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Biggio JR. Prenatal screening for fetal aneuploidy: time to examine where we are and where we are going. Am J Obstet Gynecol 2016; 214:673-5. [PMID: 27235718 DOI: 10.1016/j.ajog.2016.02.038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 02/16/2016] [Indexed: 11/27/2022]
Affiliation(s)
- Joseph R Biggio
- Department of Obstetrics and Gynecology, Center for Women's Reproductive Health, University of Alabama at Birmingham, Birmingham, AL.
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Norton ME, Baer RJ, Wapner RJ, Kuppermann M, Jelliffe-Pawlowski LL, Currier RJ. Cell-free DNA vs sequential screening for the detection of fetal chromosomal abnormalities. Am J Obstet Gynecol 2016; 214:727.e1-6. [PMID: 26709085 DOI: 10.1016/j.ajog.2015.12.018] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 11/19/2015] [Accepted: 12/14/2015] [Indexed: 01/28/2023]
Abstract
BACKGROUND Sequential and cell-free DNA (cfDNA) screening are both tests for the common aneuploidies. Although cfDNA has a greater detection rate (DR) for trisomy 21, sequential screening also can identify risk for other aneuploidies. The comparative DR for all chromosomal abnormalities is unknown. OBJECTIVE To compare sequential and cfDNA screening for detection of fetal chromosomal abnormalities in a general prenatal cohort. STUDY DESIGN The performance of sequential screening for the detection of chromosome abnormalities in a cohort of patients screened through the California Prenatal Screening Program with estimated due dates between August 2009 and December 2012 was compared with the estimated DRs and false-positive rates (FPRs) of cfDNA screening if used as primary screening in this same cohort. DR and FPR for cfDNA screening were abstracted from the published literature, as were the rates of "no results" in euploid and aneuploid cases. Chromosome abnormalities in the entire cohort were categorized as detectable (trisomies 13, 18, and 21, and sex chromosome aneuploidy), or not detectable (other chromosome abnormalities) by cfDNA screening. DR and FPR were compared for individual and all chromosome abnormalities. DR and FPR for the cohort were compared if "no results" cases were considered "screen negative" or "screen positive" for aneuploidy. DR and FPR rates were compared by use of the Fisher exact test. RESULTS Of 452,901 women who underwent sequential screening during the time period of the study, 2575 (0.57%) had a fetal chromosomal abnormality; 2101 were detected for a DR of 81.6%, and 19,929 euploid fetuses had positive sequential screening for an FPR rate of 4.5%. If no results cases were presumed normal, cfDNA screening would have detected 1820 chromosome abnormalities (70.7%) with an FPR of 0.7%. If no results cases were considered screen positive, 1985 (77.1%) cases would be detected at a total screen positive rate of 3.7%. In either case, the detection rate of sequential screening for all aneuploidies in the cohort was greater than cfDNA (P<.0001). CONCLUSION For primary population screening, cfDNA provides lower DR than sequential screening if considering detection of all chromosomal abnormalities. Assuming that no results cfDNA cases are high-risk improves cfDNA detection but with a greater FPR. cfDNA should not be adopted as primary screening without further evaluation of the implications for detection of all chromosomal abnormalities and how to best evaluate no results cases.
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Benn P. Posttest risk calculation following positive noninvasive prenatal screening using cell-free DNA in maternal plasma. Am J Obstet Gynecol 2016; 214:676.e1-7. [PMID: 26772793 DOI: 10.1016/j.ajog.2016.01.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 12/31/2015] [Accepted: 01/04/2016] [Indexed: 11/18/2022]
Abstract
Noninvasive prenatal screening (NIPS) for fetal chromosome defects has high sensitivity and specificity but is not fully diagnostic. In response to a desire to provide more information to individual women with positive NIPS results, 2 online calculators have been developed to calculate posttest risk (PTR). Use of these calculators is critically reviewed. There is a mathematically dictated requirement for a precise estimate for the specificity to provide an accurate PTR. This is illustrated by showing that a 0.1% decrease in the value for specificities for trisomies 21, 18, and 13 can reduce the PTR from 79-64% for trisomy 21, 39-27% for trisomy 18, and 21-13% for trisomy 13, respectively. Use of the calculators assumes that sensitivity and specificity are constant for all women receiving the test but there is evidence that discordancy between screening results and true fetal karyotype is more common for older women. Use of an appropriate value for the prior risk is also important and for rare disorders there is considerable uncertainty regarding prevalence. For example, commonly used rates for trisomy 13, monosomy-X, triploidy, and 22q11.2 deletion syndrome can vary by >4-fold and this can translate into large differences in PTR. When screening for rare disorders, it may not be possible to provide a reliable PTR if there is uncertainty over the false-positive rate and/or prevalence. These limitations, per se, do not negate the value of screening for rare conditions. However, counselors need to carefully weigh the validity of PTR before presenting them to patients. Additional epidemiologic and NIPS outcome data are needed.
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Affiliation(s)
- Peter Benn
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT.
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Mackie FL, Hemming K, Allen S, Morris RK, Kilby MD. The accuracy of cell-free fetal DNA-based non-invasive prenatal testing in singleton pregnancies: a systematic review and bivariate meta-analysis. BJOG 2016; 124:32-46. [DOI: 10.1111/1471-0528.14050] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/09/2016] [Indexed: 12/18/2022]
Affiliation(s)
- FL Mackie
- Centre for Women's & Newborn Health and the Institute of Metabolism and Systems Research; University of Birmingham; Birmingham UK
| | - K Hemming
- Public Health, Epidemiology and Biostatistics; Institute of Applied Health Sciences; University of Birmingham; Birmingham UK
| | - S Allen
- West Midlands Regional Genetics Laboratory; Birmingham Women's Hospital NHS Foundation Trust; Birmingham UK
| | - RK Morris
- Centre for Women's & Newborn Health and the Institute of Metabolism and Systems Research; University of Birmingham; Birmingham UK
- Fetal Medicine Centre; Birmingham Women's Hospital NHS Foundation Trust; Birmingham UK
| | - MD Kilby
- Centre for Women's & Newborn Health and the Institute of Metabolism and Systems Research; University of Birmingham; Birmingham UK
- Fetal Medicine Centre; Birmingham Women's Hospital NHS Foundation Trust; Birmingham UK
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105
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Gerundino F, Giachini C, Contini E, Benelli M, Marseglia G, Giuliani C, Marin F, Nannetti G, Lisi E, Sbernini F, Periti E, Cordisco A, Colosi E, D'ambrosio V, Mazzi M, Rossi M, Staderini L, Minuti B, Pelo E, Cicatiello R, Maruotti GM, Sglavo G, Conti A, Frusconi S, Pescucci C, Torricelli F. Validation of a method for noninvasive prenatal testing for fetal aneuploidies risk and considerations for its introduction in the Public Health System. J Matern Fetal Neonatal Med 2016; 30:710-716. [PMID: 27226231 DOI: 10.1080/14767058.2016.1183633] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
OBJECTIVE The aim of this study was to validate noninvasive prenatal testing (NIPT) for fetal aneuploidies by whole-genome massively parallel sequencing (MPS). METHODS MPS was performed on cell-free DNA (cfDNA) isolated from maternal plasma in two groups: a first set of 186 euploid samples and a second set of 195 samples enriched of aneuploid cases (n = 69); digital PCR for fetal fraction (FF) assessment was performed on 178/381 samples. Cases with <10 × 106 reads (n = 54) were excluded for downstream data analysis. Follow-up data (invasive testing results or neonatal information) were available for all samples. Performances in terms of specificity/sensitivity and Z-score distributions were evaluated. RESULTS All positive samples for trisomy 21 (T21) (n = 43), trisomy 18 (T18) (n = 6) and trisomy 13 (T13) (n = 7) were correctly identified (sensitivity: 99.9%); 5 false positive results were reported: 3 for T21 (specificity = 98.9%) and 2 for T13 (specificity = 99.4%). Besides FF, total cfDNA concentration seems another important parameter for MPS, since it influences the number of reads. CONCLUSIONS The overall test accuracy allowed us introducing NIPT for T21, T18 and T13 as a clinical service for pregnant women after 10 + 4 weeks of gestation. Sex chromosome aneuploidy assessment needs further validation due to the limited number of aneuploid cases in this study.
