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Performance of Semiconductor sequencing platform for non-invasive prenatal genetic screening for fetal aneuploidies: results from a multicenter prospective cohort study in a clinical setting

hal.structure.identifierAP-HP - Hôpital Cochin Broca Hôtel Dieu [Paris]
hal.structure.identifierNational Institutes of Health [Bethesda, MD, USA] [NIH]
dc.contributor.authorALLACH EL KHATTABI, Laïla
hal.structure.identifierCentre Hospitalier Universitaire de Bordeaux [CHU Bordeaux]
dc.contributor.authorBRUN, Stéphanie
hal.structure.identifierCentre Hospitalier Régional Universitaire de Brest [CHRU Brest]
dc.contributor.authorGUÉGUEN, Paul
hal.structure.identifierUniversité Claude Bernard Lyon 1 [UCBL]
dc.contributor.authorCHATRON, Nicolas
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorGUICHOUX, Erwan
hal.structure.identifierCentre Hospitalier Régional Universitaire de Brest [CHRU Brest]
dc.contributor.authorSCHUTZ, Sacha
hal.structure.identifierAP-HP - Hôpital Cochin Broca Hôtel Dieu [Paris]
hal.structure.identifierNational Institutes of Health [Bethesda, MD, USA] [NIH]
dc.contributor.authorNECTOUX, Juliette
hal.structure.identifierCentre Hospitalier Régional Universitaire de Nancy [CHRU Nancy]
dc.contributor.authorSORLIN, Arthur
hal.structure.identifierCentre Hospitalier Universitaire de Nice [CHU Nice]
dc.contributor.authorQUERE, Manal
hal.structure.identifierDépartement de Génétique Médicale
dc.contributor.authorBOUDJARANE, John
hal.structure.identifierMaternité Port-Royal [CHU Cochin]
dc.contributor.authorTSATSARIS, Vassilis
hal.structure.identifierAssistance publique - Hôpitaux de Paris (AP-HP) [AP-HP]
dc.contributor.authorMANDELBROT, Laurent
hal.structure.identifierUniversité Claude Bernard Lyon 1 [UCBL]
dc.contributor.authorSCHLUTH-BOLARD, Caroline
hal.structure.identifierAP-HP - Hôpital Cochin Broca Hôtel Dieu [Paris]
dc.contributor.authorDUPONT, Jean Michel
hal.structure.identifierService de génétique médicale
dc.contributor.authorROORYCK, Caroline
dc.date.issued2019
dc.identifier.issn0960-7692
dc.description.abstractEn<strong>Objectives</strong> To validate and evaluate an integrated protocol for non‐invasive prenatal genetic screening (NIPS) for common fetal aneuploidies in a clinical setting, using the semiconductor sequencing technology, Ion Proton. <strong>Methods</strong> This prospective cohort study included 2505 pregnant women from seven academic genetic laboratories (695 high risk pregnancies in a validation study and 1810 pregnancies with a risk higher than 1/250 without ultrasound anomalies, in a real NIPS clinical setting). Cell free DNA from plasma samples was sequenced using Ion Proton sequencer, and sequencing data were analyzed using the open‐access software WISECONDOR. Performance metrics for detection of trisomies 21, 18 and 13, were calculated based on either fetal karyotype result or clinical data collected at birth. We also evaluated the failure rate and compared three methods of fetal fraction quantification (RASSF1A assay, DEFRAG and SANEFALCON software). <strong>Results</strong> Sensitivities and specificities were: 98.3% (95%CI: 93.5 ‐ 99.7) and 99.9% (95%CI: 99.4 ‐ 100) for T21, 96.7% (95%CI: 80.9 ‐ 99.8) and 100% (95%CI: 99.6 ‐ 100) for T18, 94.1% (95%CI: 69.2 ‐ 99.7) and 100% (95%CI: 99.6 ‐ 100) for T13. Our failure rate was 1.2% at first and as low as 0.6% after re‐testing some of the failed samples. Fetal fraction estimation by RASSF1A assay was consistent with DEFRAG results, both of which are adequate for routine diagnosis. <strong>Conclusions</strong> We describe one of the largest studies evaluating the Ion Proton based NIPS and the first clinical study reporting pregnancy outcome in a large set of patients. We demonstrate that this platform is highly efficient in detecting the three most common trisomies. Our protocol is robust and can be easily implemented in any medical genetics laboratory.
dc.language.isoen
dc.publisherWiley-Blackwell
dc.title.enPerformance of Semiconductor sequencing platform for non-invasive prenatal genetic screening for fetal aneuploidies: results from a multicenter prospective cohort study in a clinical setting
dc.typeArticle de revue
dc.identifier.doi10.1002/uog.20112
dc.subject.halSciences du Vivant [q-bio]
bordeaux.journalUltrasound in Obstetrics and Gynecology = Ultrasound in Obstetrics & Gynecology
bordeaux.page246-254
bordeaux.volume54
bordeaux.issue2
bordeaux.peerReviewedoui
hal.identifierhal-02625704
hal.version1
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-02625704v1
bordeaux.COinSctx_ver=Z39.88-2004&amp;rft_val_fmt=info:ofi/fmt:kev:mtx:journal&amp;rft.jtitle=Ultrasound%20in%20Obstetrics%20and%20Gynecology%20=%20Ultrasound%20in%20Obstetrics%20&%20Gynecology&amp;rft.date=2019&amp;rft.volume=54&amp;rft.issue=2&amp;rft.spage=246-254&amp;rft.epage=246-254&amp;rft.eissn=0960-7692&amp;rft.issn=0960-7692&amp;rft.au=ALLACH%20EL%20KHATTABI,%20La%C3%AFla&amp;BRUN,%20St%C3%A9phanie&amp;GU%C3%89GUEN,%20Paul&amp;CHATRON,%20Nicolas&amp;GUICHOUX,%20Erwan&amp;rft.genre=article


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