fixed FPRs of 3 and 5%, the T13 detection rate in our study reached 90 and 93%, respectively, in the USG arm and 92 and 96%, respectively, in the CSG arm. MA influenced the T13 screening performance in the USG arm and reduced the DR in patients <31 years. Such influence was not detected in the CSG arm. CONCLUSIONS Classic CST was more effective in detecting T13 than the ultrasound-only approach. However, the recommended cutoff of 1/50 showed unsatisfactory results for both traditional CST and the multiparameter sonographic test we proposed.
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Affiliation(s)
- Bartosz Rajs
- Jagiellonian University in Krakow, Kraków, Poland
| | | | | | - Anna Matyszkiewicz
- Jagiellonian University in Krakow, Kraków, Poland.,Ultrasound Group Practice, "MWU DOBREUSG", Kraków, Poland
| | | | | | | | | | - Judene Mavrikis
- Collegium Medicum, School of Medicine in English, Jagiellonian University, Kraków, Poland
| | - Marcin Wiecheć
- Jagiellonian University in Krakow, Kraków, Poland.,Ultrasound Group Practice, "MWU DOBREUSG", Kraków, Poland
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116
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Korostin DO, Plakhina DA, Belova VA. Noninvasive prenatal testing: the aspects of its introduction into clinical practice. BULLETIN OF RUSSIAN STATE MEDICAL UNIVERSITY 2019. [DOI: 10.24075/brsmu.2019.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The last couple of years have witnessed the rapid development of prenatal molecular-based screening for fetal aneuploidies that utilizes the analysis of cell-free DNA circulating in the bloodstream of a pregnant woman. The present review looks at the potential and limitations of such testing and the possible causes of false-positive and false-negative results. The review also describes the underlying principles of data acquisition and analysis the testing involves. In addition, we talk about the opinions held by the expert community and some aspects of legislation on the use of noninvasive prenatal testing (NIPT) in clinical practice in the countries where NIPT is much more widespread than in Russia.
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Affiliation(s)
- D. O. Korostin
- Pirogov Russian National Research Medical University, Moscow, Russia; Genotek Ltd., Moscow, Russia
| | | | - V. A. Belova
- Pirogov Russian National Research Medical University, Moscow, Russia; Genotek Ltd., Moscow, Russia
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117
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Wang J, Wang ZW, Zhou Q, Zhang B, Yin T, Yu B, Wang LL. Lower detectability of non-invasive prenatal testing compared to prenatal diagnosis in high-risk pregnant women. ANNALS OF TRANSLATIONAL MEDICINE 2019; 7:319. [PMID: 31475189 PMCID: PMC6694278 DOI: 10.21037/atm.2019.06.70] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 04/26/2019] [Indexed: 11/06/2022]
Abstract
BACKGROUND To investigate the detectability of non-invasive prenatal testing (NIPT) after prenatal screening to detect foetal chromosomal abnormalities in pregnant women at high risk, and the number of foetal abnormalities could be missed by NIPT. METHODS From January 2009 to March 2018, 3,099 pregnant women at high risk for trisomy 21 and 18 according to the results of prenatal serological screening were enrolled in this study. The women underwent amniocentesis at 18-23 weeks, as well as karyotype testing and/or chromosomal microarray analyses (CMA). We assessed the ability of NIPT to detect chromosomal abnormalities. RESULTS In all, 177 (5.7%, 177/3,099) chromosomal abnormalities were identified. These included 129 (72.9%) abnormal numbers of chromosomes, 6 (3.4%) chromosome structural abnormalities, and 42 (23.7%) other abnormalities, including copy number variation, inversions, and chromosome additions/deletions. Of the 177 (70.0%) chromosomal abnormalities, 124 were detected and 53 were missed by NIPT. CONCLUSIONS NIPT could miss 30.0% of the chromosomal abnormalities detected by amniocentesis and cytogenetic testing. This proportion will likely decrease in the future due to further development of NIPT.
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Affiliation(s)
- Jing Wang
- Department of Medical Genetics, Changzhou Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, Changzhou 213003, China
| | - Zhi-Wei Wang
- Department of Medical Genetics, Lianyungang Maternal and Child Health Hospital Affiliated to Yangzhou University, Lianyungang 222000, China
| | - Qin Zhou
- Department of Medical Genetics, Changzhou Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, Changzhou 213003, China
| | - Bin Zhang
- Department of Medical Genetics, Changzhou Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, Changzhou 213003, China
| | - Ting Yin
- Department of Medical Genetics, Lianyungang Maternal and Child Health Hospital Affiliated to Yangzhou University, Lianyungang 222000, China
| | - Bin Yu
- Department of Medical Genetics, Changzhou Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, Changzhou 213003, China
| | - Lei-Lei Wang
- Department of Medical Genetics, Lianyungang Maternal and Child Health Hospital Affiliated to Yangzhou University, Lianyungang 222000, China
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118
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Tobin M, Gunaji R, Walsh JC, Grice GP. A review of genetic factors underlying craniorachischisis and omphalocele: Inspired by a unique trisomy 18 case. Am J Med Genet A 2019; 179:1642-1651. [PMID: 31184807 DOI: 10.1002/ajmg.a.61255] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 04/29/2019] [Accepted: 05/21/2019] [Indexed: 11/11/2022]
Abstract
Very few cases of craniorachischisis (CRN) with concomitant omphalocele (OMP) in the setting of trisomy 18 are reported in literature. Solitary midline closure defects are estimated to be more prevalent in trisomy 18 compared to the general population. Neurulation defect comparisons include anencephaly 0-2% versus 0.0206%, spina bifida 1-3% versus 0.0350%, and encephalocele 0-2% versus 0.0082% [Parker et al. (2010); Birth Defects Research. Part A: Clinical and Molecular Teratology, 88:1008-1016; Springett et al. (2015); American Journal of Medical Genetics. Part A, 167A:3062-3069]. The solitary anterior malformation OMP has been reported as high as 6% with trisomy 18 [Springett et al. (2015); American Journal of Medical Genetics. Part A, 167A:3062-3069]. We report the third published case of CRN with concomitant OMP observed in a likely trisomy 18 fetus that screened positive by noninvasive prenatal screening. Furthermore, we review and analyze the current literature to augment understanding of the genetic basis for anterior and posterior closure defects such as CRN and OMP. Although the current genetic lexicon lacks any definitive association with the simultaneous defects presented, previous research elucidated various genes related to anterior or posterior closure interruption individually. By consolidating current research, the authors advance knowledge of interconnected genetic pathology and direct future genetic mapping efforts.
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Affiliation(s)
- Michael Tobin
- CPT, Medical Corps, US Army, PGY-1 Emergency Medicine Resident, Madigan Army Medical Center, Joint Base Lewis-McChord, Washington
| | - Rajesh Gunaji
- LT, Medical Corps, US Navy, F. Edward Hébert School of Medicine, Class of 2019, Uniformed Services University of the Health Sciences, Bethesda, MD
| | - John C Walsh
- Laboratory Department, LCDR, Medical Corps (FS), US Navy, PGY-5 Pathology Resident, Naval Medical Center, San Diego, California
| | - Guerard P Grice
- Laboratory Department, CAPT (Ret.), Medical Corps, US Navy, Naval Medical Center, San Diego, California
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119
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Deng C, Zhu Q, Liu S, Liu J, Bai T, Jing X, Xia T, Liu Y, Cheng J, Li Z, Wei X, Xing L, Luo Y, Liu H. Clinical application of noninvasive prenatal screening for sex chromosome aneuploidies in 50,301 pregnancies: initial experience in a Chinese hospital. Sci Rep 2019; 9:7767. [PMID: 31123326 PMCID: PMC6533246 DOI: 10.1038/s41598-019-44018-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 05/07/2019] [Indexed: 11/10/2022] Open
Abstract
To evaluate the clinical performance of noninvasive prenatal screening (NIPS) for fetal sex chromosome aneuploidies (SCAs), pregnant women were recruited in this retrospective observational study. The NIPS test was undertaken using high-throughput gene sequencing. In total,50,301 pregnant women were analysed for demographic characteristics and medical history. Of them, 308 women (0.61%) had high risk for fetal SCAs, including 138 for 45,X, 111 for 47,XXY, 42 for 47,XXX, and 17 for 47,XYY. After the pre-test counselling, 182 participants chose to undergo invasive prenatal diagnosis, confirming 59 positive cases. The combined positive predictive value of NIPS was 32.42% (59/182), 18.39% (16/87), 44.4% (12/27), 39.29% (22/56), and 75% (9/12) for detecting SCAs, 45,X, 47,XXX, 47,XXY, and 47,XYY, respectively. NIPS can be a useful method to detect the fetal SCAs using high-throughput gene sequencing, though accuracy can still be improved, especially for 45,X. Although the value of NIPS compare favorably with those seen in traditional screening approaches for SCAs, it is important to highlight the limitations of NIPS while educating clinicians and patients.
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Affiliation(s)
- Cechuan Deng
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University,, Chengdu, 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, China
| | - Qian Zhu
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University,, Chengdu, 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, China
| | - Sha Liu
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University,, Chengdu, 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, China
| | - Jianlong Liu
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University,, Chengdu, 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, China
| | - Ting Bai
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University,, Chengdu, 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, China
| | - Xiaosha Jing
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University,, Chengdu, 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, China
| | - Tianyu Xia
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University,, Chengdu, 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, China
| | - Yunyun Liu
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University,, Chengdu, 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, China
| | - Jing Cheng
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University,, Chengdu, 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, China
| | - Zhunduo Li
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University,, Chengdu, 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, China
| | - Xiang Wei
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University,, Chengdu, 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, China
| | - Lingling Xing
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University,, Chengdu, 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, China
| | - Yuan Luo
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University,, Chengdu, 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, China
| | - Hongqian Liu
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University,, Chengdu, 610041, China.
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, China.
