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Williams J, Benn P. Single gene non-invasive prenatal testing when the father is not available for testing; concerns regarding Wynn et al., Prenatal Diagnosis 2023. 43:1344-54. Prenat Diagn 2024; 44:527-528. [PMID: 37991283 DOI: 10.1002/pd.6468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023]
Affiliation(s)
- John Williams
- Reproductive Genetics, Cedars-Sinai Medical Center, Los Angeles, California, USA
- David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Peter Benn
- UConn Health, Farmington, Connecticut, USA
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Souter V, Becraft E, Brummitt S, Gall BJ, Prigmore B, Wang Y, Benn P. Reproductive Carrier Screening: Identifying Families at Risk for Familial Hypercholesterolemia in the United States. Circ Genom Precis Med 2024; 17:e004457. [PMID: 38506081 PMCID: PMC11019987 DOI: 10.1161/circgen.123.004457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 03/10/2024] [Indexed: 03/21/2024]
Abstract
BACKGROUND Familial hypercholesterolemia is a treatable genetic condition but remains underdiagnosed. We reviewed the frequency of pathogenic or likely pathogenic (P/LP) variants in the LDLR gene in female individuals receiving reproductive carrier screening. METHODS This retrospective observational study included samples from female patients (aged 18-55 years) receiving a 274-gene carrier screening panel from January 2020 to September 2022. LDLR exons and their 10 base pair flanking regions were sequenced. Carrier frequency for P/LP variants was calculated for the entire population and by race/ethnicity. The most common variants and their likely functional effects were evaluated. RESULTS A total of 91 637 tests were performed on women with race/ethnicity reported as Asian (8.8%), Black (6.1%), Hispanic (8.5%), White (29.0%), multiple or other (15.0%), and missing (33.0%). Median age was 32.8 years with 83 728 (91%) <40 years. P/LP LDLR variants were identified in 283 samples (1 in 324). No patients were identified with >1 P/LP variant. LDLR carrier frequency was higher in Asian (1 in 191 [95% CI, 1 in 142-258]) compared with White (1 in 417 [95% CI, 1 in 326-533]; P<0.001) or Black groups (1 in 508 [95% CI, 1 in 284-910]; P=0.004). The most common variants differed between populations. Of all variants, at least 25.0% were predicted as null variants. CONCLUSIONS P/LP variants in LDLR are common. Expanding the use of reproductive carrier screening to include genes associated with FH presents another opportunity to identify people predisposed to cardiovascular disease.
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Affiliation(s)
- Vivienne Souter
- Natera, Inc, Austin, TX (V.S., E.B., S.B., B.J.G., B.P., Y.W.)
| | - Emily Becraft
- Natera, Inc, Austin, TX (V.S., E.B., S.B., B.J.G., B.P., Y.W.)
| | | | - Bryan J. Gall
- Natera, Inc, Austin, TX (V.S., E.B., S.B., B.J.G., B.P., Y.W.)
| | | | - Yang Wang
- Natera, Inc, Austin, TX (V.S., E.B., S.B., B.J.G., B.P., Y.W.)
| | - Peter Benn
- University of Connecticut Health Center, Farmington, CT (P.B.)
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Souter V, Prigmore B, Becraft E, Repass E, Smart T, Sanapareddy N, Schweitzer M, Ortiz JB, Wang Y, Benn P. Reproductive Carrier Screening Results With Maternal Health Implications During Pregnancy. Obstet Gynecol 2023; 142:1208-1216. [PMID: 37562044 DOI: 10.1097/aog.0000000000005318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 06/22/2023] [Indexed: 08/12/2023]
Abstract
OBJECTIVE To identify conditions on a reproductive carrier screening panel with the potential for carrier manifestations during pregnancy and review the implications for obstetric care. METHODS This was a retrospective cross-sectional study of consecutive samples from female patients aged 18-55 years submitted to a commercial laboratory for a 274-gene carrier screening panel (January 2020 to September 2022). A literature review was performed to identify genes on the panel with potential for pregnancy complications in carriers. Carrier expression and published recommendations for clinical management were reviewed. RESULTS We identified 12 genes with potential for carrier manifestations during pregnancy based on reports in the literature: nine with manifestations irrespective of the fetal genetic status ( ABCB11 , COL4A3 , COL4A4 , COL4A5 , DMD , F9 , F11 , GLA , and OTC ) and three ( CPT1A , CYP19A1 , and HADHA ) with manifestations only if the fetus is affected by the condition. Manifestations included cardiomyopathy, hemorrhage, gestational hypertensive disorders, cholestasis of pregnancy, acute fatty liver, hyperammonemic crisis, and maternal virilization. Published recommendations for carrier management were identified for 11 of the 12 genes. Of 91,637 tests performed during the study period, a pathogenic or likely pathogenic variant was identified in 2,139 (2.3%), giving a carrier frequency for any of the 12 genes of 1 in 43 (95% CI 1/41-45) 1,826 (2.0%) of the study population were identified as carriers for one of the nine genes with the potential for carrier manifestations irrespective of an affected or unaffected fetus. CONCLUSION Approximately 1 in 40 female patients were identified as carriers for a condition with potential for maternal manifestations in pregnancy, including some serious or even life-threatening complications. Obstetric care professionals should be aware of the possibility of pregnancy complications among carriers and the available recommendations for management. FUNDING SOURCE This study was funded by Natera, Inc.
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Affiliation(s)
- Vivienne Souter
- Natera, Inc., Austin, Texas; and the University of Connecticut Health Center, Farmington, Connecticut
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Benn P. Correspondence on "Maternal carrier screening with single-gene NIPS provides accurate fetal risk assessments for recessive conditions" by Hoskovec et al. Genet Med 2023; 25:100902. [PMID: 37522893 DOI: 10.1016/j.gim.2023.100902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 02/16/2023] [Accepted: 02/22/2023] [Indexed: 08/01/2023] Open
Affiliation(s)
- Peter Benn
- Professor Emeritus, Department of Obstetrics and Gynecology, UCONN Health, Farmington, CT.
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Benn P, Cuckle H. Overview of Noninvasive Prenatal Testing (NIPT) for the Detection of Fetal Chromosome Abnormalities; Differences in Laboratory Methods and Scope of Testing. Clin Obstet Gynecol 2023; 66:536-556. [PMID: 37650667 DOI: 10.1097/grf.0000000000000803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Although nearly all noninvasive prenatal testing is currently based on analyzing circulating maternal cell-free DNA, the technical methods usedvary considerably. We review the different methods. Based on validation trials and clinical experience, there are mostly relatively small differences in screening performance for trisomies 21, 18, and 13 in singleton pregnancies. Recent reports show low no-call rates for all methods, diminishing its importance when choosing a laboratory. However, method can be an important consideration for twin pregnancies, screening for sex chromosome abnormalities, microdeletion syndromes, triploidy, molar pregnancies, rare autosomal trisomies, and segmental imbalances, and detecting maternal chromosome abnormalities.
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Affiliation(s)
- Peter Benn
- Department of Obstetrics and Gynecology, University of Connecticut Health Center, Farmington, Connecticut
| | - Howard Cuckle
- Department of Obstetrics and Gynecology, Faculty of Medicine, Tel Aviv University, Israel
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Affiliation(s)
- Peter Benn
- Department of Genetics and Genome Sciences, UConn Health, 263 Farmington Avenue, Farmington, CT, 06032, USA.
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Grati FR, Bestetti I, De Siero D, Malvestiti F, Villa N, Sala E, Crosti F, Parisi V, Nardone AM, Di Giacomo G, Pettinari A, Tortora G, Montaldi A, Calò A, Saccilotto D, Zanchetti S, Celli P, Guerneri S, Silipigni R, Cardarelli L, Lippi E, Cavani S, Malacarne M, Genesio R, Beltrami N, Pittalis MC, Desiderio L, Gentile M, Ficarella R, Recalcati MP, Catusi I, Garzo M, Miele L, Corti C, Ghezzo S, Bertini V, Cambi F, Valetto A, Facchinetti B, Bernardini L, Capalbo A, Balducci F, Pelo E, Minuti B, Pescucci C, Giuliani C, Renieri A, Longo I, Tita R, Castello G, Casalone R, Righi R, Raso B, Civolani A, Muzi MC, di Natale M, Varriale L, Gasperini D, Nuzzi MC, Cellamare A, Casieri P, Busuito R, Ceccarini C, Cesarano C, Privitera O, Melani D, Menozzi C, Falcinelli C, Calabrese O, Battaglia P, Tanzariello A, Stampalija T, Ardisia C, Gasparini P, Benn P, Novelli A. Positive predictive values and outcomes for uninformative cell-free DNA tests: An Italian multicentric Cytogenetic and cytogenomic Audit of diagnOstic testing (ICARO study). Prenat Diagn 2022; 42:1575-1586. [PMID: 36403097 DOI: 10.1002/pd.6271] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 11/10/2022] [Accepted: 11/11/2022] [Indexed: 11/21/2022]
Abstract
OBJECTIVES To establish the positive predictive values (PPV) of cfDNA testing based on data from a nationwide survey of independent clinical cytogenetics laboratories. METHODS Prenatal diagnostic test results obtained by Italian laboratories between 2013 and March 2020 were compiled for women with positive non-invasive prenatal tests (NIPT), without an NIPT result, and cases where there was sex discordancy between the NIPT and ultrasound. PPV and other summary data were reviewed. RESULTS Diagnostic test results were collected for 1327 women with a positive NIPT. The highest PPVs were for Trisomy (T) 21 (624/671, 93%) and XYY (26/27, 96.3%), while rare autosomal trisomies (9/47, 19.1%) and recurrent microdeletions (8/55, 14.5%) had the lowest PPVs. PPVs for T21, T18, and T13 were significantly higher when diagnostic confirmation was carried out on chorionic villi (97.5%) compared to amniotic fluid (89.5%) (p < 0.001). In 19/139 (13.9%), of no result cases, a cytogenetic abnormality was detected. Follow-up genetic testing provided explanations for 3/6 cases with a fetal sex discordancy between NIPT and ultrasound. CONCLUSIONS NIPT PPVs differ across the conditions screened and the tissues studied in diagnostic testing. This variability, issues associated with fetal sex discordancy, and no results, illustrate the importance of pre- and post-test counselling.
