Noninvasive prenatal testing using a novel analysis pipeline to screen for all autosomal fetal aneuploidies improves pregnancy management
Noninvasive prenatal testing by massive parallel sequencing of maternal plasma DNA has rapidly been adopted as a mainstream method for detection of fetal trisomy 21, 18 and 13. Despite the relative high accuracy of current NIPT testing, a substantial number of false-positive and false-negative test...
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Veröffentlicht in: | European journal of human genetics : EJHG 2015-10, Vol.23 (10), p.1286-1293 |
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creator | Bayindir, Baran Dehaspe, Luc Brison, Nathalie Brady, Paul Ardui, Simon Kammoun, Molka Van der Veken, Lars Lichtenbelt, Klaske Van den Bogaert, Kris Van Houdt, Jeroen Peeters, Hilde Van Esch, Hilde de Ravel, Thomy Legius, Eric Devriendt, Koen Vermeesch, Joris R |
description | Noninvasive prenatal testing by massive parallel sequencing of maternal plasma DNA has rapidly been adopted as a mainstream method for detection of fetal trisomy 21, 18 and 13. Despite the relative high accuracy of current NIPT testing, a substantial number of false-positive and false-negative test results remain. Here, we present an analysis pipeline, which addresses some of the technical as well as the biologically derived causes of error. Most importantly, it differentiates high z-scores due to fetal trisomies from those due to local maternal CNVs causing false positives. This pipeline was retrospectively validated for trisomy 18 and 21 detection on 296 samples demonstrating a sensitivity and specificity of 100%, and applied prospectively to 1350 pregnant women in the clinical diagnostic setting with a result reported in 99.9% of cases. In addition, values indicative for trisomy were observed two times for chromosome 7 and once each for chromosomes 15 and 16, and once for a segmental trisomy 18. Two of the trisomies were confirmed to be mosaic, one of which contained a uniparental disomy cell line. As placental trisomies pose a risk for low-grade fetal mosaicism as well as uniparental disomy, genome-wide noninvasive aneuploidy detection is improving prenatal management. |
doi_str_mv | 10.1038/ejhg.2014.282 |
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Despite the relative high accuracy of current NIPT testing, a substantial number of false-positive and false-negative test results remain. Here, we present an analysis pipeline, which addresses some of the technical as well as the biologically derived causes of error. Most importantly, it differentiates high z-scores due to fetal trisomies from those due to local maternal CNVs causing false positives. This pipeline was retrospectively validated for trisomy 18 and 21 detection on 296 samples demonstrating a sensitivity and specificity of 100%, and applied prospectively to 1350 pregnant women in the clinical diagnostic setting with a result reported in 99.9% of cases. In addition, values indicative for trisomy were observed two times for chromosome 7 and once each for chromosomes 15 and 16, and once for a segmental trisomy 18. Two of the trisomies were confirmed to be mosaic, one of which contained a uniparental disomy cell line. As placental trisomies pose a risk for low-grade fetal mosaicism as well as uniparental disomy, genome-wide noninvasive aneuploidy detection is improving prenatal management.</description><identifier>ISSN: 1018-4813</identifier><identifier>EISSN: 1476-5438</identifier><identifier>DOI: 10.1038/ejhg.2014.282</identifier><identifier>PMID: 25585704</identifier><language>eng</language><publisher>England: Nature Publishing Group</publisher><subject>Aneuploidy ; Bioinformatics ; Chromosome 7 ; Chromosome Aberrations ; Chromosome Disorders - genetics ; Chromosomes ; Chromosomes, Human - genetics ; Chromosomes, Human, Pair 18 - genetics ; Deoxyribonucleic acid ; DNA ; DNA sequencing ; Down Syndrome - genetics ; Female ; Fetus - pathology ; Fetuses ; Genetic Testing - methods ; Genomes ; High-Throughput Nucleotide Sequencing - methods ; Humans ; Mosaicism ; Pipelines ; Placenta ; Placenta - pathology ; Plasma ; Pregnancy ; Prenatal Diagnosis - methods ; Retrospective Studies ; Trisomy ; Trisomy - genetics ; Trisomy 18 Syndrome ; Ultrasonic imaging ; Uniparental disomy ; Women</subject><ispartof>European journal of human genetics : EJHG, 2015-10, Vol.23 (10), p.1286-1293</ispartof><rights>Copyright Nature Publishing Group Oct 2015</rights><rights>Copyright © 2015 Macmillan Publishers Limited 2015 Macmillan Publishers