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Yin L, Tang Y, Lu Q, Shi M, Pan A, Chen D. Noninvasive prenatal testing detects microdeletion abnormalities of fetal chromosome 15. J Clin Lab Anal 2019; 33:e22911. [PMID: 31094035 PMCID: PMC6642313 DOI: 10.1002/jcla.22911] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 04/17/2019] [Accepted: 04/18/2019] [Indexed: 12/16/2022] Open
Abstract
OBJECTIVE Noninvasive prenatal testing (NIPT) is widely used in clinical detection of fetal autosomal duplications or deletions. The aim of this study was to investigate the clinical application of NIPT for detection of chromosomal microdeletions. METHODS Microdeletions of about 5 Mb in the long arm of chromosome 15 (q11.2-q12) were detected by NIPT and were confirmed by karyotype analysis and copy number variation (CNV) analysis based on high-throughput sequencing technology. RESULTS The CNV results of prenatal diagnosis showed that there were approximately 4.96 Mb of microdeletions in 15q11.2-q13.1, which was consistent with the NIPT results. The karyotype analysis showed no abnormalities. CONCLUSION In this study, the microdeletion fragment of fetal chromosome 15 was successfully detected and diagnosed using NIPT. This suggests that NIPT is an efficient method to gain genetic information about chromosomal abnormalities.
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Affiliation(s)
- Lianli Yin
- Department of Clinical Laboratory, Nanning Second People's Hospital, The Third Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Yinghua Tang
- Department of Clinical Laboratory, Guangxi Hospital Of Traditional Chinese Medicine, The First Affiliated Hospital of Guangxi University of Chinese Medicine, Nanning, China
| | - Qing Lu
- Department of genetic counseling, Nanning Second People's Hospital, The Third Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Mingfang Shi
- Department of Clinical Laboratory, Nanning Second People's Hospital, The Third Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Aiping Pan
- Department of Clinical Laboratory, Guangxi Hospital Of Traditional Chinese Medicine, The First Affiliated Hospital of Guangxi University of Chinese Medicine, Nanning, China
| | - Danyun Chen
- Department of Clinical Laboratory, Nanning Second People's Hospital, The Third Affiliated Hospital of Guangxi Medical University, Nanning, China
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Nomura J, Rieg G, Bluestone G, Tsai T, Lai A, Terashita D, Bercovici S, Hong DK, Lee BP. Rapid detection of invasive Mycobacterium chimaera disease via a novel plasma-based next-generation sequencing test. BMC Infect Dis 2019; 19:371. [PMID: 31046692 PMCID: PMC6498503 DOI: 10.1186/s12879-019-4001-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 04/17/2019] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND There is an ongoing outbreak of Mycobacterium chimaera infections among patients exposed to contaminated heater-cooler devices used during cardiac surgery. Recognition of M. chimaera infection is hampered by its long latency and non-specific symptoms. Standard diagnostic methods using acid-fast bacilli (AFB) culture often require invasive sampling, have low sensitivity, and can take weeks to result. We describe the performance of a plasma-based next-generation sequencing test (plasma NGS) for the diagnosis of M. chimaera infection. METHODS We conducted a retrospective study of 10 patients with a history of cardiac surgery who developed invasive M. chimaera infection and underwent testing by plasma NGS between February 2017 and April 2018. RESULTS Plasma NGS detected M. chimaera in 9 of 10 patients (90%) with invasive disease in a median of 4 days from specimen collection, including all 8 patients with disseminated infection. In 7 of these 9 cases (78%), plasma NGS was the first test to provide microbiologic confirmation of M. chimaera infection. In contrast, AFB cultures required a median of 20 days to turn positive, and the median time for confirmation of M. chimaera was 41 days. Of 24 AFB blood cultures obtained in this cohort, only 4 (17%) were positive. Invasive procedures were performed in 90% of cases, and in 5 patients (50%), mycobacterial growth was achieved only by culture of these deep sites. CONCLUSIONS Plasma NGS can accurately detect M. chimaera noninvasively and significantly faster than AFB culture, making it a promising new diagnostic tool.
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Affiliation(s)
- Jim Nomura
- Southern California Permanente Medical Group, Infectious Disease Department, Los Angeles Medical Center, 1505 N Edgemont St, Los Angeles, CA, 90027, USA.
| | - Gunter Rieg
- South Bay Medical Center, Harbor City, CA, USA
| | | | | | - Andrew Lai
- Southern California Permanente Medical Group, Infectious Disease Department, Los Angeles Medical Center, 1505 N Edgemont St, Los Angeles, CA, 90027, USA
| | - Dawn Terashita
- Los Angeles County Department of Public Health, Los Angeles, CA, USA
| | - Sivan Bercovici
- Karius, Inc, 975 Island Drive, Suite 101, Redwood City, CA, 94065, USA
| | - David K Hong
- Karius, Inc, 975 Island Drive, Suite 101, Redwood City, CA, 94065, USA
| | - Brian P Lee
- Karius, Inc, 975 Island Drive, Suite 101, Redwood City, CA, 94065, USA.
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Yu D, Zhang K, Han M, Pan W, Chen Y, Wang Y, Jiao H, Duan L, Zhu Q, Song X, Hong Y, Chen C, Wang J, Hui F, Huang L, Chen C, Du Y. Noninvasive prenatal testing for fetal subchromosomal copy number variations and chromosomal aneuploidy by low-pass whole-genome sequencing. Mol Genet Genomic Med 2019; 7:e674. [PMID: 31004415 PMCID: PMC6565572 DOI: 10.1002/mgg3.674] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 02/27/2019] [Accepted: 03/06/2019] [Indexed: 12/20/2022] Open
Abstract
Background Expanding noninvasive prenatal testing (NIPT) to include the detection of fetal subchromosomal copy number variations (CNVs) significantly decreased the sensitivity and specificity. Developing analytic pipeline to achieve high performance in the noninvasive detection of CNVs will largely contribute to the application of CNVs screening in clinical practice. Methods We developed the Noninvasively Prenatal Subchromosomal Copy number variation Detection (NIPSCCD) method based on low‐pass whole‐genome sequencing, and evaluated its efficacy in detecting fetal CNVs and chromosomal aneuploidies with 20,003 pregnant women. Results Totally, NIPSCCD identified 36 CNVs, including 29 CNVs consistent and 7 CNVs inconsistent with amniocytes tests. Additionally, seven fetal CNVs identified by amniocytes testing were undetected by NIPSCCD. The sensitivities for detecting CNVs > 10 Mb, 5 Mb–10 Mb, and CNVs < 5 Mb were 91.67%, 100.00%, and 68.42%, respectively. Moreover, NIPSCCD identified 103/ true positive trisomy 21/18/13 cases and 21 false positives, producing an overall 100.00% sensitivity and 99.89% specificity. Conclusion NIPSCCD showed a good performance in detecting fetal subchromosomal CNVs, especially for CNVs >10 Mb, and can be incorporated into the routine NIPT chromosomal aneuploidies screening with high sensitivity and specificity.
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Affiliation(s)
- Dongyi Yu
- Genetic Testing Center, Qingdao Women & Children Hospital, Qingdao University, Qingdao, China
| | - Kai Zhang
- Genetic Testing Center, Qingdao Women & Children Hospital, Qingdao University, Qingdao, China
| | - Meiyan Han
- Genetic Testing Center, Qingdao Women & Children Hospital, Qingdao University, Qingdao, China
| | - Wei Pan
- The Center of Prenatal Diagnosis, Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Ying Chen
- Central Lab, Wuxi Maternity and Child Health Care Hospital, Affiliated Wuxi Maternity and Child Health Care Hospital of Nanjing Medical University, Wuxi, Jiangsu, China
| | - Yunfeng Wang
- Annoroad Gene Technology Co., Ltd, Beijing, China
| | - Hongyan Jiao
- The Branch Center of Prenatal Diagnosis, Hebei Maternity and Child Healthcare Hospital, Shijiazhuang, China
| | - Ling Duan
- Department of Obstetrics, First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Qiying Zhu
- Department of Obstetrics, First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Xiaojie Song
- Department of Obstetrics and Gynecology, Wuhan Women and Child Care Service Hospital, Wuhan, China
| | - Yan Hong
- Annoroad Gene Technology Co., Ltd, Beijing, China
| | - Chen Chen
- Annoroad Gene Technology Co., Ltd, Beijing, China
| | - Juan Wang
- Annoroad Gene Technology Co., Ltd, Beijing, China
| | - Feng Hui
- Annoroad Gene Technology Co., Ltd, Beijing, China
| | | | | | - Yang Du
- Annoroad Gene Technology Co., Ltd, Beijing, China
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123
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The significance of trisomy 7 mosaicism in noninvasive prenatal screening. Hum Genomics 2019; 13:18. [PMID: 30971315 PMCID: PMC6458712 DOI: 10.1186/s40246-019-0201-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 03/18/2019] [Indexed: 12/18/2022] Open
Abstract
Background This study was an evaluation of the role of noninvasive prenatal testing (NIPT) in the detection of trisomy 7 in prenatal diagnosis. Method A total of 35 consecutive cases underwent screening for trisomies by cell-free DNA testing between April 2015 and November 2017 due to suspicious NIPT results; these cases represented 0.11% of patients (35/31,250) with similar frequencies of abnormal results among the laboratories performing the tests. NIPT was offered to further screen for common fetal chromosomal abnormalities. Karyotype analysis, chromosomal microarray analysis (CMA), and next-generation sequencing (NGS) were used to detect 20, 14, and 25 patients, respectively, who accepted confirmatory diagnostic testing. Results High-risk results by NIPT were recorded for trisomy 7 alone in 29 women: dual aneuploidy in 4 patients and multiple aneuploidy in 2 patients. Karyotype analysis of amniotic fluid cells was normal in all 20 pregnancies, suggesting a probability of confined placental mosaicism. Further CMA data were obtained in 14 of the cases mentioned above, and 2 fetuses were detected with positive results with copy number variation. The NGS results suggested that all these samples were placental chimerisms of chromosome 7, except for one sample that was found to be an additional chimerism of chromosome 2, which was also consistent with the NIPT result. Conclusion Our results may be useful for the counseling of pregnant women in the detection of trisomy 7 by NIPT.