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Affiliation(s)
- Francesca Romana Grati
- R&D, Cytogenetics, Molecular Genetics and Medical Genetics Unit, TOMA Advanced Biomedical Assays S.p.A, Busto Arsizio, Italy
| | - Ilaria Bestetti
- Laboratorio di Genetica Medica, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milano, Italy.,Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Milan, Italy
| | - Daria De Siero
- R&D, Cytogenetics, Molecular Genetics and Medical Genetics Unit, TOMA Advanced Biomedical Assays S.p.A, Busto Arsizio, Italy
| | - Francesca Malvestiti
- R&D, Cytogenetics, Molecular Genetics and Medical Genetics Unit, TOMA Advanced Biomedical Assays S.p.A, Busto Arsizio, Italy
| | - Nicoletta Villa
- UOS Citogenetica e Genetica Medica - ASST-Monza, Ospedale San Gerardo, Università di Milano-Bicocca, Monza, Italy
| | - Elena Sala
- UOS Citogenetica e Genetica Medica - ASST-Monza, Ospedale San Gerardo, Università di Milano-Bicocca, Monza, Italy
| | - Francesca Crosti
- UOS Citogenetica e Genetica Medica - ASST-Monza, Ospedale San Gerardo, Università di Milano-Bicocca, Monza, Italy
| | - Valentina Parisi
- U.O.C. Laboratorio di Genetica Medica, Ospedale Pediatrico del Bambino Gesù, IRCCS, Roma, Italy
| | - Anna Maria Nardone
- U.O.C. Laboratorio di Genetica Medica, Policlinico Tor Vergata, Roma, Italy
| | | | - Antonella Pettinari
- SOSD Malattie Rare e Citogenetica, Azienda Ospedaliero-Universitaria Ospedali Riuniti, Ancona, Italy
| | - Giada Tortora
- SOSD Malattie Rare e Citogenetica, Azienda Ospedaliero-Universitaria Ospedali Riuniti, Ancona, Italy
| | | | - Annapaola Calò
- U.O.S. Laboratorio di Genetica, AULSS8 Berica, Vicenza, Italy
| | | | - Sara Zanchetti
- U.O.S. Laboratorio di Genetica, AULSS8 Berica, Vicenza, Italy
| | - Paola Celli
- U.O.S. Laboratorio di Genetica, AULSS8 Berica, Vicenza, Italy
| | - Silvana Guerneri
- Laboratorio di Genetica Medica, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milano, Italy
| | - Rosamaria Silipigni
- Laboratorio di Genetica Medica, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milano, Italy
| | - Laura Cardarelli
- Laboratorio di Genetica medica, Lifebrain, Gruppo Cerba HealthCare, c/o RDI, Rete Diagnostica Italiana, Limena, Italy
| | - Elisabetta Lippi
- Laboratorio di Genetica medica, Lifebrain, Gruppo Cerba HealthCare, c/o RDI, Rete Diagnostica Italiana, Limena, Italy
| | - Simona Cavani
- U.O.C. Laboratorio di Genetica Umana, IRCCS G. Gaslini, Genova, Italy
| | - Michela Malacarne
- U.O.C. Laboratorio di Genetica Umana, IRCCS G. Gaslini, Genova, Italy
| | - Rita Genesio
- DAI medicina di laboratorio e trasfusionale AOU Federico II, Napoli, Italy
| | | | - Maria Carla Pittalis
- IRCCS Azienda Ospedaliero Universitaria di Bologna, Policlinico di Sant'Orsola, Bologna, Italy
| | - Laura Desiderio
- IRCCS Azienda Ospedaliero Universitaria di Bologna, Policlinico di Sant'Orsola, Bologna, Italy
| | - Mattia Gentile
- Dipartimento di Medicina della Riproduzione, UOC Genetica Medica, ASL BARI, Bari, Italy
| | - Romina Ficarella
- Dipartimento di Medicina della Riproduzione, UOC Genetica Medica, ASL BARI, Bari, Italy
| | - Maria Paola Recalcati
- Laboratorio di Citogenetica e Genetica Molecolare, Istituto Auxologico Italiano, IRCCS, Milano, Italy
| | - Ilaria Catusi
- Laboratorio di Citogenetica e Genetica Molecolare, Istituto Auxologico Italiano, IRCCS, Milano, Italy
| | - Maria Garzo
- Laboratorio di Citogenetica e Genetica Molecolare, Istituto Auxologico Italiano, IRCCS, Milano, Italy
| | | | | | - Sara Ghezzo
- Laboratorio di Citogenetica - U.O.C. Genetica Medica, Centro Servizi Pievesestina - Laboratorio Unico, AUSL ROMAGNA, Cesena, Italy
| | - Veronica Bertini
- SOD Citogenetica, Azienda Ospedaliero Universitaria Pisana (AOUP), Pisa, Italy
| | - Francesca Cambi
- SOD Citogenetica, Azienda Ospedaliero Universitaria Pisana (AOUP), Pisa, Italy
| | - Angelo Valetto
- SOD Citogenetica, Azienda Ospedaliero Universitaria Pisana (AOUP), Pisa, Italy
| | - Barbara Facchinetti
- UOSD SMeL 4 Citogenetica e Genetica Medica, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Laura Bernardini
- Medical Genetics Division, IRCCS Casa Sollievo della Sofferenza Foundation, San Giovanni Rotondo, Italy
| | - Anna Capalbo
- Medical Genetics Division, IRCCS Casa Sollievo della Sofferenza Foundation, San Giovanni Rotondo, Italy
| | - Federica Balducci
- TECNOBIOS PRENATALE EUROGENLAB - Gruppo LIFE BRAIN Emilia-Romagna, Bologna, Italy
| | | | | | | | | | - Alessandra Renieri
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy.,Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, Italy
| | - Ilaria Longo
- Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, Italy
| | - Rossella Tita
- Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, Italy
| | - Giuseppe Castello
- Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, Italy
| | - Rosario Casalone
- SSD SMeL Citogenetica e Genetica Medica, ASST dei Settelaghi, Varese, Italy
| | - Rossana Righi
- SSD SMeL Citogenetica e Genetica Medica, ASST dei Settelaghi, Varese, Italy
| | - Barbara Raso
- ASL ROMA 1, Centro S.Anna, Dipartimento dei Laboratori, U.O.S.D. di Genetica medica, Roma, Italy
| | - Alessandro Civolani
- ASL ROMA 1, Centro S.Anna, Dipartimento dei Laboratori, U.O.S.D. di Genetica medica, Roma, Italy
| | - Maria Cristina Muzi
- ASL ROMA 1, Centro S.Anna, Dipartimento dei Laboratori, U.O.S.D. di Genetica medica, Roma, Italy
| | - Manuela di Natale
- ASL ROMA 1, Centro S.Anna, Dipartimento dei Laboratori, U.O.S.D. di Genetica medica, Roma, Italy
| | - Luigia Varriale
- UOSD Diagnostica Alta Complessità, Settore Genetica, Azienda Ospedaliera Ospedali Riuniti Marche Nord-Pesaro, Nord-Pesaro, Italy
| | - Daniela Gasperini
- Laboratorio Genetica e Genomica, Ospedale Microcitemico A.Cao, ARNAS Brotzu Cagliari, Cagliari, Italy
| | - Maria Cristina Nuzzi
- UOC Patologia Clinica - Sezione di Genetica Medica, Ospedale SS. Annunziata Taranto - ASL TARANTO, Taranto, Italy
| | - Angelo Cellamare
- UOC Patologia Clinica - Sezione di Genetica Medica, Ospedale SS. Annunziata Taranto - ASL TARANTO, Taranto, Italy
| | - Paola Casieri
- UOC Patologia Clinica - Sezione di Genetica Medica, Ospedale SS. Annunziata Taranto - ASL TARANTO, Taranto, Italy
| | - Rosa Busuito
- Laboratorio di Genetica Molecolare e Citogenetica - Sezione di Citogenetica, UOC Laboratorio Analisi - ASST Ovest Milanese, Legnano, Italy
| | | | - Carla Cesarano
- U.O.C Genetica Medica, Policlinico Riuniti Foggia, Foggia, Italy
| | - Orsola Privitera
- SOS Genetica e Diagnostica di Laboratorio, Azienda USL Toscana Centro, Presidio Ospedale S. Stefano, Prato, Italy
| | - Daniela Melani
- SOS Genetica e Diagnostica di Laboratorio, Azienda USL Toscana Centro, Presidio Ospedale S. Stefano, Prato, Italy
| | - Cristina Menozzi
- SSD Genetica Medica, Dipartimento Materno Infantile, AOU Policlinico Modena, Modena, Italy
| | - Cristina Falcinelli
- SSD Genetica Medica, Dipartimento Materno Infantile, AOU Policlinico Modena, Modena, Italy
| | - Olga Calabrese
- SSD Genetica Medica, Dipartimento Materno Infantile, AOU Policlinico Modena, Modena, Italy
| | - Paola Battaglia
- Laboratorio di Genetica, UOC Genetica Medica, AUSL Imola, Imola, Italy
| | | | - Tamara Stampalija
- Unit of Fetal Medicine and Prenatal Diagnosis, Institute for Maternal and Child Health, IRCCS Burlo Garofolo, Trieste, Italy.,Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
| | - Carmela Ardisia
- Genetica Medica IRCCS Ospedale "Burlo Garofolo", Trieste, Italy
| | - Paolo Gasparini
- Genetica Medica IRCCS Ospedale "Burlo Garofolo", Trieste, Italy
| | - Peter Benn
- Department of Obstetrics and Gynecology, University of Connecticut Health Center, Farmington, Connecticut, USA
| | - Antonio Novelli
- U.O.C. Laboratorio di Genetica Medica, Ospedale Pediatrico del Bambino Gesù, IRCCS, Roma, Italy
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Gall BJ, Smart TB, Munch R, Kolluri S, Tadepally H, Lim KPH, Demko ZP, Benn P, Souter V, Sanapareddy N, Keen‐Kim D. Assessment of an automated approach for variant interpretation in screening for monogenic disorders: A single-center study. Mol Genet Genomic Med 2022; 10:e2085. [PMID: 36333997 PMCID: PMC9747559 DOI: 10.1002/mgg3.2085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 10/21/2022] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND Automation has been introduced into variant interpretation, but it is not known how automated variant interpretation performs on a stand-alone basis. The purpose of this study was to evaluate a fully automated computerized approach. METHOD We reviewed all variants encountered in a set of carrier screening panels over a 1-year interval. Observed variants with high-confidence ClinVar interpretations were included in the analysis; those without high-confidence ClinVar entries were excluded. RESULTS Discrepancy rates between automated interpretations and high-confidence ClinVar entries were analyzed. Of the variants interpreted as positive (likely pathogenic or pathogenic) based on ClinVar information, 22.6% were classified as negative (variants of uncertain significance, likely benign or benign) variants by the automated method. Of the ClinVar negative variants, 1.7% were classified as positive by the automated software. On a per-case basis, which accounts for variant frequency, 63.4% of cases with a ClinVar high-confidence positive variant were classified as negative by the automated method. CONCLUSION While automation in genetic variant interpretation holds promise, there is still a need for manual review of the output. Additional validation of automated variant interpretation methods should be conducted.
