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Series GSE228150 Query DataSets for GSE228150
Status Public on Oct 05, 2023
Title Prevalence of chromosomal alterations in first-trimester spontaneous pregnancy loss
Organism Homo sapiens
Experiment type Genome variation profiling by array
Summary Extensive genome analysis of pregnancy loss products by genome haplarithmisis.
Pregnancy loss (PL) is the primary pregnancy complication, mostly caused by chromosomal abnormalities of the conceptus. However, the nature and prevalence of these abnormalities and the allocation of (ab)normal cells in embryonic and placental compartments during intrauterine development remains elusive. We analyzed 1,745 spontaneous PLs and found that ~50% were karyotypically normal. We applied genome haplarithmisis to 91 PL families with normal karyotypes, following whole-genome genotypes of the parents as well as of the extraembryonic mesoderm (EM) and chorionic villi (CV), representing embryonic and placental cells, of the product of conception (POC), which allowed characterizing genomic landscape of both lineages. 36.4% of these PLs have chromosomal aberrations not previously detected by karyotyping. In contrast to viable pregnancies where mosaic chromosomal abnormalities are often restricted to the CV, we find that in spontaneous abortions, the situation is reversed with a higher degree of mosaic chromosomal imbalances in EM rather than CV.
 
Overall design From 1987 to 2021, A total of 1745 spontaneous PLs were analyzed using karyotyping. 866 (49.6%) were classified as normal and 879 (50.4%) as abnormal. The karyotypes of fetal tissue was determined by conventional metaphase analysis (n=1745) or additional testing by comparative genomic hybridization (CGH) and fluorescence in situ hybridization (FISH), as described previously37,38. All the samples with abnormal karyotype were excluded for downstream haplarithmisis. Of the karyotypically normal cases, 111 families were randomly selected for SNP haplotyping, given that fetal (EM and CV) and parental blood samples were available without previously identified genetic predisposition was in any of the couples. Twenty families have been excluded due to the DNA of one or more family members being of insufficient quality causing low SNP call rates or due to one or both parents not being the biological parent, making proper haplotyping analysis impossible . Ninety-one families have been successfully analyzed by haplarithmisis. Of those, forty-two were categorized as SPL (loss of one pregnancy) and forty-nine as RPL (loss of two or more consecutive pregnancies).
The data is provided in quartest structure,including Father, Mother, chrionic villi (CV) sample and extra-embryonic mesoderm (EM).
Please note that each processed data file was generated from multiple samples as inidcated in the corresponding sample description.
 
Contributor(s) Essers R, Lebedev IN, Kurg A, Fonova EA, Stevens SJ, Koeck R, von Rango U, Brandts L, Deligiannis SP, Nikitina TV, Sazhenova EA, Tolmacheva EN, Kashevarova AA, Fedotov DA, Demeneva VV, Drozdov GV, Al-Nasiry S, Macville MV, van den Wijngaard A, Dreesen J, Paulussen A, Hoschen A, Brunner HG, Salumets A, Esteki MZ
Citation(s) 37996709
Submission date Mar 24, 2023
Last update date Dec 22, 2023
Contact name Rick Essers
E-mail(s) rick.essers@mumc.nl
Organization name Maastricht University Medical Centre (MUMC+)
Department Clinical Genetics
Street address P. Debyelaan 25
City Maastricht
State/province Limburg
ZIP/Postal code 6229HX
Country Netherlands
 
Platforms (1)
GPL28939 Illumina Infinium Global Screening Array-24 BeadChip (customizable)
Samples (450)
GSM7115145 Chorionic villi fetal biopsy [PL1063_CV2009]
GSM7115146 Extraembryonic mesoderm fetal biopsy [PL1063_EM2009]
GSM7115147 Periferal blood father [PL1063_Father]
This SubSeries is part of SuperSeries:
GSE228151 Prevalence of chromosomal alterations in first-trimester spontaneous pregnancy loss
Relations
BioProject PRJNA948400