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Fleddermann L, Hashmi SS, Stevens B, Murphy L, Rodriguez-Buritica D, Friel LA, Singletary C. Current genetic counseling practice in the United States following positive non-invasive prenatal testing for sex chromosome abnormalities. J Genet Couns 2019; 28:802-811. [PMID: 30946507 DOI: 10.1002/jgc4.1122] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 03/04/2019] [Accepted: 03/05/2019] [Indexed: 11/06/2022]
Abstract
The purpose of this study was to describe current genetic counseling practice in the United States following a non-invasive prenatal testing (NIPT) result positive for a sex chromosome abnormality (SCA). Screening for SCAs can be confounded by confined placental mosaicism, natural loss of the X chromosome from maternal cells during aging, and undiagnosed maternal SCA or copy number variant (CNV). Furthermore, with the exception of 45,X, individuals with SCAs usually have no ultrasound or postnatal findings. This makes follow-up for unresolved positive NIPT necessary; however, there are currently no clinical guidelines. This study used a cross-sectional design with an anonymous questionnaire to survey 176 genetic counselors. The majority of prenatal respondents always offered diagnostic testing (>88%) and anatomy ultrasound (~90%), but the percent consistently offering maternal karyotype (22%-52%) and postnatal evaluation (28%-87%) varied. Maternal karyotype was offered more often when NIPT was positive for 45,X or 47,XXX and patients had normal prenatal diagnostic testing (p < 0.02) or declined testing (p < 0.02). Offer of postnatal evaluation was more likely when diagnostic testing was declined (p < 0.001). The majority of pediatric providers always offered a postnatal karyotype for the newborn (>72%) but the percent offering maternal karyotype (6%-46%) varied widely. With the current inconsistencies, many newborns with undiagnosed SCAs who could benefit from growth hormone therapy, early intervention, and/or targeted surveillance may be missed. Therefore, there is a need for professional guidelines to help improve the consistency of clinical care for patients with NIPT results positive for SCAs.
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Affiliation(s)
- Lauren Fleddermann
- UTHealth Graduate School of Biomedical Sciences, MD Anderson Cancer Center, The University of Texas, Houston, Texas.,Maternal Fetal Medicine Clinic, North Memorial Health Hospital, Robbinsdale, Minnesota
| | - Syed Shahrukh Hashmi
- UTHealth Graduate School of Biomedical Sciences, MD Anderson Cancer Center, The University of Texas, Houston, Texas.,Department of Pediatrics, McGovern Medical School at the University of Texas Health Science Center at Houston, Houston, Texas
| | - Blair Stevens
- UTHealth Graduate School of Biomedical Sciences, MD Anderson Cancer Center, The University of Texas, Houston, Texas.,Department of Obstetrics, Gynecology and Reproductive Sciences, McGovern Medical School at the University of Texas Health Science Center at Houston, Houston, Texas
| | - Lauren Murphy
- UTHealth Graduate School of Biomedical Sciences, MD Anderson Cancer Center, The University of Texas, Houston, Texas.,Department of Obstetrics, Gynecology and Reproductive Sciences, McGovern Medical School at the University of Texas Health Science Center at Houston, Houston, Texas
| | - David Rodriguez-Buritica
- UTHealth Graduate School of Biomedical Sciences, MD Anderson Cancer Center, The University of Texas, Houston, Texas.,Department of Pediatrics, McGovern Medical School at the University of Texas Health Science Center at Houston, Houston, Texas
| | - Lara A Friel
- UTHealth Graduate School of Biomedical Sciences, MD Anderson Cancer Center, The University of Texas, Houston, Texas.,Department of Obstetrics, Gynecology and Reproductive Sciences, McGovern Medical School at the University of Texas Health Science Center at Houston, Houston, Texas
| | - Claire Singletary
- UTHealth Graduate School of Biomedical Sciences, MD Anderson Cancer Center, The University of Texas, Houston, Texas.,Department of Pediatrics, McGovern Medical School at the University of Texas Health Science Center at Houston, Houston, Texas.,Department of Obstetrics, Gynecology and Reproductive Sciences, McGovern Medical School at the University of Texas Health Science Center at Houston, Houston, Texas
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Deans ZC, Allen S, Jenkins L, Khawaja F, Gutowska-Ding W, Patton SJ, Chitty LS, Hastings RJ. Ensuring high standards for the delivery of NIPT world-wide: Development of an international external quality assessment scheme. Prenat Diagn 2019; 39:379-387. [PMID: 30767256 PMCID: PMC6619285 DOI: 10.1002/pd.5438] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 02/04/2019] [Accepted: 02/11/2019] [Indexed: 02/05/2023]
Abstract
Objective To ensure accurate and appropriate reporting of non‐invasive prenatal testing (NIPT) results, the standard of testing should be measured and monitored by participation in external quality assessment (EQA) schemes. The findings from international pilot EQAs for NIPT for the common trisomies are presented. Methods In the first pilot, three EQA providers used artificially manufactured reference materials to deliver an EQA for NIPT. The second pilot used clinically collected maternal plasma samples. The testing and reporting for aneuploidy status was performed by participating laboratories using routine procedures. Reports were assessed against peer ratified criteria and EQA scores were returned to participants. Results Forty laboratories participated in the first. Genotyping accuracy was high; four laboratories reported a critical genotyping error (10%) and two reported partial results. Eighty seven laboratories participated in the second pilot using maternal plasma, two reporting a critical genotyping error (2.3%). For both rounds, report content was variable with key information frequently omitted or difficult to identify within the report. Conclusions We have successfully delivered an international pilot EQA for NIPT. When compared with currently available manufactured materials, EQA for NIPT was best performed using clinically collected maternal plasma. Work is required to define and improve the standard of reporting. What is already known about this topic?
To ensure laboratories deliver accurate, appropriate, and effective reporting of tests performed in their laboratories participation in external quality assessment (EQA) schemes is required by accrediting bodies. There is no international EQA scheme available for NIPT for aneuploidy.
What does this study add?
EQA for the common trisomies can be successfully delivered across multiple laboratories worldwide. The EQA is best delivered using clinically collected maternal plasma samples which can be transported at room temperature. Reporting standards are very variable with key information often omitted. Further work is required to develop internationally acceptable EQA for NIPT aneuploidy including reporting standards. The high level of participation in these pilots suggests the need for continued delivery of EQA.
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Affiliation(s)
- Zandra C Deans
- UK NEQAS for Molecular Genetics/GenQA, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Stephanie Allen
- West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Birmingham, UK
| | - Lucy Jenkins
- Great Ormond Street Hospital, North East Thames Regional Genetics Laboratory, London, UK
| | - Farrah Khawaja
- UK NEQAS for Molecular Genetics/GenQA, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Weronika Gutowska-Ding
- EMQN, Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| | - Simon J Patton
- EMQN, Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| | - Lyn S Chitty
- UCL Great Ormond Street Institute of Child Health and Great Ormond Street NHS Foundation Trust, London, UK
| | - Ros J Hastings
- CEQAS/GenQA, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
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126
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Clinical utility of noninvasive prenatal screening for expanded chromosome disease syndromes. Genet Med 2019; 21:1998-2006. [PMID: 30828085 DOI: 10.1038/s41436-019-0467-4] [Citation(s) in RCA: 151] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 02/12/2019] [Indexed: 12/11/2022] Open
Abstract
PURPOSE To assess the clinical performance of an expanded noninvasive prenatal screening (NIPS) test ("NIPS-Plus") for detection of both aneuploidy and genome-wide microdeletion/microduplication syndromes (MMS). METHODS A total of 94,085 women with a singleton pregnancy were prospectively enrolled in the study. The cell-free plasma DNA was directly sequenced without intermediate amplification and fetal abnormalities identified using an improved copy-number variation (CNV) calling algorithm. RESULTS A total of 1128 pregnancies (1.2%) were scored positive for clinically significant fetal chromosome abnormalities. This comprised 965 aneuploidies (1.026%) and 163 (0.174%) MMS. From follow-up tests, the positive predictive values (PPVs) for T21, T18, T13, rare trisomies, and sex chromosome aneuploidies were calculated as 95%, 82%, 46%, 29%, and 47%, respectively. For known MMS (n = 32), PPVs were 93% (DiGeorge), 68% (22q11.22 microduplication), 75% (Prader-Willi/Angleman), and 50% (Cri du Chat). For the remaining genome-wide MMS (n = 88), combined PPVs were 32% (CNVs ≥10 Mb) and 19% (CNVs <10 Mb). CONCLUSION NIPS-Plus yielded high PPVs for common aneuploidies and DiGeorge syndrome, and moderate PPVs for other MMS. Our results present compelling evidence that NIPS-Plus can be used as a first-tier pregnancy screening method to improve detection rates of clinically significant fetal chromosome abnormalities.