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Affiliation(s)
| | | | | | | | | | | | | | - Peter Benn
- Genetics and Genome SciencesUniversity of Connecticut Health CenterFarmingtonConnecticutUSA
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Demko Z, Prigmore B, Benn P. A Critical Evaluation of Validation and Clinical Experience Studies in Non-Invasive Prenatal Testing for Trisomies 21, 18, and 13 and Monosomy X. J Clin Med 2022; 11:jcm11164760. [PMID: 36012999 PMCID: PMC9410356 DOI: 10.3390/jcm11164760] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 07/28/2022] [Accepted: 08/11/2022] [Indexed: 11/25/2022] Open
Abstract
Non-invasive prenatal testing (NIPT) for trisomies 21, 18, 13 and monosomy X is widely utilized with massively parallel shotgun sequencing (MPSS), digital analysis of selected regions (DANSR), and single nucleotide polymorphism (SNP) analyses being the most widely reported methods. We searched the literature to find all NIPT clinical validation and clinical experience studies between January 2011 and January 2022. Meta-analyses were performed using bivariate random-effects and univariate regression models for estimating summary performance measures across studies. Bivariate meta-regression was performed to explore the influence of testing method and study design. Subgroup and sensitivity analyses evaluated factors that may have led to heterogeneity. Based on 55 validation studies, the detection rate (DR) was significantly higher for retrospective studies, while the false positive rate (FPR) was significantly lower for prospective studies. Comparing the performance of NIPT methods for trisomies 21, 18, and 13 combined, the SNP method had a higher DR and lower FPR than other methods, significantly so for MPSS, though not for DANSR. The performance of the different methods in the 84 clinical experience studies was consistent with validation studies. Clinical positive predictive values of all NIPT methods improved over the last decade. We conclude that all NIPT methods are highly effective for fetal aneuploidy screening, with performance differences across methodologies.
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Affiliation(s)
| | | | - Peter Benn
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT 06030, USA
- Correspondence:
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Cuckle H, Benn P, Yaron Y. A Founding Father of Reproductive Genetics: Eugene Pergament (1933-2022). Prenat Diagn 2022; 42:959-961. [PMID: 35621153 DOI: 10.1002/pd.6187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
A Founding Father of Reproductive Genetics: Eugene Pergament (1933-2022) This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Howard Cuckle
- Columbia University Medical Center, Obstetrics and Gynecology, New York, New York, US
| | - Peter Benn
- University of Connecticut Health Center, Department of Genetics and Genome Sciences, Farmington, Connecticut, US
| | - Yuval Yaron
- Tel Aviv Sourasky Medical Center, Prenatal Diagnosis Unit, Genetic Institute, 6 Weizmann Street, Tel Aviv, Israel
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Kantor V, Jelsema R, Xu W, DiNonno W, Young K, Demko Z, Benn P. Non‐invasive prenatal screening for fetal triploidy using single nucleotide polymorphism (SNP)‐based testing: Differential Diagnosis And Clinical Management In Cases Showing An Extra Haplotype. Prenat Diagn 2022; 42:994-999. [PMID: 35574995 PMCID: PMC9539994 DOI: 10.1002/pd.6169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 05/06/2022] [Accepted: 05/11/2022] [Indexed: 12/02/2022]
Abstract
Objective An extra haplotype is infrequently encountered in single nucleotide polymorphism(SNP)‐based non‐invasive prenatal testing (NIPT) and is usually attributed to an undetected twin or triploidy. We reviewed a large series to establish relative frequencies of these outcomes and identify alternative causes. Methods In 515,804 women receiving NIPT from September 2017 through March 2019, all results with an extra haplotype were reviewed. Known viable and vanished twin pregnancies were excluded. For positive cases, pregnancy outcome information was sought. Results Of 1005 results with an extra haplotype (1 in 513), pregnancy outcome was available for 773 cases: 11% were confirmed or suspected triploidy; 65% to vanished twin; 10% with pregnancy loss. Rare explanations included complete mole, chimera, undisclosed donor egg pregnancy, maternal organ transplant and one instance of maternal neoplasm. Among triploid cases that were detected and independently confirmed, 23/27 (85%) were diandric. Conclusion SNP‐based NIPT, with detection of an extra haplotype, is 11% predictive of triploidy. For results with an extra haplotype, ultrasound is recommended to establish viability, evaluate for twins (viable or vanished), and detect findings consistent with triploidy. Review of patient history, serum screening, and ultrasound will reduce the number of CVS or amniocenteses necessary to confirm a diagnosis of triploidy.
What's already known about this topic?
Both digynic and diandric triploidy are occasionally seen in pregnancies but are extremely rare in live‐births In cell‐free DNA prenatal screening, the presence of an extra haplotype could be indicative of either twin pregnancy or triploidy
What does this study add?
Outcomes for a large series of prenatal screening tests where an extra haplotype was identified in cell‐free DNA Complete moles, chimeras, transplantation, and donor egg are additional explanations for extra haplotypes We discuss prenatal management when an extra haplotype is observed in cell‐free DNA
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Affiliation(s)
| | | | | | | | | | | | - Peter Benn
- Department of Genetics and Genome Sciences UConn Health Farmington San Carlos CT USA
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Mohan P, Lemoine J, Trotter C, Rakova I, Billings P, Peacock S, Kao C, Wang Y, Xia F, Eng CM, Benn P. Clinical experience with non-invasive prenatal screening for single-gene disorders. Ultrasound Obstet Gynecol 2022; 59:33-39. [PMID: 34358384 PMCID: PMC9302116 DOI: 10.1002/uog.23756] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 07/29/2021] [Accepted: 08/02/2021] [Indexed: 05/10/2023]
Abstract
OBJECTIVE To assess the performance of a non-invasive prenatal screening test (NIPT) for a panel of dominant single-gene disorders (SGD) with a combined population incidence of 1 in 600. METHODS Cell-free fetal DNA isolated from maternal plasma samples accessioned from 14 April 2017 to 27 November 2019 was analyzed by next-generation sequencing, targeting 30 genes, to look for pathogenic or likely pathogenic variants implicated in 25 dominant conditions. The conditions included Noonan spectrum disorders, skeletal disorders, craniosynostosis syndromes, Cornelia de Lange syndrome, Alagille syndrome, tuberous sclerosis, epileptic encephalopathy, SYNGAP1-related intellectual disability, CHARGE syndrome, Sotos syndrome and Rett syndrome. NIPT-SGD was made available as a clinical service to women with a singleton pregnancy at ≥ 9 weeks' gestation, with testing on maternal and paternal genomic DNA to assist in interpretation. A minimum of 4.5% fetal fraction was required for test interpretation. Variants identified in the mother were deemed inconclusive with respect to fetal carrier status. Confirmatory prenatal or postnatal diagnostic testing was recommended for all screen-positive patients and follow-up information was requested. The screen-positive rates with respect to the clinical indication for testing were evaluated. RESULTS A NIPT-SGD result was available for 2208 women, of which 125 (5.7%) were positive. Elevated test-positive rates were observed for referrals with a family history of a disorder on the panel (20/132 (15.2%)) or a primary indication of fetal long-bone abnormality (60/178 (33.7%)), fetal craniofacial abnormality (6/21 (28.6%)), fetal lymphatic abnormality (20/150 (13.3%)) or major fetal cardiac defect (4/31 (12.9%)). For paternal age ≥ 40 years as a sole risk factor, the test-positive rate was 2/912 (0.2%). Of the 125 positive cases, follow-up information was available for 67 (53.6%), with none classified as false-positive. No false-negative cases were identified. CONCLUSIONS NIPT can assist in the early detection of a set of SGD, particularly when either abnormal ultrasound findings or a family history is present. Additional clinical studies are needed to evaluate the optimal design of the gene panel, define target populations and assess patient acceptability. NIPT-SGD offers a safe and early prenatal screening option. © 2021 The Authors. Ultrasound in Obstetrics & Gynecology published by John Wiley & Sons Ltd on behalf of International Society of Ultrasound in Obstetrics and Gynecology.
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Affiliation(s)
| | | | | | | | | | | | | | - Y. Wang
- Baylor GeneticsHoustonTXUSA
- Baylor College of MedicineHoustonTXUSA
| | - F. Xia
- Baylor GeneticsHoustonTXUSA
- Baylor College of MedicineHoustonTXUSA
| | - C. M. Eng
- Baylor GeneticsHoustonTXUSA
- Baylor College of MedicineHoustonTXUSA
| | - P. Benn
- Department of Genetics and Genome SciencesUniversity of Connecticut Health CenterFarmingtonCTUSA
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Benn P, Rebarber A. Non-invasive prenatal testing in the management of twin pregnancies. Prenat Diagn 2021; 41:1233-1240. [PMID: 34170028 PMCID: PMC8518532 DOI: 10.1002/pd.5989] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 06/03/2021] [Accepted: 06/05/2021] [Indexed: 12/02/2022]
Abstract
Twin pregnancies are common and associated with pregnancy complications and adverse outcomes. Prenatal clinical management is intensive and has been hampered by inferior screening and less acceptable invasive testing. For aneuploidy screening, meta‐analyses show that non‐invasive prenatal testing (NIPT) through analysis of cell‐free DNA (cf‐DNA) is superior to serum and ultrasound‐based tests. The positive predictive value for NIPT is driven strongly by the discriminatory power of the assay and only secondarily by the prior risk. Uncertainties in a priori risks for aneuploidies in twin pregnancies are therefore of lesser importance with NIPT. Additional information on zygosity can be obtained using NIPT. Establishing zygosity can be helpful when chorionicity was not reliably established early in pregnancy or where the there is a concern for one versus two affected fetuses. In dizygotic twin pregnancies, individual fetal fractions can be measured to ensure that both values are satisfactory. Vanishing twins can be identified by NIPT. Although clinical utility of routinely detecting vanishing twins has not yet been demonstrated, there are individual cases where cf‐DNA analysis could be helpful in explaining unusual clinical or laboratory observations. We conclude that cf‐DNA analysis and ultrasound have synergistic roles in the management of multiple gestational pregnancies.
What's already known about this topic?
In singleton pregnancies, non‐invasive prenatal testing (NIPT) for fetal aneuploidy is more effective than conventional serum and ultrasound‐based screening tests. NIPT is more complex in dizygotic twin pregnancies due to the presence of two fetal genotypes. Overall fetal fraction is higher in twin pregnancies but the individual contribution for each fetus is lower.
What does this study add?
A review of cell‐free DNA testing in twin pregnancies. Individual fetal fractions in dizygotic twin pregnancies can be measured. Zygosity can be established using NIPT and this can be particularly useful when there are concerns about chorionicity or determining whether one versus two fetuses are affected. Vanishing twins can be detected through NIPT and this testing could be considered for some apparently singleton pregnancies with complications.