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Affiliation(s)
| | - Claudia Giachini
- a Diagnostic Genetics Unit, Careggi University Hospital , Firenze , Italy
| | - Elisa Contini
- a Diagnostic Genetics Unit, Careggi University Hospital , Firenze , Italy
| | - Matteo Benelli
- a Diagnostic Genetics Unit, Careggi University Hospital , Firenze , Italy
| | | | - Costanza Giuliani
- a Diagnostic Genetics Unit, Careggi University Hospital , Firenze , Italy
| | - Francesca Marin
- a Diagnostic Genetics Unit, Careggi University Hospital , Firenze , Italy
| | - Genni Nannetti
- a Diagnostic Genetics Unit, Careggi University Hospital , Firenze , Italy
| | - Ermanna Lisi
- a Diagnostic Genetics Unit, Careggi University Hospital , Firenze , Italy
| | - Fiammetta Sbernini
- a Diagnostic Genetics Unit, Careggi University Hospital , Firenze , Italy
| | - Enrico Periti
- b Prenatal Diagnosis Unit, Azienda Sanitaria Firenze , Firenze , Italy
| | - Adalgisa Cordisco
- b Prenatal Diagnosis Unit, Azienda Sanitaria Firenze , Firenze , Italy
| | - Enrico Colosi
- c Department of Obstetrics and Gynecology , Reproductive Medicine and Prenatal Care Unit, Misericordia Hospital , Grosseto , Italy
| | - Valentina D'ambrosio
- c Department of Obstetrics and Gynecology , Reproductive Medicine and Prenatal Care Unit, Misericordia Hospital , Grosseto , Italy
| | - Marta Mazzi
- d Division of Molecular and Reproduction Diagnostics , Misericordia Hospital , Grosseto , Italy
| | - Maya Rossi
- d Division of Molecular and Reproduction Diagnostics , Misericordia Hospital , Grosseto , Italy
| | - Lucia Staderini
- a Diagnostic Genetics Unit, Careggi University Hospital , Firenze , Italy
| | - Barbara Minuti
- a Diagnostic Genetics Unit, Careggi University Hospital , Firenze , Italy
| | - Elisabetta Pelo
- e Medical Genetics Unit, Azienda Sanitaria Firenze , Firenze , Italy
| | - Rita Cicatiello
- f Department of Molecular Medicine and Medical Biotechnology University "Federico II" , Napoli , Italy
| | | | - Gabriella Sglavo
- g Department of Gynecology and Obstetrics , University "Federico II" , Napoli , Italy
| | - Anna Conti
- f Department of Molecular Medicine and Medical Biotechnology University "Federico II" , Napoli , Italy
| | - Sabrina Frusconi
- a Diagnostic Genetics Unit, Careggi University Hospital , Firenze , Italy
| | - Chiara Pescucci
- a Diagnostic Genetics Unit, Careggi University Hospital , Firenze , Italy
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106
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Song Y, Zhou X, Huang S, Li X, Qi Q, Jiang Y, Liu Y, Ma C, Li Z, Xu M, Cram DS, Liu J. Quantitation of fetal DNA fraction in maternal plasma using circulating single molecule amplification and re-sequencing technology (cSMART). Clin Chim Acta 2016; 456:151-156. [DOI: 10.1016/j.cca.2016.03.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 03/08/2016] [Accepted: 03/11/2016] [Indexed: 10/22/2022]
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Arbabi A, Rampášek L, Brudno M. Cell-free DNA fragment-size distribution analysis for non-invasive prenatal CNV prediction. Bioinformatics 2016; 32:1662-9. [PMID: 27153615 DOI: 10.1093/bioinformatics/btw178] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 03/31/2016] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Non-invasive detection of aneuploidies in a fetal genome through analysis of cell-free DNA circulating in the maternal plasma is becoming a routine clinical test. Such tests, which rely on analyzing the read coverage or the allelic ratios at single-nucleotide polymorphism (SNP) loci, are not sensitive enough for smaller sub-chromosomal abnormalities due to sequencing biases and paucity of SNPs in a genome. RESULTS We have developed an alternative framework for identifying sub-chromosomal copy number variations in a fetal genome. This framework relies on the size distribution of fragments in a sample, as fetal-origin fragments tend to be smaller than those of maternal origin. By analyzing the local distribution of the cell-free DNA fragment sizes in each region, our method allows for the identification of sub-megabase CNVs, even in the absence of SNP positions. To evaluate the accuracy of our method, we used a plasma sample with the fetal fraction of 13%, down-sampled it to samples with coverage of 10X-40X and simulated samples with CNVs based on it. Our method had a perfect accuracy (both specificity and sensitivity) for detecting 5 Mb CNVs, and after reducing the fetal fraction (to 11%, 9% and 7%), it could correctly identify 98.82-100% of the 5 Mb CNVs and had a true-negative rate of 95.29-99.76%. AVAILABILITY AND IMPLEMENTATION Our source code is available on GitHub at https://github.com/compbio-UofT/FSDA CONTACT: : brudno@cs.toronto.edu.
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Affiliation(s)
- Aryan Arbabi
- Department of Computer Science, University of Toronto, Toronto, ON M5S 2E4, Canada Centre for Computational Medicine, Hospital for Sick Children, Toronto, ON M5G 1L7, Canada and
| | - Ladislav Rampášek
- Department of Computer Science, University of Toronto, Toronto, ON M5S 2E4, Canada Genetics and Genome Biology, Hospital for Sick Children, Toronto, ON M5G 1L7, Canada
| | - Michael Brudno
- Department of Computer Science, University of Toronto, Toronto, ON M5S 2E4, Canada Centre for Computational Medicine, Hospital for Sick Children, Toronto, ON M5G 1L7, Canada and Genetics and Genome Biology, Hospital for Sick Children, Toronto, ON M5G 1L7, Canada
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108
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Yaron Y. The implications of non-invasive prenatal testing failures: a review of an under-discussed phenomenon. Prenat Diagn 2016; 36:391-6. [DOI: 10.1002/pd.4804] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 02/08/2016] [Accepted: 02/29/2016] [Indexed: 12/14/2022]
Affiliation(s)
- Yuval Yaron
- Genetic Institute, Tel Aviv Sourasky Medical Center; Tel Aviv University; Tel Aviv Israel
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109
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Ryan A, Hunkapiller N, Banjevic M, Vankayalapati N, Fong N, Jinnett KN, Demko Z, Zimmermann B, Sigurjonsson S, Gross SJ, Hill M. Validation of an Enhanced Version of a Single-Nucleotide Polymorphism-Based Noninvasive Prenatal Test for Detection of Fetal Aneuploidies. Fetal Diagn Ther 2016; 40:219-223. [PMID: 27028530 DOI: 10.1159/000442931] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 11/12/2015] [Indexed: 11/19/2022]
Abstract
OBJECTIVE To validate an updated version (Version 2) of a single-nucleotide polymorphism (SNP)-based noninvasive prenatal test (NIPT) and to determine the likelihood of success when testing for fetal aneuploidies following a redraw. METHODS Version 2 was analytically validated using 587 plasma samples with known genotype (184 trisomy 21, 37 trisomy 18, 15 trisomy 13, 9 monosomy X, 4 triploidy and 338 euploid). Sensitivity, specificity and no-call rate were calculated, and a fetal-fraction adjustment was applied to enable projection of these values in a commercial distribution. Likelihood of success of a second blood draw was computed based on fetal fraction and maternal weight from the first draw. RESULTS Validation of this methodology yielded high sensitivities (≥99.4%) and specificities (100%) for all conditions tested with an observed no-call rate of 2.3%. The no-call threshold for sample calling was reduced to 2.8% fetal fraction. The redraw success rate was driven by higher initial fetal fractions and lower maternal weights, with the fetal fraction being the more significant variable. CONCLUSIONS The enhanced version of this SNP-based NIPT method showed a reduced no-call rate and a reduced fetal-fraction threshold for sample calling in comparison to the earlier version, while maintaining high sensitivity and specificity.
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110
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Abstract
Cell-free fetal DNA screening for Down syndrome has gained rapid acceptance over the past few years with increasing market penetration. Three main laboratory methodologies are currently used: a massive parallel shotgun sequencing (MPSS), a targeted massive parallel sequencing (t-MPS) and a single nucleotide polymorphism (SNP) based approach. Although each of these technologies has its own advantages and disadvantages, the performance of all was shown to be comparable and superior to that of traditional first-trimester screening for the detection of trisomy 21 in a routine prenatal population. Differences in performance were predominantly shown for chromosomal anomalies other than trisomy 21. Understanding the limitations and benefits of each technology is essential for proper counseling to patients. These technologies, as well as few investigational technologies described in this review, carry a great potential beyond screening for the common aneuploidies.
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Affiliation(s)
- Pe'er Dar
- Department of Obstetrics & Gynecology and Women's Health, Montefiore Medical Center, Albert Einstein College of Medicine, 1695 Eastchester Road, Bronx, New York 10461, USA
| | - Hagit Shani
- Department of Obstetrics & Gynecology and Women's Health, Montefiore Medical Center, Albert Einstein College of Medicine, 1695 Eastchester Road, Bronx, New York 10461, USA
| | - Mark I Evans
- Department of Obstetrics and Gynecology, Mt. Sinai School of Medicine, New York, NY, USA; Comprehensive Genetics and Fetal Medicine Foundation of America, 131 East 65th Street, New York, NY 10065, USA.
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Abstract
Maternal plasma cell-free (cf) DNA testing has higher discriminatory power for aneuploidy than any conventional multi-marker screening test. Several strategies have been suggested for introducing it into clinical practice. Secondary cfDNA, restricted only to women with positive conventional screening test, is generally cost saving and minimizes the need for invasive prenatal diagnosis but leads to a small loss in detection. Primary cfDNA, replacing conventional screening or retaining the nuchal translucency scan, is not currently cost-effective for third-party payers. Contingent cfDNA, testing about 20% of women with the highest risks based on a conventional test, is the preferred approach.