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Bayón JC, Orruño E, Portillo MI, Asua J. The consequences of implementing non-invasive prenatal testing with cell-free foetal DNA for the detection of Down syndrome in the Spanish National Health Service: a cost-effectiveness analysis. COST EFFECTIVENESS AND RESOURCE ALLOCATION 2019; 17:6. [PMID: 30867656 PMCID: PMC6397500 DOI: 10.1186/s12962-019-0173-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 02/17/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND DNA-based non-invasive prenatal testing (NIPT) using maternal blood constitutes an emerging technology for the detection of Down syndrome (DS). The aim of the study was to conduct a cost-effectiveness analysis to evaluate the economic costs and health implications of the introduction of NIPT based on cell-free foetal DNA analysis through different screening strategies for the detection of DS. METHODS An analytical short-term decision model was developed, from the payer´s perspective (Spanish National Health Service). The main outcome measure was the number of DS cases detected. Secondary measures included associated miscarriages, women undergoing current screening, women undergoing NIPT, positive NIPT and invasive procedures performed. The study setting was the Spanish National Health Service. Three strategies were compared: (a) first- and second-trimester screening (current screening); (b) NIPT as contingent testing; and (c) NIPT as first-line testing. Modelling was based on a hypothetical cohort of 100,000 Spanish pregnant women. Population data were obtained from the database of the Basque Antenatal Screening Programme. Deterministic sensitivity analyses were performed to assess variations in the cost of NIPT, screening risk cut-off, screening uptake-rate and rate of failure of NIPT. RESULTS NIPT as contingent testing (strategy b) led to fewer miscarriages following invasive procedures and a slight reduction in the number of DS cases detected compared to current screening. However, lowering the screening cut-off to ≥ 1:500 would improve the overall effectiveness of NIPT as contingent testing, increasing the number of DS cases detected and decreasing foetal losses as compared to the current screening, despite there would be an extra-cost of 3.5%. When NIPT was used as first-line testing (strategy c), the screening would be more effective but also more expensive, with incremental cost-effectiveness ratios (ICERs) per additional case of DS detected of €1,299,763 and €1,232,763, compared with strategies a and b, respectively. Results were sensitive to the different parameters considered in the analysis. CONCLUSIONS Both, as first-line testing and as contingent testing when screening cut-off was lowered ≥ 1:500, NIPT would lead to more favourable outcomes as compared to the current screening (both in terms of DS cases detected and miscarriages avoided), but at a greater cost.
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Affiliation(s)
- J. C. Bayón
- Basque Office for Health Technology Assessment (OSTEBA), Ministry of Health, Basque Government, c/Donostia 1, 01010 Vitoria-Gasteiz, Basque Country Spain
| | - E. Orruño
- Bioaraba Health Research Institute, Methodology and Statistics Unit, Araba University Hospital, Txagorritxu Headquarters, 4th Floor, c/José Achótegui, 01009 Vitoria-Gasteiz, Basque Country Spain
| | - M. I. Portillo
- Colorectal and Prenatal Screening Coordinating Centre, Basque Health Service, Bilbao, Basque Country Spain
| | - J. Asua
- Basque Office for Health Technology Assessment (OSTEBA), Ministry of Health, Basque Government, c/Donostia 1, 01010 Vitoria-Gasteiz, Basque Country Spain
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Wilkins-Haug L, Zhang C, Cerveira E, Ryan M, Mil-Homens A, Zhu Q, Reddi H, Lee C, Bianchi DW. Biological explanations for discordant noninvasive prenatal test results: Preliminary data and lessons learned. Prenat Diagn 2019; 38:445-458. [PMID: 29633279 DOI: 10.1002/pd.5260] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 03/25/2018] [Accepted: 03/29/2018] [Indexed: 12/14/2022]
Abstract
OBJECTIVE Maternal plasma cell-free DNA (cfDNA) analysis is a powerful screening tool for Down syndrome. In a pilot series, we examined biologic causes of discordance between the cfDNA test results and the fetal karyotype. We also explored the feasibility of obtaining trio biospecimens by using parental engagement. METHODS A convenience sample of women with discordant cfDNA results were recruited by their care providers. We provided shipping materials and instructions for biospecimen collection. Maternal, newborn, and placental samples were examined with droplet digital PCR. RESULTS Thirteen of 15 women successfully had biospecimens obtained remotely. High-quality DNA was extracted in 12 of 13 women. Presumed biologic etiologies for discordance were identified in 7 of 12 women: 3 cases from additional clinical review (male renal transplant, vanishing twin, and colon cancer) and 4 cases from additional laboratory investigation using droplet digital PCR (3 with confined placental mosaicism and 1 with true fetal mosaicism). CONCLUSIONS Understanding the biology behind cfDNA-fetal karyotype discordancy is useful for follow-up clinical care. Our study suggests that most cases could be resolved by using a trio biospecimen protocol and parental involvement. To improve accuracy, additional sequencing of biospecimens will be required.
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Affiliation(s)
- Louise Wilkins-Haug
- Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Eliza Cerveira
- Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Mallory Ryan
- Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Adam Mil-Homens
- Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Qihui Zhu
- Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Honey Reddi
- Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Charles Lee
- Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Diana W Bianchi
- Mother Infant Research Institute, Tufts Medical Center, Boston, MA, USA.,Prenatal Genomics and Therapy Section, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
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129
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Ashoor Al Mahri G, Nicolaides KH. Evolution in screening for Down syndrome. ACTA ACUST UNITED AC 2019. [DOI: 10.1111/tog.12534] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Ghalia Ashoor Al Mahri
- London Deanery and Out Of Programme for Training at Corniche Hospital Abu Dhabi United Arab Emirates
| | - KH Nicolaides
- Harris Birthright Research Centre for Fetal Medicine King's College Hospital London SE5 9RS UK
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Discordant sex between fetal screening and postnatal phenotype requires evaluation. J Perinatol 2019; 39:28-33. [PMID: 30459335 PMCID: PMC6340391 DOI: 10.1038/s41372-018-0278-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 09/27/2018] [Accepted: 10/16/2018] [Indexed: 12/13/2022]
Abstract
OBJECTIVE Non-invasive prenatal screening (NIPS) utilizes circulating cell-free DNA (cfDNA) to screen for fetal genetic abnormalities. NIPS is the first widely-available prenatal screen to assess genotypic sex. Most pediatricians have limited familiarity with NIPS technology and potential etiologies of discordant results. Increased familiarity may provide diagnostic insight and improve clinical care. STUDY DESIGN We reviewed all patients with discordant genotypic fetal sex assessed by cfDNA and neonatal phenotypic sex referred to our medical center. RESULT Four infants with discordant cfDNA result and phenotypic sex were identified. Etiologies include vanishing twin syndrome, difference of sexual development, sex chromosome aneuploidy and maternal chimerism. CONCLUSIONS We present four cases illustrating potential etiologies of discordant cfDNA result and postnatal phenotypic sex. Unanticipated cfDNA results offer the perinatologist a unique opportunity for early diagnosis and targeted treatment of various conditions, many of which may not have otherwise been detected in the perinatal period.
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131
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Rezaei M, Winter M, Zander-Fox D, Whitehead C, Liebelt J, Warkiani ME, Hardy T, Thierry B. A Reappraisal of Circulating Fetal Cell Noninvasive Prenatal Testing. Trends Biotechnol 2018; 37:632-644. [PMID: 30501925 DOI: 10.1016/j.tibtech.2018.11.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 11/04/2018] [Accepted: 11/05/2018] [Indexed: 01/09/2023]
Abstract
New tools for higher-resolution fetal genome analysis including microarray and next-generation sequencing have revolutionized prenatal screening. This article provides commentary on this rapidly advancing field and a future perspective emphasizing circulating fetal cell (CFC) utility. Despite the tremendous technological challenges associated with their reliable and cost-effective isolation from maternal blood, CFCs have a strong potential to bridge the gap between the diagnostic sensitivity of invasive procedures and the desirable noninvasive nature of cell-free fetal DNA (cffDNA). Considering the rapid advances in both rare cell isolation and low-input DNA analysis, we argue here that CFC-based noninvasive prenatal testing is poised to be implemented clinically in the near future.
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Affiliation(s)
- Meysam Rezaei
- Future Industries Institute and ARC Centre of Excellence in Convergent Bio and Nano Science and Technology, University of South Australia, Mawson Lakes Campus, Mawson Lakes, South Australia, Australia; Joint first authors. https://twitter.com/@CBNSSA
| | - Marnie Winter
- Future Industries Institute and ARC Centre of Excellence in Convergent Bio and Nano Science and Technology, University of South Australia, Mawson Lakes Campus, Mawson Lakes, South Australia, Australia; Joint first authors. https://twitter.com/@CBNSSA
| | | | - Clare Whitehead
- Department of Obstetrics and Gynaecology, University of Toronto, Toronto, ON, Canada
| | - Jan Liebelt
- South Australian Clinical Genetics Service, Women's and Children's Hospital, Adelaide, Australia
| | - Majid Ebrahimi Warkiani
- School of Biomedical Engineering, University of Technology Sydney, Sydney, Ultimo NSW 2007, Australia; Institute of Molecular Medicine, Sechenov First Moscow State University, Moscow 119991, Russia
| | - Tristan Hardy
- SA Pathology, Adelaide, Australia; Repromed, Dulwich, South Australia, Australia.
| | - Benjamin Thierry
- Future Industries Institute and ARC Centre of Excellence in Convergent Bio and Nano Science and Technology, University of South Australia, Mawson Lakes Campus, Mawson Lakes, South Australia, Australia; http://bionanoengineering.com/. https://twitter.com/@CBNSSA
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Affiliation(s)
- Wolfgang Holzgreve
- MD, FRCOG, FACOG, MBA, Professor of Obstetrics and Gynecology, Medical Director and CEO, University Medical Center Bonn, Sigmund-Freud-Strasse 25, 53105 Bonn, Germany, Tel.: +49 228.287-10900, Fax: +49 228.287-90 10900, Mobile: +49 151.58 233 667, E-mail:
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Huang T, Dougan S, Walker M, Armour CM, Okun N. Trends in the use of prenatal testing services for fetal aneuploidy in Ontario: a descriptive study. CMAJ Open 2018; 6:E436-E444. [PMID: 30291139 PMCID: PMC6182116 DOI: 10.9778/cmajo.20180046] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND In 2014, Ontario augmented its publicly funded multiple-marker screening program for prenatal aneuploidy by incorporating cell-free fetal DNA (cffDNA) analysis for high-risk pregnancies. We assessed trends in the use of multiple-marker screening, cffDNA screening and prenatal diagnostic testing before and after implementation of public funding. METHODS We conducted a descriptive study based on data from the Better Outcomes Registry & Network (BORN) Ontario. The study population included all pregnant women in Ontario with a singleton pregnancy and an expected date of delivery between July 1, 2012, and Mar. 31, 2016, with pregnancy data captured in BORN. Pregnancy losses and terminations before 20 weeks' gestation not captured in BORN were excluded. We generated descriptive statistics to show trends and regional variations in use. RESULTS The study sample included 534 210 singleton pregnancies. After cffDNA screening was funded for specific indications, uptake of multiple-marker screening increased slightly, from 66.5% to 68.1% (p < 0.001). Uptake of cffDNA screening among women with a positive multiple-marker screening result increased substantially, from 3.2% to 48.8% (p < 0.001). In contrast, the rate of prenatal diagnostic testing in this group decreased from 54.8% to 30.8% (p < 0.001). Although women aged 40 years or older are eligible for primary cffDNA screening, only a small decrease in the use of multiple-marker screening was observed in this group. The greatest use of cffDNA screening and greatest decline in prenatal diagnostic testing were seen in women with a level of risk for trisomy 21 of 1:101-1:200 based on multiple-marker screening. INTERPRETATION After public funding of cffDNA screening was implemented in Ontario, there was a significant increase in cffDNA screening and a significant decrease in prenatal diagnostic testing among women with a positive multiple-marker screening result. These changing patterns show the significant impact of public policy and funding decisions on women's choices regarding prenatal testing.
