Prenatal exome sequencing and impact on perinatal outcome: cohort study
ABSTRACT Objectives First, to determine the uptake of prenatal exome sequencing (pES) and the diagnostic yield of pathogenic (causative) variants in a UK tertiary fetal medicine unit following the introduction of the NHS England Rapid Exome Sequencing Service for fetal anomalies testing (R21 pathway...
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| Veröffentlicht in: | Ultrasound in obstetrics & gynecology 2023-03, Vol.61 (3), p.339-345 |
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| creator | Poljak, B. Agarwal, U. Alfirevic, Z. Allen, S. Canham, N. Higgs, J. Kaelin Agten, A. Khalil, A. Roberts, D. Mone, F. Navaratnam, K. |
| description | ABSTRACT
Objectives
First, to determine the uptake of prenatal exome sequencing (pES) and the diagnostic yield of pathogenic (causative) variants in a UK tertiary fetal medicine unit following the introduction of the NHS England Rapid Exome Sequencing Service for fetal anomalies testing (R21 pathway). Second, to identify how the decision to proceed with pES and identification of a causative variant affect perinatal outcomes, specifically late termination of pregnancy (TOP) at or beyond 22 weeks' gestation.
Methods
This was a retrospective cohort study of anomalous fetuses referred to the Liverpool Women's Hospital Fetal Medicine Unit between 1 March 2021 and 28 February 2022. pES was performed as part of the R21 pathway. Trio exome sequencing was performed using an Illumina next‐generation sequencing platform assessing coding and splice regions of a panel of 974 prenatally relevant genes and 231 expert reviewed genes. Data on demographics, phenotype, pES result and perinatal outcome were extracted and compared. Descriptive statistics and the χ‐square or Fisher's exact test were performed using IBM SPSS version 28.0.1.0.
Results
In total, 72 cases were identified and two‐thirds of eligible women (n = 48) consented to trio pES. pES was not feasible in one case owing to a low DNA yield and, therefore, was performed in 47 cases. In one‐third of cases (n = 24), pES was not proposed or agreed. In 58.3% (14/24) of these cases, this was because invasive testing was declined and, in 41.7% (10/24) of cases, women opted for testing and underwent chromosomal microarray analysis only. The diagnostic yield of pES was 23.4% (11/47). There was no overall difference in the proportion of women who decided to have late TOP in the group in which pES was agreed compared with the group in which pES was not proposed or agreed (25.0% (12/48) vs 25.0% (6/24); P = 1.0). However, the decision to have late TOP was significantly more frequent when a causative variant was detected compared with when pES was uninformative (63.6% (7/11) vs 13.9% (5/36); P |
| doi_str_mv | 10.1002/uog.26141 |
| format | Article |
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Objectives
First, to determine the uptake of prenatal exome sequencing (pES) and the diagnostic yield of pathogenic (causative) variants in a UK tertiary fetal medicine unit following the introduction of the NHS England Rapid Exome Sequencing Service for fetal anomalies testing (R21 pathway). Second, to identify how the decision to proceed with pES and identification of a causative variant affect perinatal outcomes, specifically late termination of pregnancy (TOP) at or beyond 22 weeks' gestation.
Methods
This was a retrospective cohort study of anomalous fetuses referred to the Liverpool Women's Hospital Fetal Medicine Unit between 1 March 2021 and 28 February 2022. pES was performed as part of the R21 pathway. Trio exome sequencing was performed using an Illumina next‐generation sequencing platform assessing coding and splice regions of a panel of 974 prenatally relevant genes and 231 expert reviewed genes. Data on demographics, phenotype, pES result and perinatal outcome were extracted and compared. Descriptive statistics and the χ‐square or Fisher's exact test were performed using IBM SPSS version 28.0.1.0.