Limited</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c518t-9f3c70463c76cb2c1055ca7204f0b530cf6fcf740712c660605c24f15bcea98c3</citedby><cites>FETCH-LOGICAL-c518t-9f3c70463c76cb2c1055ca7204f0b530cf6fcf740712c660605c24f15bcea98c3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4592078/pdf/$$EPDF$$P50$$Gpubmedcentral$$H</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4592078/$$EHTML$$P50$$Gpubmedcentral$$H</linktohtml><link.rule.ids>230,315,729,782,786,887,27931,27932,53798,53800</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/25585704$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Bayindir, Baran</creatorcontrib><creatorcontrib>Dehaspe, Luc</creatorcontrib><creatorcontrib>Brison, Nathalie</creatorcontrib><creatorcontrib>Brady, Paul</creatorcontrib><creatorcontrib>Ardui, Simon</creatorcontrib><creatorcontrib>Kammoun, Molka</creatorcontrib><creatorcontrib>Van der Veken, Lars</creatorcontrib><creatorcontrib>Lichtenbelt, Klaske</creatorcontrib><creatorcontrib>Van den Bogaert, Kris</creatorcontrib><creatorcontrib>Van Houdt, Jeroen</creatorcontrib><creatorcontrib>Peeters, Hilde</creatorcontrib><creatorcontrib>Van Esch, Hilde</creatorcontrib><creatorcontrib>de Ravel, Thomy</creatorcontrib><creatorcontrib>Legius, Eric</creatorcontrib><creatorcontrib>Devriendt, Koen</creatorcontrib><creatorcontrib>Vermeesch, Joris R</creatorcontrib><title>Noninvasive prenatal testing using a novel analysis pipeline to screen for all autosomal fetal aneuploidies improves pregnancy management</title><title>European journal of human genetics : EJHG</title><addtitle>Eur J Hum Genet</addtitle><description>Noninvasive prenatal testing by massive parallel sequencing of maternal plasma DNA has rapidly been adopted as a mainstream method for detection of fetal trisomy 21, 18 and 13. Despite the relative high accuracy of current NIPT testing, a substantial number of false-positive and false-negative test results remain. Here, we present an analysis pipeline, which addresses some of the technical as well as the biologically derived causes of error. Most importantly, it differentiates high z-scores due to fetal trisomies from those due to local maternal CNVs causing false positives. This pipeline was retrospectively validated for trisomy 18 and 21 detection on 296 samples demonstrating a sensitivity and specificity of 100%, and applied prospectively to 1350 pregnant women in the clinical diagnostic setting with a result reported in 99.9% of cases. In addition, values indicative for trisomy were observed two times for chromosome 7 and once each for chromosomes 15 and 16, and once for a segmental trisomy 18. Two of the trisomies were confirmed to be mosaic, one of which contained a uniparental disomy cell line. As placental trisomies pose a risk for low-grade fetal mosaicism as well as uniparental disomy, genome-wide noninvasive aneuploidy detection is improving prenatal management.</description><subject>Aneuploidy</subject><subject>Bioinformatics</subject><subject>Chromosome 7</subject><subject>Chromosome Aberrations</subject><subject>Chromosome Disorders - genetics</subject><subject>Chromosomes</subject><subject>Chromosomes, Human - genetics</subject><subject>Chromosomes, Human, Pair 18 - genetics</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA sequencing</subject><subject>Down Syndrome - genetics</subject><subject>Female</subject><subject>Fetus - pathology</subject><subject>Fetuses</subject><subject>Genetic Testing - methods</subject><subject>Genomes</subject><subject>High-Throughput Nucleotide Sequencing - methods</subject><subject>Humans</subject><subject>Mosaicism</subject><subject>Pipelines</subject><subject>Placenta</subject><subject>Placenta - pathology</subject><subject>Plasma</subject><subject>Pregnancy</subject><subject>Prenatal Diagnosis - methods</subject><subject>Retrospective Studies</subject><subject>Trisomy</subject><subject>Trisomy - genetics</subject><subject>Trisomy 18 Syndrome</subject><subject>Ultrasonic imaging</subject><subject>Uniparental disomy</subject><subject>Women</subject><issn>1018-4813</issn><issn>1476-5438</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2015</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNqNkkFrFDEUxwdRbK0evUrAi5dZk0kyyV4EKdUKRS96Dtn0ZZolk4zJzMJ-BL-1b-harCcvL4H8-OW9x79pXjO6YZTr97C_GzYdZWLT6e5Jc86E6lspuH6Kd8p0KzTjZ82LWvcUKaXY8-ask1JLRcV58-trTiEdbA0HIFOBZGcbyQx1DmkgS12rJSkfIBKbbDzWUMkUJoghAZkzqa4AJOJzITYis8y55hEdHlaTTbBMMYfbAJWEcSpoqutHQ7LJHcmI0gFGSPPL5pm3scKr03nR_Ph09f3yur359vnL5ceb1kmm53brucPOe6y923WOUSmdVR0Vnu4kp8733nklqGKd63vaU-k64ZncObBb7fhF8-HeOy27EW4dfl1sNFMJoy1Hk20wj19SuDNDPhghtx1VGgXvToKSfy64KTOG6iBGnDUv1TDVyy2iWv4HyvhWciU4om__Qfd5KbjxE6V6LEi195QrudYC_qFvRs2aB7Pmwax5MJgH5N_8PewD_ScA_DeKZLTo</recordid><startdate>20151001</startdate><enddate>20151001</enddate><creator>Bayindir, Baran</creator><creator>Dehaspe, Luc</creator><creator>Brison, Nathalie</creator><creator>Brady, Paul</creator><creator>Ardui, Simon</creator><creator>Kammoun, Molka</creator><creator>Van