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Affiliation(s)
- Tianhua Huang
- Ontario Prenatal Screening Program, Better Outcomes Registry & Network (BORN) Ontario (Huang, Dougan, Walker, Armour, Okun), Ottawa, Ont.; Genetic Program (Huang), North York General Hospital, Toronto, Ont.; Regional Genetics Program (Armour), Children's Hospital of Eastern Ontario, Ottawa, Ont.; Maternal Fetal Medicine Program (Okun), Mt. Sinai Hospital, University of Toronto, Toronto, Ont.
| | - Shelley Dougan
- Ontario Prenatal Screening Program, Better Outcomes Registry & Network (BORN) Ontario (Huang, Dougan, Walker, Armour, Okun), Ottawa, Ont.; Genetic Program (Huang), North York General Hospital, Toronto, Ont.; Regional Genetics Program (Armour), Children's Hospital of Eastern Ontario, Ottawa, Ont.; Maternal Fetal Medicine Program (Okun), Mt. Sinai Hospital, University of Toronto, Toronto, Ont
| | - Mark Walker
- Ontario Prenatal Screening Program, Better Outcomes Registry & Network (BORN) Ontario (Huang, Dougan, Walker, Armour, Okun), Ottawa, Ont.; Genetic Program (Huang), North York General Hospital, Toronto, Ont.; Regional Genetics Program (Armour), Children's Hospital of Eastern Ontario, Ottawa, Ont.; Maternal Fetal Medicine Program (Okun), Mt. Sinai Hospital, University of Toronto, Toronto, Ont
| | - Christine M Armour
- Ontario Prenatal Screening Program, Better Outcomes Registry & Network (BORN) Ontario (Huang, Dougan, Walker, Armour, Okun), Ottawa, Ont.; Genetic Program (Huang), North York General Hospital, Toronto, Ont.; Regional Genetics Program (Armour), Children's Hospital of Eastern Ontario, Ottawa, Ont.; Maternal Fetal Medicine Program (Okun), Mt. Sinai Hospital, University of Toronto, Toronto, Ont
| | - Nan Okun
- Ontario Prenatal Screening Program, Better Outcomes Registry & Network (BORN) Ontario (Huang, Dougan, Walker, Armour, Okun), Ottawa, Ont.; Genetic Program (Huang), North York General Hospital, Toronto, Ont.; Regional Genetics Program (Armour), Children's Hospital of Eastern Ontario, Ottawa, Ont.; Maternal Fetal Medicine Program (Okun), Mt. Sinai Hospital, University of Toronto, Toronto, Ont
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134
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Lambert-Messerlian G, Palomaki GE. Fewer women aged 35 and older choose serum screening for Down's syndrome: Impact and implications. J Med Screen 2018; 26:59-66. [PMID: 30253677 DOI: 10.1177/0969141318797961] [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: 11/15/2022]
Abstract
OBJECTIVE To quantify changes in the proportion of women aged 35 and older choosing serum screening for Down's syndrome over time and the effect on false positive and detection rates. METHODS From Rhode Island hospital-based laboratory prenatal screening records (2013-2017) we extracted the test performed (Integrated, Combined, Quadruple), maternal age, and Down's syndrome risk; documented observed changes in maternal age distributions and false positive rates, and modelled the impact of varying proportions of older women choosing screening on each test's performance using the 2015 United States birth cohort as baseline. RESULTS Over five years, observed false positive rates for Integrated testing declined from 1.9 to 1.3% (-32%). The proportion of older women tested declined from 14.9 to 8.5%, from which modelling predicts a 16% decline in the false positive rate. This is lower than our observed change but consistent with a reduction driven by declining participation by older women. Modelling predicted a detection rate reduction from 89 to 87%. Larger detection rate impacts were predicted for Combined and Quadruple testing. CONCLUSIONS This study documents, for the first time, the declining proportion of older women choosing Down's syndrome serum screening and subsequent impact on screening performance. The American College of Obstetrics and Gynecology recommends offering cell-free DNA screening for these 'high risk' pregnancies and uptake may increase further. Screening programmes could consider increasing use of Integrated testing over other serum screening tests or lowering risk cut-offs so false positive rates approach those of 2012 to regain lost detection.
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Affiliation(s)
- Geralyn Lambert-Messerlian
- 1 Department of Pathology and Laboratory Medicine, Women & Infants Hospital and the Alpert Medical School at Brown University, Providence, USA.,2 Obstetrics and Gynecology, Women & Infants Hospital and the Alpert Medical School at Brown University, Providence, USA
| | - Glenn E Palomaki
- 1 Department of Pathology and Laboratory Medicine, Women & Infants Hospital and the Alpert Medical School at Brown University, Providence, USA
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135
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Zhou F, Liu S, Wang H. Noninvasively diagnosing for fetal trisomy 21 by examining heterozygous single nucleotide polymorphisms in the placental specific genes on chromosome 21. Eur J Obstet Gynecol Reprod Biol 2018; 233:19-25. [PMID: 30544028 DOI: 10.1016/j.ejogrb.2018.09.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 09/03/2018] [Accepted: 09/10/2018] [Indexed: 10/28/2022]
Abstract
OBJECTIVE Noninvasive prenatal diagnosing for fetal trisomy 21 could help to avoid unnecessary amniocentesis. It is feasible to target the cell-free placental-specific mRNA in maternal plasma, thus eliminating the interference from the maternal genetic background. STUDY DESIGN In this study, placental-specific genes on chromosome 21 were identified by searching the TiGER database and reviewing the published literature. These cell-free placental-specific mRNA fragments in maternal plasma were amplified and sequenced. Then, the allelic ratio of heterozygous single-nucleotide polymorphisms(SNPs) was analyzed. RESULTS Four placental-specific genes (DNMT3L, KRTAP26-1, PLAC4, DSCR4) were identified. This study included 42 cases of normal pregnancies and 19 cases of trisomy 21 pregnancies. The probability density function showed that the allelic ratio of heterozygous SNPs in normal pregnancy reached a peak at 1.0, and that in the trisomy 21 pregnancy was a double-peaked curve in both 0.5 and 2.0. However, the allelic ratio of heterozygous SNPs demonstrated no statistical difference between the normal and trisomy 21 pregnancies. CONCLUSION Fetal trisomy 21 could not be diagnosed by examining the heterozygous SNPs of cell-free placental-specific mRNA on chromosome 21. This might be because the low quantity and quality of cell-free placental-specific mRNA fragments in maternal plasma, and the limited available heterozygous SNPs on the placental-specific genes.
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Affiliation(s)
- Fan Zhou
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China; Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Shanling Liu
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China; Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - He Wang
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China; Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China.
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136
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García-Pérez L, Linertová R, Álvarez-de-la-Rosa M, Bayón JC, Imaz-Iglesia I, Ferrer-Rodríguez J, Serrano-Aguilar P. Cost-effectiveness of cell-free DNA in maternal blood testing for prenatal detection of trisomy 21, 18 and 13: a systematic review. THE EUROPEAN JOURNAL OF HEALTH ECONOMICS : HEPAC : HEALTH ECONOMICS IN PREVENTION AND CARE 2018; 19:979-991. [PMID: 29249015 DOI: 10.1007/s10198-017-0946-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 11/29/2017] [Indexed: 06/07/2023]
Abstract
The aim of this paper was to conduct a systematic review of the cost-effectiveness of the analysis of cell-free DNA in maternal blood, often called the non-invasive prenatal test (NIPT), in the prenatal screening of trisomy in chromosomes 21, 18 and 13. MEDLINE, MEDLINE in process, EMBASE, and Cochrane Library were searched in April 2017. We selected: (1) economic evaluations that estimated the costs and detected cases of trisomy 21, 18 or 13; (2) comparisons of prenatal screening with NIPT (universal or contingent strategies) and the usual screening without NIPT, (3) in pregnant women with any risk of foetal anomalies. Studies were reviewed by two researchers. Data were extracted, the methodological quality was assessed and a narrative synthesis was prepared. In total, 12 studies were included, four of them performed in Europe. Three studies evaluated NIPT as a contingent test, three studies evaluated a universal NIPT, and six studies evaluated both. The results are heterogeneous, especially for the contingent NIPT where the results range from NIPT being dominant to a dominated strategy. Universal NIPT was found to be more effective but also costlier than the usual screening, with very high incremental cost-effectiveness ratios. One advantage of screening with NIPT is lower invasive procedure-related foetal losses than with usual screening. In conclusion, the cost-effectiveness of contingent NIPT is uncertain according to several studies, while the universal NIPT is not cost-effective currently.
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Affiliation(s)
- Lidia García-Pérez
- Servicio de Evaluación, Servicio Canario de la Salud, Camino Candelaria Nº 44, 1ª planta, El Rosario, 38109, Santa Cruz De Tenerife, Canary Islands, Spain.