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112
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Fiorentino F, Bono S, Pizzuti F, Mariano M, Polverari A, Duca S, Sessa M, Baldi M, Diano L, Spinella F. The importance of determining the limit of detection of non-invasive prenatal testing methods. Prenat Diagn 2016; 36:304-11. [DOI: 10.1002/pd.4780] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 01/07/2016] [Accepted: 01/24/2016] [Indexed: 12/12/2022]
Affiliation(s)
- Francesco Fiorentino
- GENOMA Group, Molecular Genetics Laboratory; Via di Castel Giubileo 11 00138 Rome Italy
| | - Sara Bono
- GENOMA Group, Molecular Genetics Laboratory; Via di Castel Giubileo 11 00138 Rome Italy
| | - Francesca Pizzuti
- GENOMA Group, Molecular Genetics Laboratory; Via di Castel Giubileo 11 00138 Rome Italy
| | - Martina Mariano
- GENOMA Group, Molecular Genetics Laboratory; Via di Castel Giubileo 11 00138 Rome Italy
| | - Arianna Polverari
- GENOMA Group, Molecular Genetics Laboratory; Via di Castel Giubileo 11 00138 Rome Italy
| | - Sara Duca
- GENOMA Group, Molecular Genetics Laboratory; Via di Castel Giubileo 11 00138 Rome Italy
| | - Mariateresa Sessa
- GENOMA Group, Molecular Genetics Laboratory; Via di Castel Giubileo 11 00138 Rome Italy
| | - Marina Baldi
- GENOMA Group, Molecular Genetics Laboratory; Via di Castel Giubileo 11 00138 Rome Italy
| | - Laura Diano
- GENOMA Group, Molecular Genetics Laboratory; Via di Castel Giubileo 11 00138 Rome Italy
| | - Francesca Spinella
- GENOMA Group, Molecular Genetics Laboratory; Via di Castel Giubileo 11 00138 Rome Italy
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Persico N, Boito S, Ischia B, Cordisco A, De Robertis V, Fabietti I, Periti E, Volpe P, Fedele L, Rembouskos G. Cell-free DNA testing in the maternal blood in high-risk pregnancies after first-trimester combined screening. Prenat Diagn 2016; 36:232-6. [DOI: 10.1002/pd.4773] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 12/30/2015] [Accepted: 01/05/2016] [Indexed: 12/14/2022]
Affiliation(s)
- Nicola Persico
- Department of Obstetrics and Gynecology ‘L. Mangiagalli’, Fondazione IRCCS ‘Ca’ Granda; Ospedale Maggiore Policlinico; Milan Italy
| | - Simona Boito
- Department of Obstetrics and Gynecology ‘L. Mangiagalli’, Fondazione IRCCS ‘Ca’ Granda; Ospedale Maggiore Policlinico; Milan Italy
| | - Benedetta Ischia
- Department of Obstetrics and Gynecology ‘L. Mangiagalli’, Fondazione IRCCS ‘Ca’ Granda; Ospedale Maggiore Policlinico; Milan Italy
| | | | | | - Isabella Fabietti
- Department of Obstetrics and Gynecology ‘L. Mangiagalli’, Fondazione IRCCS ‘Ca’ Granda; Ospedale Maggiore Policlinico; Milan Italy
| | - Enrico Periti
- Fetal Medicine Unit; Palagi Hospital; Florence Italy
| | - Paolo Volpe
- Fetal Medicine Unit; Di Venere and Sarcone Hospitals; Bari Italy
| | - Luigi Fedele
- Department of Obstetrics and Gynecology ‘L. Mangiagalli’, Fondazione IRCCS ‘Ca’ Granda; Ospedale Maggiore Policlinico; Milan Italy
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Krishna I, Badell M, Loucks TL, Lindsay M, Samuel A. Adverse perinatal outcomes are more frequent in pregnancies with a low fetal fraction result on noninvasive prenatal testing. Prenat Diagn 2016; 36:210-5. [DOI: 10.1002/pd.4779] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2015] [Revised: 01/12/2016] [Accepted: 01/15/2016] [Indexed: 12/25/2022]
Affiliation(s)
- Iris Krishna
- Department of Gynecology and Obstetrics, Division of Maternal-Fetal Medicine; Emory University School of Medicine; Atlanta GA USA
| | - Martina Badell
- Department of Gynecology and Obstetrics, Division of Maternal-Fetal Medicine; Emory University School of Medicine; Atlanta GA USA
| | - Tammy L. Loucks
- Department of Gynecology and Obstetrics, Division of Maternal-Fetal Medicine; Emory University School of Medicine; Atlanta GA USA
| | - Michael Lindsay
- Department of Gynecology and Obstetrics, Division of Maternal-Fetal Medicine; Emory University School of Medicine; Atlanta GA USA
| | - Amber Samuel
- Maternal-Fetal Medicine; Obstetrix Medical Group of Houston; The Woodlands TX USA
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Steinbach RJ, Allyse M, Michie M, Liu EY, Cho MK. "This lifetime commitment": Public conceptions of disability and noninvasive prenatal genetic screening. Am J Med Genet A 2016; 170A:363-374. [PMID: 26566970 PMCID: PMC4948186 DOI: 10.1002/ajmg.a.37459] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 10/20/2015] [Indexed: 12/15/2022]
Abstract
Recently, new noninvasive prenatal genetic screening technologies for Down syndrome and other genetic conditions have become commercially available. Unique characteristics of these screening tests have reignited long-standing concerns about prenatal testing for intellectual and developmental disabilities. We conducted a web-based survey of a sample of the US public to examine how attitudes towards disability inform views of prenatal testing in the context of these rapidly advancing prenatal genetic screening technologies. Regardless of opinion toward disability, the majority of respondents supported both the availability of screening and the decision to continue a pregnancy positive for aneuploidy. Individuals rationalized their support with various conceptions of disability; complications of the expressivist argument and other concerns from the disability literature were manifested in many responses analyzed.
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Affiliation(s)
| | - Megan Allyse
- Biomedical Ethics Research Program and Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905 U.S.A
| | - Marsha Michie
- Institute for Health and Aging, University of California, San Francisco, CA 94118 U.S.A
| | - Emily Y. Liu
- Stanford Center for Biomedical Ethics, Stanford, CA 94305 U.S.A
| | - Mildred K. Cho
- Stanford Center for Biomedical Ethics, Stanford, CA 94305 U.S.A
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Gross SJ, Stosic M, McDonald‐McGinn DM, Bassett AS, Norvez A, Dhamankar R, Kobara K, Kirkizlar E, Zimmermann B, Wayham N, Babiarz JE, Ryan A, Jinnett KN, Demko Z, Benn P. Clinical experience with single-nucleotide polymorphism-based non-invasive prenatal screening for 22q11.2 deletion syndrome. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2016; 47:177-83. [PMID: 26396068 PMCID: PMC5064640 DOI: 10.1002/uog.15754] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 09/09/2015] [Accepted: 09/14/2015] [Indexed: 05/09/2023]
Abstract
OBJECTIVES To evaluate the performance of a single-nucleotide polymorphism (SNP)-based non-invasive prenatal test (NIPT) for the detection of fetal 22q11.2 deletion syndrome in clinical practice, assess clinical follow-up and review patient choices for women with high-risk results. METHODS In this study, 21 948 samples were submitted for screening for 22q11.2 deletion syndrome using a SNP-based NIPT and subsequently evaluated. Follow-up was conducted for all cases with a high-risk result. RESULTS Ninety-five cases were reported as high risk for fetal 22q11.2 deletion. Diagnostic testing results were available for 61 (64.2%) cases, which confirmed 11 (18.0%) true positives and identified 50 (82.0%) false positives, resulting in a positive predictive value (PPV) of 18.0%. Information regarding invasive testing was available for 84 (88.4%) high-risk cases: 57.1% (48/84) had invasive testing and 42.9% (36/84) did not. Ultrasound anomalies were present in 81.8% of true-positive and 18.0% of false-positive cases. Two additional cases were high risk for a maternal 22q11.2 deletion; one was confirmed by diagnostic testing and one had a positive family history. There were three pregnancy terminations related to screening results of 22q11.2 deletion, two of which were confirmed as true positive by invasive testing. CONCLUSIONS Clinical experience with this SNP-based non-invasive screening test for 22q11.2 deletion syndrome indicates that these deletions have a frequency of approximately 1 in 1000 in the referral population with most identifiable through this test. Use of this screening method requires the availability of counseling and other management resources for high-risk pregnancies.
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Affiliation(s)
| | | | - D. M. McDonald‐McGinn
- Division of Human Genetics, The Children's Hospital of PhiladelphiaPerelman School of Medicine at the University of PennsylvaniaPhiladelphiaPAUSA
| | - A. S. Bassett
- Clinical Genetics Research ProgramCentre for Addiction and Mental HealthTorontoOntarioCanada
| | | | | | | | | | | | | | | | | | | | | | - P. Benn
- Division of Human Genetics, Department of Genetics and Genome SciencesUniversity of Connecticut Health CenterFarmingtonCTUSA
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Alberti A, Salomon LJ, Le Lorc'h M, Couloux A, Bussières L, Goupil S, Malan V, Pelletier E, Hyon C, Vialard F, Rozenberg P, Bouhanna P, Oury JF, Schmitz T, Romana S, Weissenbach J, Vekemans M, Ville Y. Non-invasive prenatal testing for trisomy 21 based on analysis of cell-free fetal DNA circulating in the maternal plasma. Prenat Diagn 2016; 35:471-6. [PMID: 25643828 DOI: 10.1002/pd.4561] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Revised: 01/04/2015] [Accepted: 01/14/2015] [Indexed: 12/23/2022]
Abstract
OBJECTIVE By-the-book implementation of non-invasive prenatal test and clinical validation for trisomy 21. STUDY DESIGN Publicly funded prospective study of 225 cases. Women at risk for trisomy 21 > 1/250 based on combined ultrasound and serum markers during first or second trimester were eligible following an informed consent. The technique was established from the available literature and performed on 10 mL of venous blood collected prior to chorionic villus sampling or amniocentesis. Investigators were blinded to the fetal karyotype. Results were expressed in Z-scores of the percentage of each chromosome. RESULTS Among 976 eligible cases, 225 were processed: 8 were used for pretesting phase and 23 to build a reference set. One hundred thirty six euploid cases and 47 with trisomy 21 were then run randomly. Eleven cases yielded no result (4.8%). Z-scores were above 3 (7.58+/-2.41) for chromosome 21 in all 47 trisomies and in none of the euploid cases (0.11+/-1.0). Z-scores were within normal range for the other chromosomes in both groups. Using a cut-off of 3, sensitivity and specificity were of 100% 95% CI [94.1, 100] and 100% 95% CI [98, 100], respectively. CONCLUSION Non-invasive prenatal test for trisomy 21 is a robust strategy that can be translated from seminal publications. Publicly funded studies should refine its indications and cost-effectiveness in prenatal screening and diagnosis. © 2015 John Wiley & Sons, Ltd.
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Walker BS, Jackson BR, LaGrave D, Ashwood ER, Schmidt RL. A cost-effectiveness analysis of cell free DNA as a replacement for serum screening for Down syndrome. Prenat Diagn 2016; 35:440-6. [PMID: 25273838 DOI: 10.1002/pd.4511] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Revised: 08/07/2014] [Accepted: 09/26/2014] [Indexed: 12/23/2022]
Abstract
OBJECTIVE The aim of this article is to determine the cost effectiveness of cell free DNA (cfDNA) as a replacement for integrated screening using a societal cost perspective. METHOD This study used Monte-Carlo simulation with one-way and probabilistic sensitivity analysis. RESULTS Cell free DNA is more effective and less costly than integrated screening. The incremental cost-effectiveness ratio for cfDNA relative to the integrated test was -$277 955 per case detected (95th percent confidence interval -$881 882 to $532 785). CONCLUSION Cell free DNA screening is a cost-effective replacement for maternal serum screening when the lifetime costs of Down syndrome live births are considered. The adoption of cfDNA screening would save approximately $277 955 for each additional case detected over integrated screening.