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Affiliation(s)
- Peter Benn
- Department of Genetics and Genome Sciences, UConn Health, Farmington, Connecticut, USA
| | - Andrei Rebarber
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Division of Maternal Fetal Medicine, Englewood Hospital, Englewood, New Jersey, USA
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14
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Grati FR, Malvestiti F, Gallazzi G, Saragozza S, Grimi B, Agrati C, Branca L, Palumbo F, Trotta A, Chinetti S, Simoni G, Ferreira J, Benn P. Performance of conventional cytogenetic analysis on chorionic villi when only one cell layer, cytotrophoblast or mesenchyme alone, is analyzed. Prenat Diagn 2021; 41:652-660. [PMID: 33782989 DOI: 10.1002/pd.5941] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 03/11/2021] [Accepted: 03/22/2021] [Indexed: 02/04/2023]
Abstract
OBJECTIVE To provide an estimation of the probability of error when chorionic villi (CV) cytogenetic analysis is limited to a single placental layer; either a direct preparation (Dir) or long-term culture (LTC). METHODS We retrospectively reviewed cytogenetic studies on 81,593 consecutive CV samples in which both Dir and LTC were analyzed. All mosaic cases received amniocentesis. The false omission and false discovery rates were calculated by assessing the results that would have been reported when analysis was limited to either Dir or LTC. RESULTS For all abnormalities combined, the proportion of normal Dir or LTC only reports that would have been inconsistent with a subsequent amniocentesis was 0.09% and 0.03%, respectively (false omissions). Among abnormal reports based on Dir or LTC alone, 8.01% and 3.17%, respectively, would be inconsistent with a subsequent amniocentesis result (false discoveries). Differences are present for individual abnormalities. CONCLUSIONS From the perspective of identifying all abnormalities of potential clinical significance, the analysis of both placental layers is optimal. LTC alone is the preferred approach if only one layer of placenta is to be analyzed. Although rare, it is important to acknowledge that one cell layer analysis alone can cause misdiagnosis due to undetected mosaicism.
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Affiliation(s)
- Francesca Romana Grati
- Unit of Research and Development, Cytogenetics and Medical Genetics TOMA, Advanced Biomedical Assays, Impact Lab, Varese, Italy
| | - Francesca Malvestiti
- Unit of Research and Development, Cytogenetics and Medical Genetics TOMA, Advanced Biomedical Assays, Impact Lab, Varese, Italy
| | - Gloria Gallazzi
- Unit of Research and Development, Cytogenetics and Medical Genetics TOMA, Advanced Biomedical Assays, Impact Lab, Varese, Italy
| | - Silvia Saragozza
- Unit of Research and Development, Cytogenetics and Medical Genetics TOMA, Advanced Biomedical Assays, Impact Lab, Varese, Italy
| | - Beatrice Grimi
- Unit of Research and Development, Cytogenetics and Medical Genetics TOMA, Advanced Biomedical Assays, Impact Lab, Varese, Italy
| | - Cristina Agrati
- Unit of Research and Development, Cytogenetics and Medical Genetics TOMA, Advanced Biomedical Assays, Impact Lab, Varese, Italy
| | - Lara Branca
- Unit of Research and Development, Cytogenetics and Medical Genetics TOMA, Advanced Biomedical Assays, Impact Lab, Varese, Italy
| | - Federica Palumbo
- Unit of Research and Development, Cytogenetics and Medical Genetics TOMA, Advanced Biomedical Assays, Impact Lab, Varese, Italy
| | - Anna Trotta
- Unit of Research and Development, Cytogenetics and Medical Genetics TOMA, Advanced Biomedical Assays, Impact Lab, Varese, Italy
| | - Sara Chinetti
- Unit of Research and Development, Cytogenetics and Medical Genetics TOMA, Advanced Biomedical Assays, Impact Lab, Varese, Italy
| | - Giuseppe Simoni
- Unit of Research and Development, Cytogenetics and Medical Genetics TOMA, Advanced Biomedical Assays, Impact Lab, Varese, Italy
| | - Jose Ferreira
- Faculty of Medicine, Eduardo Mondlane University, Maputo, Mozambique.,Department of Obstetrics and Gynecology, Maputo Central Hospital, Maputo, Mozambique
| | - Peter Benn
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, Connecticut, USA
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Abstract
The presence of high levels of aneuploidy in oocytes and early embryos and their fate is of considerable scientific and clinical importance. The Origins of Aneuploidy Research Consortium (OARC) was established to promote interdisciplinary communication and collaborative research into this topic. Under the umbrella of OARC, a series of papers has now been published in this Special Issue of Prenatal Diagnosis. Recent studies have transformed the view that aneuploidy is usually attributable to meiotic non-disjunction. The molecular basis for the association between meiotic error and maternal age is becoming understood. The clinical significance of mitotic instability in the earliest cells divisions of the embryo is also becoming clearer. An error in the segregation of one or more whole chromosomes from a parent does not invariably result in a non-viable pregnancy or an abnormal outcome. Epidemiologic data allows an assessment of in utero viability, the effect of maternal age, and secondary factors that may affect aneuploidy prevalence. We advocate careful use of nomenclature and revision of educational materials to more accurately explain the complex and often nuanced mechanisms. OARC plans to hold additional workshops, promote additional publications and offer educational resources.
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Affiliation(s)
- Peter Benn
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, Connecticut, USA
| | - Howard Cuckle
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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Benn P. Uniparental disomy: Origin, frequency, and clinical significance. Prenat Diagn 2021; 41:564-572. [PMID: 33179335 DOI: 10.1002/pd.5837] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 06/28/2020] [Accepted: 09/29/2020] [Indexed: 02/06/2023]
Abstract
Uniparental disomy (UPD) is defined as two copies of a whole chromosome derived from the same parent. There can be multiple mechanisms that lead to UPD; these are reviewed in the context of contemporary views on the mechanism leading to aneuploidy. Recent studies indicate that UPD is rare in an apparently healthy population and also rare in spontaneous abortion tissues. The most common type of UPD is a maternal heterodisomy (both maternal allele sets present). Isodisomy (a duplicated single set of alleles) or segmental loss of heterozygosity is sometimes encountered in SNP-based microarray referrals. Decisions regarding the most appropriate follow-up testing should consider the possibility of consanguinity (that will generally involve multiple regions), an imprinted gene disorder (chromosomes 6, 7, 11, 14, 15, 20), expression of an autosomal recessive disorder, and an occult aneuploid cell line that may be confined to the placenta. Upd(16)mat, per se, does not appear to be associated with an abnormal phenotype. UPD provides an insight into the history of early chromosome segregation error and understanding the rates and fate of these events are of key importance in the provision of fertility management and prenatal healthcare.
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Affiliation(s)
- Peter Benn
- Department of Genetics and Genome Sciences, UConn Health, Farmington, Connecticut, USA
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17
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Benn P. Obituary: Lillian
YF
Hsu,
MD
,
FFACMG. Prenat Diagn 2020. [DOI: 10.1002/pd.5773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Peter Benn
- Department of Genetics and Genome Sciences UCONN Health Farmington Connecticut USA
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18
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Cuckle H, Benn P. Review of epidemiological factors (other than maternal age) that determine the prevalence of common autosomal trisomies. Prenat Diagn 2020; 41:536-544. [PMID: 32895968 DOI: 10.1002/pd.5822] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 07/24/2020] [Accepted: 09/02/2020] [Indexed: 12/22/2022]
Abstract
The birth prevalence of each common autosomal trisomy (21, 18 and 13) increases with advancing maternal age and this is the most important epidemiological risk factor. Prevalence during pregnancy is also dependent on gestational age. Other factors claimed to influence prevalence include paternal age, ethnicity, family history, premature reproductive aging, parity, twinning, smoking, environmental exposures, maternal medical conditions, and predispositions. We review the evidence for these associations since they may provide insights into causal mechanisms. When investigating potential co-factors it is important to adequately allow for maternal age and minimize its confounding contribution. This is well illustrated by reports of an inverse paternal age effect where there is strong correlation between parental ages. Gestational age at diagnosis, availability of prenatal screening, diagnostic testing, and elective termination of affected pregnancies and healthcare disparities also confound the studies on ethnicity, medical conditions, and predispositions or environmental factors. Data from twin zygosity studies demonstrate the importance of differences in fetal viability for affected pregnancies. We conclude that existing epidemiological evidence for most of the co-factors discussed should currently be considered tenuous; history of Down syndrome, albeit biased, may be an exception. The co-factors may yet provide clues to hitherto poorly understood causal pathways.
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Affiliation(s)
- Howard Cuckle
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Peter Benn
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, Connecticut, USA
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Benn P, Grati FR. Aneuploidy in first trimester chorionic villi and spontaneous abortions: Windows into the origin and fate of aneuploidy through embryonic and fetal development. Prenat Diagn 2020; 41:519-524. [PMID: 32677063 DOI: 10.1002/pd.5795] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 05/25/2020] [Accepted: 07/13/2020] [Indexed: 12/12/2022]
Abstract
OBJECTIVE To review the mosaic autosomal trisomies in chorionic villi sample (CVS) trophoblasts, mesenchyme, and both cell lineages and to compare them with trisomies in spontaneous abortions. METHODS Mosaic autosomal trisomies from 76 102 diagnostic CVS tests were classified as involving trophoblasts, involving mesenchyme, or present in both. Autosomal trisomies in products of conception were based on 18 published studies. We evaluated correlates between trisomy frequency with chromosome size or number of protein coding genes in the imbalance. RESULTS Distinctly different patterns of trisomy were found in trophoblasts, mesenchyme, or both. In trisomic spontaneous abortions, there was a weak, borderline significant, inverse association between frequency and trisomic chromosome size and also with the number of protein coding genes involved (r = 0.43, P = 0.04 and r = 0.39, P = 0.07, respectively). These associations became stronger after excluding trisomy 16 (r = 0.52, P = 0.01 and r = 0.64, P = 0.001, respectively). Only CVS trisomies in both trophoblasts and mesenchyme resembled the trisomies found in spontaneous abortions and these were also associated with chromosome size and protein coding genes (r = 0.42, P = 0.05 and r = 0.57, P = 0.006, respectively). CONCLUSION The abnormalities seen in CVS differ from those reported in early embryos. From conception through birth, there are lineage-specific, evolving spectrums of aneuploidy in trophoblasts, mesenchyme, and fetus.
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Affiliation(s)
- Peter Benn
- Department of Genetics and Genome Sciences, UConn Health, Farmington, Connecticut, USA
| | - Francesca Romana Grati
- Unit of Research and Development, Cytogenetics and Medical Genetics, TOMA, Advanced Biomedical Assays S.p.A., Impact Lab Group, Busto Arsizio, Italy
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Okoli C, Schwenk A, Radford M, Myland M, Taylor S, Darley A, Barnes J, Fox A, Grimson F, Reeves I, Munshi S, Croucher A, Boxall N, Benn P, Paice A, van Wyk J, Khoo S. Polypharmacy and potential drug-drug interactions for people with HIV in the UK from the Climate-HIV database. HIV Med 2020; 21:471-480. [PMID: 32671950 PMCID: PMC7497154 DOI: 10.1111/hiv.12879] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/28/2020] [Indexed: 11/30/2022]
Abstract
Objectives People with HIV (PWHIV) are likely to need therapies for comorbidities as they age. We assessed risk of drug–drug interactions (DDIs) in PWHIV. Methods The Climate‐HIV electronic recording system was used to cross‐sectionally analyse records from PWHIV aged ≥ 18 years attending four UK HIV units with a current antiretroviral (ARV) prescription in February 2018. Antiretroviral and non‐ARV medications were categorized by clinical significance of DDIs (University of Liverpool DDI tool). Potential DDIs were predicted using treatment guidelines for commonly recorded comorbidities. Results Among 4630 PWHIV (44% female), 41% were ≥ 50 years old. The average number of non‐ARV comedications increased from < 1 for patients aged ≤ 24 years to > 5 for patients aged ≥ 75 years; 65% were taking one or more non‐ARV comedications. The median (interquartile range) number of non‐ARVs was 1 (0–2) and 2 (1–5) for those aged < 50 and ≥ 50 years, respectively. Common comorbidities/concurrent health conditions occurred more frequently in patients aged ≥ 50 years vs. < 50 (53% vs. 34%). Boosted protease inhibitors were associated with the highest proportion of contraindicated comedications; dolutegravir and raltegravir had the fewest. For non‐ARVs, sildenafil and quetiapine were most likely to result in DDIs. Guideline‐recommended treatments for hepatitis C, hepatitis B, and tuberculosis had the highest proportions of contraindications when combined with ARV regimens, while treatments for hepatitis C, malignancy, and mental health conditions had the highest proportion of combinations potentially causing DDIs requiring dose monitoring or adjustment. Conclusions Non‐ARV use by PWHIV is high and increases with age. Treatment decisions for ageing PWHIV should consider guideline recommendations for comorbidities.