- Fundación Canaria de Investigación Sanitaria (FUNCANIS), Camino Candelaria Nº 44, 1ª planta, El Rosario, 38109, Santa Cruz De Tenerife, Canary Islands, Spain.
- Red de Investigación en Servicios de Salud en Enfermedades Crónicas (REDISSEC), Madrid, Spain.
- Centro de Investigaciones Biomédicas de Canarias (CIBICAN), Universidad de La Laguna, La Laguna, Spain.
- Facultad de Ciencias Económicas y Empresariales, Universidad de La Laguna, Campus de Guajara, Camino de la Hornera s/n, La Laguna, 38071, Santa Cruz De Tenerife, Spain.
| | - Renata Linertová
- Servicio de Evaluación, Servicio Canario de la Salud, Camino Candelaria Nº 44, 1ª planta, El Rosario, 38109, Santa Cruz De Tenerife, Canary Islands, Spain
- Fundación Canaria de Investigación Sanitaria (FUNCANIS), Camino Candelaria Nº 44, 1ª planta, El Rosario, 38109, Santa Cruz De Tenerife, Canary Islands, Spain
- Red de Investigación en Servicios de Salud en Enfermedades Crónicas (REDISSEC), Madrid, Spain
- Centro de Investigaciones Biomédicas de Canarias (CIBICAN), Universidad de La Laguna, La Laguna, Spain
| | - Margarita Álvarez-de-la-Rosa
- Obstetrics and Gynecology Department, Hospital Universitario de Canarias (HUC), Universidad de La Laguna (ULL), Carretera de Ofra s/n, La Cuesta, La Laguna, 38320, Santa Cruz De Tenerife, Spain
| | - Juan Carlos Bayón
- Department of Health, Basque Government, Basque Office for Health Technology Assessment (OSTEBA), Alameda Rekalde Nº 39, 48008, Bilbao, Spain
| | - Iñaki Imaz-Iglesia
- Red de Investigación en Servicios de Salud en Enfermedades Crónicas (REDISSEC), Madrid, Spain
- Instituto de Salud Carlos III, Monforte de Lemos Nº 5, 28029, Madrid, Spain
| | - Jorge Ferrer-Rodríguez
- Fundación Canaria de Investigación Sanitaria (FUNCANIS), Camino Candelaria Nº 44, 1ª planta, El Rosario, 38109, Santa Cruz De Tenerife, Canary Islands, Spain
| | - Pedro Serrano-Aguilar
- Servicio de Evaluación, Servicio Canario de la Salud, Camino Candelaria Nº 44, 1ª planta, El Rosario, 38109, Santa Cruz De Tenerife, Canary Islands, Spain
- Red de Investigación en Servicios de Salud en Enfermedades Crónicas (REDISSEC), Madrid, Spain
- Centro de Investigaciones Biomédicas de Canarias (CIBICAN), Universidad de La Laguna, La Laguna, Spain
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137
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Ren Y, Zhao J, Li R, Xie Y, Jiang S, Zhou H, Liu H, You Y, Chen F, Wang W, Gao Y, Meng Y, Lu Y. Noninvasive prenatal test for FGFR3-related skeletal dysplasia based on next-generation sequencing and plasma cell-free DNA: Test performance analysis and feasibility exploration. Prenat Diagn 2018; 38:821-828. [PMID: 30048571 DOI: 10.1002/pd.5334] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 07/13/2018] [Accepted: 07/14/2018] [Indexed: 12/22/2022]
Abstract
OBJECTIVE To explore the feasibility and accuracy of a noninvasive prenatal test for fibroblast growth factor receptor 3 (FGFR3)-related skeletal dysplasia based on next-generation sequencing (NGS) of plasma cell-free DNA. METHOD Fragmented genome DNA (gDNA) of fetuses with achondroplasia (ACH) and thanatophoric dysplasia type I (TD I) was mixed with postdelivery maternal plasma cell-free DNA to generate spiked samples of different modeled fetal fractions. Multiplex polymerase chain reaction was used to amplify the 19 FGFR3 loci, and the amplification products were then sequenced by NGS to detect the fetal mutant alleles. Then, maternal plasma samples of pregnant women carrying ACH (n = 4) and TD I fetuses (n = 2), as well as healthy controls (n = 15), were tested by NGS, and the test performance was evaluated. RESULTS Fetal FGFR3 mutations were detected in all artificial mixtures with fetal gDNA concentrations above 3%. In clinical validation, our method identified all fetal FGFR3 mutant alleles from maternal plasma, with no false positive results. The sensitivity and specificity of our method were 100% (95% CI, 54.1%-100%) and 100% (78.2%-100%), respectively. CONCLUSION Our method had a favorable performance for noninvasively detecting fetal FGFR3 mutations in maternal plasma, highlighting its promising value in developing a noninvasive prenatal test for de novo and paternally inherited disorders.
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Affiliation(s)
- Yuan Ren
- Department of Obstetrics and Gynecology, Chinese PLA General Hospital, Beijing, China
| | - Jia Zhao
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Ruibing Li
- Department of Obstetrics and Gynecology, Chinese PLA General Hospital, Beijing, China
| | | | - Shufang Jiang
- Department of Obstetrics and Gynecology, Chinese PLA General Hospital, Beijing, China
| | - Honghui Zhou
- Department of Obstetrics and Gynecology, Chinese PLA General Hospital, Beijing, China
| | | | - Yanqin You
- Department of Obstetrics and Gynecology, Chinese PLA General Hospital, Beijing, China
| | - Fang Chen
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Ya Gao
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Yuanguang Meng
- Department of Obstetrics and Gynecology, Chinese PLA General Hospital, Beijing, China
| | - Yanping Lu
- Department of Obstetrics and Gynecology, Chinese PLA General Hospital, Beijing, China
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138
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Ramdaney A, Hoskovec J, Harkenrider J, Soto E, Murphy L. Clinical experience with sex chromosome aneuploidies detected by noninvasive prenatal testing (NIPT): Accuracy and patient decision-making. Prenat Diagn 2018; 38:841-848. [PMID: 30068017 DOI: 10.1002/pd.5339] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 06/21/2018] [Accepted: 07/21/2018] [Indexed: 12/14/2022]
Abstract
OBJECTIVE The objectives of the study are to assess the accuracy of noninvasive prenatal testing (NIPT) for sex chromosome aneuploidies (SCAs) and to investigate patient decision-making in clinical practice. STUDY DESIGN This is a retrospective cohort study review of positive NIPT results for SCAs from January 2013 to September 2017. RESULTS Of the 136 positive NIPT results for SCAs, 73 (53.7%) were positive for 45,X, 62 (45.6%) were a sex chromosome trisomy, and 1 was a sex chromosome tetrasomy. Of the 134 viable pregnancies, 46 (34.3%) elected to pursue prenatal diagnosis. Fewer women underwent invasive prenatal testing when counseled regarding a positive NIPT for monosomy X in the presence of suggestive ultrasound findings (4/23; 17.4%) compared with those who had a positive NIPT result without ultrasound findings (24/46, 52.2%). Abnormal karyotypes consistent with the NIPT result were confirmed in 30/64 (46.9%). Even in the context of ultrasound abnormalities, there was not 100% concordance. CONCLUSIONS The majority (88/134; 65.7%) of patients in our cohort declined prenatal diagnosis even in the presence of associated ultrasound findings. Comprehensive pretest and posttest counseling is recommended and should address the importance of confirmatory testing and benefits of early diagnosis. Practice guidelines are needed to address provider responsibilities about postnatal testing.
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Affiliation(s)
- Aarti Ramdaney
- Department of Obstetrics, Gynecology and Reproductive Sciences, McGovern Medical School at the University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Jennifer Hoskovec
- Department of Obstetrics, Gynecology and Reproductive Sciences, McGovern Medical School at the University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Jacqueline Harkenrider
- Department of Obstetrics, Gynecology and Reproductive Sciences, McGovern Medical School at the University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Eleazar Soto
- Department of Obstetrics, Gynecology and Reproductive Sciences, McGovern Medical School at the University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Lauren Murphy
- Department of Obstetrics, Gynecology and Reproductive Sciences, McGovern Medical School at the University of Texas Health Science Center at Houston, Houston, TX, USA
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139
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Genome-wide detection of additional fetal chromosomal abnormalities by cell-free DNA testing of 15,626 consecutive pregnant women. SCIENCE CHINA-LIFE SCIENCES 2018; 62:215-224. [PMID: 30076564 DOI: 10.1007/s11427-017-9344-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 06/21/2018] [Indexed: 12/18/2022]
Abstract
Cell-free DNA (cfDNA) testing for common fetal trisomies (T21, T18, T13) is highly effective. However, the usefulness of cfDNA testing in detecting other chromosomal abnormalities is unclear. We evaluated the performance of cfDNA testing for genome-wide abnormalities, and analyzed the incremental yield by reporting extra abnormalities. We performed genome-wide cfDNA testing in 15,626 consecutive pregnancies prospectively enrolled in this study. cfDNA testing results were reported and counseling was given depending on the presence of extra chromosomal abnormalities. cfDNA testing identified 190 cases (1.2%) of chromosomal abnormalities including 100 common trisomies and 90 additional abnormalities. By expanding the cfDNA reporting range to genome-wide abnormalities, the false positive rate increased to 0.39% (P<0.001) and positive predictive value (PPV) was reduced to 65.58% (P=0.42). However, the detection yield increased from 0.44% to 0.65% (P=0.014), and cfDNA testing detected 38.61% (39/101) additional abnormalities with no ultrasound and biochemical screening findings. cfDNA testing outperformed biochemical screening by showing 60 times higher true positive rate and fewer false negative results. Genome-wide cfDNA testing significantly increased the diagnostic yield by detecting extra abnormalities, especially those without diagnostic indications. Genome-wide cfDNA testing has fewer false positive and false negative results compared with biochemical screening.