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Affiliation(s)
- Brandon S Walker
- Department of Pathology and ARUP Laboratories, School of Medicine, University of Utah, Salt Lake City, UT, USA
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Taylor-Phillips S, Freeman K, Geppert J, Agbebiyi A, Uthman OA, Madan J, Clarke A, Quenby S, Clarke A. Accuracy of non-invasive prenatal testing using cell-free DNA for detection of Down, Edwards and Patau syndromes: a systematic review and meta-analysis. BMJ Open 2016; 6:e010002. [PMID: 26781507 PMCID: PMC4735304 DOI: 10.1136/bmjopen-2015-010002] [Citation(s) in RCA: 223] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
OBJECTIVE To measure test accuracy of non-invasive prenatal testing (NIPT) for Down, Edwards and Patau syndromes using cell-free fetal DNA and identify factors affecting accuracy. DESIGN Systematic review and meta-analysis of published studies. DATA SOURCES PubMed, Ovid Medline, Ovid Embase and the Cochrane Library published from 1997 to 9 February 2015, followed by weekly autoalerts until 1 April 2015. ELIGIBILITY CRITERIA FOR SELECTING STUDIES English language journal articles describing case-control studies with ≥ 15 trisomy cases or cohort studies with ≥ 50 pregnant women who had been given NIPT and a reference standard. RESULTS 41, 37 and 30 studies of 2012 publications retrieved were included in the review for Down, Edwards and Patau syndromes. Quality appraisal identified high risk of bias in included studies, funnel plots showed evidence of publication bias. Pooled sensitivity was 99.3% (95% CI 98.9% to 99.6%) for Down, 97.4% (95.8% to 98.4%) for Edwards, and 97.4% (86.1% to 99.6%) for Patau syndrome. The pooled specificity was 99.9% (99.9% to 100%) for all three trisomies. In 100,000 pregnancies in the general obstetric population we would expect 417, 89 and 40 cases of Downs, Edwards and Patau syndromes to be detected by NIPT, with 94, 154 and 42 false positive results. Sensitivity was lower in twin than singleton pregnancies, reduced by 9% for Down, 28% for Edwards and 22% for Patau syndrome. Pooled sensitivity was also lower in the first trimester of pregnancy, in studies in the general obstetric population, and in cohort studies with consecutive enrolment. CONCLUSIONS NIPT using cell-free fetal DNA has very high sensitivity and specificity for Down syndrome, with slightly lower sensitivity for Edwards and Patau syndrome. However, it is not 100% accurate and should not be used as a final diagnosis for positive cases. TRIAL REGISTRATION NUMBER CRD42014014947.
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Affiliation(s)
| | - Karoline Freeman
- Warwick Medical School, The University of Warwick, Coventry, West Midlands, UK
| | - Julia Geppert
- Warwick Medical School, The University of Warwick, Coventry, West Midlands, UK
| | - Adeola Agbebiyi
- Warwick Medical School, The University of Warwick, Coventry, West Midlands, UK
| | - Olalekan A Uthman
- Warwick Medical School, The University of Warwick, Coventry, West Midlands, UK
| | - Jason Madan
- Warwick Medical School, The University of Warwick, Coventry, West Midlands, UK
| | - Angus Clarke
- Institute of Cancer & Genetics, Cardiff University School of Medicine, Cardiff, UK
| | - Siobhan Quenby
- Warwick Medical School, The University of Warwick, Coventry, West Midlands, UK
| | - Aileen Clarke
- Warwick Medical School, The University of Warwick, Coventry, West Midlands, UK
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Affiliation(s)
- Felix C.K. Wong
- Centre for Research into Circulating Fetal Nucleic Acids, Li Ka Shing Institute of Health Sciences, and
- Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China; ,
| | - Y.M. Dennis Lo
- Centre for Research into Circulating Fetal Nucleic Acids, Li Ka Shing Institute of Health Sciences, and
- Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China; ,
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Kazemi M, Salehi M, Kheirollahi M. Down Syndrome: Current Status, Challenges and Future Perspectives. INTERNATIONAL JOURNAL OF MOLECULAR AND CELLULAR MEDICINE 2016. [PMID: 27942498 DOI: 10.22088/acadpub.bums.5.3.125] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
Down syndrome (DS) is a birth defect with huge medical and social costs, caused by trisomy of whole or part of chromosome 21. It is the most prevalent genetic disease worldwide and the common genetic cause of intellectual disabilities appearing in about 1 in 400-1500 newborns. Although the syndrome had been described thousands of years before, it was named after John Langdon Down who described its clinical description in 1866. Scientists have identified candidate genes that are involved in the formation of specific DS features. These advances in turn may help to develop targeted therapy for persons with trisomy 21. Screening for DS is an important part of routine prenatal care. Until recently, noninvasive screening for aneuploidy depends on the measurement of maternal serum analytes and ultrasonography. More recent progress has resulted in the development of noninvasive prenatal screening (NIPS) test using cell-free fetal DNA sequences isolated from a maternal blood sample. A review on those achievements is discussed.
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Affiliation(s)
- Mohammad Kazemi
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran.; Medical Genetic Center of Genome, Isfahan, Iran.; Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Non-communicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mansoor Salehi
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran.; Medical Genetic Center of Genome, Isfahan, Iran.; Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Non-communicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Majid Kheirollahi
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran.; Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Non-communicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
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Abstract
Prenatal diagnosis and screening have undergone rapid development in recent years, with advances in molecular technology driving the change. Noninvasive prenatal testing (NIPT) for Down syndrome as a highly sensitive screening test is now available worldwide through the commercial sector with many countries moving toward implementation into their publically funded maternity systems. Noninvasive prenatal diagnosis (NIPD) can now be performed for definitive diagnosis of some recessive and X-linked conditions, rather than just paternally inherited dominant and de novo conditions. NIPD/T offers pregnant couples greater choice during their pregnancy as these safer methods avoid the risk of miscarriage associated with invasive testing. As the cost of sequencing falls and technology develops further, there may well be potential for whole exome and whole genome sequencing of the unborn fetus using cell-free DNA in the maternal plasma. How such assays can or should be implemented into the clinical setting remain an area of significant debate, but it is clear that the progress made to date for safer prenatal testing has been welcomed by expectant couples and their healthcare professionals.
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123
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Zhang R, Zhang H, Li Y, Han Y, Xie J, Li J. External Quality Assessment for Detection of Fetal Trisomy 21, 18, and 13 by Massively Parallel Sequencing in Clinical Laboratories. J Mol Diagn 2015; 18:244-52. [PMID: 26747585 DOI: 10.1016/j.jmoldx.2015.10.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Revised: 09/24/2015] [Accepted: 10/21/2015] [Indexed: 01/24/2023] Open
Abstract
An external quality assessment for detection of trisomy 21, 18, and 13 by massively parallel sequencing was implemented by the National Center for Clinical Laboratories of People's Republic of China in 2014. Simulated samples were prepared by mixing fragmented abnormal DNA with plasma from non-pregnant women. The external quality assessment panel, comprising 5 samples from pregnant healthy women, 2 samples with sex chromosome aneuploidies, and 13 samples with different concentrations of fetal fractions positive for trisomy 21, 18, and 13, was then distributed to participating laboratories. In total, 55.6% (47 of 84) of respondents correctly identified each of the samples in the panel. Seventeen false-negative and 87 gray zone results were reported, most [102 of 104 (98.1%)] of which were derived from for trisomy samples with effective fetal fractions <4%. No laboratories generated false-positive results. In addition, we observed varied diagnostic capabilities of different assays, with the assay on the basis of NextSeq CN500 performing better than others, whereas Z values generated by BGISEQ-100 fluctuated greatly. There were no significant correlations between the numbers of unique sequence reads and Z values from any trisomy sample generated by BGISEQ-100. Overall, most clinical laboratories detected samples containing effective fetal fractions >4%. Our study shows need for further laboratory training in the management of samples with low fetal fractions. For some assays, precision of Z values needs to be improved.
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Affiliation(s)
- Rui Zhang
- National Center for Clinical Laboratories, Beijing Hospital, Beijing, People's Republic of China
| | - Hongyun Zhang
- BGI Clinical Laboratories-Shenzhen, Shenzhen, People's Republic of China
| | - Yulong Li
- Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, National Center for Clinical Laboratories, Beijing Hospital, Beijing, People's Republic of China
| | - Yanxi Han
- National Center for Clinical Laboratories, Beijing Hospital, Beijing, People's Republic of China
| | - Jiehong Xie
- National Center for Clinical Laboratories, Beijing Hospital, Beijing, People's Republic of China
| | - Jinming Li
- National Center for Clinical Laboratories, Beijing Hospital, Beijing, People's Republic of China.