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Affiliation(s)
- C Okoli
- ViiV Healthcare, Brentford, UK
| | - A Schwenk
- North Middlesex University Hospital NHS Trust, London, UK
| | | | - M Myland
- IQVIA Real World Insights, UK & Ireland, London, UK
| | - S Taylor
- Birmingham Heartlands HIV Service, Department of Infection and Immunology, Birmingham Heartlands Hospital, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - A Darley
- Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - J Barnes
- Birmingham Heartlands HIV Service, Department of Infection and Immunology, Birmingham Heartlands Hospital, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - A Fox
- Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - F Grimson
- IQVIA Real World Insights, UK & Ireland, London, UK
| | - I Reeves
- Homerton University Hospital NHS Foundation Trust, London, UK
| | - S Munshi
- Homerton University Hospital NHS Foundation Trust, London, UK
| | - A Croucher
- Homerton University Hospital NHS Foundation Trust, London, UK
| | - N Boxall
- IQVIA Real World Insights, UK & Ireland, London, UK
| | - P Benn
- ViiV Healthcare, Brentford, UK
| | - A Paice
- ViiV Healthcare, Brentford, UK
| | | | - S Khoo
- University of Liverpool, Liverpool, UK
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Westemeyer M, Saucier J, Wallace J, Prins SA, Shetty A, Malhotra M, Demko ZP, Eng CM, Weckstein L, Boostanfar R, Rabinowitz M, Benn P, Keen-Kim D, Billings P. Correction: Clinical experience with carrier screening in a general population: support for a comprehensive pan-ethnic approach. Genet Med 2020; 22:1282. [PMID: 32483296 PMCID: PMC7332416 DOI: 10.1038/s41436-020-0853-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Benn P, Martin K, McKanna T, Valenti E, Billings P, Demko Z. Combining the use of a fetal fraction-based risk algorithm and probability of an informative redraw in noninvasive prenatal testing for fetal aneuploidy. J Genet Couns 2019; 29:800-806. [PMID: 31872514 PMCID: PMC7586960 DOI: 10.1002/jgc4.1208] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 11/27/2019] [Accepted: 12/02/2019] [Indexed: 12/14/2022]
Abstract
Some women undergoing noninvasive prenatal testing (NIPT) do not receive an informative result due to low fetal fraction (FF). A proportion of these are at increased risk for fetal trisomy 13, 18, or triploidy, while others have no change from their prior risk. Women with an initial uninformative NIPT need to be counseled about any such change in their risk for fetal abnormality and also the probability that a redraw will be informative. To help in the decision making, we reviewed a dataset of single nucleotide polymorphism‐based NIPT with uninformative results where a redraw was received. Risk for trisomy 13, 18, or triploidy was evaluated using a fetal fraction‐based risk (FFBR) algorithm. Risk‐unchanged women were further analyzed using a regression model to determine the likelihood of an informative redraw. Of 2,644 women with an uninformative NIPT and a redraw, 1,147 (43.4%) were high risk for trisomy 13, 18, or triploidy. 1,497 (56.6%) were risk unchanged and, of these, 975 (65.1%) cases had an informative redraw (i.e., risks were available for 2,122 (80%) of those initially classified as uninformative). The regression model for the risk‐unchanged cases provided a new table for predicting an informative redraw. Likelihood of a successful redraw was significantly (p < .001) dependent on the initial FF, maternal weight, and time between blood draws. We conclude that the FFBR algorithm and the predictive model for an informative redraw provide complementary additions in the management of women presented with an initially uninformative SNP‐based NIPT due to low FF. We suggest approaches for the counseling and follow‐up testing for women with an initially uninformative NIPT.
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Hedriana H, Martin K, Saltzman D, Billings P, Demko Z, Benn P. Cell-free DNA fetal fraction in twin gestations in single-nucleotide polymorphism-based noninvasive prenatal screening. Prenat Diagn 2019; 40:179-184. [PMID: 31711265 PMCID: PMC7027570 DOI: 10.1002/pd.5609] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 10/19/2019] [Accepted: 10/26/2019] [Indexed: 12/14/2022]
Abstract
Objectives The performance of noninvasive prenatal screening (NIPS) for fetal aneuploidy in twin pregnancies is dependent on the amount of placentally derived cell‐free DNA, the “fetal fraction (FF),” present in maternal plasma. We report FF values in monozygotic (MZ) and dizygotic (DZ) pregnancies. Methods We reviewed FF in pregnancies at 10 to 20 completed weeks gestational age based on single‐nucleotide polymorphism (SNP)‐based NIPS where zygosity was routinely established in twin pregnancies. The cohort included 121 446 (96.3%) singleton, 1454 (1.2%) MZ, and 3161 (2.5%) DZ pregnancies. For DZ twins, individual FFs were measured. Results Combined FF for DZ and MZ fetuses were 35% and 26% greater than singletons, respectively. The individual FF contributions from each fetus in DZ twins were, on average, 32% less than singletons. FF in DZ twin pairs were moderately correlated (Pearson correlation coefficient.66). When a threshold of 2.8% FF was applied to define uninterpretable results, 1.7% (2102/121 446) of singletons, 0.8% (11/1454) of MZ pairs, and 5.6% (178/3161) of DZ pairs were uninterpretable. Conclusion For optimal aneuploidy NIPS in twin pregnancies, zygosity should be established and in DZ twins FF for both fetuses should be determined to identify those cases where results can be reliably interpreted. What's already known about this topic?
Adequate cell‐free fetal DNA (fetal fraction [FF]) is essential for noninvasive prenatal screening. FFs in twin pregnancies may be higher or lower than that found in singleton pregnancies.
What does this study add?
In this large series of twin pregnancies, the average total FF was higher than for singletons but the per fetus FF was lower. There can be large differences in the two FFs in dizygotic twin pregnancies. Optimal prenatal aneuploidy screening in twin pregnancies requires information on both zygosity and the individual FFs.
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Affiliation(s)
- Herman Hedriana
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of California Davis Health, Sacramento, CA
| | | | | | | | | | - Peter Benn
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT
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Affiliation(s)
- Peter Benn
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT, USA
| | - Francesca Romana Grati
- Unit of Research and Development, Cytogenetics and Medical Genetics TOMA, Advanced Biomedical Assays, Impact Lab Group, Busto Arsizio, Varese, Italy.
| | - Jose Ferreira
- Faculty of medicine, Eduardo Mondlane University, Maputo, Mozambique.,Department of Obstetrics and Gynecology, Maputo Central Hospital, Maputo, Mozambique; 5 Genomed S.A., Warsaw, Poland
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Benn P, Malvestiti F, Grimi B, Maggi F, Simoni G, Grati FR. Rare autosomal trisomies: comparison of detection through cell-free DNA analysis and direct chromosome preparation of chorionic villus samples. Ultrasound Obstet Gynecol 2019; 54:458-467. [PMID: 31237735 DOI: 10.1002/uog.20383] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 05/24/2019] [Accepted: 06/15/2019] [Indexed: 06/09/2023]
Abstract
OBJECTIVE Direct chromosome preparations of chorionic villus samples (CVS) and cell-free DNA (cfDNA) testing both involve analysis of the trophoblastic cell lineage. The aim of this study was to compare the spectrum of rare autosomal trisomies (RATs) detected by these two approaches and assess the available information on their clinical significance. METHODS Data from 10 reports on genome-wide cfDNA testing were pooled to determine which chromosomes were most frequently involved in RAT-positive cases, and pregnancy outcome information was reviewed. CVS information was obtained from an updated database of 76 102 consecutive CVS analyses performed over a period of 18 years at TOMA laboratory, in which trophoblastic and mesenchymal layers were analyzed and amniotic fluid cell analysis was recommended for RAT-positive cases. Chromosomes involved and presence of confined placental mosaicism, true fetal mosaicism and uniparental disomy (UPD) for imprinted chromosomes were assessed. Also evaluated were the frequency and types of RATs in products of conception. RESULTS RATs were present in 634 of 196 662 (0.32%) cfDNA samples and 237 of 57 539 (0.41%) CVS trophoblast samples (P < 0.01). The frequency of RATs varied over 8-fold between the cfDNA reports. Confirmation of abnormality through amniocentesis was more likely when RATs were ascertained through cfDNA (14 of 151; 9.3%) than through CVS trophoblasts (seven of 237; 3.0%) (P < 0.01). In cfDNA-ascertained cases, trisomies 15, 16 and 22, which are associated with fetal loss, were identified proportionately more often. Of 151 cases with RAT identified by cfDNA and outcome information available, 41.1% resulted in normal live birth; 27.2% in fetal loss; 7.3% had phenotypic abnormality detected through ultrasound or other follow-up evaluation; 2.0% had a clinically significant UPD; and 14.6% had fetal growth restriction or low birth weight. All autosomes were involved in trisomies in products of conception; the most common RATs detected were trisomies 16, 22 and 15 with a frequency of > 9% each. CONCLUSIONS Although there are strong parallels between RATs ascertained through cfDNA analysis and direct chromosome preparation of CVS, caution is needed in applying conclusions from CVS analysis to cfDNA testing, and vice versa. RATs identified through genome-wide cfDNA tests have uncertain risks for fetal loss, growth restriction or fetal abnormality. Copyright © 2019 ISUOG. Published by John Wiley & Sons Ltd.