der Veken, Lars</creator><creator>Lichtenbelt, Klaske</creator><creator>Van den Bogaert, Kris</creator><creator>Van Houdt, Jeroen</creator><creator>Peeters, Hilde</creator><creator>Van Esch, Hilde</creator><creator>de Ravel, Thomy</creator><creator>Legius, Eric</creator><creator>Devriendt, Koen</creator><creator>Vermeesch, Joris R</creator><general>Nature Publishing Group</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>8AO</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M7P</scope><scope>P64</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20151001</creationdate><title>Noninvasive prenatal testing using a novel analysis pipeline to screen for all autosomal fetal aneuploidies improves pregnancy management</title><author>Bayindir, Baran ; Dehaspe, Luc ; Brison, Nathalie ; Brady, Paul ; Ardui, Simon ; Kammoun, Molka ; Van der Veken, Lars ; Lichtenbelt, Klaske ; Van den Bogaert, Kris ; Van Houdt, Jeroen ; Peeters, Hilde ; Van Esch, Hilde ; de Ravel, Thomy ; Legius, Eric ; Devriendt, Koen ; Vermeesch, Joris R</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c518t-9f3c70463c76cb2c1055ca7204f0b530cf6fcf740712c660605c24f15bcea98c3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2015</creationdate><topic>Aneuploidy</topic><topic>Bioinformatics</topic><topic>Chromosome 7</topic><topic>Chromosome Aberrations</topic><topic>Chromosome Disorders - 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>European journal of human genetics : EJHG</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Bayindir, Baran</au><au>Dehaspe, Luc</au><au>Brison, Nathalie</au><au>Brady, Paul</au><au>Ardui, Simon</au><au>Kammoun, Molka</au><au>Van der Veken, Lars</au><au>Lichtenbelt, Klaske</au><au>Van den Bogaert, Kris</au><au>Van Houdt, Jeroen</au><au>Peeters, Hilde</au><au>Van Esch, Hilde</au><au>de Ravel, Thomy</au><au>Legius, Eric</au><au>Devriendt, Koen</au><au>Vermeesch, Joris R</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Noninvasive prenatal testing using a novel analysis pipeline to screen for all autosomal fetal aneuploidies improves pregnancy management</atitle><jtitle>European journal of human genetics : EJHG</jtitle><addtitle>Eur J Hum Genet</addtitle><date>2015-10-01</date><risdate>2015</risdate><volume>23</volume><issue>10</issue><spage>1286</spage><epage>1293</epage><pages>1286-1293</pages><issn>1018-4813</issn><eissn>1476-5438</eissn><abstract>Noninvasive prenatal testing by massive parallel sequencing of maternal plasma DNA has rapidly been adopted as a mainstream method for detection of fetal trisomy 21, 18 and 13. Despite the relative high accuracy of current NIPT testing, a substantial number of false-positive and false-negative test results remain. Here, we present an analysis pipeline, which addresses some of the technical as well as the biologically derived causes of error. Most importantly, it differentiates high z-scores due to fetal trisomies from those due to local maternal CNVs causing false positives. This pipeline was retrospectively validated for trisomy 18 and 21 detection on 296 samples demonstrating a sensitivity and specificity of 100%, and applied prospectively to 1350 pregnant women in the clinical diagnostic setting with a result reported in 99.9% of cases. In addition, values indicative for trisomy were observed two times for chromosome 7 and once each for chromosomes 15 and 16, and once for a segmental trisomy 18. Two of the trisomies were confirmed to be mosaic, one of which contained a uniparental disomy cell line. As placental trisomies pose a risk for low-grade fetal mosaicism as well as uniparental disomy, genome-wide noninvasive aneuploidy detection is improving prenatal management.</abstract><cop>England</cop><pub>Nature Publishing Group</pub><pmid>25585704</pmid><doi>10.1038/ejhg.2014.282</doi><tpages>8</tpages><oa>free_for_read</oa></addata></record> |
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subjects | Aneuploidy Bioinformatics Chromosome 7 Chromosome Aberrations Chromosome Disorders - genetics Chromosomes Chromosomes, Human - genetics Chromosomes, Human, Pair 18 - genetics Deoxyribonucleic acid DNA DNA sequencing Down Syndrome - genetics Female Fetus - pathology Fetuses Genetic Testing - methods Genomes High-Throughput Nucleotide Sequencing - methods Humans Mosaicism Pipelines Placenta Placenta - pathology Plasma Pregnancy Prenatal Diagnosis - methods Retrospective Studies Trisomy Trisomy - genetics Trisomy 18 Syndrome Ultrasonic imaging Uniparental disomy Women |
title | Noninvasive prenatal testing using a novel analysis pipeline to screen for all autosomal fetal aneuploidies improves pregnancy management |
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