Results
In total, 72 cases were identified and two‐thirds of eligible women (n = 48) consented to trio pES. pES was not feasible in one case owing to a low DNA yield and, therefore, was performed in 47 cases. In one‐third of cases (n = 24), pES was not proposed or agreed. In 58.3% (14/24) of these cases, this was because invasive testing was declined and, in 41.7% (10/24) of cases, women opted for testing and underwent chromosomal microarray analysis only. The diagnostic yield of pES was 23.4% (11/47). There was no overall difference in the proportion of women who decided to have late TOP in the group in which pES was agreed compared with the group in which pES was not proposed or agreed (25.0% (12/48) vs 25.0% (6/24); P = 1.0). However, the decision to have late TOP was significantly more frequent when a causative variant was detected compared with when pES was uninformative (63.6% (7/11) vs 13.9% (5/36); P < 0.0009). The median turnaround time for results was longer in cases in which a causative variant was identified than in those in which pES was uninformative (22 days (interquartile range (IQR), 19–34) days vs 14 days (IQR, 10–15 days); P < 0.0001).
Conclusions
This study demonstrates the potential impact of identification of a causative variant by pES on decision to have late TOP. As the R21 pathway continues to evolve, we urge clinicians and policymakers to consider introducing earlier screening for anomalies, developing robust guidance for late TOP and ensuring optimized support for couples. © 2022 The Authors. Ultrasound in Obstetrics & Gynecology published by John Wiley & Sons Ltd on behalf of International Society of Ultrasound in Obstetrics and Gynecology.</description><identifier>ISSN: 0960-7692</identifier><identifier>EISSN: 1469-0705</identifier><identifier>DOI: 10.1002/uog.26141</identifier><identifier>PMID: 36508432</identifier><language>eng</language><publisher>Chichester, UK: John Wiley & Sons, Ltd</publisher><subject>Anomalies ; Cohort analysis ; Cohort Studies ; Demographics ; Diagnostic systems ; DNA microarrays ; Exome Sequencing ; Female ; Fetus - diagnostic imaging ; Fetuses ; Genes ; Gynecology ; Humans ; Medicine ; Obstetrics ; Phenotypes ; Pregnancy ; prenatal ; Prenatal Diagnosis - methods ; R21 ; Retrospective Studies ; Statistical analysis ; termination of pregnancy ; Ultrasonic imaging ; Ultrasonography, Prenatal ; Ultrasound</subject><ispartof>Ultrasound in obstetrics & gynecology, 2023-03, Vol.61 (3), p.339-345</ispartof><rights>2022 The Authors. Ultrasound in Obstetrics & Gynecology published by John Wiley & Sons Ltd on behalf of International Society of Ultrasound in Obstetrics and Gynecology.</rights><rights>2022. This article is published under http://creativecommons.org/licenses/by-nc-nd/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c3881-2dccdd17e5901adb9d7a2a1c5b257f64ee32fc632a8972aceed075d45502a07e3</citedby><cites>FETCH-LOGICAL-c3881-2dccdd17e5901adb9d7a2a1c5b257f64ee32fc632a8972aceed075d45502a07e3</cites><orcidid>0000-0002-3344-0315 ; 0000-0003-0888-1650 ; 0000-0001-7600-5359 ; 0000-0001-9276-518X ; 0000-0003-2802-7670 ; 0000-0002-0718-7547</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1002%2Fuog.26141$$EPDF$$P50$$Gwiley$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1002%2Fuog.26141$$EHTML$$P50$$Gwiley$$Hfree_for_read</linktohtml><link.rule.ids>314,776,780,1411,1427,27901,27902,45550,45551,46384,46808</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/36508432$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Poljak, B.</creatorcontrib><creatorcontrib>Agarwal, U.</creatorcontrib><creatorcontrib>Alfirevic, Z.</creatorcontrib><creatorcontrib>Allen, S.</creatorcontrib><creatorcontrib>Canham, N.</creatorcontrib><creatorcontrib>Higgs, J.</creatorcontrib><creatorcontrib>Kaelin Agten, A.</creatorcontrib><creatorcontrib>Khalil, A.</creatorcontrib><creatorcontrib>Roberts, D.</creatorcontrib><creatorcontrib>Mone, F.</creatorcontrib><creatorcontrib>Navaratnam, K.</creatorcontrib><title>Prenatal exome sequencing and impact on perinatal outcome: cohort study</title><title>Ultrasound in obstetrics & gynecology</title><addtitle>Ultrasound Obstet Gynecol</addtitle><description>ABSTRACT
Objectives
First, to determine the uptake of prenatal exome sequencing (pES) and the diagnostic yield of pathogenic (causative) variants in a UK tertiary fetal medicine unit following the introduction of the NHS England Rapid Exome Sequencing Service for fetal anomalies testing (R21 pathway). Second, to identify how the decision to proceed with pES and identification of a causative variant affect perinatal outcomes, specifically late termination of pregnancy (TOP) at or beyond 22 weeks' gestation.