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Affiliation(s)
- P Benn
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT, USA
| | - F Malvestiti
- Unit of Research and Development, Cytogenetics and Medical Genetics, TOMA, Advanced Biomedical Assays S.p.A., Busto Arsizio, Varese, Italy
| | - B Grimi
- Unit of Research and Development, Cytogenetics and Medical Genetics, TOMA, Advanced Biomedical Assays S.p.A., Busto Arsizio, Varese, Italy
| | - F Maggi
- Unit of Research and Development, Cytogenetics and Medical Genetics, TOMA, Advanced Biomedical Assays S.p.A., Busto Arsizio, Varese, Italy
| | - G Simoni
- Unit of Research and Development, Cytogenetics and Medical Genetics, TOMA, Advanced Biomedical Assays S.p.A., Busto Arsizio, Varese, Italy
| | - F R Grati
- Unit of Research and Development, Cytogenetics and Medical Genetics, TOMA, Advanced Biomedical Assays S.p.A., Busto Arsizio, Varese, Italy
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DiNonno W, Demko Z, Martin K, Billings P, Egbert M, Zneimer S, Keen-Kim D, Benn P. Quality Assurance of Non-Invasive Prenatal Screening (NIPS) for Fetal Aneuploidy Using Positive Predictive Values as Outcome Measures. J Clin Med 2019; 8:jcm8091311. [PMID: 31454954 PMCID: PMC6780279 DOI: 10.3390/jcm8091311] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 08/21/2019] [Accepted: 08/22/2019] [Indexed: 12/28/2022] Open
Abstract
Non-invasive prenatal screening (NIPS) based on the analysis of cell-free DNA in maternal plasma has been shown to have high sensitivity and specificity. We gathered follow-up information for pregnancies in women with test-positive NIPS results from 2014–2017 with quarterly assessments of positive predictive values (PPVs). A non-inferiority analysis with a minimum requirement of 70%/80% of expected performance for trisomy 21 and 18 was used to ensure testing met expectations. PPVs were evaluated in the context of changes in the population receiving testing. For all quarters, PPVs for trisomies 21 and 18 exceeded the requirement of > 70% of the reference PPV. Overall observed PPVs for trisomy 21, 18, 13 and monosomy X were similar for women aged <35 (90.9%, 95% Confidence Interval (CI) 88.6–92.7%) compared to women with advanced maternal age (94.5%, 95% CI 93.1–95.6%). Despite significant declines in test-positive rates from 1.18% to 0.62% for trisomy 21, and from 0.75% to 0.48% for trisomies 18, 13 and monosomy X combined, PPVs remained stable through the four-year interval. We conclude that quarterly evaluation of PPV provides an overview of past testing and helps demonstrate long-term consistency in test performance, even in the setting of increasing use by women with lower a priori risks.
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Affiliation(s)
| | | | | | | | | | | | | | - Peter Benn
- UConn Health, Farmington, CT 06030, USA.
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Lo LM, Shiau CS, Chen KC, Shaw SWS, Benn P. Screening for 22q11.2 deletion syndrome by two non-invasive prenatal testing methodologies: A case with discordant results. Taiwan J Obstet Gynecol 2019; 58:40-42. [PMID: 30638477 DOI: 10.1016/j.tjog.2018.11.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/29/2018] [Indexed: 01/09/2023] Open
Abstract
OBJECTIVE Non-invasive prenatal testing (NIPT) through the analysis of cell-free DNA in maternal plasma has bee expanded to include clinically-relevant microdeletions such as the 22q11.2 deletion syndrome (22q11.2DS). CASE REPORT We present a pregnancy where the fetus was affected with 22q11.2DS based on chromosome microarray analysis. Discordant results were obtained through two different NIPT methodologies. The pregnancy was identified as high risk by a SNP-based approach but low risk using a genome-wide counting methodology. A review of the technical methods used for these tests provides insight into why they may provide conflicting results and emphasizes the importance of chromosome microarray studies for diagnostic confirmation and defining the deletion. CONCLUSION Currently available NIPT for 22q11.2DS use different technologies that are not equivalent. The genome-wide counting methodology has the potential to detect deletions outside the critical 22q11.2 A-D region but current data suggests it may have a lower sensitivity for deletions within the critical region.
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Affiliation(s)
- Liang-Ming Lo
- Department of Obstetrics and Gynecology, Taipei Chang Gung Memorial Hospital, Taipei, Taiwan; College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chii-Shinn Shiau
- Department of Obstetrics and Gynecology, Taipei Chang Gung Memorial Hospital, Taipei, Taiwan; College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Kuang-Chao Chen
- Department of Obstetrics and Gynecology, Taipei Chang Gung Memorial Hospital, Taipei, Taiwan; College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - S W S Shaw
- Department of Obstetrics and Gynecology, Taipei Chang Gung Memorial Hospital, Taipei, Taiwan; College of Medicine, Chang Gung University, Taoyuan, Taiwan; Prenatal Cell and Gene Therapy Group, Institute for Women's Health, University College London, London, UK.
| | - Peter Benn
- Genetics and Genome Sciences, UCONN Health, 263 Farmington Avenue, E3050, Farmington, CT, USA
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McKanna T, Ryan A, Krinshpun S, Kareht S, Marchand K, Grabarits C, Ali M, McElheny A, Gardiner K, LeChien K, Hsu M, Saltzman D, Stosic M, Martin K, Benn P. Fetal fraction-based risk algorithm for non-invasive prenatal testing: screening for trisomies 13 and 18 and triploidy in women with low cell-free fetal DNA. Ultrasound Obstet Gynecol 2019; 53:73-79. [PMID: 30014528 PMCID: PMC6587793 DOI: 10.1002/uog.19176] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 06/13/2018] [Accepted: 07/10/2018] [Indexed: 05/09/2023]
Abstract
OBJECTIVE To identify pregnancies at increased risk for trisomy 13, trisomy 18 or triploidy attributable to low fetal fraction (FF). METHODS A FF-based risk (FFBR) model was built using data from more than 165 000 singleton pregnancies referred for single-nucleotide polymorphism (SNP)-based non-invasive prenatal testing (NIPT). Based on maternal weight and gestational age (GA), FF distributions for normal, trisomy 13, trisomy 18 and triploid pregnancies were constructed and used to adjust prior risks for these abnormalities. A risk cut-off of ≥ 1% was chosen to define pregnancies at high risk for trisomy 13, trisomy 18 or triploidy (high FFBR score). The model was evaluated on an independent blinded set of pregnancies for which SNP-based NIPT did not return a result, and for which pregnancy outcome information was gathered retrospectively. RESULTS The evaluation cohort comprised 1148 cases, of which approximately half received a high FFBR score. Compared with rates expected based on maternal age (MA) and GA, cases with a high FFBR score had a significantly increased rate of trisomy 13, trisomy 18 or triploidy combined (5.7% vs 0.7%; P < 0.001) and also of unexplained pregnancy loss (14.7% vs 10.4%; P < 0.001). For cases that did not receive a high FFBR score, the incidence of a chromosomal abnormality or pregnancy loss was not significantly different from that expected based on MA and GA. In this study cohort, the sensitivity of the FFBR model for detection of trisomy 13, trisomy 18 or triploidy was 91.4% (95% CI, 76.9-98.2%) with a positive predictive value of 5.7% (32/564; 95% CI, 3.9-7.9%). CONCLUSIONS For pregnancies with a FF too low to receive a result on standard NIPT, the FFBR algorithm identified a subset of cases at increased risk for trisomy 13, trisomy 18 or triploidy. For the remainder of cases, the risk of a fetal chromosomal abnormality was unchanged from that expected based on MA and GA. © 2018 The Authors. Ultrasound in Obstetrics & Gynecology published by John Wiley & Sons Ltd on behalf of the International Society of Ultrasound in Obstetrics and Gynecology.
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Affiliation(s)
| | | | | | | | - K. Marchand
- Beth Israel Deaconess Medical CenterBostonMAUSA
| | - C. Grabarits
- Vanderbilt University Medical CenterNashvilleTNUSA
| | - M. Ali
- Weill Cornell MedicineNew YorkNYUSA
| | - A. McElheny
- St Louis University School of MedicineSt LouisMOUSA
| | | | | | - M. Hsu
- Northshore University Health SystemChicagoILUSA
| | - D. Saltzman
- Icahn School of Medicine at Mount SinaiNew YorkNYUSA
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Benn P, Plon SE, Bianchi DW. Current Controversies in Prenatal Diagnosis 2: NIPT results suggesting maternal cancer should always be disclosed. Prenat Diagn 2018; 39:339-343. [PMID: 30398677 DOI: 10.1002/pd.5379] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 10/08/2018] [Accepted: 10/10/2018] [Indexed: 12/16/2022]
Affiliation(s)
- Peter Benn
- Department of Genetics and Genome Sciences, UCONN Health, Farmington, Connecticut
| | - Sharon E Plon
- Departments of Pediatrics and Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Diana W Bianchi
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
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Benn P, Grati FR. Genome-wide non-invasive prenatal screening for all cytogenetically visible imbalances. Ultrasound Obstet Gynecol 2018; 51:429-433. [PMID: 29363829 DOI: 10.1002/uog.19014] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 11/28/2017] [Accepted: 01/15/2018] [Indexed: 06/07/2023]
Affiliation(s)
- P Benn
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT, USA
| | - F R Grati
- TOMA, Advanced Biomedical Assays S.p.A, Busto Arsizio, Varese, Italy
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Guanciali Franchi P, Palka C, Morizio E, Sabbatinelli G, Alfonsi M, Fantasia D, Sitar G, Benn P, Calabrese G. Sequential combined test, second trimester maternal serum markers, and circulating fetal cells to select women for invasive prenatal diagnosis. PLoS One 2017; 12:e0189235. [PMID: 29216282 PMCID: PMC5720779 DOI: 10.1371/journal.pone.0189235] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 11/21/2017] [Indexed: 12/19/2022] Open
Abstract
From January 1st 2013 to August 31st 2016, 24408 pregnant women received the first trimester Combined test and contingently offered second trimester maternal serum screening to identify those women who would most benefit from invasive prenatal diagnosis (IPD). The screening was based on first trimester cut-offs of ≥1:30 (IPD indicated), 1:31 to 1:899 (second trimester screening indicated) and ≤1:900 (no further action), and a second trimester cut-off of ≥1:250. From January 2014, analysis of fetal cells from peripheral maternal blood was also offered to women with positive screening results. For fetal Down syndrome, the overall detection rate was 96.8% for a false-positive rate of 2.8% resulting in an odds of being affected given a positive result (OAPR) of 1:11, equivalent to a positive predictive value (PPV) of 8.1%. Additional chromosome abnormalities were also identified resulting in an OAPR for any chromosome abnormality of 1:6.6 (PPV 11.9%). For a sub-set of cases with positive contingent test results, FISH analysis of circulating fetal cells in maternal circulation identified 7 abnormal and 39 as normal cases with 100% specificity and 100% sensitivity. We conclude that contingent screening using conventional Combined and second trimester screening tests is effective but can potentially be considerably enhanced through the addition of fetal cell analysis.
