Ena-DATASET-DTU-22-02-2017-08:21:35:017-10 - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001003188 | EGA |
REPOSITORIES: EGA
Publications
Sequencing and de novo assembly of 150 genomes from Denmark as a population reference.
Maretty Lasse L Jensen Jacob Malte JM Petersen Bent B Sibbesen Jonas Andreas JA Liu Siyang S Villesen Palle P Skov Laurits L Belling Kirstine K Theil Have Christian C Izarzugaza Jose M G JMG Grosjean Marie M Bork-Jensen Jette J Grove Jakob J Als Thomas D TD Huang Shujia S Chang Yuqi Y Xu Ruiqi R Ye Weijian W Rao Junhua J Guo Xiaosen X Sun Jihua J Cao Hongzhi H Ye Chen C van Beusekom Johan J Espeseth Thomas T Flindt Esben E Friborg Rune M RM Halager Anders E AE Le Hellard Stephanie S Hultman Christina M CM Lescai Francesco F Li Shengting S Lund Ole O Løngren Peter P Mailund Thomas T Matey-Hernandez Maria Luisa ML Mors Ole O Pedersen Christian N S CNS Sicheritz-Pontén Thomas T Sullivan Patrick P Syed Ali A Westergaard David D Yadav Rachita R Li Ning N Xu Xun X Hansen Torben T Krogh Anders A Bolund Lars L Sørensen Thorkild I A TIA Pedersen Oluf O Gupta Ramneek R Rasmussen Simon S Besenbacher Søren S Børglum Anders D AD Wang Jun J Eiberg Hans H Kristiansen Karsten K Brunak Søren S Schierup Mikkel Heide MH
Nature 20170726 7665
Hundreds of thousands of human genomes are now being sequenced to characterize genetic variation and use this information to augment association mapping studies of complex disorders and other phenotypic traits. Genetic variation is identified mainly by mapping short reads to the reference genome or by performing local assembly. However, these approaches are biased against discovery of structural variants and variation in the more complex parts of the genome. Hence, large-scale de novo assembly i ...[more]
Similar Datasets
Project description:Alignment of Genome Denmark Phase II dataset to GRCh38. The dataset consists of 150 Danish individuals (50 trios) sequenced to 80X. The BAM-file contains data from multiple libraries created from one individual with libraries of 180, 500, 800, 2000, 5000, 10000 and 20000 bp. The libraries were created using standard Illumina protocols for paired end reads (180-800bp libraries) and mate pair libraries (2kb-20kb).
| EGAD00001003157 | EGA
Project description:The MHC vcf call set was generated using a modified AsmVar and BayesTyper pipeline. In contrast to the original pipeline, where variant calling is performed using alignment of collapsed assemblies to a reference genome, the MHC call set was produced using alignment of phased MHC haplotypes. Two iterations of BayesTyper was run, a first iteration for each haplotype seperately and a second iteration performing joint variant calling on all haplotypes. The sample IDs for the fathers and mothers are TrioID-01 and TrioID-02, respectively, and the IDs for the children are TrioID-0x, where x is a number between 3 and 7.
| EGAD00001003455 | EGA
Project description:Female Crlj:CD1(ICR) mice were fed diets containing 0 (control), 5000 and 10000 ppm permethrin and 2500 ppm isoniazid (positive control for tumor induction) for periods of 7 and 14 days. We used microarrays to evaluate gene expression profiling in mouse lung at the early phase of treatment with permethrin and isoniazid.
2018-12-21 | GSE92688 | GEO
Project description:In socially monogamous prairie voles (Microtus ochrogaster), parental behaviors not only occur in mothers and fathers, but also can exist in virgin males. However, some virgin males display aggressive behaviors towards conspecific pups. Although this behavioral dichotomy in response to pup exposure has been well documented in male virgin voles, little is known about the gene expression changes underlie the parental behavioral differences and their regulatory mechanisms. To address this, we profiled the transcriptome and DNA methylome of hippocampal dentate gyrus of four prairie vole groups, attacker virgin males, parental virgin males, fathers, and mothers. We found a concordant pattern of gene transcription in parental virgin males and fathers, when comparing to the attacker group. The methylome analysis also revealed pathways with genes enriched for epigenetic changes involving both receptor-mediated and secondary messenger signaling across both behavioral phenotypes and sexual experiences. Furthermore, we found correlations between gene expression changes and DNA methylation differences between attacker and parental virgin males, which suggests a canonical gene expression regulatory role of DNA methylation in paternal care. Therefore, our study presents an integrated view of transcriptome and epigenome that provides a DNA epigenetic based molecular insight of paternal behavior.