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
GSE228150_PL1063.adj.txt.gz 29.2 Mb (ftp)(http) TXT
GSE228150_PL1246.adj.txt.gz 30.0 Mb (ftp)(http) TXT
GSE228150_PL129.adj.txt.gz 28.7 Mb (ftp)(http) TXT
GSE228150_PL135.adj.txt.gz 29.3 Mb (ftp)(http) TXT
GSE228150_PL1359.adj.txt.gz 29.6 Mb (ftp)(http) TXT
GSE228150_PL1362.adj.txt.gz 30.4 Mb (ftp)(http) TXT
GSE228150_PL137.adj.txt.gz 29.9 Mb (ftp)(http) TXT
GSE228150_PL1373.adj.txt.gz 29.0 Mb (ftp)(http) TXT
GSE228150_PL1397.adj.txt.gz 29.9 Mb (ftp)(http) TXT
GSE228150_PL140.adj.txt.gz 29.7 Mb (ftp)(http) TXT
GSE228150_PL1400.adj.txt.gz 32.5 Mb (ftp)(http) TXT
GSE228150_PL142.adj.txt.gz 31.6 Mb (ftp)(http) TXT
GSE228150_PL150.adj.txt.gz 29.9 Mb (ftp)(http) TXT
GSE228150_PL1547.adj.txt.gz 29.9 Mb (ftp)(http) TXT
GSE228150_PL158.adj.txt.gz 30.5 Mb (ftp)(http) TXT
GSE228150_PL1595.adj.txt.gz 29.0 Mb (ftp)(http) TXT
GSE228150_PL1618.adj.txt.gz 29.2 Mb (ftp)(http) TXT
GSE228150_PL164.adj.txt.gz 30.5 Mb (ftp)(http) TXT
GSE228150_PL166.adj.txt.gz 13.8 Mb (ftp)(http) TXT
GSE228150_PL167.adj.txt.gz 29.6 Mb (ftp)(http) TXT
GSE228150_PL1681.adj.txt.gz 29.6 Mb (ftp)(http) TXT
GSE228150_PL1682.adj.txt.gz 29.4 Mb (ftp)(http) TXT
GSE228150_PL1701.adj.txt.gz 28.9 Mb (ftp)(http) TXT
GSE228150_PL1710_1.adj.txt.gz 28.6 Mb (ftp)(http) TXT
GSE228150_PL1710_2.adj.txt.gz 28.6 Mb (ftp)(http) TXT
GSE228150_PL1710_3.adj.txt.gz 28.8 Mb (ftp)(http) TXT
GSE228150_PL1744.adj.txt.gz 29.4 Mb (ftp)(http) TXT
GSE228150_PL1758.adj.txt.gz 29.5 Mb (ftp)(http) TXT
GSE228150_PL1776.adj.txt.gz 30.2 Mb (ftp)(http) TXT
GSE228150_PL1783.adj.txt.gz 29.6 Mb (ftp)(http) TXT
GSE228150_PL1790.adj.txt.gz 30.7 Mb (ftp)(http) TXT
GSE228150_PL180.adj.txt.gz 31.1 Mb (ftp)(http) TXT
GSE228150_PL1800.adj.txt.gz 29.6 Mb (ftp)(http) TXT
GSE228150_PL1809.adj.txt.gz 28.8 Mb (ftp)(http) TXT
GSE228150_PL1824.adj.txt.gz 29.3 Mb (ftp)(http) TXT
GSE228150_PL1873.adj.txt.gz 30.6 Mb (ftp)(http) TXT
GSE228150_PL1892.adj.txt.gz 29.6 Mb (ftp)(http) TXT
GSE228150_PL1896.adj.txt.gz 29.3 Mb (ftp)(http) TXT
GSE228150_PL1941.adj.txt.gz 28.8 Mb (ftp)(http) TXT
GSE228150_PL1965.adj.txt.gz 28.6 Mb (ftp)(http) TXT
GSE228150_PL1973.adj.txt.gz 29.2 Mb (ftp)(http) TXT
GSE228150_PL2016.adj.txt.gz 29.5 Mb (ftp)(http) TXT
GSE228150_PL2019.adj.txt.gz 30.3 Mb (ftp)(http) TXT
GSE228150_PL203.adj.txt.gz 29.5 Mb (ftp)(http) TXT
GSE228150_PL2030.adj.txt.gz 30.2 Mb (ftp)(http) TXT
GSE228150_PL2074.adj.txt.gz 29.6 Mb (ftp)(http) TXT
GSE228150_PL2081.adj.txt.gz 29.2 Mb (ftp)(http) TXT
GSE228150_PL2087.adj.txt.gz 30.0 Mb (ftp)(http) TXT
GSE228150_PL2115.adj.txt.gz 28.9 Mb (ftp)(http) TXT
GSE228150_PL2130.adj.txt.gz 29.3 Mb (ftp)(http) TXT
GSE228150_PL2137.adj.txt.gz 30.4 Mb (ftp)(http) TXT
GSE228150_PL2178.adj.txt.gz 31.2 Mb (ftp)(http) TXT
GSE228150_PL2194.adj.txt.gz 30.2 Mb (ftp)(http) TXT
GSE228150_PL2223.adj.txt.gz 29.2 Mb (ftp)(http) TXT
GSE228150_PL2261.adj.txt.gz 29.2 Mb (ftp)(http) TXT
GSE228150_PL228.adj.txt.gz 32.2 Mb (ftp)(http) TXT
GSE228150_PL2377.adj.txt.gz 29.9 Mb (ftp)(http) TXT
GSE228150_PL2409.adj.txt.gz 30.2 Mb (ftp)(http) TXT