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Tynan JA, Kim SK, Mazloom AR, Zhao C, McLennan G, Tim R, Liu L, Hannum G, Hull A, Bombard AT, Oeth P, Burcham T, van den Boom D, Ehrich M. Application of risk score analysis to low-coverage whole genome sequencing data for the noninvasive detection of trisomy 21, trisomy 18, and trisomy 13. Prenat Diagn 2015; 36:56-62. [DOI: 10.1002/pd.4712] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 09/18/2015] [Accepted: 10/22/2015] [Indexed: 12/22/2022]
Affiliation(s)
| | - S. K. Kim
- Sequenom Laboratories; San Diego CA USA
| | | | - C. Zhao
- Sequenom Laboratories; San Diego CA USA
| | | | - R. Tim
- Sequenom Laboratories; San Diego CA USA
| | - L. Liu
- Sequenom Laboratories; San Diego CA USA
| | - G. Hannum
- Sequenom Laboratories; San Diego CA USA
| | - A. Hull
- School of Medicine; University of California; San Diego CA USA
| | - A. T. Bombard
- Sequenom, Inc.; San Diego CA USA
- School of Medicine; University of California; San Diego CA USA
| | - P. Oeth
- Sequenom Laboratories; San Diego CA USA
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125
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de Graaf G, Buckley F, Skotko BG. Estimates of the live births, natural losses, and elective terminations with Down syndrome in the United States. Am J Med Genet A 2015; 167A:756-67. [PMID: 25822844 DOI: 10.1002/ajmg.a.37001] [Citation(s) in RCA: 146] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 01/19/2015] [Indexed: 01/20/2023]
Abstract
The present and future live birth prevalence of Down syndrome (DS) is of practical importance for planning services and prioritizing research to support people living with the condition. Live birth prevalence is influenced by changes in prenatal screening technologies and policies. To predict the future impact of these changes, a model for estimating the live births of people with DS is required. In this study, we combine diverse and robust datasets with validated estimation techniques to describe the non-selective and live birth prevalence of DS in the United States from 1900-2010. Additionally, for the period 1974-2010, we estimate the impact of DS-related elective pregnancy terminations (following a prenatal diagnosis of DS) on the live births with DS. The live birth prevalence for DS in the most recent years (2006-2010) was estimated at 12.6 per 10,000 (95% CI 12.4-12.8), with around 5,300 births annually. During this period, an estimated 3,100 DS-related elective pregnancy terminations were performed in the U.S. annually. As of 2007, the estimated rates at which live births with DS were reduced as a consequence of DS-related elective pregnancy terminations were 30% (95% CI: 27.3-31.9) for the U.S. as a whole. Our results and our model provide data on the impact of elective pregnancy terminations on live births with DS and may provide a baseline from which future trends for live births with DS can be estimated.
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Affiliation(s)
- Gert de Graaf
- Dutch Down Syndrome Foundation, Meppel, the Netherlands
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126
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Allyse M, Chandrasekharan S. Too much, too soon?: Commercial provision of noninvasive prenatal screening for subchromosomal abnormalities and beyond. Genet Med 2015; 17:958-61. [PMID: 25790161 PMCID: PMC4993715 DOI: 10.1038/gim.2015.23] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 01/26/2015] [Indexed: 02/02/2023] Open
Affiliation(s)
- Megan Allyse
- Institute for Health and Aging, University of California San Francisco, San Francisco, CA
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127
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Kirkizlar E, Zimmermann B, Constantin T, Swenerton R, Hoang B, Wayham N, Babiarz JE, Demko Z, Pelham RJ, Kareht S, Simon AL, Jinnett KN, Rabinowitz M, Sigurjonsson S, Hill M. Detection of Clonal and Subclonal Copy-Number Variants in Cell-Free DNA from Patients with Breast Cancer Using a Massively Multiplexed PCR Methodology. Transl Oncol 2015; 8:407-416. [PMID: 26500031 PMCID: PMC4631096 DOI: 10.1016/j.tranon.2015.08.004] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 07/31/2015] [Accepted: 08/10/2015] [Indexed: 12/20/2022] Open
Abstract
We demonstrate proof-of-concept for the use of massively multiplexed PCR and next-generation sequencing (mmPCR-NGS) to identify both clonal and subclonal copy-number variants (CNVs) in circulating tumor DNA. This is the first report of a targeted methodology for detection of CNVs in plasma. Using an in vitro model of cell-free DNA, we show that mmPCR-NGS can accurately detect CNVs with average allelic imbalances as low as 0.5%, an improvement over previously reported whole-genome sequencing approaches. Our method revealed differences in the spectrum of CNVs detected in tumor tissue subsections and matching plasma samples from 11 patients with stage II breast cancer. Moreover, we showed that liquid biopsies are able to detect subclonal mutations that may be missed in tumor tissue biopsies. We anticipate that this mmPCR-NGS methodology will have broad applicability for the characterization, diagnosis, and therapeutic monitoring of CNV-enriched cancers, such as breast, ovarian, and lung cancer.
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Affiliation(s)
- Eser Kirkizlar
- Natera Inc., 201 Industrial Road, Suite 410, San Carlos, CA 94070
| | | | - Tudor Constantin
- Natera Inc., 201 Industrial Road, Suite 410, San Carlos, CA 94070
| | - Ryan Swenerton
- Natera Inc., 201 Industrial Road, Suite 410, San Carlos, CA 94070
| | - Bin Hoang
- Natera Inc., 201 Industrial Road, Suite 410, San Carlos, CA 94070
| | - Nicholas Wayham
- Natera Inc., 201 Industrial Road, Suite 410, San Carlos, CA 94070
| | - Joshua E Babiarz
- Natera Inc., 201 Industrial Road, Suite 410, San Carlos, CA 94070
| | - Zachary Demko
- Natera Inc., 201 Industrial Road, Suite 410, San Carlos, CA 94070
| | - Robert J Pelham
- Natera Inc., 201 Industrial Road, Suite 410, San Carlos, CA 94070
| | - Stephanie Kareht
- Natera Inc., 201 Industrial Road, Suite 410, San Carlos, CA 94070
| | | | | | | | | | - Matthew Hill
- Natera Inc., 201 Industrial Road, Suite 410, San Carlos, CA 94070.
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128
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Leiva Portocarrero ME, Garvelink MM, Becerra Perez MM, Giguère A, Robitaille H, Wilson BJ, Rousseau F, Légaré F. Decision aids that support decisions about prenatal testing for Down syndrome: an environmental scan. BMC Med Inform Decis Mak 2015; 15:76. [PMID: 26404088 PMCID: PMC4583147 DOI: 10.1186/s12911-015-0199-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 09/16/2015] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Prenatal screening tests for Down syndrome (DS) are routine in many developed countries and new tests are rapidly becoming available. Decisions about prenatal screening are increasingly complex with each successive test, and pregnant women need information about risks and benefits as well as clarity about their values. Decision aids (DAs) can help healthcare providers support women in this decision. Using an environmental scan, we aimed to identify publicly available DAs focusing on prenatal screening/diagnosis for Down syndrome that provide effective support for decision making. METHODS Data sources searched were the Decision Aids Library Inventory (DALI) of the Ottawa Patient Decision Aids Research Group at the Ottawa Health Research Institute; Google searches on the internet; professional organizations, academic institutions and other experts in the field; and references in existing systematic reviews on DAs. Eligible DAs targeted pregnant women, focused on prenatal screening and/or diagnosis, applied to tests for fetal abnormalities or aneuploidies, and were in French, English, Spanish or Portuguese. Pairs of reviewers independently identified eligible DAs and extracted characteristics including the presence of practical decision support tools and features to aid comprehension. They then performed quality assessment using the 16 minimum standards established by the International Patient Decision Aids Standards (IPDASi v4.0). RESULTS Of 543 potentially eligible DAs (512 in DALI, 27 from experts, and four on the internet), 23 were eligible and 20 were available for data extraction. DAs were developed from 1996 to 2013 in six countries (UK, USA, Canada, Australia, Sweden, and France). Five DAs were for prenatal screening, three for prenatal diagnosis and 12 for both). Eight contained values clarification methods (personal worksheets). The 20 DAs scored a median of 10/16 (range 6-15) on the 16 IPDAS minimum standards. DISCUSSION None of the 20 included DAs met all 16 IPDAS minimum standards, and few included practical decision support tools or aids to comprehension. CONCLUSIONS Our results indicate there is a need for DAs that effectively support decision making regarding prenatal testing for Down syndrome, especially in light of the recently available non-invasive prenatal screening tests.
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Affiliation(s)
- Maria Esther Leiva Portocarrero
- />Research Axis of Population Health and Practice-Changing Research, CHU de Québec Research Centre, Saint-François-d’Assise Hospital, 10, rue de l’Espinay, Quebec, QC G1L 3L5 Canada
| | - Mirjam M Garvelink
- />Research Axis of Population Health and Practice-Changing Research, CHU de Québec Research Centre, Saint-François-d’Assise Hospital, 10, rue de l’Espinay, Quebec, QC G1L 3L5 Canada
| | - Maria Margarita Becerra Perez
- />Research Axis of Population Health and Practice-Changing Research, CHU de Québec Research Centre, Saint-François-d’Assise Hospital, 10, rue de l’Espinay, Quebec, QC G1L 3L5 Canada
| | - Anik Giguère
- />Centre d’excellence sur le vieillissement de Québec, CHU de Québec Research Centre, Saint-François-d’Assise Hospital, 10, rue de l’Espinay, Quebec, QC G1L 3L5 Canada
- />Department of Family Medicine and Emergency Medicine, Pavillon Ferdinand-Vandry, Université Laval, 1050, avenue de la Médecine, Quebec, QC G1V 0A6 Canada
| | - Hubert Robitaille
- />Research Axis of Population Health and Practice-Changing Research, CHU de Québec Research Centre, Saint-François-d’Assise Hospital, 10, rue de l’Espinay, Quebec, QC G1L 3L5 Canada
| | - Brenda J. Wilson
- />Department of Epidemiology and Community Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5 Canada
| | - François Rousseau
- />Department of Molecular biology, Medical Biochemistry and Pathology, Faculty of Medicine, Pavillon Ferdinand-Vandry, Université Laval, 1050, avenue de la Médecine, Quebec, QC G1V 0A6 Canada
- />MSSS/FRQS/CHUQ Research Chair in Health Technology Assessment and Evidence-based Laboratory Medicine, Saint-François-d’Assise Hospital, 10, rue de l’Espinay, Quebec, QC G1L 3L5 Canada
| | - France Légaré
- />Research Axis of Population Health and Practice-Changing Research, CHU de Québec Research Centre, Saint-François-d’Assise Hospital, 10, rue de l’Espinay, Quebec, QC G1L 3L5 Canada
- />Department of Family Medicine and Emergency Medicine, Pavillon Ferdinand-Vandry, Université Laval, 1050, avenue de la Médecine, Quebec, QC G1V 0A6 Canada
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Sun K, Jiang P, Chan KCA. The impact of digital DNA counting technologies on noninvasive prenatal testing. Expert Rev Mol Diagn 2015; 15:1261-8. [PMID: 26358092 DOI: 10.1586/14737159.2015.1084227] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The discovery of cell-free DNA molecules in maternal plasma has opened up numerous opportunities for noninvasive prenatal testing. The advent of new digital counting technologies, including digital polymerase chain reaction and massive parallel sequencing, has provided the opportunity to quantify the cell-free DNA molecules in maternal plasma in an unprecedentedly precise manner. Powered by these technologies, prenatal testing of different kinds of hereditary conditions, ranging from monogenic diseases to chromosome aneuploidies, has been shown to be possible through the analysis of maternal plasma DNA. Discussed here are the principles of the approaches used in the noninvasive testing of different fetal conditions, with an emphasis on the impact that different digital DNA counting strategies have made on the development of these tests.
