Feasibility of Optical Genome Mapping from Placental and Umbilical Cord Sampled after Spontaneous or Therapeutic Pregnancy Termination
Carole Goumy,
Zangbéwendé Guy Ouedraogo,
Elodie Bellemonte,
Eleonore Eymard-Pierre,
Gwendoline Soler,
Isabelle Perthus,
Céline Pebrel-Richard,
Laetitia Gouas,
Gaëlle Salaun,
Lauren Véronèse,
Hélène Laurichesse,
Claude Darcha,
Andrei Tchirkov
Affiliations
Carole Goumy
Cytogénétique Médicale, Centre Hospitalier Universitaire de Clermont-Ferrand, CHU Estaing, 63000 Clermont-Ferrand, France
Zangbéwendé Guy Ouedraogo
Cytogénétique Médicale, Centre Hospitalier Universitaire de Clermont-Ferrand, CHU Estaing, 63000 Clermont-Ferrand, France
Elodie Bellemonte
UMR 1095 INRAE/UCA Génétique, Diversité et Ecophysiologie des Céréales (GDEC), Genotyping and Sequencing Plateform Gentyane, 63000 Clermont-Ferrand, France
Eleonore Eymard-Pierre
Cytogénétique Médicale, Centre Hospitalier Universitaire de Clermont-Ferrand, CHU Estaing, 63000 Clermont-Ferrand, France
Gwendoline Soler
Cytogénétique Médicale, Centre Hospitalier Universitaire de Clermont-Ferrand, CHU Estaing, 63000 Clermont-Ferrand, France
Isabelle Perthus
Service de Génétique Médicale, CHU Clermont-Ferrand, CHU Estaing, 63000 Clermont-Ferrand, France
Céline Pebrel-Richard
Cytogénétique Médicale, Centre Hospitalier Universitaire de Clermont-Ferrand, CHU Estaing, 63000 Clermont-Ferrand, France
Laetitia Gouas
Cytogénétique Médicale, Centre Hospitalier Universitaire de Clermont-Ferrand, CHU Estaing, 63000 Clermont-Ferrand, France
Gaëlle Salaun
Cytogénétique Médicale, Centre Hospitalier Universitaire de Clermont-Ferrand, CHU Estaing, 63000 Clermont-Ferrand, France
Lauren Véronèse
Cytogénétique Médicale, Centre Hospitalier Universitaire de Clermont-Ferrand, CHU Estaing, 63000 Clermont-Ferrand, France
Hélène Laurichesse
Service d’Anatomie et de Cytologie Pathologique, Centre Hospitalier Universitaire de Clermont-Ferrand, CHU Estaing, 63000 Clermont-Ferrand, France
Claude Darcha
Service d’Anatomie et de Cytologie Pathologique, Centre Hospitalier Universitaire de Clermont-Ferrand, CHU Estaing, 63000 Clermont-Ferrand, France
Andrei Tchirkov
Cytogénétique Médicale, Centre Hospitalier Universitaire de Clermont-Ferrand, CHU Estaing, 63000 Clermont-Ferrand, France
Optical genome mapping (OGM) is an alternative to classical cytogenetic techniques to improve the detection rate of clinically significant genomic abnormalities. The isolation of high-molecular-weight (HMW) DNA is critical for a successful OGM analysis. HMW DNA quality depends on tissue type, sample size, and storage conditions. We assessed the feasibility of OGM analysis of DNA from nine umbilical cord (UC) and six chorionic villus (CV) samples collected after the spontaneous or therapeutic termination of pregnancy. We analyzed quality control metrics provided by the Saphyr system (Bionano Genomics) and assessed the length of extracted DNA molecules using pulsed-field capillary electrophoresis. OMG data were successfully analyzed for all six CV samples. Five of the UC samples did not meet the Saphyr quality criteria, mainly due to poor DNA quality. In this regard, we found that DNA quality assessment with pulsed-field capillary electrophoresis can predict a successful OGM analysis. OGM data were fully concordant with the results of standard cytogenetic methods. Moreover, OGM detected an average of 14 additional structural variants involving OMIM genes per sample. On the basis of our results, we established the optimal conditions for sample storage and preparation required for a successful OGM analysis. We recommend checking DNA quality before analysis with pulsed-field capillary electrophoresis if the storage conditions were not ideal or if the quality of the sample is poor. OGM can therefore be performed on fetal tissue harvested after the termination of pregnancy, which opens up the perspective for improved diagnostic yield.