2023-07-12 | GSE214798 | GEO
Project description:In socially monogamous prairie voles (Microtus ochrogaster), parental behaviors not only occur in mothers and fathers, but also can exist in virgin males. However, some virgin males display aggressive behaviors towards conspecific pups. Although this behavioral dichotomy in response to pup exposure has been well documented in male virgin voles, little is known about the gene expression changes underlie the parental behavioral differences and their regulatory mechanisms. To address this, we profiled the transcriptome and DNA methylome of hippocampal dentate gyrus of four prairie vole groups, attacker virgin males, parental virgin males, fathers, and mothers. We found a concordant pattern of gene transcription in parental virgin males and fathers, when comparing to the attacker group. The methylome analysis also revealed pathways with genes enriched for epigenetic changes involving both receptor-mediated and secondary messenger signaling across both behavioral phenotypes and sexual experiences. Furthermore, we found correlations between gene expression changes and DNA methylation differences between attacker and parental virgin males, which suggests a canonical gene expression regulatory role of DNA methylation in paternal care. Therefore, our study presents an integrated view of transcriptome and epigenome that provides a DNA epigenetic based molecular insight of paternal behavior.
2023-07-12 | GSE214797 | GEO
Project description:Nonsyndromic cleft lip with or without palate (NSCL/P) are common birth defects of complex etiology. Multiple interacting loci with possible additional environment factors influence the risk for NSCL/P. 12 single nucleotide polymorphisms (SNPs) in 7 candidate genes were tested using an allele-specific primer extension for both case-control and case-parents analyses in northeast China (236 unrelated patients, 185 mothers and 154 fathers, including 128 complete trios, 400 control individuals). TGFA and IRF6 genes showed a significant associations with NSCL/P. For IRF6, statistical evidence of association between rs2235371 (P=0.003), rs2013162 (P=0.000) and NSCL/P was found in case-control analyses. The Family Based Association Tests (FBAT) showed an over-transmission for C allele of rs2235371 polymorphic (p=0.007). For TGFA, associations between rs3771494, rs3771523 (G3822A), rs11466285 (T3851C) and NSCL/P could be observed both in case-control and FBAT analyses. However, we found no associations between other genes (BCL3, TGFB3, MTHFR1, PVRL1 and SUMO1) and NSCL/P. In the study present, 236 unrelated patient with NSCL/P addition with 185 mothers and 154 fathers and 400 control individuals were tested with the allele special primer extension microarray.
2013-04-09 | E-GEOD-45770 | biostudies-arrayexpress
Project description:Motherhood is characterized by dramatic changes in brain and behavior, but less is known about fatherhood. Here we report that male sticklebacks – a small fish in which fathers provide care – experience dramatic changes in neurogenomic state as they become fathers. Some genes are unique to different stages of paternal care, some genes are shared across stages, and some genes are added to the previously acquired neurogenomic state. Comparative genomic analysis suggests that some of these neurogenomic dynamics resemble changes associated with pregnancy and reproduction in mammalian mothers. Moreover, gene regulatory analysis identified transcription factors that are regulated in opposite directions in response to a territorial challenge versus during paternal care. Altogether these results show that some of the molecular mechanisms of parental care might be deeply conserved and might not be sex-specific, and suggest that tradeoffs between opposing social behaviors are managed at the gene regulatory level.