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Affiliation(s)
- Kun Sun
- a Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Peiyong Jiang
- a Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
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131
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Kotsopoulou I, Tsoplou P, Mavrommatis K, Kroupis C. Non-invasive prenatal testing (NIPT): limitations on the way to become diagnosis. ACTA ACUST UNITED AC 2015. [PMID: 29540035 DOI: 10.1515/dx-2015-0002] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
With the discovery of existing circulating cell-free fetal DNA (ccffDNA) in maternal plasma and the advent of next-generation sequencing (NGS) technology, there is substantial hope that prenatal diagnosis will become a predominately non-invasive process in the future. At the moment, non-invasive prenatal testing (NIPT) is available for high-risk pregnancies with significant better sensitivity and specificity than the other existing non-invasive methods (biochemical and ultrasonographical). Mainly it is performed by NGS methods in a few commercial labs worldwide. However, it is expected that many other labs will offer analogous services in the future in this fast-growing field with a multiplicity of in-house methods (e.g., epigenetic, etc.). Due to various limitations of the available methods and technologies that are explained in detail in this manuscript, NIPT has not become diagnostic yet and women may still need to undergo risky invasive procedures to verify a positive finding or to secure (or even expand) a negative one. Efforts have already started to make the NIPT technologies more accurate (even at the level of a complete fetal genome) and cheaper and thus more affordable, in order to become diagnostic screening tests for all pregnancies in the near future.
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Affiliation(s)
- Ioanna Kotsopoulou
- 1Department of Clinical Biochemistry, Attikon University General Hospital, University of Athens Medical School, Athens, Greece
| | | | | | - Christos Kroupis
- 1Department of Clinical Biochemistry, Attikon University General Hospital, University of Athens Medical School, Athens, Greece
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Non-invasive Prenatal Screening for Fetal Aneuploidy: Comparison with Cytogenetic Results. CURRENT GENETIC MEDICINE REPORTS 2015. [DOI: 10.1007/s40142-015-0072-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Meck JM, Kramer Dugan E, Matyakhina L, Aviram A, Trunca C, Pineda-Alvarez D, Aradhya S, Klein RT, Cherry AM. Noninvasive prenatal screening for aneuploidy: positive predictive values based on cytogenetic findings. Am J Obstet Gynecol 2015; 213:214.e1-5. [PMID: 25843063 DOI: 10.1016/j.ajog.2015.04.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 03/13/2015] [Accepted: 04/01/2015] [Indexed: 01/26/2023]
Abstract
OBJECTIVE We sought to determine the positive predictive value (PPV) of noninvasive prenatal screening (NIPS) for various aneuploidies based on cases referred for follow-up cytogenetic testing. Secondarily, we wanted to determine the false-negative (FN) rate for those cases with a negative NIPS result. STUDY DESIGN We compared the cytogenetic findings (primarily from chromosome analysis) from 216 cases referred to our laboratories with either a positive or negative NIPS result, and classified NIPS results as true positive, false positive, true negative, or FN. Diagnostic cytogenetic testing was performed on the following tissue types: amniotic fluid (n = 137), chorionic villi (n = 69), neonatal blood (n = 6), and products of conception (n = 4). RESULTS The PPV for NIPS were as follows: 93% for trisomy (T)21 (n = 99; 95% confidence interval [CI], 86-97.1%), 58% for T18 (n = 24; 95% CI, 36.6-77.9%), 45% for T13 (n = 11; 95% CI, 16.7-76.6%), 23% for monosomy X (n = 26; 95% CI, 9-43.6%), and 67% for XXY (n = 6; 95% CI, 22.3-95.7%). Of the 26 cases referred for follow-up cytogenetics after a negative NIPS result, 1 (4%) was FN (T13). Two cases of triploidy, a very serious condition but one not claimed to be detectable by the test providers, were among those classified as true negatives. CONCLUSION T21, which has the highest prevalence of all aneuploidies, demonstrated a high true-positive rate, resulting in a high PPV. However, the other aneuploidies, with their lower prevalence, displayed relatively high false-positive rates and, therefore, lower PPV. Patients and physicians must fully understand the limitations of this screening test and the need in many cases to follow up with appropriate diagnostic testing to obtain an accurate diagnosis.
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134
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Chitty LS, Lo YMD. Noninvasive Prenatal Screening for Genetic Diseases Using Massively Parallel Sequencing of Maternal Plasma DNA. Cold Spring Harb Perspect Med 2015; 5:a023085. [PMID: 26187875 PMCID: PMC4561399 DOI: 10.1101/cshperspect.a023085] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The identification of cell-free fetal DNA (cffDNA) in maternal plasma in 1997 heralded the most significant change in obstetric care for decades, with the advent of safer screening and diagnosis based on analysis of maternal blood. Here, we describe how the technological advances offered by next-generation sequencing have allowed for the development of a highly sensitive screening test for aneuploidies as well as definitive prenatal molecular diagnosis for some monogenic disorders.
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Affiliation(s)
- Lyn S Chitty
- UCL Institute of Child Health, Genetics and Genomic Medicine, London WC1N 1EH, United Kingdom; University College London Hospitals NHS Foundation Trust, London NW1 2PG, United Kingdom; NE Thames Regional Genetics Service, Great Ormond Street Hospital for Children NHS Foundation Trust, 37 Queen Square, London WC1N 3BH, United Kingdom
| | - Y M Dennis Lo
- Centre for Research into Circulating Fetal Nucleic Acids, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China; Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, NT, Hong Kong SAR, China
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135
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Tartaglia N, Howell S, Wilson R, Janusz J, Boada R, Martin S, Frazier JB, Pfeiffer M, Regan K, McSwegin S, Zeitler P. The eXtraordinarY Kids Clinic: an interdisciplinary model of care for children and adolescents with sex chromosome aneuploidy. J Multidiscip Healthc 2015; 8:323-34. [PMID: 26229481 PMCID: PMC4514383 DOI: 10.2147/jmdh.s80242] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Purpose Individuals with sex chromosome aneuploidies (SCAs) are born with an atypical number of X and/or Y chromosomes, and present with a range of medical, developmental, educational, behavioral, and psychological concerns. Rates of SCA diagnoses in infants and children are increasing, and there is a need for specialized interdisciplinary care to address associated risks. The eXtraordinarY Kids Clinic was established to provide comprehensive and experienced care for children and adolescents with SCA, with an interdisciplinary team composed of developmental–behavioral pediatrics, endocrinology, genetic counseling, child psychology, pediatric neuropsychology, speech–language pathology, occupational therapy, nursing, and social work. The clinic model includes an interdisciplinary approach to care, where assessment results by each discipline are integrated to develop unified diagnostic impressions and treatment plans individualized for each patient. Additional objectives of the eXtraordinarY Kids Clinic program include prenatal genetic counseling, research, education, family support, and advocacy. Methods Satisfaction surveys were distributed to 496 patients, and responses were received from 168 unique patients. Results Satisfaction with the overall clinic visit was ranked as “very satisfied” in 85%, and as “satisfied” in another 9.8%. Results further demonstrate specific benefits from the clinic experience, the importance of a knowledgeable clinic coordinator, and support the need for similar clinics across the country. Three case examples of the interdisciplinary approach to assessment and treatment are included.
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Affiliation(s)
- Nicole Tartaglia
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, USA ; Child Development Unit, Children's Hospital Colorado, Aurora, CO, USA
| | - Susan Howell
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, USA ; Child Development Unit, Children's Hospital Colorado, Aurora, CO, USA
| | - Rebecca Wilson
- Child Development Unit, Children's Hospital Colorado, Aurora, CO, USA
| | - Jennifer Janusz
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, USA ; Child Development Unit, Children's Hospital Colorado, Aurora, CO, USA
| | - Richard Boada
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, USA ; Child Development Unit, Children's Hospital Colorado, Aurora, CO, USA
| | - Sydney Martin
- Child Development Unit, Children's Hospital Colorado, Aurora, CO, USA
| | | | - Michelle Pfeiffer
- Child Development Unit, Children's Hospital Colorado, Aurora, CO, USA
| | - Karen Regan
- Child Development Unit, Children's Hospital Colorado, Aurora, CO, USA
| | - Sarah McSwegin
- Child Development Unit, Children's Hospital Colorado, Aurora, CO, USA
| | - Philip Zeitler
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, USA ; Child Development Unit, Children's Hospital Colorado, Aurora, CO, USA
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136
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Gross SJ, Kareht S, Ryan A. Prenatal screening: Focus on more specific fetal testing. Nature 2015; 523:290. [PMID: 26178955 DOI: 10.1038/523290d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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137
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Kinnings SL, Geis JA, Almasri E, Wang H, Guan X, McCullough RM, Bombard AT, Saldivar JS, Oeth P, Deciu C. Factors affecting levels of circulating cell-free fetal DNA in maternal plasma and their implications for noninvasive prenatal testing. Prenat Diagn 2015; 35:816-22. [DOI: 10.1002/pd.4625] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Revised: 05/15/2015] [Accepted: 05/17/2015] [Indexed: 12/26/2022]
Affiliation(s)
| | | | | | | | | | | | | | | | - Paul Oeth
- Sequenom Laboratories; San Diego CA USA
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138
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Eiben B, Krapp M, Borth H, Kutur N, Kreiselmaier P, Glaubitz R, Deutinger J, Merz E. Single Nucleotide Polymorphism-Based Analysis of Cell-Free Fetal DNA in 3000 Cases from Germany and Austria. Ultrasound Int Open 2015; 1:E8-E11. [PMID: 27689149 PMCID: PMC5023199 DOI: 10.1055/s-0035-1555765] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 05/29/2015] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND & PATIENT Data from 3 008 patients, who underwent single-nucleotide-polymorphism (SNP)-based noninvasive prenatal testing (NIPT) are presented. METHOD The PanoramaTM test (Natera, San Carlos, CA) was used to analyze cell-free fetal DNA from maternal blood for trisomies 21, 18, and 13, triploidy and sex-chromosome aneuploidies. RESULT In 2 942 (97.8%) cases, a result was obtained. The average fetal fraction was 10.2%. A high-risk result for fetal aneuploidy was made for 65 (2.2%) cases. In 59 (90.8%) of these cases, invasive testing confirmed the aneuploidy. There were 6 false-positive cases. In the false-positive group, the fetal fraction was significantly lower. The overall positive predictive value was 90.8%. No false-negative cases were reported but many patients in this study have not delivered yet. Therefore, exact data cannot be given for potential false-negative cases. CONCLUSION SNP-based NIPT is a reliable screening method for evaluating the risk of aneuploidies of chromosomes 21, 18 and 13. By using NIPT, the number of invasive procedures may be reduced significantly compared to maternal age and first-trimester screening.
