Definitive SNP/CNV haplotype map of Asians determined using a collection of complete hydatidiform moles
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE18701 | GEO | 2010/05/17
SECONDARY ACCESSION(S): PRJNA121489
REPOSITORIES: GEO
Similar Datasets
Project description:This SuperSeries is composed of the following subset Series: GSE18642: Definitive SNP/CNV haplotype map of Asians determined using a collection of complete hydatidiform moles (Affymetrix) GSE18663: Definitive SNP/CNV haplotype map of Asians determined using a collection of complete hydatidiform moles (Illumina) Refer to individual Series
2010-05-17 | E-GEOD-18701 | biostudies-arrayexpress
Project description:Copy number variations (CNVs) are abundant, possibly variable among populations, and can confer various phenotypic variations such as risk to complex disease. We determined a genome-wide high resolution SNP/CNV haplotype structure of Asians, by analyzing a collection of complete hydatidiform moles (CHMs) of Japanese, using high-density DNA arrays. CHMs are tissues carrying duplicated haploid genomes that originated from single sperm, and have advantages as materials over conventional diploid cells in detecting CNVs by hybridization, because greater S/N ratios are expected, and overlapping CNV segments are independently detected without being bothered by possible heterozygous situations. Overall occupancy of CNV segments per haploid found here was at a level similar to previous reports. Approximately a half of our polymorphic CNV regions have not been described in the previous report for Asians, but the frequencies of most of these new CNV regions were low. The limited number of examined samples is likely to be the reason that they have escaped detection in the previous report. Many common CNV regions are resolvable to clusters of CNV segmets (that is, CNV events) on the basis of mutual overlap of the segments. The similarity of haplotype backgrounds surrounding different CNV events within the same CNV regions suggests that ancestral recurrences of CNV events were predominantly haplotype preferential.
2010-05-17 | GSE18642 | GEO
Project description:Copy number variations (CNVs) are abundant, possibly variable among populations, and can confer various phenotypic variations such as risk to complex disease. We determined a genome-wide high resolution SNP/CNV haplotype structure of Asians, by analyzing a collection of complete hydatidiform moles (CHMs) of Japanese, using high-density DNA arrays. CHMs are tissues carrying duplicated haploid genomes that originated from single sperm, and have advantages as materials over conventional diploid cells in detecting CNVs by hybridization, because greater S/N ratios are expected, and overlapping CNV segments are independently detected without being bothered by possible heterozygous situations. Overall occupancy of CNV segments per haploid found here was at a level similar to previous reports. Approximately a half of our polymorphic CNV regions have not been described in the previous report for Asians, but the frequencies of most of these new CNV regions were low. The limited number of examined samples is likely to be the reason that they have escaped detection in the previous report. Many common CNV regions are resolvable to clusters of CNV segmets (that is, CNV events) on the basis of mutual overlap of the segments. The similarity of haplotype backgrounds surrounding different CNV events within the same CNV regions suggests that ancestral recurrences of CNV events were predominantly haplotype preferential.
2010-05-17 | GSE18663 | GEO
Project description:Copy number variations (CNVs) are abundant, possibly variable among populations, and can confer various phenotypic variations such as risk to complex disease. We determined a genome-wide high resolution SNP/CNV haplotype structure of Asians, by analyzing a collection of complete hydatidiform moles (CHMs) of Japanese, using high-density DNA arrays. CHMs are tissues carrying duplicated haploid genomes that originated from single sperm, and have advantages as materials over conventional diploid cells in detecting CNVs by hybridization, because greater S/N ratios are expected, and overlapping CNV segments are independently detected without being bothered by possible heterozygous situations. Overall occupancy of CNV segments per haploid found here was at a level similar to previous reports. Approximately a half of our polymorphic CNV regions have not been described in the previous report for Asians, but the frequencies of most of these new CNV regions were low. The limited number of examined samples is likely to be the reason that they have escaped detection in the previous report. Many common CNV regions are resolvable to clusters of CNV segmets (that is, CNV events) on the basis of mutual overlap of the segments. The similarity of haplotype backgrounds surrounding different CNV events within the same CNV regions suggests that ancestral recurrences of CNV events were predominantly haplotype preferential. Illumina Human1M-Duov3 BeadChip analyses were performed according to the manufacturer's directions on DNA extracted from 5 complete hydatidiform moles (CHMs) tissues collected throughout Japan.
2010-05-17 | E-GEOD-18663 | biostudies-arrayexpress
Project description:The haplotype map constructed by the International HapMap Project is a valuable source for the studies of disease genes, population structure, and evolution. In the Project, haplotypes have been inferred from experimentally determined genotypes, and are fairly accurate for Caucasians and Africans since the inference was based on the genotypes of trios. However, the inference for the Asians populations was less accurate, because of the lack of familial information. Here we assessed how the error in the inference can affect downstream studies, especially the analysis of recent positive selections, by comparing the results of the analyses using the data of HapMap JPT and of definitive haplotypes (DHaplo-DB) determined by us from a collection of Japanese complete hydatidiform moles (CHM), each of which carries a genome derived from a single sperm. We found that the error in JPT was not uniform throughout the genome, and the statistics for recent positive selection was significantly affected. Keywords: Definitive haplotype determination using CHMs, which carry haploid genomes.
