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All-in-one whole exome sequencing strategy with simultaneous copy number variant, single nucleotide variant and absence-of-heterozygosity analysis in fetuses with structural ultrasound anomalies: A 1-year experience.
Faas, Brigitte H W; Westra, Dineke; de Munnik, Sonja A; van Rij, Maartje; Marcelis, Carlo; Joosten, Sara; Krapels, Ingrid; Vernimmen, Vivian; Heijligers, Malou; Willemsen, Marjolein H; de Leeuw, Nicole; Rinne, Tuula; Pfundt, Rolph; Smeekens, Sanne P; Stegmann, Sander P A; Macville, Merryn; Sikkel, Esther; Coumans, Audrey; Wijnberger, Lia; Derks, Irma; van Lent-Albrechts, Josefa; Hofste, Tom; Timmermans, Raoul; van den End, Janneke; Stevens, Servi J C; Feenstra, Ilse.
Afiliación
  • Faas BHW; Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.
  • Westra D; Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.
  • de Munnik SA; Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.
  • van Rij M; Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, The Netherlands.
  • Marcelis C; Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.
  • Joosten S; Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.
  • Krapels I; Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.
  • Vernimmen V; Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, The Netherlands.
  • Heijligers M; Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, The Netherlands.
  • Willemsen MH; Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, The Netherlands.
  • de Leeuw N; Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.
  • Rinne T; Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.
  • Pfundt R; Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.
  • Smeekens SP; Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.
  • Stegmann SPA; Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.
  • Macville M; Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, The Netherlands.
  • Sikkel E; Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, The Netherlands.
  • Coumans A; Department of Obstetrics and Gynaecology, Radboud University Medical Center, Nijmegen, The Netherlands.
  • Wijnberger L; Department of Obstetrics and Gynaecology, Maastricht University Medical Centre, Maastricht, The Netherlands.
  • Derks I; Department of Obstetrics and Gynaecology, Rijnstate Hospital, Arnhem, The Netherlands.
  • van Lent-Albrechts J; Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.
  • Hofste T; Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, The Netherlands.
  • Timmermans R; Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.
  • van den End J; Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.
  • Stevens SJC; Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.
  • Feenstra I; Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, The Netherlands.
Prenat Diagn ; 43(4): 527-543, 2023 04.
Article en En | MEDLINE | ID: mdl-36647814
OBJECTIVE: We performed a 1-year evaluation of a novel strategy of simultaneously analyzing single nucleotide variants (SNVs), copy number variants (CNVs) and copy-number-neutral Absence-of-Heterozygosity from Whole Exome Sequencing (WES) data for prenatal diagnosis of fetuses with ultrasound (US) anomalies and a non-causative QF-PCR result. METHODS: After invasive diagnostics, whole exome parent-offspring trio-sequencing with exome-wide CNV analysis was performed in pregnancies with fetal US anomalies and a non-causative QF-PCR result (WES-CNV). On request, additional SNV-analysis, restricted to (the) requested gene panel(s) only (with the option of whole exome SNV-analysis afterward) was performed simultaneously (WES-CNV/SNV) or as rapid SNV-re-analysis, following a normal CNV analysis. RESULTS: In total, 415 prenatal samples were included. Following a non-causative QF-PCR result, WES-CNV analysis was initially requested for 74.3% of the chorionic villus (CV) samples and 45% of the amniotic fluid (AF) samples. In case WES-CNV analysis did not reveal a causative aberration, SNV-re-analysis was requested in 41.7% of the CV samples and 17.5% of the AF samples. All initial analyses could be finished within 2 weeks after sampling. For SNV-re-analysis during pregnancy, turn-around-times (TATs) varied between one and 8 days. CONCLUSION: We show a highly efficient all-in-one WES-based strategy, with short TATs, and the option of rapid SNV-re-analysis after a normal CNV result.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Variaciones en el Número de Copia de ADN / Feto Límite: Female / Humans / Pregnancy Idioma: En Revista: Prenat Diagn Año: 2023 Tipo del documento: Article País de afiliación: Países Bajos Pais de publicación: Reino Unido
Texto completo
Añadir a Mi BVS
Imprimir
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PubMed Links
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Variaciones en el Número de Copia de ADN / Feto Límite: Female / Humans / Pregnancy Idioma: En Revista: Prenat Diagn Año: 2023 Tipo del documento: Article País de afiliación: Países Bajos Pais de publicación: Reino Unido