title: Competence Classification of Cumulus and Granulosa Cell Transcriptome in Embryos Matched by Morphology and Female Age.
abstract: By focussing on differences in the mural granulosa cell (MGC) and cumulus cell (CC) transcriptomes from follicles resulting in competent (live birth) and non-competent (no pregnancy) oocytes the study aims on defining a competence classifier expression profile in the two cellular compartments.
  
  
  
  A case-control study.
  
  
  
  University based facilities for clinical services and research.
  
  
  
  MGC and CC samples from 60 women undergoing IVF treatment following the long GnRH-agonist protocol were collected. Samples from 16 oocytes where live birth was achieved and 16 age- and embryo morphology matched incompetent oocytes were included in the study.
  
  
  
  MGC and CC were isolated immediately after oocyte retrieval. From the 16 competent and non-competent follicles, mRNA was extracted and expression profile generated on the Human Gene 1.0 ST Affymetrix array. Live birth prediction analysis using machine learning algorithms (support vector machines) with performance estimation by leave-one-out cross validation and independent validation on an external data set.
  
  
  
  We defined a signature of 30 genes expressed in CC predictive of live birth. This live birth prediction model had an accuracy of 81%, a sensitivity of 0.83, a specificity of 0.80, a positive predictive value of 0.77, and a negative predictive value of 0.86. Receiver operating characteristic analysis found an area under the curve of 0.86, significantly greater than random chance. When applied on 3 external data sets with the end-point outcome measure of blastocyst formation, the signature resulted in 62%, 75% and 88% accuracy, respectively. The genes in the classifier are primarily connected to apoptosis and involvement in formation of extracellular matrix. We were not able to define a robust MGC classifier signature that could classify live birth with accuracy above random chance level.
  
  
  
  We have developed a cumulus cell classifier, which showed a promising performance on external data. This suggests that the gene signature at least partly include genes that relates to competence in the developing blastocyst.
authors.affiliation: Center for Genomic Medicine, University Hospital of Copenhagen, Rigshospitalet, Copenhagen, Denmark.
authors.forename: Rehannah
authors.identifier: 0000-0002-6947-9094
authors.initials: R
authors.lastname: Borup
authors.affiliation: Fertility Clinic, University Hospital of Copenhagen, Rigshospitalet, Copenhagen, Denmark.
authors.forename: Lea Langhoff
authors.initials: LL
authors.lastname: Thuesen
authors.affiliation: Laboratory of Reproductive Biology, University Hospital of Copenhagen, Rigshospitalet, Copenhagen, Denmark.
authors.forename: Claus Yding
authors.initials: CY
authors.lastname: Andersen
authors.affiliation: Fertility Clinic, University Hospital of Copenhagen, Rigshospitalet, Copenhagen, Denmark.
authors.forename: Anders
authors.initials: A
authors.lastname: Nyboe-Andersen
authors.affiliation: Fertility Clinic, University Hospital of Copenhagen, Rigshospitalet, Copenhagen, Denmark.
authors.forename: Søren
authors.initials: S
authors.lastname: Ziebe
authors.affiliation: Bioinformatics Center, Department of Biology and Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark.
authors.forename: Ole
authors.initials: O
authors.lastname: Winther
authors.affiliation: Fertility Clinic, University Hospital of Copenhagen, Herlev Hospital, Copenhagen, Denmark.
authors.forename: Marie Louise
authors.initials: ML
authors.lastname: Grøndahl
mesh_terms: D000328:Adult; D016022:Case-Control Studies; D054885:Cumulus Cells / Q000145:classification* / Q000378:metabolism*; D047108:Embryonic Development / Q000235:genetics; D005260:Female; D005307:Fertilization in Vitro; D053263:Gene Regulatory Networks; D006107:Granulosa Cells / Q000145:classification* / Q000378:metabolism*; D006801:Humans; D007231:Infant, Newborn; D054315:Oocyte Retrieval; D011247:Pregnancy; D011256:Pregnancy Outcome; D059467:Transcriptome