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Affiliation(s)
- Paolo Guanciali Franchi
- Department of Medical, Oral and Biotechnological Science, Chieti-Pescara University, Chieti, Italy
- * E-mail:
| | - Chiara Palka
- Department of Medical, Oral and Biotechnological Science, Chieti-Pescara University, Chieti, Italy
| | - Elisena Morizio
- Department of Medical, Oral and Biotechnological Science, Chieti-Pescara University, Chieti, Italy
| | - Giulia Sabbatinelli
- Department of Medical, Oral and Biotechnological Science, Chieti-Pescara University, Chieti, Italy
| | - Melissa Alfonsi
- Department of Medical, Oral and Biotechnological Science, Chieti-Pescara University, Chieti, Italy
| | | | - Giammaria Sitar
- Department of Medical, Oral and Biotechnological Science, Chieti-Pescara University, Chieti, Italy
| | - Peter Benn
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT, United States of America
| | - Giuseppe Calabrese
- Department of Medical, Oral and Biotechnological Science, Chieti-Pescara University, Chieti, Italy
- Department of Hematology, Pescara Hospital, Pescara, Italy
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Martin K, Iyengar S, Kalyan A, Lan C, Simon AL, Stosic M, Kobara K, Ravi H, Truong T, Ryan A, Demko ZP, Benn P. Clinical experience with a single-nucleotide polymorphism-based non-invasive prenatal test for five clinically significant microdeletions. Clin Genet 2017; 93:293-300. [PMID: 28696552 DOI: 10.1111/cge.13098] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 06/30/2017] [Indexed: 01/06/2023]
Abstract
Single-nucleotide polymorphism (SNP)-based non-invasive prenatal testing (NIPT) can currently predict a subset of submicroscopic abnormalities associated with severe clinical manifestations. We retrospectively analyzed the performance of SNP-based NIPT in 80 449 referrals for 22q11.2 deletion syndrome and 42 326 referrals for 1p36, cri-du-chat, Prader-Willi, and Angelman microdeletion syndromes over a 1-year period, and compared the original screening protocol with a revision that reflexively sequenced high-risk calls at a higher depth of read. The prevalence of these microdeletion syndromes was also estimated in the referral population. The positive predictive value of the original test was 15.7% for 22q11.2 deletion syndrome, and 5.2% for the other 4 disorders combined. With the revised protocol, these values increased to 44.2% for 22q11.2 and 31.7% for the others. The 0.33% false-positive rate (FPR) for 22q11.2 deletion syndrome decreased to 0.07% with the revised protocol. Similarly, the FPR for the other 4 disorders combined decreased from 0.56% to 0.07%. Minimal prevalences were estimated to be 1 in 1255 for 22q11.2 deletion syndrome and 1 in 1464 for 1p36, cri-du-chat, and Angelman syndromes combined. Our results show that these microdeletions are relatively common in the referral population, and that the performance of SNP-based NIPT is improved with high-depth resequencing.
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Affiliation(s)
- K Martin
- Natera, Inc., San Carlos, California
| | - S Iyengar
- Natera, Inc., San Carlos, California
| | - A Kalyan
- Natera, Inc., San Carlos, California
| | - C Lan
- Natera, Inc., San Carlos, California
| | - A L Simon
- Natera, Inc., San Carlos, California
| | - M Stosic
- Natera, Inc., San Carlos, California
| | - K Kobara
- Natera, Inc., San Carlos, California
| | - H Ravi
- Natera, Inc., San Carlos, California
| | - T Truong
- Natera, Inc., San Carlos, California
| | - A Ryan
- Natera, Inc., San Carlos, California
| | - Z P Demko
- Natera, Inc., San Carlos, California
| | - P Benn
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, Connecticut
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Grati FR, Benn P. Comment on “The clinical utility of genome-wide non invasive prenatal screening”. Prenat Diagn 2017; 37:1050-1052. [DOI: 10.1002/pd.5098] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 06/18/2017] [Indexed: 01/18/2023]
Affiliation(s)
| | - Peter Benn
- Department of Genetics and Genome Sciences; University of Connecticut Health Center; Farmington CT USA
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Benn P, Iyengar S, Crowley TB, Zackai EH, Burrows EK, Moshkevich S, McDonald-McGinn DM, Sullivan KE, Demko Z. Pediatric healthcare costs for patients with 22q11.2 deletion syndrome. Mol Genet Genomic Med 2017; 5:631-638. [PMID: 29178641 PMCID: PMC6234953 DOI: 10.1002/mgg3.310] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 06/02/2017] [Accepted: 06/06/2017] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND The 22q11.2 deletion syndrome is a variably expressed disorder that can include cardiac, palate, and other physical abnormalities, immunodeficiency, and hypocalcemia. Because of the extreme variability in phenotype, there has been no available estimate of the total medical expenditure associated with the average case. METHODS We have developed a model to estimate the cost from the time of diagnosis to age 20. Costs were based on patients seen at a specialty center but also considered those components of care expected to have been provided by external healthcare facilities. Expense was based on billed medical charges extracted from the electronic medical billing system for all patients with a diagnosis of DiGeorge or velocardiofacial syndrome from 1993-2015. Expenditures included maternal prenatal care directly related to an affected pregnancy, molecular/cytogenetic diagnosis, consultations, surgery, and/or other treatment and management. Most mental health services (except inpatient), therapy related to cognitive, behavioral, speech, pharmacy, and nonmedical costs (special education, vocational, respite, lost earnings) were not included. RESULTS Data were available for 642 patients with 50.7% diagnosed prenatally or in the first year of life. The average cost for a patient was $727,178. Costs were highest for patients ascertained prenatally ($2,599,955) or in the first year of life ($1,043,096), those with cardiac abnormalities or referred for cardiac evaluation ($751,535), and patients with low T-cell counts ($1,382,222). CONCLUSION This study demonstrates that there are significant medical costs associated with 22q11.2 deletion syndrome.
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Affiliation(s)
- Peter Benn
- University of Connecticut Health Center, Farmington, Connecticut
| | | | - Terrence Blaine Crowley
- Children's Hospital of Philadelphia and the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Elaine H Zackai
- Children's Hospital of Philadelphia and the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Evanette K Burrows
- Children's Hospital of Philadelphia and the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | | | - Donna M McDonald-McGinn
- Children's Hospital of Philadelphia and the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Kathleen E Sullivan
- Children's Hospital of Philadelphia and the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
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Benn P. The Significance of Test Failures in Noninvasive Prenatal Screening for Fetal Aneuploidy Using Cell-free DNA. J Fetal Med 2017. [DOI: 10.1007/s40556-016-0109-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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36
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Calabrese G, Fantasia D, Alfonsi M, Morizio E, Celentano C, Guanciali Franchi P, Sabbatinelli G, Palka C, Benn P, Sitar G. Aneuploidy screening using circulating fetal cells in maternal blood by dual-probe FISH protocol: a prospective feasibility study on a series of 172 pregnant women. Mol Genet Genomic Med 2016; 4:634-640. [PMID: 27896286 PMCID: PMC5118208 DOI: 10.1002/mgg3.249] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 08/25/2016] [Accepted: 08/29/2016] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND A long sought goal in medical genetics has been the replacement of invasive procedures for the detection of chromosomal aneuploidies by isolating and analyzing fetal cells or free fetal DNA from maternal blood, avoiding risk to the fetus. However, a rapid, simple, consistent, and low-cost procedure suitable for routine clinical practice has not yet been achieved. The purpose of this study was to assess the feasibility of predicting fetal aneuploidy by applying our recently established dual-probe FISH protocol to fetal cells isolated and enriched from maternal blood. METHODS A total of 172 pregnant women underwent prospective testing for fetal aneuploidy by FISH analysis of fetal cells isolated from maternal blood. Results were compared with the karyotype determined through invasive procedures or at birth. RESULTS Seven of the samples exhibited fetal aneuploidy, which was confirmed by invasive prenatal diagnosis procedures. After enrichment for fetal cells, the frequency of trisomic cells was at least double in samples from aneuploid pregnancies (range 0.38-0.90%) compared to samples from normal pregnancies (≤0.18%). One false negative result was also obtained. CONCLUSIONS Noninvasive prenatal aneuploidy screening using fetal cells isolated from maternal blood is feasible and could substantially reduce the need for invasive procedures.
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Affiliation(s)
| | | | - Melissa Alfonsi
- Genetica Medica Università Chieti-Pescara Chieti Scalo Italy
| | - Elisena Morizio
- Genetica Medica Università Chieti-Pescara Chieti Scalo Italy
| | | | | | | | - Chiara Palka
- Genetica Medica Università Chieti-Pescara Chieti Scalo Italy
| | - Peter Benn
- University of Connecticut Health Center Farmington Connecticut
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Benn P, Norwitz ER, Pergament E. Cell-free DNA vs sequential screening for the detection of fetal chromosomal abnormalities. Am J Obstet Gynecol 2016; 215:252-3. [PMID: 27091082 DOI: 10.1016/j.ajog.2016.04.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 04/08/2016] [Indexed: 10/21/2022]
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38
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Benn P. Expanding non-invasive prenatal testing beyond chromosomes 21, 18, 13, X and Y. Clin Genet 2016; 90:477-485. [PMID: 27283893 DOI: 10.1111/cge.12818] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 06/05/2016] [Accepted: 06/07/2016] [Indexed: 12/16/2022]
Abstract
Non-invasive prenatal testing (NIPT) based on cell-free DNA in maternal plasma is being expanded to include additional chromosome abnormalities beyond those involving chromosomes 21, 18, 13, X and Y. Review of population cytogenetic data provides insight into the likely number of additional abnormalities detectable. Additional clinically significant and cytogenetically recognizable abnormalities are present in less than 0.1% of newborns but clinically significant, or potentially significant, sub-microscopic imbalances are expected to be present in 1.7%. Cytogenetic studies on chorionic villus samples suggests that after excluding abnormalities involving chromosomes 21, 18, 13, X and Y, approximately 0.6% of NIPT results may be positive for an unbalanced abnormality attributable to mosaicism but most of these will not be confirmed at amniocentesis or in newborns. NIPT has also been developed for specific microdeletion syndromes and initial experience is now available. Laboratory procedures such as deeper sequencing and additional data analytics are rapidly evolving but even with existing protocols, it is already clear that NIPT does not necessarily need to be limited to trisomies 21, 18, 13 and the sex-chromosome abnormalities. Patient educational materials and genetic counseling services need to be available for women offered expanded NIPT.
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Affiliation(s)
- P Benn
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT, USA
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Hamill M, Benn P, Carder C, Copas A, Ward H, Ison C, French P. The clinical manifestations of anorectal infection with lymphogranuloma venereum (LGV) versus non-LGV strains of Chlamydia trachomatis: a case–control study in homosexual men. Int J STD AIDS 2016; 18:472-5. [PMID: 17623505 DOI: 10.1258/095646207781147319] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Lymphogranuloma venereum (LGV) has recently been reported in men who have sex with men. In a case–control study we compared behavioural and clinical features of 32 men with LGV (cases) and 31 men with non-LGV chlamydial proctitis (controls). LGV was associated with rectal discharge (odds ratio [OR] 4.15, 95% confidence interval [CI] 1.42, 12.2), and there was a tendency to association with HIV infection (OR 3.60, CI 0.67–19.4), sexual contact in the UK (OR 3.03, CI 1.02–9.01) and fisting (OR 5.04, CI 0.98–26.1). LGV should be considered a possible diagnosis in men with rectal discharge.
