Noninvasive prenatal detection and selective analysis of cell-free DNA obtained from maternal blood: evaluation for trisomy 21 and trisomy 18

We sought to develop a novel biochemical assay and algorithm for the prenatal evaluation of risk for fetal trisomy 21 (T21) and trisomy 18 (T18) using cell-free DNA obtained from maternal blood. We assayed cell-free DNA from a training set and a blinded validation set of pregnant women, comprising 2...

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Published in:	American journal of obstetrics and gynecology Vol. 206; no. 4; pp. 319.e1 - 319.e9
Main Authors:	Sparks, Andrew B., Struble, Craig A., Wang, Eric T., Song, Ken, Oliphant, Arnold
Format:	Journal Article
Language:	English
Published:	New York, NY Mosby, Inc 01.04.2012 Elsevier
Subjects:	Adult aneuploidy detection Biological and medical sciences Case-Control Studies Chromosome aberrations Chromosomes, Human, Pair 18 - genetics DNA - blood DNA - genetics Down syndrome Down Syndrome - diagnosis Female Fetus Gynecology. Andrology. Obstetrics Humans Male Medical genetics Medical sciences noninvasive prenatal diagnostics Obstetrics and Gynecology Pregnancy Pregnancy Trimester, First - blood Prenatal Diagnosis - methods Risk Sensitivity and Specificity trisomy Trisomy - diagnosis aneuploidy detection noninvasive prenatal diagnostics Down syndrome trisomy Chromosomal aberration Trisomy Gynecology Aneuploidy Obstetrics Blood Chromosome E18 Prenatal diagnosis Mother DNA Cell Edwards syndrome
ISSN:	0002-9378, 1097-6868, 1097-6868
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Abstract	We sought to develop a novel biochemical assay and algorithm for the prenatal evaluation of risk for fetal trisomy 21 (T21) and trisomy 18 (T18) using cell-free DNA obtained from maternal blood. We assayed cell-free DNA from a training set and a blinded validation set of pregnant women, comprising 250 disomy, 72 T21, and 16 T18 pregnancies. We used digital analysis of selected regions in combination with a novel algorithm, fetal-fraction optimized risk of trisomy evaluation (FORTE), to determine trisomy risk for each subject. In all, 163/171 subjects in the training set passed quality control criteria. Using a Z statistic, 35/35 T21 cases and 7/7 T18 cases had Z statistic >3 and 120/121 disomic cases had Z statistic <3. FORTE produced an individualized trisomy risk score for each subject, and correctly discriminated all T21 and T18 cases from disomic cases. All 167 subjects in the blinded validation set passed quality control and FORTE performance matched that observed in the training set correctly discriminating 36/36 T21 cases and 8/8 T18 cases from 123/123 disomic cases. Digital analysis of selected regions and FORTE enable accurate, scalable noninvasive fetal aneuploidy detection.
AbstractList	We sought to develop a novel biochemical assay and algorithm for the prenatal evaluation of risk for fetal trisomy 21 (T21) and trisomy 18 (T18) using cell-free DNA obtained from maternal blood. We assayed cell-free DNA from a training set and a blinded validation set of pregnant women, comprising 250 disomy, 72 T21, and 16 T18 pregnancies. We used digital analysis of selected regions in combination with a novel algorithm, fetal-fraction optimized risk of trisomy evaluation (FORTE), to determine trisomy risk for each subject. In all, 163/171 subjects in the training set passed quality control criteria. Using a Z statistic, 35/35 T21 cases and 7/7 T18 cases had Z statistic >3 and 120/121 disomic cases had Z statistic <3. FORTE produced an individualized trisomy risk score for each subject, and correctly discriminated all T21 and T18 cases from disomic cases. All 167 subjects in the blinded validation set passed quality control and FORTE performance matched that observed in the training set correctly discriminating 36/36 T21 cases and 8/8 T18 cases from 123/123 disomic cases. Digital analysis of selected regions and FORTE enable accurate, scalable noninvasive fetal aneuploidy detection. We sought to develop a novel biochemical assay and algorithm for the prenatal evaluation of risk for fetal trisomy 21 (T21) and trisomy 18 (T18) using cell-free DNA obtained from maternal blood.OBJECTIVEWe sought to develop a novel biochemical assay and algorithm for the prenatal evaluation of risk for fetal trisomy 21 (T21) and trisomy 18 (T18) using cell-free DNA obtained from maternal blood.We assayed cell-free DNA from a training set and a blinded validation set of pregnant women, comprising 250 disomy, 72 T21, and 16 T18 pregnancies. We used digital analysis of selected regions in combination with a novel algorithm, fetal-fraction optimized risk of trisomy evaluation (FORTE), to determine trisomy risk for each subject.STUDY DESIGNWe assayed cell-free DNA from a training set and a blinded validation set of pregnant women, comprising 250 disomy, 72 T21, and 16 T18 pregnancies. We used digital analysis of selected regions in combination with a novel algorithm, fetal-fraction optimized risk of trisomy evaluation (FORTE), to determine trisomy risk for each subject.In all, 163/171 subjects in the training set passed quality control criteria. Using a Z statistic, 35/35 T21 cases and 7/7 T18 cases had Z statistic >3 and 120/121 disomic cases had Z statistic <3. FORTE produced an individualized trisomy risk score for each subject, and correctly discriminated all T21 and T18 cases from disomic cases. All 167 subjects in the blinded validation set passed quality control and FORTE performance matched that observed in the training