2019-09-15 | GSE134508 | GEO
Project description:Background: Normal cell BRCA1 epimutations have been associated with increased risk of triple-negative breast cancer (TNBC). However, the fraction of TNBCs that may have BRCA1 epimutations as their underlying cause is unknown. Neither are the time of occurrence and the potential inheritance patterns of BRCA1 epimutations established. Methods: To address these questions, we analyzed BRCA1 methylation status in breast cancer tissue and matched white blood cells (WBC) from 408 patients with 411 primary breast cancers, including 66 TNBCs, applying a highly sensitive sequencing assay, allowing allele-resolved methylation assessment. Further, to assess the time of origin and the characteristics of normal cell BRCA1 methylation, we analyzed umbilical cord blood of 1260 newborn girls and 200 newborn boys. Finally, we assessed BRCA1 methylation status among 575 mothers and 531 fathers of girls with (n = 102) and without (n = 473) BRCA1 methylation. Results: We found concordant tumor and mosaic WBC BRCA1 epimutations in 10 out of 66 patients with TNBC and in four out of six patients with estrogen receptor (ER)-low expression (<10%) tumors (combined: 14 out of 72; 19.4%; 95% CI 11.1–30.5). In contrast, we found concordance in only three out of 220 patients with 221 ER≥10% tumors and zero out of 114 patients with 116 HER2-positive tumors. Intraindividually, BRCA1 epimutations affected the same allele in normal and tumor cells. Assessing BRCA1 methylation in umbilical WBCs from girls, we found mosaic, predominantly monoallelic BRCA1 epimutations, with qualitative features similar to those in adults, in 113/1260 (9.0%) of individuals, but no correlation to BRCA1 methylation status either in mothers or fathers. A significantly lower fraction of newborn boys carried BRCA1 methylation (9 / 200; 4.5%) as compared to girls (p = 0.038). Similarly, WBC BRCA1 methylation was found less common among fathers (16/531; 3.0%), as compared to mothers (46 / 575; 8.0%; p = 0.0003). Conclusions: Our findings suggest prenatal BRCA1 epimutations might be the underlying cause of around 20% of TNBC and low-ER expression breast cancers. Such constitutional mosaic BRCA1 methylation likely arise through gender-related mechanisms in utero, independent of Mendelian inheritance.
2023-10-26 | GSE243963 | GEO
Project description:Background: Normal cell BRCA1 epimutations have been associated with increased risk of triple-negative breast cancer (TNBC). However, the fraction of TNBCs that may have BRCA1 epimutations as their underlying cause is unknown. Neither are the time of occurrence and the potential inheritance patterns of BRCA1 epimutations established. Methods: To address these questions, we analyzed BRCA1 methylation status in breast cancer tissue and matched white blood cells (WBC) from 408 patients with 411 primary breast cancers, including 66 TNBCs, applying a highly sensitive sequencing assay, allowing allele-resolved methylation assessment. Further, to assess the time of origin and the characteristics of normal cell BRCA1 methylation, we analyzed umbilical cord blood of 1260 newborn girls and 200 newborn boys. Finally, we assessed BRCA1 methylation status among 575 mothers and 531 fathers of girls with (n = 102) and without (n = 473) BRCA1 methylation. Results: We found concordant tumor and mosaic WBC BRCA1 epimutations in 10 out of 66 patients with TNBC and in four out of six patients with estrogen receptor (ER)-low expression (<10%) tumors (combined: 14 out of 72; 19.4%; 95% CI 11.1–30.5). In contrast, we found concordance in only three out of 220 patients with 221 ER≥10% tumors and zero out of 114 patients with 116 HER2-positive tumors. Intraindividually, BRCA1 epimutations affected the same allele in normal and tumor cells. Assessing BRCA1 methylation in umbilical WBCs from girls, we found mosaic, predominantly monoallelic BRCA1 epimutations, with qualitative features similar to those in adults, in 113/1260 (9.0%) of individuals, but no correlation to BRCA1 methylation status either in mothers or fathers. A significantly lower fraction of newborn boys carried BRCA1 methylation (9 / 200; 4.5%) as compared to girls (p = 0.038). Similarly, WBC BRCA1 methylation was found less common among fathers (16/531; 3.0%), as compared to mothers (46 / 575; 8.0%; p = 0.0003). Conclusions: Our findings suggest prenatal BRCA1 epimutations might be the underlying cause of around 20% of TNBC and low-ER expression breast cancers. Such constitutional mosaic BRCA1 methylation likely arise through gender-related mechanisms in utero, independent of Mendelian inheritance.
2023-10-26 | GSE243956 | GEO