GSE228150_PL241.adj.txt.gz 29.7 Mb (ftp)(http) TXT
GSE228150_PL245.adj.txt.gz 31.1 Mb (ftp)(http) TXT
GSE228150_PL2451.adj.txt.gz 30.1 Mb (ftp)(http) TXT
GSE228150_PL2452.adj.txt.gz 29.5 Mb (ftp)(http) TXT
GSE228150_PL246.adj.txt.gz 30.3 Mb (ftp)(http) TXT
GSE228150_PL250.adj.txt.gz 31.5 Mb (ftp)(http) TXT
GSE228150_PL2596.adj.txt.gz 28.9 Mb (ftp)(http) TXT
GSE228150_PL2597.adj.txt.gz 30.0 Mb (ftp)(http) TXT
GSE228150_PL2617.adj.txt.gz 29.3 Mb (ftp)(http) TXT
GSE228150_PL2621.adj.txt.gz 29.9 Mb (ftp)(http) TXT
GSE228150_PL2631.adj.txt.gz 29.2 Mb (ftp)(http) TXT
GSE228150_PL2650.adj.txt.gz 29.0 Mb (ftp)(http) TXT
GSE228150_PL2652.adj.txt.gz 29.6 Mb (ftp)(http) TXT
GSE228150_PL2653.adj.txt.gz 28.9 Mb (ftp)(http) TXT
GSE228150_PL2660.adj.txt.gz 28.9 Mb (ftp)(http) TXT
GSE228150_PL2662.adj.txt.gz 28.3 Mb (ftp)(http) TXT
GSE228150_PL2666.adj.txt.gz 28.7 Mb (ftp)(http) TXT
GSE228150_PL2678.adj.txt.gz 28.5 Mb (ftp)(http) TXT
GSE228150_PL2682.adj.txt.gz 29.1 Mb (ftp)(http) TXT
GSE228150_PL2701.adj.txt.gz 29.2 Mb (ftp)(http) TXT
GSE228150_PL2702.adj.txt.gz 28.9 Mb (ftp)(http) TXT
GSE228150_PL2706.adj.txt.gz 28.9 Mb (ftp)(http) TXT
GSE228150_PL2708.adj.txt.gz 28.9 Mb (ftp)(http) TXT
GSE228150_PL271.adj.txt.gz 29.4 Mb (ftp)(http) TXT
GSE228150_PL2711.adj.txt.gz 29.2 Mb (ftp)(http) TXT
GSE228150_PL2712.adj.txt.gz 28.9 Mb (ftp)(http) TXT
GSE228150_PL2717.adj.txt.gz 29.3 Mb (ftp)(http) TXT
GSE228150_PL2726.adj.txt.gz 29.1 Mb (ftp)(http) TXT
GSE228150_PL2727.adj.txt.gz 30.0 Mb (ftp)(http) TXT
GSE228150_PL2728.adj.txt.gz 29.5 Mb (ftp)(http) TXT
GSE228150_PL2730.adj.txt.gz 30.4 Mb (ftp)(http) TXT
GSE228150_PL2733.adj.txt.gz 30.1 Mb (ftp)(http) TXT
GSE228150_PL2734.adj.txt.gz 29.7 Mb (ftp)(http) TXT
GSE228150_PL2738.adj.txt.gz 28.8 Mb (ftp)(http) TXT
GSE228150_PL278.adj.txt.gz 30.9 Mb (ftp)(http) TXT
GSE228150_PL281.adj.txt.gz 30.0 Mb (ftp)(http) TXT
GSE228150_PL290.adj.txt.gz 29.9 Mb (ftp)(http) TXT
GSE228150_PL379.adj.txt.gz 31.5 Mb (ftp)(http) TXT
GSE228150_PL383.adj.txt.gz 30.1 Mb (ftp)(http) TXT
GSE228150_PL384.adj.txt.gz 31.8 Mb (ftp)(http) TXT
GSE228150_PL401.adj.txt.gz 29.4 Mb (ftp)(http) TXT
GSE228150_PL444.adj.txt.gz 30.5 Mb (ftp)(http) TXT
GSE228150_PL445.adj.txt.gz 31.3 Mb (ftp)(http) TXT
GSE228150_PL455.adj.txt.gz 30.2 Mb (ftp)(http) TXT
GSE228150_PL524_1.adj.txt.gz 30.9 Mb (ftp)(http) TXT
GSE228150_PL524_2.adj.txt.gz 30.7 Mb (ftp)(http) TXT
GSE228150_PL588.adj.txt.gz 29.7 Mb (ftp)(http) TXT
GSE228150_PL649.adj.txt.gz 29.0 Mb (ftp)(http) TXT
GSE228150_PL668.adj.txt.gz 29.1 Mb (ftp)(http) TXT
GSE228150_PL714.adj.txt.gz 29.3 Mb (ftp)(http) TXT
GSE228150_PL777.adj.txt.gz 29.1 Mb (ftp)(http) TXT
GSE228150_PL822.adj.txt.gz 30.1 Mb (ftp)(http) TXT
GSE228150_PL915.adj.txt.gz 30.9 Mb (ftp)(http) TXT
GSE228150_PL920.adj.txt.gz 30.8 Mb (ftp)(http) TXT
GSE228150_PL934.adj.txt.gz 31.2 Mb (ftp)(http) TXT
GSE228150_PL947.adj.txt.gz 29.5 Mb (ftp)(http) TXT
GSE228150_RAW.tar 4.7 Gb (http)(custom) TAR (of IDAT)
Processed data are available on Series record

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