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Affiliation(s)
- M Hamill
- Department of Genitourinary Medicine, The Mortimer Market Centre, Camden PCT, London, UK.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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 Obstet Gynecol 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Rose NC, Benn P, Milunsky A. Current controversies in prenatal diagnosis 1: should NIPT routinely include microdeletions/microduplications? Prenat Diagn 2015; 36:10-4. [PMID: 26492631 DOI: 10.1002/pd.4710] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Revised: 10/14/2015] [Accepted: 10/15/2015] [Indexed: 12/24/2022]
Affiliation(s)
- Nancy C Rose
- Intermountain Healthcare, Salt Lake City, UT, USA.,University of Utah, Salt Lake City, UT, USA
| | - Peter Benn
- University of Connecticut Health Center, Farmington, CT, USA
| | - Aubrey Milunsky
- Center for Human Genetics, Cambridge, MA, USA.,Tufts University School of Medicine, Boston, MA, USA
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43
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Dar P, Gross SJ, Benn P. Positive predictive values and false-positive results in noninvasive prenatal screening. Am J Obstet Gynecol 2015; 213:595-6. [PMID: 26070701 DOI: 10.1016/j.ajog.2015.06.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 06/01/2015] [Indexed: 10/23/2022]
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Gross SJ, Ryan A, Benn P. Noninvasive prenatal testing for 22q11.2 deletion syndrome: deeper sequencing increases the positive predictive value. Am J Obstet Gynecol 2015; 213:254-5. [PMID: 25986033 DOI: 10.1016/j.ajog.2015.05.028] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 05/12/2015] [Indexed: 11/16/2022]
Affiliation(s)
- Susan J Gross
- Natera Inc, 201 Industrial Rd., San Carlos, CA 94070
| | - Allison Ryan
- Natera Inc, 201 Industrial Rd., San Carlos, CA 94070
| | - Peter Benn
- Division of Human Genetics, Department of Genetics and Genome Sciences, University of Connecticut Health Center, 236 Farmington Ave., Farmington, CT 06030-3808.
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45
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Benn P, Curnow KJ, Chapman S, Michalopoulos SN, Hornberger J, Rabinowitz M. An Economic Analysis of Cell-Free DNA Non-Invasive Prenatal Testing in the US General Pregnancy Population. PLoS One 2015; 10:e0132313. [PMID: 26158465 PMCID: PMC4497716 DOI: 10.1371/journal.pone.0132313] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 06/11/2015] [Indexed: 11/23/2022] Open
Abstract
OBJECTIVE Analyze the economic value of replacing conventional fetal aneuploidy screening approaches with non-invasive prenatal testing (NIPT) in the general pregnancy population. METHODS Using decision-analysis modeling, we compared conventional screening to NIPT with cell-free DNA (cfDNA) analysis in the annual US pregnancy population. Sensitivity and specificity for fetal aneuploidies, trisomy 21, trisomy 18, trisomy 13, and monosomy X, were estimated using published data and modeling of both first- and second trimester screening. Costs were assigned for each prenatal test component and for an affected birth. The overall cost to the healthcare system considered screening costs, the number of aneuploid cases detected, invasive procedures performed, procedure-related euploid losses, and affected pregnancies averted. Sensitivity analyses evaluated the effect of variation in parameters. Costs were reported in 2014 US Dollars. RESULTS Replacing conventional screening with NIPT would reduce healthcare costs if it can be provided for $744 or less in the general pregnancy population. The most influential variables were timing of screening entry, screening costs, and pregnancy termination rates. Of the 13,176 affected pregnancies undergoing screening, NIPT detected 96.5% (12,717/13,176) of cases, compared with 85.9% (11,314/13,176) by conventional approaches. NIPT reduced invasive procedures by 60.0%, with NIPT and conventional methods resulting in 24,596 and 61,430 invasive procedures, respectively. The number of procedure-related euploid fetal losses was reduced by 73.5% (194/264) in the general screening population. CONCLUSION Based on our analysis, universal application of NIPT would increase fetal aneuploidy detection rates and can be economically justified. Offering this testing to all pregnant women is associated with substantial prenatal healthcare benefits.
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Affiliation(s)
- Peter Benn
- Division of Human Genetics, Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT, United States of America
| | | | | | | | - John Hornberger
- Cedar Associates, Menlo Park, CA, United States of America
- Stanford University, Stanford, CA, United States of America
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47
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Benn P, Borrell A, Chiu RWK, Cuckle H, Dugoff L, Faas B, Gross S, Huang T, Johnson J, Maymon R, Norton M, Odibo A, Schielen P, Spencer K, Wright D, Yaron Y. Position statement from the Chromosome Abnormality Screening Committee on behalf of the Board of the International Society for Prenatal Diagnosis. Prenat Diagn 2015; 35:725-34. [DOI: 10.1002/pd.4608] [Citation(s) in RCA: 206] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Accepted: 04/24/2015] [Indexed: 12/12/2022]
Affiliation(s)
- Peter Benn
- Department of Genetics and Genome Sciences; University of Connecticut Health Center; Farmington CT USA
| | - Antoni Borrell
- Prenatal Diagnosis Unit, Institute of Gynecology, Obstetrics and Neonatology, Hospital Clinic, Maternitat Campus; University of Barcelona Medical School; Catalonia Spain
| | - Rossa W. K. Chiu
- Department of Chemical Pathology; The Chinese University of Hong Kong, Prince of Wales Hospital; Hong Kong
| | - Howard Cuckle
- Department of Obstetrics and Gynecology; Columbia University Medical Center; New York NY USA
| | - Lorraine Dugoff
- Department of Obstetrics and Gynecology; University of Pennsylvania; Philadelphia PA USA
| | - Brigitte Faas
- Department of Human Genetics; Radboud University Nijmegen Medical Centre; Nijmegen The Netherlands
| | - Susan Gross
- Department of Obstetrics and Gynecology; Albert Einstein College of Medicine; New York NY USA
| | - Tianhua Huang
- Genetics Program; North York General Hospital; Toronto ON Canada
| | - Joann Johnson
- Department of Obstetrics and Gynecology; University of Calgary; Calgary AB Canada
| | - Ron Maymon
- Department of Obstetrics and Gynecology, Assaf Harofe Medical Center, Sackler Faculty of Medicine; Tel Aviv University; Tel Aviv Israel
| | - Mary Norton
- Department of Obstetrics and Gynecology; Stanford University School of Medicine; Stanford CA USA
| | - Anthony Odibo
- Department of Obstetrics and Gynecology; University of South Florida; Tampa FL USA
| | - Peter Schielen
- Laboratory for Infectious Diseases and Perinatal Screening; National Institute for Public Health and the Environment (RIVM); Bilthoven The Netherlands
| | - Kevin Spencer
- Prenatal Screening Unit, Clinical Biochemistry Department; Barking Havering & Redbridge University Hospitals, King George Hospital; Goodmayes UK
| | - Dave Wright
- Department of Statistics; University of Exeter; Exeter UK
| | - Yuval Yaron
- Prenatal Diagnosis Unit, Genetic Institute; Sourasky Medical Center; Tel Aviv Israel
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Benn P. Re: Non-invasive prenatal testing for trisomies 21, 18 and 13: clinical experience from 146 958 pregnancies. H. Zhang, Y. Gao, F. Jiang, M. Fu, Y. Yuan, Y. Guo, Z. Zhu, M. Lin, Q. Liu, Z. Tian, H. Zhang, F. Chen, T. K. Lau, L. Zhao, X. Yi, Y. Yin and W. Wang. Ultrasound Obstet Gynecol 2015; 45: 530-538. Ultrasound Obstet Gynecol 2015; 45:512-513. [PMID: 25914392 DOI: 10.1002/uog.14846] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Affiliation(s)
- P Benn
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, CT 06030-3808, USA.
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Wapner RJ, Babiarz JE, Levy B, Stosic M, Zimmermann B, Sigurjonsson S, Wayham N, Ryan A, Banjevic M, Lacroute P, Hu J, Hall MP, Demko Z, Siddiqui A, Rabinowitz M, Gross SJ, Hill M, Benn P. Expanding the scope of noninvasive prenatal testing: detection of fetal microdeletion syndromes. Am J Obstet Gynecol 2015; 212:332.e1-9. [PMID: 25479548 DOI: 10.1016/j.ajog.2014.11.041] [Citation(s) in RCA: 218] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 11/05/2014] [Accepted: 11/30/2014] [Indexed: 11/26/2022]
Abstract
OBJECTIVE The purpose of this study was to estimate the performance of a single-nucleotide polymorphism (SNP)-based noninvasive prenatal test for 5 microdeletion syndromes. STUDY DESIGN Four hundred sixty-nine samples (358 plasma samples from pregnant women, 111 artificial plasma mixtures) were amplified with the use of a massively multiplexed polymerase chain reaction, sequenced, and analyzed with the use of the Next-generation Aneuploidy Test Using SNPs algorithm for the presence or absence of deletions of 22q11.2, 1p36, distal 5p, and the Prader-Willi/Angelman region. RESULTS Detection rates were 97.8% for a 22q11.2 deletion (45/46) and 100% for Prader-Willi (15/15), Angelman (21/21), 1p36 deletion (1/1), and cri-du-chat syndromes (24/24). False-positive rates were 0.76% for 22q11.2 deletion syndrome (3/397) and 0.24% for cri-du-chat syndrome (1/419). No false positives occurred for Prader-Willi (0/428), Angelman (0/442), or 1p36 deletion syndromes (0/422). CONCLUSION SNP-based noninvasive prenatal microdeletion screening is highly accurate. Because clinically relevant microdeletions and duplications occur in >1% of pregnancies, regardless of maternal age, noninvasive screening for the general pregnant population should be considered.
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50
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Cuckle H, Benn P, Pergament E. Cell-free DNA screening for fetal aneuploidy as a clinical service. Clin Biochem 2015; 48:932-41. [PMID: 25732593 DOI: 10.1016/j.clinbiochem.2015.02.011] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Revised: 01/19/2015] [Accepted: 02/12/2015] [Indexed: 12/25/2022]
Abstract
Non-invasive prenatal testing (NIPT) through the analysis of cell free (cf)DNA is revolutionizing prenatal screening for fetal aneuploidy. Current methods used in clinical practice include shotgun massively parallel sequencing (s-MPS); targeted (t-MPS); and an approach that takes advantage of single nucleotide polymorphism (SNP) differences between mother and fetus. Efficacy of cfDNA testing for the common autosomal trisomies far exceeds that of conventional screening. Depending on the methodology used, reasons for discordancy between cfDNA results and fetal karyotype can include true fetal mosaicism, confined placental mosaicism, presence of a maternal karyotype abnormality, insufficient counting due to low fetal fraction, and a vanishing twin. Among the possible cfDNA strategies a Primary test has the highest performance but is expensive, while a Contingent cfDNA test can achieve high performance at a relatively low cost. Practicalities to be considered in the provision of testing include pretest counseling about the scope and accuracy of the testing, the interpretation of results when there is a low fetal fraction and follow-up studies for positive test results. The role of first trimester nuchal translucency measurement and conventional biochemical testing needs to be reassessed in the context of the use of cfDNA.
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Affiliation(s)
- Howard Cuckle
- Department of Obstetrics and Gynecology, Columbia University Medical Center, New York, NY 10032, USA.
| | - Peter Benn
- Department of Genetics and Developmental Biology, University of Connecticut Health Center, Farmington, CT 06030, USA
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