Methods
This was a retrospective cohort study of anomalous fetuses referred to the Liverpool Women's Hospital Fetal Medicine Unit between 1 March 2021 and 28 February 2022. pES was performed as part of the R21 pathway. Trio exome sequencing was performed using an Illumina next‐generation sequencing platform assessing coding and splice regions of a panel of 974 prenatally relevant genes and 231 expert reviewed genes. Data on demographics, phenotype, pES result and perinatal outcome were extracted and compared. Descriptive statistics and the χ‐square or Fisher's exact test were performed using IBM SPSS version 28.0.1.0.
Results
In total, 72 cases were identified and two‐thirds of eligible women (n = 48) consented to trio pES. pES was not feasible in one case owing to a low DNA yield and, therefore, was performed in 47 cases. In one‐third of cases (n = 24), pES was not proposed or agreed. In 58.3% (14/24) of these cases, this was because invasive testing was declined and, in 41.7% (10/24) of cases, women opted for testing and underwent chromosomal microarray analysis only. The diagnostic yield of pES was 23.4% (11/47). There was no overall difference in the proportion of women who decided to have late TOP in the group in which pES was agreed compared with the group in which pES was not proposed or agreed (25.0% (12/48) vs 25.0% (6/24); P = 1.0). However, the decision to have late TOP was significantly more frequent when a causative variant was detected compared with when pES was uninformative (63.6% (7/11) vs 13.9% (5/36); P < 0.0009). The median turnaround time for results was longer in cases in which a causative variant was identified than in those in which pES was uninformative (22 days (interquartile range (IQR), 19–34) days vs 14 days (IQR, 10–15 days); P < 0.0001).
Conclusions
This study demonstrates the potential impact of identification of a causative variant by pES on decision to have late TOP. As the R21 pathway continues to evolve, we urge clinicians and policymakers to consider introducing earlier screening for anomalies, developing robust guidance for late TOP and ensuring optimized support for couples. © 2022 The Authors. Ultrasound in Obstetrics & Gynecology published by John Wiley & Sons Ltd on behalf of International Society of Ultrasound in Obstetrics and Gynecology.</description><subject>Anomalies</subject><subject>Cohort analysis</subject><subject>Cohort Studies</subject><subject>Demographics</subject><subject>Diagnostic systems</subject><subject>DNA microarrays</subject><subject>Exome Sequencing</subject><subject>Female</subject><subject>Fetus - diagnostic imaging</subject><subject>Fetuses</subject><subject>Genes</subject><subject>Gynecology</subject><subject>Humans</subject><subject>Medicine</subject><subject>Obstetrics</subject><subject>Phenotypes</subject><subject>Pregnancy</subject><subject>prenatal</subject><subject>Prenatal Diagnosis - methods</subject><subject>R21</subject><subject>Retrospective Studies</subject><subject>Statistical analysis</subject><subject>termination of pregnancy</subject><subject>Ultrasonic imaging</subject><subject>Ultrasonography, Prenatal</subject><subject>Ultrasound</subject><issn>0960-7692</issn><issn>1469-0705</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2023</creationdate><recordtype>article</recordtype><sourceid>24P</sourceid><sourceid>EIF</sourceid><recordid>eNp10MFLwzAUx_Egis7pwX9ACl70UH1JmqT1JkOnMJgHPZcsedOOtplJi-6_N9rpQfD0Lh9-PL6EnFC4pADsqncvl0zSjO6QEc1kkYICsUtGUEhIlSzYATkMYQUAMuNynxxwKSDPOBuR6aPHVne6TvDDNZgEfOuxNVX7kujWJlWz1qZLXJus0VcDdH1nIr1OjHt1vktC19vNEdlb6jrg8faOyfPd7dPkPp3Npw-Tm1lqeJ7TlFljrKUKRQFU20VhlWaaGrFgQi1lhsjZ0kjOdF4opg2iBSVsJgQwDQr5mJwPu2vv4qehK5sqGKxr3aLrQ8mU4FIqKvNIz_7Qlet9G7-LKgep8oJDVBeDMt6F4HFZrn3VaL8pKZRfdctYt_yuG-3pdrFfNGh_5U_OCK4G8F7VuPl_qXyeT4fJTzGtg18</recordid><startdate>202303</startdate><enddate>202303</enddate><creator>Poljak, B.</creator><creator>Agarwal, U.</creator><creator>Alfirevic, Z.</creator><creator>Allen, S.