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140
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Vičić A, Hafner T, Bekavac Vlatković I, Korać P, Habek D, Stipoljev F. Prenatal diagnosis of Down syndrome: A 13-year retrospective study. Taiwan J Obstet Gynecol 2018; 56:731-735. [PMID: 29241910 DOI: 10.1016/j.tjog.2017.10.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/05/2017] [Indexed: 10/18/2022] Open
Abstract
OBJECTIVE The aim of this study is to summarize the experience on prenatal diagnosis of Down syndrome. MATERIALS AND METHODS The study includes a retrospective data analysis of 157 prenatally detected cases of Down syndrome, routinely diagnosed among 6448 prenatal investigations performed during a 13-year period (2002-2014) in a single tertiary center. RESULTS The prevalence of diagnosed Down syndrome cases was 2.4%. Maternal age alone was indication for prenatal diagnosis in 47 cases (45.2%), increased first-/second-trimester biochemical screening test in 34 cases (21.7%), abnormal ultrasound examination in 69 cases (43.9%), positive familial history for chromosomal abnormalities in four cases, and high risk for trisomy 21 revealed by cell-free DNA testing in three cases. Ultrasound anomalies were present in total of 94 fetuses (59.8%). The most common abnormality was cystic hygroma found in 46 cases (29.3%). A regular form of Down syndrome (trisomy 21) was found in 147 cases (93.6%), Robertsonian translocation in six cases (3.8%), and mosaic form in four cases (2.6%). CONCLUSION In prenatal diagnosis of Down syndrome noninvasive screening methods are important for estimation of individual risks, in both, young population of woman and older mothers, while conventional and molecular cytogenetic methods are essential for definite diagnosis and proper genetic counseling.
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Affiliation(s)
- Ana Vičić
- Department of Obstetrics and Gynecology, Clinical Hospital "Sveti Duh", Zagreb, Croatia.
| | - Tomislav Hafner
- Department of Obstetrics and Gynecology, Clinical Hospital "Sveti Duh", Zagreb, Croatia
| | | | - Petra Korać
- Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Dubravko Habek
- Department of Obstetrics and Gynecology, Clinical Hospital "Sveti Duh", Zagreb, Croatia
| | - Feodora Stipoljev
- Department of Obstetrics and Gynecology, Clinical Hospital "Sveti Duh", Zagreb, Croatia; Faculty of Medicine Osijek, Josip Juraj Strossmayer University of Osijek, Osijek, Croatia
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141
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Abstract
New genetic tests have rapidly entered clinical care with little consistency in laboratory testing and reporting. Non-invasive prenatal screening using cell free DNA (cfDNA) may either screen for common aneuploidies alone or include chromosomal microdeletions. All cfDNA screening tests have false positives and false negatives, and accordingly laboratories should report positive and negative predictive values. In addition, since fetal fraction plays a significant role in the reliability of results, this should also be reported with all test results. Chromosomal microarray addresses significant clinically relevant information beyond that detected with standard karyotype testing but may, in less than one percent of cases, result in a variant of uncertain significance (VUS). Laboratories should indicate their policies for reporting these VUS findings. In addition, physicians using this testing should be aware of the advantages and disadvantages of the laboratory platforms. Whole-exome and whole-genome sequencing are just entering clinical care and issues of VUS, incidental findings, and phenotype/genotype correlations need to be investigated before these techniques enter routine clinical care.
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Affiliation(s)
- Karen Wou
- Division of Medical Genetics, Department of Pediatrics, Columbia University, United States
| | - Wendy K Chung
- Division of Medical Genetics, Department of Pediatrics, Columbia University, United States
| | - Ronald J Wapner
- Division of Reproductive Genetics, Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, 622 W. 168th St, PH-16-66, New York, NY 10032, United States.
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142
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Kim SY, Lee SM, Jun JK, Han YJ, Kim MH, Shim JY, Lee MY, Oh SY, Lee J, Kim SH, Cha DH, Cho GJ, Kwon HS, Kim BJ, Park MH, Cho HY, Ko HS, Ahn J, Ryu HM. Prospective observations study protocol to investigate cost-effectiveness of various prenatal test strategies after the introduction of noninvasive prenatal testing. BMC Pregnancy Childbirth 2018; 18:307. [PMID: 30041617 PMCID: PMC6056912 DOI: 10.1186/s12884-018-1930-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 06/28/2018] [Indexed: 01/15/2023] Open
Abstract
Background Among the non-invasive screening methods for the identification of fetal aneuploidy, NIPT (non-invasive prenatal testing) shows the highest sensitivity and specificity in high-risk pregnancies. Due to the low false positive rate of NIPT, it is assumed that the implementation of NIPT as a primary screening method may reduce the number of invasive fetal tests and result in a similar or lowered cost in the overall detection of Down syndrome. However, most previous studies are based on theoretical economic analysis. This study aims to determine the cost effectiveness of various prenatal test strategies, including NIPT, in real clinical settings in both low risk and high risk pregnancies. Methods/design In this prospective observational study, women (< 24 weeks) with singleton or twin pregnancies will be enrolled in 12 different healthcare institutions. The participants will be grouped based on the risks of fetal chromosomal abnormalities and will be counseled on the various screening or diagnostic methods, including NIPT, according to the aneuploidy risk. The final decision on screening or diagnostic methods will be made by patients after counseling. Questionnaires regarding factors affecting the decision on prenatal test will be answered by the participants and physicians. The economic analysis on final total costs will be compared according to the various prenatal test strategies. Discussion The results of present study are expected to have a significant impact on national policies in determining Korean prenatal screening test strategies and to help in developing novel and effective prenatal screening tests in the future. Electronic supplementary material The online version of this article (10.1186/s12884-018-1930-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- So Yeon Kim
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Seung Mi Lee
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul, Republic of Korea.
| | - Jong Kwan Jun
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - You Jung Han
- Department of Obstetrics and Gynecology, Cheil General Hospital and Women's Healthcare Center, Dankook University College of Medicine, Seoul, Republic of Korea
| | - Min Hyoung Kim
- Department of Obstetrics and Gynecology, Cheil General Hospital and Women's Healthcare Center, Dankook University College of Medicine, Seoul, Republic of Korea
| | - Jae-Yoon Shim
- Department of Obstetrics and Gynecology, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Republic of Korea
| | - Mi-Young Lee
- Department of Obstetrics and Gynecology, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Republic of Korea
| | - Soo-Young Oh
- Department of Obstetrics and Gynecology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - JoonHo Lee
- Department of Obstetrics and Gynecology, Institute of Women's Life Medical Science, Yonsei University College of Medicine, Yonsei University Health System, Seoul, Republic of Korea
| | - Soo Hyun Kim
- Department of Obstetrics and Gynecology, CHA Gangnam Medical Center, CHA University, Seoul, Republic of Korea
| | - Dong Hyun Cha
- Department of Obstetrics and Gynecology, CHA Gangnam Medical Center, CHA University, Seoul, Republic of Korea
| | - Geum Joon Cho
- Department of Obstetrics and Gynecology, Korea University College of Medicine, Seoul, Republic of Korea
| | - Han-Sung Kwon
- Department of Obstetrics and Gynecology, Konkuk University School of Medicine, Seoul, Republic of Korea
| | - Byoung Jae Kim
- Department of Obstetrics and Gynecology, Seoul Metropolitan Government Seoul National University Boramae Medical Center, Seoul, Republic of Korea
| | - Mi Hye Park
- Department of Obstetrics and Gynecology, Ewha Womans University, Seoul, Republic of Korea
| | - Hee Young Cho
- Department of Obstetrics and Gynecology, Bundang CHA Medical Center, CHA University School of Medicine, Seongnam, Republic of Korea
| | - Hyun Sun Ko
- Department of Obstetrics and Gynecology, Catholic University of Korea College of Medicine, Seoul, Republic of Korea
| | - Jeonghoon Ahn
- Department of Health Convergence, Ewha Womans University, Seoul, Republic of Korea
| | - Hyun Mee Ryu
- Department of Obstetrics and Gynecology, Cheil General Hospital and Women's Healthcare Center, Dankook University College of Medicine, Seoul, Republic of Korea.
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143
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Huang T, Meschino WS, Rashid S, Dennis A, Mak-Tam E, Cuckle H. Enhanced First Trimester Aneuploidy Screening with Placental Growth Factor and Alpha Feto-Protein: Detection of Trisomies 18 and 13. JOURNAL OF OBSTETRICS AND GYNAECOLOGY CANADA 2018; 40:1295-1301. [PMID: 30025867 DOI: 10.1016/j.jogc.2018.01.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 01/03/2018] [Accepted: 01/03/2018] [Indexed: 01/19/2023]
Abstract
OBJECTIVES To assess the performance of first trimester combined screening (FTS) when enhanced with placental growth factor and alpha feto-protein in the detection of trisomies 18 and 13. METHODS A retrospective case-control study. Marker parameters were derived using frozen serum samples. Multivariate Gaussian modelling predicted the detection rate (DR) and false-positive rate (FPR) for trisomies 18 and 13 with FTS and enhanced first trimester screening (eFTS) using the risk of trisomy 21 alone and an additional risk cut-off for trisomy 18, or trisomies 18 or 13. RESULTS There were 83 trisomy 18, 22 trisomy 13, and 588 controls. The median placental growth factor levels in trisomies 18 and 13 were 0.75 and 0.65 multiple of the median of controls, respectively (both P < 0.0001). There were no statistically significant differences in alpha feto-protein levels. Modelling predicts that using a trisomy 21 risk cut-off alone, at FPR of 3%, eFTS increases the DR for trisomies 18 and 13 by 0.6-0.8% compared with FTS. Additionally using a trisomy 18 risk cut-off, at an extra FPR of 0.2%, eFTS increased the DR by 0.6-0.9% over FTS; using a trisomy 18 or 13 risk cut-off did not further increase detection for FTS or eFTS. The increase in DR was greater at higher FPR. CONCLUSION eFTS increases the detection of trisomies 18 and 13 to a small extent.