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Affiliation(s)
- B. Eiben
- Institut für Klinische Genetik Nordrhein, Essen, Germany
| | - M. Krapp
- amedes Hamburg, Zentrum für Endokrinologie, Kinderwunsch und Pränatale Medizin, Hamburg, Germany
| | - H. Borth
- Genetic Department, amedes Institut f. Labormedizin und Klinische Genetik Institut f. Labormedizin und Klinische Genetik Rhein/ Ruhr MVZ GmbH, Essen, Germany
| | - N. Kutur
- Genetic Department, amedes Institut f. Labormedizin und Klinische Genetik Rhein/ Ruhr MVZ GmbH, Essen, Germany
| | - P. Kreiselmaier
- MVZ FCH, amedes Hamburg, Zentrum für Pränatale Medizin, Hamburg, Germany
| | - R. Glaubitz
- amedes Labor, Human Genetics, Hannover, Germany
| | - J. Deutinger
- UFK Wien, Dep. for Prenatal Diagnostic and Therapy, Wien, Austria
| | - E. Merz
- KH Nordwest, Obstetrics & Gynecology, Frankfurt/Main, Germany
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Grace MR, Hardisty E, Green NS, Davidson E, Stuebe AM, Vora NL. Cell free DNA testing-interpretation of results using an online calculator. Am J Obstet Gynecol 2015; 213:30.e1-30.e4. [PMID: 25957020 DOI: 10.1016/j.ajog.2015.05.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2015] [Revised: 04/21/2015] [Accepted: 05/02/2015] [Indexed: 12/12/2022]
Abstract
All pregnant women, regardless of age, should be offered screening or invasive testing for chromosomal abnormalities at <20 weeks' gestation. Noninvasive prenatal screening for fetal aneuploidy with the use of cell-free DNA (cfDNA) is a screening method that offers high sensitivity and specificity in validation studies and has reduced the need for unnecessary invasive procedures. Laboratories often advertise and report a test's sensitivity and specificity as a means to describe the test's accuracy. The positive predictive value (PPV) of a screening test (the proportion of positive results that are truly positive) is a function of the prevalence of the condition in a population and often is not reported in direct-to-patient advertising. False-positive cfDNA screening tests have been reported, and there is evidence that some women are deciding to terminate their pregnancy without confirmatory testing. We believe that laboratories should disclose the patient-specific PPV of cfDNA screening for aneuploidy on result reports. To assist with counseling patients about the benefits, risks, and limitations of aneuploidy screening with the use of cfDNA and to demonstrate the relationship between an a priori risk and PPV, we developed a web-based calculator to estimate the PPV of the 4 commercially available cfDNA testing platforms for which data have been published. Estimates are made with the use of a patient's age and gestational age-related risk of trisomy 21, 18 and 13 or an a priori risk that is based on other findings. This web-based calculator is an aid for providers and genetic counselors to illustrate the relationship between disease prevalence and a test's PPV. It has enhanced our counseling of patients both before they elect noninvasive prenatal screening and after they receive a positive result.
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140
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Kim SK, Hannum G, Geis J, Tynan J, Hogg G, Zhao C, Jensen TJ, Mazloom AR, Oeth P, Ehrich M, van den Boom D, Deciu C. Determination of fetal DNA fraction from the plasma of pregnant women using sequence read counts. Prenat Diagn 2015; 35:810-5. [PMID: 25967380 DOI: 10.1002/pd.4615] [Citation(s) in RCA: 143] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
OBJECTIVE This study introduces a novel method, referred to as SeqFF, for estimating the fetal DNA fraction in the plasma of pregnant women and to infer the underlying mechanism that allows for such statistical modeling. METHODS Autosomal regional read counts from whole-genome massively parallel single-end sequencing of circulating cell-free DNA (ccfDNA) from the plasma of 25 312 pregnant women were used to train a multivariate model. The pretrained model was then applied to 505 pregnant samples to assess the performance of SeqFF against known methodologies for fetal DNA fraction calculations. RESULTS Pearson's correlation between chromosome Y and SeqFF for pregnancies with male fetuses from two independent cohorts ranged from 0.932 to 0.938. Comparison between a single-nucleotide polymorphism-based approach and SeqFF yielded a Pearson's correlation of 0.921. Paired-end sequencing suggests that shorter ccfDNA, that is, less than 150 bp in length, is nonuniformly distributed across the genome. Regions exhibiting an increased proportion of short ccfDNA, which are more likely of fetal origin, tend to provide more information in the SeqFF calculations. CONCLUSION SeqFF is a robust and direct method to determine fetal DNA fraction. Furthermore, the method is applicable to both male and female pregnancies and can greatly improve the accuracy of noninvasive prenatal testing for fetal copy number variation.
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Affiliation(s)
- Sung K Kim
- Sequenom Laboratories, San Diego, CA, USA
| | | | | | - John Tynan
- Sequenom Laboratories, San Diego, CA, USA
| | - Grant Hogg
- Sequenom Laboratories, San Diego, CA, USA
| | - Chen Zhao
- Sequenom Laboratories, San Diego, CA, USA
| | | | | | - Paul Oeth
- Sequenom Laboratories, San Diego, CA, USA
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141
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#36: Prenatal aneuploidy screening using cell-free DNA. Am J Obstet Gynecol 2015; 212:711-6. [PMID: 25813012 DOI: 10.1016/j.ajog.2015.03.043] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 03/20/2015] [Indexed: 02/05/2023]
Abstract
Recent advances in technology have created exciting opportunities to expand and improve genetic testing options that are available to women during pregnancy. However, the novelty and complexity of these technologies, combined with the commercial interest to implement these tests rapidly into routine clinical care, have created challenges for physicians and patients and potentially will lead to misunderstanding, misuse, and unintended consequences. The purpose of this document was to aid clinicians in their day-to-day practice of counseling patients regarding prenatal aneuploidy testing options with cell-free DNA screening, which includes how it compares to current testing methods, potential benefits and harms, and its limitations and caveats.
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142
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Wou K, Feinberg JL, Wapner RJ, Simpson JL. Cell-free DNA versus intact fetal cells for prenatal genetic diagnostics: what does the future hold? Expert Rev Mol Diagn 2015; 15:989-98. [DOI: 10.1586/14737159.2015.1051529] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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143
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Greeley ET, Kessler KA, Vohra N. Clinical Applications of Noninvasive Prenatal Testing. JOURNAL OF FETAL MEDICINE 2015. [DOI: 10.1007/s40556-015-0035-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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144
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Emad A, Lamoureux J, Ouellet A, Drouin R. Rapid Aneuploidy Detection of Chromosomes 13, 18, 21, X and Y Using Quantitative Fluorescent Polymerase Chain Reaction with Few Microdissected Fetal Cells. Fetal Diagn Ther 2015; 38:65-76. [DOI: 10.1159/000365810] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 07/07/2014] [Indexed: 11/19/2022]
Abstract
Objectives: Analysis of DNA from small numbers of cells, such as fetal cells in maternal blood, is a major limiting factor for their use in clinical applications. Traditional methods of single-cells whole genome amplification (SCs-WGA) and accurate analysis have been challenging to date. Our purpose was to assess the feasibility of using a few fetal cells to determine fetal sex and major chromosomal abnormalities by quantitative fluorescent polymerase chain reaction (QF-PCR). Methods: Cultured cells from 26 amniotic fluid samples were used for standard DNA extraction and recovery of 5 fetal cells by laser-capture microdissection. SCs-WGA was performed using the DNA from the microdissected cells. PCR amplification of short tandem repeats specific for chromosomes 13, 18, 21, X and Y was performed on extracted and amplified DNA. Allele dosage and sexing were quantitatively analyzed following separation by capillary electrophoresis. Results: Microsatellite QF-PCR analysis showed high concordance in chromosomal copy number between extracted and amplified DNA when 5 or more cells were used. Results were in concordance with that of conventional cytogenetic analysis. Conclusion: Satisfactory genomic coverage can be obtained from SCs-WGA. Clinically, SCs-WGA coupled with QF-PCR can provide a reliable, accurate, rapid and cost-effective method for detection of major fetal chromosome abnormalities.
