Project description:Illumina Infinium 450k Human DNA Methylation BeadChip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in Osteosarcoma and Colon Cancer PDXs Bisulphite converted DNA from each sample was hybridised to the Illumina Infinium 450k Human Methylation BeadChip.
Project description:Validation of methylation data for 9 osteosarcoma Patient tumours and PDXs by MeDIP followed by next generation sequencing 9 samples, MeDIP done with Diagenode kit and libraries prepped using NEB kit, sequenced on HiSeq 2000
Project description:Microarrays were used to assess differences between 1) human tumours that did and did not engraft, 2) human tumours and their matched primary xenografts, 3) early and late passage primary xenografts and 4) small and large primary xenografts for a series of esophageal patient and primary xenograft tumours Overall design: Patient esophageal tumour samples were obtained and inplanted in NOD/SCID mice; xenografts that formed were passaged from mouse to mouse. Samples of different passages were selected for profiling.
Project description:A study to evaluate techniques for repairing DNA from formalin-fixed paraffin-embedded (FFPE) tissue samples by direct comparison of FFPE DNA repair methods prior to analysis on genome-wide methylation array to matched fresh frozen (FF) tissues. Formalin-fixed paraffin-embedded tissue from three colon adenocarcinoma samples were subjected to different FFPE-oriented DNA repair approaches and sequences, then compared with corresponding fresh frozen tissues. All samples were hybridized to the Illumina Infinium 450k Human Methylation BeadChip.
Project description:The maternal and paternal copies of the genome are both required for mammalian development and this is primarily due to imprinted genes, those that are mono-allelically expressed based on parent-of-origin. Typically, this pattern of expression is regulated by differentially methylated regions (DMRs) that are established in the germline and maintained after fertilisation. There are a large number of germline DMRs that have not yet been associated with imprinting and their function in development is unknown. In this study, we developed a genome-wide approach to identify novel imprinted DMRs, specifically in the human placenta, and investigated the dynamics of imprinted DMRs during development in somatic and extra-embryonic tissues. DNA methylation was evaluated using the Illumina HumanMethylation450 array in 116 human tissue samples, publically available reduced representation bisulfite sequencing in the human embryo and germ cells, and targeted bisulfite sequencing in term placentas. 43 known and 101 novel imprinted DMRs were identified in the human placenta, by comparing methylation between diandric and digynic triploids and female and male gametes. 72 novel DMRs showed a pattern consistent with placental-specific imprinting and this mono-allelic methylation was entirely maternal in origin. Strikingly, these DMRs exhibited polymorphic imprinted methylation specifically in placenta. These data suggest that imprinting in human development is far more extensive and dynamic than previously reported and that the placenta preferentially maintains maternal germline-derived DNA methylation For the identification of imprinted DMRs in the placenta, chorionic villous samples from 5 diandric and 5 digynic triploids pregnancies were assayed, along with a pooled sample of complete hydatiform moles (CHM). Placental chorionic villous samples (n=63) included 29 control pregnancies delivered at term, while the remaining 34 were delivered preterm or miscarried, or had abnormal MSS results, IUGR or LOPET. The preterm births were associated with one or more of: preterm labour, premature rupture of membranes (PROM), chorioamnionitis, placental abruption, and incompetent cervix. All samples were determined to be chromosomally normal using standard karyotyping or comparative genome hybridization, as previously described (Robinson et al. 2010). Two to four independent sites were taken from each placenta and after DNA extraction from chorionic villous, the DNA was pooled before being utilized in this study. Thirty-three fetal tissues, including brain (n=8), spinal cord (n=7), muscle (n=9), and kidney (n=9) were collected from second trimester foetuses, as previously described (Price et al. 2012). Adult female whole blood samples (n=10) were collected from control women. Extra-embryonic cell types (n=19), including cord blood (embryonic), cord, amniotic membrane, chorionic membrane, 1st, 2nd and 3rd trimester trophoblast and mesenchyme, and decidua (maternal), were isolated from control placental samples.
Project description:Genome wide DNA methylation profiling of smokers and non-smokers in PBMC samples. The Illumina Infinium 450k Human DNA methylation Beadchip v1.1 was used to obtain DNA methylation profiles across 485,577 CpGs in PBMC samples. Samples included 50 smokers and 61 non-smokers. Bisulfite converted DNA from the 111 samples were hybridized to the Illumina Infinium 450k Human Methylation Beadchip v1.1
Project description:Genome-wide DNA methylation profiling of individuals consuming alcohol and controls in LC samples. Individuals consuming alcohol were profiled at time of intake (T1) into treatment facility and four weeks into treatment (T2). Controls were profiled once. The Illumina Infinium 450k Human DNA Methylation BeadChip v1.0 was used to obtain DNA methylation profiles across 485,577 CpGs in LC samples. Samples included 33 case subjects at T1, 26 case subjects at T2 and 33 controls. Bisulfite-converted DNA from 92 samples were hybridized to the Illumina Infinium 450k Human Methylation BeadChip v1.0.
Project description:The origin of aberrant DNA methylation in cancer remains largely unknown. In this study, we elucidated the DNA methylome in primary Acute Promyelocytic Leukemia (APL) and the role of PML-RARa in establishing these patterns. APL patients showed increased genome-wide DNA methylation with higher variability than healthy CD34+ cells, promyelocytes and remission bone marrow. A core set of differentially methylated regions in APL was identified. Age at diagnosis, Sanz score and Flt3-mutation status characterized methylation subtypes. Transcription factor binding sites, e.g. c-myc binding sites were associated with low methylation. SUZ12 and REST binding sites identified in embryonic stem cells were, however, preferentially DNA hypermethylated in APL. Unexpectedly, PML-RARa binding sites were also protected from aberrant DNA methylation in APL. In line, myeloid cells from pre-leukemic PML-RARa knock-in mice did not show altered DNA methylation and expression of PML-RARa in hematopoietic progenitor cells prevented differentiation without affecting DNA methylation. ATRA treatment of APL blasts did also not result in DNA methylation changes. These results suggest that aberrant DNA methylation is associated with leukemia phenotype but not required for PML-RARa-mediated initiation of leukemogenesis. Bisulphite converted DNA from the 10 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip
Project description:Illumina Infinium 450k Human DNA Methylation BeadChip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in 51 central chondrosarcoma. Bisulphite converted DNA from each sample was hybridised to the Illumina Infinium 450k Human Methylation BeadChip.