</creator><creator>Canham, N.</creator><creator>Higgs, J.</creator><creator>Kaelin Agten, A.</creator><creator>Khalil, A.</creator><creator>Roberts, D.</creator><creator>Mone, F.</creator><creator>Navaratnam, K.</creator><general>John Wiley & Sons, Ltd</general><general>Wiley Subscription Services, Inc</general><scope>24P</scope><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>7QO</scope><scope>8FD</scope><scope>FR3</scope><scope>K9.</scope><scope>P64</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0002-3344-0315</orcidid><orcidid>https://orcid.org/0000-0003-0888-1650</orcidid><orcidid>https://orcid.org/0000-0001-7600-5359</orcidid><orcidid>https://orcid.org/0000-0001-9276-518X</orcidid><orcidid>https://orcid.org/0000-0003-2802-7670</orcidid><orcidid>https://orcid.org/0000-0002-0718-7547</orcidid></search><sort><creationdate>202303</creationdate><title>Prenatal exome sequencing and impact on perinatal outcome: cohort study</title><author>Poljak, B. ; Agarwal, U. ; Alfirevic, Z. ; Allen, S. ; Canham, N. ; Higgs, J. ; Kaelin Agten, A. ; Khalil, A. ; Roberts, D. ; Mone, F. ; Navaratnam, K.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c3881-2dccdd17e5901adb9d7a2a1c5b257f64ee32fc632a8972aceed075d45502a07e3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2023</creationdate><topic>Anomalies</topic><topic>Cohort analysis</topic><topic>Cohort Studies</topic><topic>Demographics</topic><topic>Diagnostic systems</topic><topic>DNA microarrays</topic><topic>Exome Sequencing</topic><topic>Female</topic><topic>Fetus - diagnostic imaging</topic><topic>Fetuses</topic><topic>Genes</topic><topic>Gynecology</topic><topic>Humans</topic><topic>Medicine</topic><topic>Obstetrics</topic><topic>Phenotypes</topic><topic>Pregnancy</topic><topic>prenatal</topic><topic>Prenatal Diagnosis - methods</topic><topic>R21</topic><topic>Retrospective Studies</topic><topic>Statistical analysis</topic><topic>termination of pregnancy</topic><topic>Ultrasonic imaging</topic><topic>Ultrasonography, Prenatal</topic><topic>Ultrasound</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Poljak, B.</creatorcontrib><creatorcontrib>Agarwal, U.</creatorcontrib><creatorcontrib>Alfirevic, Z.</creatorcontrib><creatorcontrib>Allen, S.</creatorcontrib><creatorcontrib>Canham, N.</creatorcontrib><creatorcontrib>Higgs, J.</creatorcontrib><creatorcontrib>Kaelin Agten, A.</creatorcontrib><creatorcontrib>Khalil, A.</creatorcontrib><creatorcontrib>Roberts, D.</creatorcontrib><creatorcontrib>Mone, F.</creatorcontrib><creatorcontrib>Navaratnam, K.</creatorcontrib><collection>Wiley Online Library Open Access</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Biotechnology Research Abstracts</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Ultrasound in obstetrics & gynecology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Poljak, B.</au><au>Agarwal, U.</au><au>Alfirevic, Z.</au><au>Allen, S.</au><au>Canham, N.</au><au>Higgs, J.</au><au>Kaelin Agten, A.</au><au>Khalil, A.</au><au>Roberts, D.</au><au>Mone, F.</au><au>Navaratnam, K.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Prenatal exome sequencing and impact on perinatal outcome: cohort study</atitle><jtitle>Ultrasound in obstetrics & gynecology</jtitle><addtitle>Ultrasound Obstet Gynecol</addtitle><date>2023-03</date><risdate>2023</risdate><volume>61</volume><issue>3</issue><spage>339</spage><epage>345</epage><pages>339-345</pages><issn>0960-7692</issn><eissn>1469-0705</eissn><abstract>ABSTRACT
Objectives
First, to determine the uptake of prenatal exome sequencing (pES) and the diagnostic yield of pathogenic (causative) variants in a UK tertiary fetal medicine unit following the introduction of the NHS England Rapid Exome Sequencing Service for fetal anomalies testing (R21 pathway). Second, to identify how the decision to proceed with pES and identification of a causative variant affect perinatal outcomes, specifically late termination of pregnancy (TOP) at or beyond 22 weeks' gestation.