2009-05-12 | GSE12713 | GEO
Project description:The haplotype map constructed by the International HapMap Project is a valuable source for the studies of disease genes, population structure, and evolution. In the Project, haplotypes have been inferred from experimentally determined genotypes, and are fairly accurate for Caucasians and Africans since the inference was based on the genotypes of trios. However, the inference for the Asians populations was less accurate, because of the lack of familial information. Here we assessed how the error in the inference can affect downstream studies, especially the analysis of recent positive selections, by comparing the results of the analyses using the data of HapMap JPT and of definitive haplotypes (DHaplo-DB) determined by us from a collection of Japanese complete hydatidiform moles (CHM), each of which carries a genome derived from a single sperm. We found that the error in JPT was not uniform throughout the genome, and the statistics for recent positive selection was significantly affected. Keywords: Definitive haplotype determination using CHMs, which carry haploid genomes. 100 CHM samples collected throughout Japan were analyzed by Affymetrix Genechip Mapping 500K Set array.
2010-04-05 | E-GEOD-12713 | biostudies-arrayexpress
Project description:The haplotype map constructed by the HapMap Project is a valuable resource in the genetic studies of disease genes, population structure, and evolution. In the Project, Caucasian and African haplotypes are fairly accurately inferred, based mainly on the rules of Mendelian inheritance using the genotypes of trios. However, the Asian haplotypes are inferred from the genotypes of unrelated individuals based on population genetics, and are less accurate. Thus, the effects of this inaccuracy on downstream analyses needs to be assessed. We determined true Japanese haplotypes by genotyping 100 complete hydatidiform moles (CHM), each carrying a genome derived from a single sperm, using Affymetrix 500 K Arrays. We then assessed how inferred haplotypes can differ from true haplotypes, by phasing pseudo-individualized true haplotypes using the programs PHASE, fastPHASE, and Beagle. We found that, at various genomic regions, especially the MHC locus, the expansion of extended haplotype homozygosity (EHH), which is a measure of positive selection, is obscured when inferred Asian haplotype data is used to detect the expansion. We then mapped the genome using a new statistic, XDiHH, which directly detects the difference between the true and inferred haplotypes, in the determination of EHH expansion. We also show that the true haplotype data presented here is useful to assess and improve the accuracy of phasing of Asian genotypes.
| S-EPMC2670534 | biostudies-literature
Project description:Gene expression studies of molar pregnancy have been limited to a small number of candidate loci. We analyzed high-dimensional RNA and protein data to characterize molecular features of complete hydatidiform moles (CHMs) and corresponding pathologic pathways. CHMs and first trimester placentas were collected, histopathologically examined, then flash-frozen or paraffin-embedded. Frozen CHMs and control placentas were subjected to RNA-Seq, with resulting data and published placental RNA-Seq data subjected to bioinformatics analyses. Paraffin-embedded tissues from CHMs and control placentas were used for tissue microarray (TMA) construction, immunohistochemistry, and immunoscoring for galectin-14. Of the 14,022 protein-coding genes expressed in all samples, 3,729 were differentially expressed (DE) in CHMs, of which 72% were up-regulated. DE genes were enriched in placenta-specific genes (OR = 1.88, p = 0.0001), of which 79% were down-regulated, imprinted genes (OR = 2.38, p = 1.54 × 10-6), and immune genes (OR = 1.82, p = 7.34 × 10-18), of which 73% were up-regulated. DNA methylation-related enzymes and histone demethylases were dysregulated. "Cytokine-cytokine receptor interaction" was the most impacted of 38 dysregulated pathways, among which 17 were immune-related pathways. TMA-based immunoscoring validated the lower expression of galectin-14 in CHM. In conclusion, placental functions were down-regulated, imprinted gene expression was altered, and immune pathways were activated, indicating complex dysregulation of placental developmental and immune processes in CHMs.
| S-EPMC6829352 | biostudies-literature
Project description:Complete hydatidiform moles (CHMs) are tissues carrying duplicated haploid genomes derived from single sperms, and detecting copy number variations (CNVs) in CHMs is assumed to be sensitive and straightforward methods. We genotyped 108 CHM genomes using Affymetrix SNP 6.0 (GEO#: GSE18642) and Illumina 1 M-duo (GEO#: GSE54948). After quality control, we obtained 84 definitive haplotype consisting of 1.7 million SNPs and 2339 CNV regions. The results are presented in the database of our web site (http://orca.gen.kyushu-u.ac.jp/cgi-bin/gbrowse/humanBuild37D4_1/).
| S-EPMC4535890 | biostudies-literature
Project description:We analyzed high-dimensional RNA data to characterize molecular features of complete hydatidiform moles (CHMs) and corresponding pathologic pathways. CHMs and first trimester placentas were collected, histopathologically examined, then flash-frozen. Frozen CHMs and control placentas were subjected to RNA-Seq, with resulting data and published placental RNA-Seq data subjected to bioinformatics analyses. Of the 14,022 protein-coding genes expressed in all samples, 3729 were differentially expressed (DE) in CHMs of which 72% were up-regulated. DE genes were enriched in placenta-specific genes (OR = 1.88, p = 0.0001) of which 79% were down-regulated, imprinted genes (OR = 2.38, p = 1.54 × 10−6), and immune genes (OR = 1.82, p = 7.34 × 10−18), of which 73% were up-regulated. DNA methylation enzymes and histone demethylases were dysregulated. “Cytokine–cytokine receptor interaction” was the most impacted of 38 dysregulated pathways, among which 17 were immune-related pathways.
2019-10-31 | GSE138250 | GEO