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Series GSE138864 Query DataSets for GSE138864
Status Public on Nov 21, 2019
Title A KHDC3L mutation resulting in recurrent hydatidiform mole causes genome-wide DNA methylation loss in oocytes and persistent imprinting defects post-fertilisation.
Organism Homo sapiens
Experiment type Methylation profiling by genome tiling array
Summary Maternal-effect mutations in components of the subcortical maternal complex (SCMC) of the human oocyte can cause early embryonic failure, gestational abnormalities and recurrent pregnancy loss. Enigmatically, they are also associated with DNA methylation abnormalities at imprinted genes in conceptuses, in the devastating gestational abnormality biparental complete hydatidiform mole (BiCHM) or in multi-locus imprinting disease (MLID). However, the developmental timing, genomic extent and mechanistic basis of these imprinting defects are unknown. Here, we studied methylation level of a women reported with familial recurrent hydatidiform mole and multiple pregnancy loss. Genotype analysis revealed homozygous mutation in KHDC3L. We obtained biparental mole from patient (Patient D) and compared it’s whole-genome methylation profile with respect to control placentas and sporadic mole (AnCHM) using Infinium MethylationEPIC BeadChip (WG-317-1001, Illumina). We also used endometrium samples from their respective mother for the comparison purposes. Molar conceptuses were observed with methylation defects at genome-wide level and profound loss of methylation at multiple genome-derived differentially methylated regions (gDMRs) confirming MLID.
 
Overall design DNA samples from control placenta, biparental mole and sporadic mole were analysed using using Infinium MethylationEPIC 850K Bead Chip and pyrosequencing. Methylation level was assesed at genome-wide level and specific genome features (eg. gDMRs and CpG Islands).
 
Contributor(s) Demond H, Anvar Z, Jahromi BN, Sparago A, Verma A, Davari M, Calzari L, Russo S, Jahromi MA, Monk D, Andrews S, Riccio A, Kelsey G
Citation(s) 31847873
Submission date Oct 15, 2019
Last update date Dec 31, 2019
Contact name Ankit Verma
E-mail(s) ankitverma9079@gmail.com
Organization name Institute of Genetics and Biophysics "A. Buzzati Traverso" (IGB-ABT)
Street address Via Pietro Castellino, 111
City Naples
State/province Naples
ZIP/Postal code 80131
Country Italy
 
Platforms (1)
GPL21145 Infinium MethylationEPIC
Samples (6)
GSM4120575 Control Placenta 01
GSM4120576 Control Placenta 02
GSM4120577 KHDC3L Mole (BiCHM)
Relations
BioProject PRJNA577637

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE138864_Matrix_processed.txt.gz 40.0 Mb (ftp)(http) TXT
GSE138864_Matrix_signal_intensities.txt.gz 27.3 Mb (ftp)(http) TXT
GSE138864_RAW.tar 242.6 Mb (http)(custom) TAR (of IDAT)
Processed data included within Sample table
Processed data are available on Series record

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