Methods
This was a retrospective cohort study of anomalous fetuses referred to the Liverpool Women's Hospital Fetal Medicine Unit between 1 March 2021 and 28 February 2022. pES was performed as part of the R21 pathway. Trio exome sequencing was performed using an Illumina next‐generation sequencing platform assessing coding and splice regions of a panel of 974 prenatally relevant genes and 231 expert reviewed genes. Data on demographics, phenotype, pES result and perinatal outcome were extracted and compared. Descriptive statistics and the χ‐square or Fisher's exact test were performed using IBM SPSS version 28.0.1.0.
Results
In total, 72 cases were identified and two‐thirds of eligible women (n = 48) consented to trio pES. pES was not feasible in one case owing to a low DNA yield and, therefore, was performed in 47 cases. In one‐third of cases (n = 24), pES was not proposed or agreed. In 58.3% (14/24) of these cases, this was because invasive testing was declined and, in 41.7% (10/24) of cases, women opted for testing and underwent chromosomal microarray analysis only. The diagnostic yield of pES was 23.4% (11/47). There was no overall difference in the proportion of women who decided to have late TOP in the group in which pES was agreed compared with the group in which pES was not proposed or agreed (25.0% (12/48) vs 25.0% (6/24); P = 1.0). However, the decision to have late TOP was significantly more frequent when a causative variant was detected compared with when pES was uninformative (63.6% (7/11) vs 13.9% (5/36); P < 0.0009). The median turnaround time for results was longer in cases in which a causative variant was identified than in those in which pES was uninformative (22 days (interquartile range (IQR), 19–34) days vs 14 days (IQR, 10–15 days); P < 0.0001).
Conclusions
This study demonstrates the potential impact of identification of a causative variant by pES on decision to have late TOP. As the R21 pathway continues to evolve, we urge clinicians and policymakers to consider introducing earlier screening for anomalies, developing robust guidance for late TOP and ensuring optimized support for couples. © 2022 The Authors. Ultrasound in Obstetrics & Gynecology published by John Wiley & Sons Ltd on behalf of International Society of Ultrasound in Obstetrics and Gynecology.</abstract><cop>Chichester, UK</cop><pub>John Wiley & Sons, Ltd</pub><pmid>36508432</pmid><doi>10.1002/uog.26141</doi><tpages>7</tpages><orcidid>https://orcid.org/0000-0002-3344-0315</orcidid><orcidid>https://orcid.org/0000-0003-0888-1650</orcidid><orcidid>https://orcid.org/0000-0001-7600-5359</orcidid><orcidid>https://orcid.org/0000-0001-9276-518X</orcidid><orcidid>https://orcid.org/0000-0003-2802-7670</orcidid><orcidid>https://orcid.org/0000-0002-0718-7547</orcidid><oa>free_for_read</oa></addata></record> |
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| source | Wiley Free Content; MEDLINE; Wiley Online Library Journals Frontfile Complete; EZB-FREE-00999 freely available EZB journals |
| subjects | Anomalies Cohort analysis Cohort Studies Demographics Diagnostic systems DNA microarrays Exome Sequencing Female Fetus - diagnostic imaging Fetuses Genes Gynecology Humans Medicine Obstetrics Phenotypes Pregnancy prenatal Prenatal Diagnosis - methods R21 Retrospective Studies Statistical analysis termination of pregnancy Ultrasonic imaging Ultrasonography, Prenatal Ultrasound |
| title | Prenatal exome sequencing and impact on perinatal outcome: cohort study |
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