set correctly discriminating 36/36 T21 cases and 8/8 T18 cases from 123/123 disomic cases.RESULTSIn all, 163/171 subjects in the training set passed quality control criteria. Using a Z statistic, 35/35 T21 cases and 7/7 T18 cases had Z statistic >3 and 120/121 disomic cases had Z statistic <3. FORTE produced an individualized trisomy risk score for each subject, and correctly discriminated all T21 and T18 cases from disomic cases. All 167 subjects in the blinded validation set passed quality control and FORTE performance matched that observed in the training set correctly discriminating 36/36 T21 cases and 8/8 T18 cases from 123/123 disomic cases.Digital analysis of selected regions and FORTE enable accurate, scalable noninvasive fetal aneuploidy detection.CONCLUSIONDigital analysis of selected regions and FORTE enable accurate, scalable noninvasive fetal aneuploidy detection. Objective We sought to develop a novel biochemical assay and algorithm for the prenatal evaluation of risk for fetal trisomy 21 (T21) and trisomy 18 (T18) using cell-free DNA obtained from maternal blood. Study Design We assayed cell-free DNA from a training set and a blinded validation set of pregnant women, comprising 250 disomy, 72 T21, and 16 T18 pregnancies. We used digital analysis of selected regions in combination with a novel algorithm, fetal-fraction optimized risk of trisomy evaluation (FORTE), to determine trisomy risk for each subject. Results In all, 163/171 subjects in the training set passed quality control criteria. Using a Z statistic, 35/35 T21 cases and 7/7 T18 cases had Z statistic >3 and 120/121 disomic cases had Z statistic <3. FORTE produced an individualized trisomy risk score for each subject, and correctly discriminated all T21 and T18 cases from disomic cases. All 167 subjects in the blinded validation set passed quality control and FORTE performance matched that observed in the training set correctly discriminating 36/36 T21 cases and 8/8 T18 cases from 123/123 disomic cases. Conclusion Digital analysis of selected regions and FORTE enable accurate, scalable noninvasive fetal aneuploidy detection.
Author	Wang, Eric T. Sparks, Andrew B. Struble, Craig A. Oliphant, Arnold Song, Ken
Author_xml	– sequence: 1 givenname: Andrew B. surname: Sparks fullname: Sparks, Andrew B. – sequence: 2 givenname: Craig A. surname: Struble fullname: Struble, Craig A. – sequence: 3 givenname: Eric T. surname: Wang fullname: Wang, Eric T. – sequence: 4 givenname: Ken surname: Song fullname: Song, Ken email: ksong@ariadx.com – sequence: 5 givenname: Arnold surname: Oliphant fullname: Oliphant, Arnold
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Copyright	2012 Mosby, Inc. Mosby, Inc. 2015 INIST-CNRS Copyright © 2012 Mosby, Inc. All rights reserved.
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Keywords	aneuploidy detection noninvasive prenatal diagnostics Down syndrome trisomy Chromosomal aberration Trisomy Gynecology Aneuploidy Obstetrics Blood Chromosome E18 Prenatal diagnosis Mother DNA Cell Edwards syndrome
Language	English
License	CC BY 4.0 Copyright © 2012 Mosby, Inc. All rights reserved.
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of fetal messenger ribonucleic acid in maternal blood to determine fetal RhD status as a strategy for noninvasive prenatal diagnosis publication-title: Am J Obstet Gynecol doi: 10.1016/S0002-9378(98)70274-1 – volume: 21 start-page: 313 year: 2003 ident: 10.1016/j.ajog.2012.01.030_bib31 article-title: Screening for chromosomal defects publication-title: Ultrasound Obstet Gynecol doi: 10.1002/uog.128 – volume: 204 start-page: 205.e1 year: 2011 ident: 10.1016/j.ajog.2012.01.030_bib20 article-title: Noninvasive detection of fetal trisomy 21 by sequencing of DNA in maternal blood: a study in a clinical setting publication-title: Am J Obstet Gynecol doi: 10.1016/j.ajog.2010.12.060 – volume: 191 start-page: 1730 year: 2004 ident: 10.1016/j.ajog.2012.01.030_bib12 article-title: Use of maternal plasma for noninvasive determination of fetal RhD status publication-title: Am J Obstet Gynecol doi: 10.1016/j.ajog.2004.06.098 – volume: 200 start-page: 543.e1 year: 2009 ident: 10.1016/j.ajog.2012.01.030_bib14 article-title: Microfluidic digital PCR enables rapid prenatal diagnosis of fetal aneuploidy publication-title: Am J Obstet Gynecol doi: 10.1016/j.ajog.2009.03.002 – reference: 22464064 - Am J Obstet Gynecol. 2012 Apr;206(4):269-75
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Snippet	We sought to develop a novel biochemical assay and algorithm for the prenatal evaluation of risk for fetal trisomy 21 (T21) and trisomy 18 (T18) using... Objective We sought to develop a novel biochemical assay and algorithm for the prenatal evaluation of risk for fetal trisomy 21 (T21) and trisomy 18 (T18)...
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SubjectTerms	Adult aneuploidy detection Biological and medical sciences Case-Control Studies Chromosome aberrations Chromosomes, Human, Pair 18 - genetics DNA - blood DNA - genetics Down syndrome Down Syndrome - diagnosis Female Fetus Gynecology. Andrology. Obstetrics Humans Male Medical genetics Medical sciences noninvasive prenatal diagnostics Obstetrics and Gynecology Pregnancy Pregnancy Trimester, First - blood Prenatal Diagnosis - methods Risk Sensitivity and Specificity trisomy Trisomy - diagnosis
Title	Noninvasive prenatal detection and selective analysis of cell-free DNA obtained from maternal blood: evaluation for trisomy 21 and trisomy 18
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