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Series GSE85424 Query DataSets for GSE85424
Status Public on Jul 22, 2018
Title Definitive classification of ovarian mature cystic teratomas origin using B allele frequency plots with SNP array analysis
Organism Homo sapiens
Experiment type Genome variation profiling by SNP array
Summary Ovarian mature cystic teratomas (MCTs) originate from postmeiotic germ cells, and some are thought to result from the fusion of two ova. The aim of this study was to determine whether this mechanism is in fact involved in MCT development. MCTs can be classified by the zygosity of the centromere and distal chromosome regions. We evaluated the zygosity of all chromosomes from 38 MCT specimens using B allele frequency (BAF) plots of single nucleotide polymorphism-array data. Theoretically, MCTs originated from the fusion of two ova should have a mixed pattern of centromeric zygosity, i.e., a combination of heterozygous and homozygous regions. However, no MCTs in this series met this criterion as evidenced by BAF plots, suggesting that the fusion of two ova is not mechanistically involved in the development of ovarian teratomas. Thus, MCTs were classified into three types originating from meiosis I and meiosis II errors, and endoduplication of a mature ovum. The numbers of recombination events occurring with type I and II MCTs were somewhat higher than in regular oogenesis. In addition, BAF plots could facilitate the construction of recombination maps at the whole-genome level for type I and II MCTs. In conclusion, our findings provide evidence against the hypothesis that MCTs originate from the fusion of two ova and indicate that BAF plots could serve as useful analytical tools for analyzing MCT cytogenetics and human oocyte meiosis.
Overall design Thirty-eight ovarian MCTs specimens from 35 MCTs were obtained from 27 patients, who were subjected to cystectomy or oophorectomy. Three sets of specimens were collected from same tumors (specimen 09 and 10 from tumor 27, specimen 23 and 24 from tumor 28, specimen 32 and 33 from tumor 12). The other specimens were sampled from independent tumors. The genomic DNAs were extracted and were analyzed by Illumina HumanCore-24v1 array.
Contributor(s) Usui H, Nakabayashi K, Maehara K, Hata K, Shozu M
Citation(s) 29700881
Submission date Aug 10, 2016
Last update date Jul 24, 2018
Contact name Hirokazu Usui
Phone 81-43-222-2121
Organization name Graduate School of Medicine, Chiba University
Department Department of Reproductive Medicine
Street address 1-8-1 Inohana, Chuo-ku
City Chiba
State/province Chiba
ZIP/Postal code 260-8670
Country Japan
Platforms (2)
GPL13829 Illumina HumanCytoSNP-12 v2.1 BeadChip
GPL24395 Illumina HumanCore-24v1-0 SNP array
Samples (38)
GSM2891113 Patient2_Tumor3_Specimen1
GSM2891114 Patient9_Tumor13_Specimen2
GSM2891115 Patient10_Tumor15_Specimen3
BioProject PRJNA338444

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
GSE85424_RAW.tar 135.5 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table

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