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145
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Bioinformatics analysis of circulating cell-free DNA sequencing data. Clin Biochem 2015; 48:962-75. [PMID: 25966961 DOI: 10.1016/j.clinbiochem.2015.04.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 03/30/2015] [Accepted: 04/29/2015] [Indexed: 12/18/2022]
Abstract
The discovery of cell-free DNA molecules in plasma has opened up numerous opportunities in noninvasive diagnosis. Cell-free DNA molecules have become increasingly recognized as promising biomarkers for detection and management of many diseases. The advent of next generation sequencing has provided unprecedented opportunities to scrutinize the characteristics of cell-free DNA molecules in plasma in a genome-wide fashion and at single-base resolution. Consequently, clinical applications of circulating cell-free DNA analysis have not only revolutionized noninvasive prenatal diagnosis but also facilitated cancer detection and monitoring toward an era of blood-based personalized medicine. With the remarkably increasing throughput and lowering cost of next generation sequencing, bioinformatics analysis becomes increasingly demanding to understand the large amount of data generated by these sequencing platforms. In this Review, we highlight the major bioinformatics algorithms involved in the analysis of cell-free DNA sequencing data. Firstly, we briefly describe the biological properties of these molecules and provide an overview of the general bioinformatics approach for the analysis of cell-free DNA. Then, we discuss the specific upstream bioinformatics considerations concerning the analysis of sequencing data of circulating cell-free DNA, followed by further detailed elaboration on each key clinical situation in noninvasive prenatal diagnosis and cancer management where downstream bioinformatics analysis is heavily involved. We also discuss bioinformatics analysis as well as clinical applications of the newly developed massively parallel bisulfite sequencing of cell-free DNA. Finally, we offer our perspectives on the future development of bioinformatics in noninvasive diagnosis.
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146
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Brady P, Brison N, Van Den Bogaert K, de Ravel T, Peeters H, Van Esch H, Devriendt K, Legius E, Vermeesch JR. Clinical implementation of NIPT - technical and biological challenges. Clin Genet 2015; 89:523-30. [PMID: 25867715 DOI: 10.1111/cge.12598] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 03/19/2015] [Accepted: 04/09/2015] [Indexed: 02/03/2023]
Abstract
Non-invasive prenatal testing (NIPT) for fetal aneuploidy detection is increasingly being offered in the clinical setting. Whereas the majority of tests only report fetal trisomies 21, 18 and 13, genome-wide analyses have the potential to detect other fetal, as well as maternal, aneuploidies. In this review, we discuss the technical and clinical advantages and challenges associated with genome-wide cell-free fetal DNA profiling.
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Affiliation(s)
- P Brady
- Centre for Human Genetics, KU Leuven, University Hospital Leuven, Leuven, Belgium
| | - N Brison
- Centre for Human Genetics, KU Leuven, University Hospital Leuven, Leuven, Belgium
| | - K Van Den Bogaert
- Centre for Human Genetics, KU Leuven, University Hospital Leuven, Leuven, Belgium
| | - T de Ravel
- Centre for Human Genetics, KU Leuven, University Hospital Leuven, Leuven, Belgium
| | - H Peeters
- Centre for Human Genetics, KU Leuven, University Hospital Leuven, Leuven, Belgium
| | - H Van Esch
- Centre for Human Genetics, KU Leuven, University Hospital Leuven, Leuven, Belgium
| | - K Devriendt
- Centre for Human Genetics, KU Leuven, University Hospital Leuven, Leuven, Belgium
| | - E Legius
- Centre for Human Genetics, KU Leuven, University Hospital Leuven, Leuven, Belgium
| | - J R Vermeesch
- Centre for Human Genetics, KU Leuven, University Hospital Leuven, Leuven, Belgium
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147
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Zhang H, Gao Y, Jiang F, Fu M, Yuan Y, Guo Y, Zhu Z, Lin M, Liu Q, Tian Z, Zhang H, Chen F, Lau TK, Zhao L, Yi X, Yin Y, Wang W. Non-invasive prenatal testing for trisomies 21, 18 and 13: clinical experience from 146,958 pregnancies. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2015; 45:530-8. [PMID: 25598039 DOI: 10.1002/uog.14792] [Citation(s) in RCA: 244] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Revised: 01/04/2015] [Accepted: 01/09/2015] [Indexed: 05/09/2023]
Abstract
OBJECTIVES To report the clinical performance of massively parallel sequencing-based non-invasive prenatal testing (NIPT) in detecting trisomies 21, 18 and 13 in over 140,000 clinical samples and to compare its performance in low-risk and high-risk pregnancies. METHODS Between 1 January 2012 and 31 August 2013, 147,314 NIPT requests to screen for fetal trisomies 21, 18 and 13 using low-coverage whole-genome sequencing of plasma cell-free DNA were received. The results were validated by karyotyping or follow-up of clinical outcomes. RESULTS NIPT was performed and results obtained in 146,958 samples, for which outcome data were available in 112,669 (76.7%). Repeat blood sampling was required in 3213 cases and 145 had test failure. Aneuploidy was confirmed in 720/781 cases positive for trisomy 21, 167/218 cases positive for trisomy 18 and 22/67 cases positive for trisomy 13 on NIPT. Nine false negatives were identified, including six cases of trisomy 21 and three of trisomy 18. The overall sensitivity of NIPT was 99.17%, 98.24% and 100% for trisomies 21, 18 and 13, respectively, and specificity was 99.95%, 99.95% and 99.96% for trisomies 21, 18 and 13, respectively. There was no significant difference in test performance between the 72,382 high-risk and 40,287 low-risk subjects (sensitivity, 99.21% vs. 98.97% (P = 0.82); specificity, 99.95% vs. 99.95% (P = 0.98)). The major factors contributing to false-positive and false-negative NIPT results were maternal copy number variant and fetal/placental mosaicism, but fetal fraction had no effect. CONCLUSIONS Using a stringent protocol, the good performance of NIPT shown by early validation studies can be maintained in large clinical samples. This technique can provide equally high sensitivity and specificity in screening for trisomy 21 in a low-risk, as compared to high-risk, population.
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Affiliation(s)
- H Zhang
- BGI-Diagnostics, Shenzhen, China; BGI Clinical Laboratories-Shenzen, Shenzhen, China
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148
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Snyder MW, Simmons LE, Kitzman JO, Coe BP, Henson JM, Daza RM, Eichler EE, Shendure J, Gammill HS. Copy-number variation and false positive prenatal aneuploidy screening results. N Engl J Med 2015; 372:1639-45. [PMID: 25830323 PMCID: PMC4411081 DOI: 10.1056/nejmoa1408408] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Investigations of noninvasive prenatal screening for aneuploidy by analysis of circulating cell-free DNA (cfDNA) have shown high sensitivity and specificity in both high-risk and low-risk cohorts. However, the overall low incidence of aneuploidy limits the positive predictive value of these tests. Currently, the causes of false positive results are poorly understood. We investigated four pregnancies with discordant prenatal test results and found in two cases that maternal duplications on chromosome 18 were the likely cause of the discordant results. Modeling based on population-level copy-number variation supports the possibility that some false positive results of noninvasive prenatal screening may be attributable to large maternal copy-number variants. (Funded by the National Institutes of Health and others.).
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Affiliation(s)
- Matthew W Snyder
- From the Department of Genome Sciences (M.W.S., J.O.K., B.P.C., R.M.D., E.E.E., J.S.), Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology (L.E.S., J.M.H., H.S.G.), and Howard Hughes Medical Institute (E.E.E.), University of Washington, and the Clinical Research Division, Fred Hutchinson Cancer Research Center (H.S.G.) - both in Seattle
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149
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Wald NJ, Bestwick JP. Performance of antenatal reflex DNA screening for Down's syndrome. J Med Screen 2015; 22:168-74. [PMID: 25882667 DOI: 10.1177/0969141315581005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 03/17/2015] [Indexed: 11/16/2022]
Abstract
OBJECTIVE Maternal plasma DNA analysis has a high but imperfect antenatal Down's syndrome screening performance. We aimed to determine the effect of combining DNA testing with current tests. METHODS In our modelled screening protocol, women provide two samples, one serum sample for a Combined test, and a plasma sample for a possible DNA test. Women with a Combined test risk above a specified level have a DNA test using the plasma sample without the need to recall them for another sample and counselling (ie. in a reflex manner). Women with a failed DNA test after a second attempt using a fresh plasma sample have an Integrated test. Screening performance was estimated according to the proportion of women reflexed to DNA testing and compared with universal DNA testing. RESULTS Reflexing 10% of women to a DNA test yields a 91% detection rate (DR) for a 0.025% false-positive rate (FPR) and no failed tests, compared with a 98% DR, 0.2% FPR and a 2.5% test failure rate with universal DNA testing (94% for 0.046% if 20% reflexed). DNA test failure rate has little influence on screening performance CONCLUSION Reflex DNA testing substantially reduces the FPR with a relatively small loss in detection compared with universal DNA testing, and reduces patient anxiety by avoiding the recall of women for DNA testing.
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Affiliation(s)
- Nicholas J Wald
- Wolfson Institute of Preventive Medicine, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ
| | - Jonathan P Bestwick
- Wolfson Institute of Preventive Medicine, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ
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Allyse M, Sayres LC, Goodspeed T, Michie M, Cho MK. "Don't Want No Risk and Don't Want No Problems": Public Understandings of the Risks and Benefits of Non-Invasive Prenatal Testing in the United States. AJOB Empir Bioeth 2015; 6:5-20. [PMID: 25932463 DOI: 10.1080/23294515.2014.994722] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
BACKGROUND The recent availability of new non-invasive prenatal genetic tests for fetal aneuploidy has raised questions concerning whether and how these new tests will be integrated into prenatal medical care. Among the many factors to be considered are public understandings and preferences about prenatal testing mechanisms and the prospect of fetal aneuploidy. METHODS To address these issues, we conducted a nation-wide mixed-method survey of 2,960 adults in the United States to explore justifications for choices among prenatal testing mechanisms. Open responses were qualitatively coded and grouped by theme. RESULTS Respondents cited accuracy, followed by cost, as the most significant aspects of prenatal testing. Acceptance of testing was predicated on differing valuations of knowledge and on personal and religious beliefs. Trust in the medical establishment, attitudes towards risk, and beliefs about health and illness were also considered relevant. CONCLUSIONS Although a significant portion of the sample population valued the additional accuracy provided by the new non-invasive tests, they nevertheless expressed concerns over high costs. Furthermore, participants continued to express reservations about the value of prenatal genetic information per se, regardless of how it was obtained.
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Affiliation(s)
- Megan Allyse
- Institute for Health and Aging, University of California San Francisco
| | | | | | - Marsha Michie
- Institute for Health and Aging, University of California San Francisco
| | - Mildred K Cho
- Stanford Center for Biomedical Ethics and Department of Pediatrics, Stanford Medical School
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