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Affiliation(s)
- Tianhua Huang
- Genetics Program, North York General Hospital, Toronto, ON; Better Outcomes Registry & Network (BORN) Ontario, Ottawa, ON; The Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON; Department of Obstetrics & Gynaecology, University of Toronto, Toronto, ON.
| | - Wendy S Meschino
- Genetics Program, North York General Hospital, Toronto, ON; Department of Paediatrics, University of Toronto, Toronto, ON
| | - Shamim Rashid
- Genetics Program, North York General Hospital, Toronto, ON
| | - Alan Dennis
- Genetics Program, North York General Hospital, Toronto, ON
| | - Ellen Mak-Tam
- Genetics Program, North York General Hospital, Toronto, ON
| | - Howard Cuckle
- Obstetrics and Gynecology, Columbia University Medical Center, New York, NY
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144
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Malcher C, Yamamoto GL, Burnham P, Ezquina SAM, Lourenço NCV, Balkassmi S, Antonio DSM, Hsia GSP, Gollop T, Pavanello RC, Lopes MA, Bakker E, Zatz M, Bertola D, Vlaminck ID, Passos-Bueno MR. Development of a comprehensive noninvasive prenatal test. Genet Mol Biol 2018; 41:545-554. [PMID: 30043834 PMCID: PMC6136382 DOI: 10.1590/1678-4685-gmb-2017-0177] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 12/26/2017] [Indexed: 12/30/2022] Open
Abstract
Our aim was to develop and apply a comprehensive noninvasive prenatal test (NIPT) by using high-coverage targeted next-generation sequencing to estimate fetal fraction, determine fetal sex, and detect trisomy and monogenic disease without parental genotype information. We analyzed 45 pregnancies, 40 mock samples, and eight mother-child pairs to generate 35 simulated datasets. Fetal fraction (FF) was estimated based on analysis of the single nucleotide polymorphism (SNP) allele fraction distribution. A Z-score was calculated for trisomy of chromosome 21 (T21), and fetal sex detection. Monogenic disease detection was performed through variant analysis. Model validation was performed using the simulated datasets. The novel model to estimate FF was robust and accurate (r2= 0.994, p-value < 2.2e-16). For samples with FF > 0.04, T21 detection had 100% sensitivity (95% CI: 63.06 to 100%) and 98.53% specificity (95% CI: 92.08 to 99.96%). Fetal sex was determined with 100% accuracy. We later performed a proof of concept for monogenic disease diagnosis of 5/7 skeletal dysplasia cases. In conclusion, it is feasible to perform a comprehensive NIPT by using only data from high coverage targeted sequencing, which, in addition to detecting trisomies, also make it possible to identify pathogenic variants of the candidate genes for monogenic diseases.
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Affiliation(s)
- Carolina Malcher
- Centro de Pesquisa sobre o Genoma Humano e Células-Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Guilherme L Yamamoto
- Centro de Pesquisa sobre o Genoma Humano e Células-Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Philip Burnham
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Suzana A M Ezquina
- Centro de Pesquisa sobre o Genoma Humano e Células-Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Naila C V Lourenço
- Centro de Pesquisa sobre o Genoma Humano e Células-Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Sahilla Balkassmi
- Department of Clinical Genetics, Laboratory for Diagnostic Genome Analysis (LDGA), Leiden University Medical Center, Leiden, The Netherlands
| | - David S Marco Antonio
- Centro de Pesquisa sobre o Genoma Humano e Células-Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Gabriella S P Hsia
- Centro de Pesquisa sobre o Genoma Humano e Células-Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Thomaz Gollop
- Faculdade de Medicina de Jundiaí, Jundiaí, SP, Brazil
| | - Rita C Pavanello
- Centro de Pesquisa sobre o Genoma Humano e Células-Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Marco Antonio Lopes
- Departamento de Obstetrícia e Ginecologia, Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Egbert Bakker
- Department of Clinical Genetics, Laboratory for Diagnostic Genome Analysis (LDGA), Leiden University Medical Center, Leiden, The Netherlands
| | - Mayana Zatz
- Centro de Pesquisa sobre o Genoma Humano e Células-Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Débora Bertola
- Centro de Pesquisa sobre o Genoma Humano e Células-Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Iwijn De Vlaminck
- Centro de Pesquisa sobre o Genoma Humano e Células-Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Maria Rita Passos-Bueno
- Centro de Pesquisa sobre o Genoma Humano e Células-Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
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145
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Non-invasive prenatal testing: use of cell-free fetal DNA in Down syndrome screening. Br J Gen Pract 2018; 67:298-299. [PMID: 28663415 DOI: 10.3399/bjgp17x691625] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
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146
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Doğan M, Eröz R, Bolu S, Yüce H. Evaluation of Karyotype Composition of Our Turner Syndrome Patients with Their Application Complaints and Anthropometric Data. KONURALP TIP DERGISI 2018. [DOI: 10.18521/ktd.414179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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147
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Non-invasive prenatal aneuploidy testing: Critical diagnostic performance parameters predict sample z-score values. Clin Biochem 2018; 59:69-77. [PMID: 29958880 DOI: 10.1016/j.clinbiochem.2018.06.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 06/21/2018] [Accepted: 06/22/2018] [Indexed: 01/01/2023]
Abstract
OBJECTIVES Non-invasive prenatal aneuploidy testing (NIPT) by next-generation sequencing of circulating cell-free DNA in maternal plasma relies on chromosomal ratio (chrratio) measurements to detect aneuploid values that depart from euploid ratios. Diagnostic performances are known to depend on the fraction of fetal DNA (FF) present in maternal plasma, although how this translates into specific quantitative changes in specificity/positive predictive values and which other variables might also be important is not well understood. DESIGN & METHODS To explore this issue, theoretical relationships between FF and various measures of diagnostic performances were assessed for a range of parameter values. Empirical data from three NIPT assays were then used to validate theoretical calculations. RESULTS For a given positivity threshold, dramatic changes in specificity and positive predictive values (PPV) as a function of both FF and the coefficient of variation (CV) of the chrratio measurement were observed. Theoretically predicted and observed chrratio z-scores agreed closely, confirming the determinant impact of small changes in both FF and chrratio CV. CONCLUSIONS Evaluation of NIPT assay performances therefore requires knowledge of the FF distribution in the population in which the test is intended to be used and, in particular, of the precise value of the assay chrratio CV for each chromosome or genomic region of interest. Laboratories offering NIPT testing should carefully measure these parameters to ensure test reliability and clinical usefulness in interpreting individual patients' results.
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148
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Eswarachari V, Kadam P, Movva S, Lingaiah S, Akther RM, Kidangan FX, Gowda KC, Golakoti RRK, Lall M, Mahajan S, Saviour P, Puri R, Verma IC, Vedam RL. Noninvasive prenatal testing (NIPT) detects variant of Turner syndrome not detectable by fluorescent in situ hybridization. J Matern Fetal Neonatal Med 2018; 32:4177-4180. [PMID: 29793366 DOI: 10.1080/14767058.2018.1481383] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
Introduction: Noninvasive prenatal testing (NIPT) is a reliable screening method for fetal aneuploidy detection of trisomy 18, 13, 21 along with few sex chromosome abnormalities monosomy X, XXX, XXY (Klinefelter), XYY (Jacob) syndromes and certain microdeletions which include cri-du-chat, DiGeorge, 1p36, Angelman, and Prader-Willi syndromes in comparison to the available screening methods. Prenatal screening of Turners syndrome is possible by ultrasound in certain conditions only. Recently benefits of early detection and treatment of Turners syndrome has been emphasized, enforcing on accurate and early screening prenatally.Case details: The current case emphasizes on the reliability of NIPT testing which comes with an advantage of early screening. A 24-year-old primi gravida was referred for NIPT as she tested for high risk on biochemical screening. The Panorama™ NIPT results showed low risk for trisomies, 21, 18, and 13 but high risk of monosomy X and was advised confirmatory amniocentesis. The fluorescence in situ hybridization (FISH) report revealed no numerical abnormality detected for any of the five chromosomes tested. On receiving this discordant report, the sample was rerun for NIPT, to rule out any laboratory-related issues. The result obtained on a rerun was consistent with the first report and showed monosomy X again. The karyotype report was available three weeks later and a rare variant of Turners syndrome was identified.Discussion: Panorama™ NIPT considers single nucleotide polymorphisms spread across the chromosomes for analysis, different variants of aneuploidy can be picked up in comparison to FISH, similar to the current case wherein it could not as it was a centromeric probe. Reported first case of X chromosome variant detected by NIPT confirmed by karyotyping, missed by FISH.
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Affiliation(s)
| | - Priya Kadam
- Medgenome Labs Ltd., Narayana Nethralaya, Bangalore, India
| | - Sireesha Movva
- Medgenome Labs Ltd., Narayana Nethralaya, Bangalore, India
| | | | - Riyaz M Akther
- Medgenome Labs Ltd., Narayana Nethralaya, Bangalore, India
| | | | - Kiran C Gowda
- Medgenome Labs Ltd., Narayana Nethralaya, Bangalore, India
| | | | - Meena Lall
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Surbhi Mahajan
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Pushpa Saviour
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Ratna Puri
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Ishwar C Verma
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
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149
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Non invasive prenatal diagnosis of fetal aneuploidy using cell free fetal DNA. Eur J Obstet Gynecol Reprod Biol 2018; 225:5-8. [DOI: 10.1016/j.ejogrb.2018.03.033] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 02/13/2018] [Accepted: 03/19/2018] [Indexed: 01/21/2023]
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150
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Dhamankar R, Valenti E, Hedriana HL. Non-invasive Prenatal Testing: A Unique Approach with Single Nucleotide Polymorphism. JOURNAL OF FETAL MEDICINE 2018. [DOI: 10.1007/s40556-018-0167-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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