4 results on '"Jasmin Gries"'
Search Results
2. Bi-PROF: bisulfite profiling of target regions using 454 GS FLX Titanium technology
- Author
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Pavlo Lutsik, Jasmin Gries, Jörn Walter, Sascha Tierling, Iduna Fichtner, Maria Rivera Markelova, Christine Sers, Julia Arand, and Dirk Schumacher
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Cancer Research ,Base pair ,Molecular Sequence Data ,Biology ,DNA sequencing ,Mice ,Animals ,Humans ,Sulfites ,Epigenetics ,Promoter Regions, Genetic ,Molecular Biology ,DNA Primers ,Genetics ,Titanium ,Base Sequence ,Titrimetry ,Methylation ,Sequence Analysis, DNA ,Amplicon ,DNA Methylation ,Xenograft Model Antitumor Assays ,Bisulfite ,Subcloning ,DNA methylation ,Colorectal Neoplasms ,Research Paper - Abstract
The use of next generation sequencing has expanded our view on whole mammalian methylome patterns. In particular, it provides a genome-wide insight of local DNA methylation diversity at single nucleotide level and enables the examination of single chromosome sequence sections at a sufficient statistical power. We describe a bisulfite-based sequence profiling pipeline, Bi-PROF, which is based on the 454 GS-FLX Titanium technology that allows to obtain up to one million sequence stretches at single base pair resolution without laborious subcloning. To illustrate the performance of the experimental workflow connected to a bioinformatics program pipeline (BiQ Analyzer HT) we present a test analysis set of 68 different epigenetic marker regions (amplicons) in five individual patient-derived xenograft tissue samples of colorectal cancer and one healthy colon epithelium sample as a control. After the 454 GS-FLX Titanium run, sequence read processing and sample decoding, the obtained alignments are quality controlled and statistically evaluated. Comprehensive methylation pattern interpretation (profiling) assessed by analyzing 10 (2)-10 (4) sequence reads per amplicon allows an unprecedented deep view on pattern formation and methylation marker heterogeneity in tissues concerned by complex diseases like cancer.
- Published
- 2013
3. Adult monozygotic twins discordant for intra-uterine growth have indistinguishable genome-wide DNA methylation profiles
- Author
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Matthias Riemenschneider, Maurice P. Zeegers, Sascha Tierling, Gilles Gasparoni, N Y Souren, Jasmin Gries, Catherine Derom, Pavlo Lutsik, Jean-Pierre Fryns, Jörn Walter, RS: NUTRIM - R4 - Gene-environment interaction, and Complexe Genetica
- Subjects
Adult ,Bisulfite sequencing ,Molecular Sequence Data ,IN-UTERO ,Biology ,DEVELOPMENTAL ORIGINS ,chemistry.chemical_compound ,Young Adult ,BECKWITH-WIEDEMANN SYNDROME ,Birth Weight ,Humans ,LOW-BIRTH-WEIGHT ,Epigenetics ,Saliva ,Gene ,HUMAN SALIVA ,Epigenomics ,Genetics ,Genome, Human ,Research ,FLOW-CYTOMETRY ,INFANT GROWTH ,High-Throughput Nucleotide Sequencing ,Methylation ,Sequence Analysis, DNA ,Twins, Monozygotic ,ASSOCIATION ,DNA Methylation ,Middle Aged ,GENE ,chemistry ,DNA methylation ,Human genome ,Female ,DNA ,RESTRICTION - Abstract
BACKGROUND: Low birth weight is associated with an increased adult metabolic disease risk. It is widely discussed that poor intra-uterine conditions could induce long-lasting epigenetic modifications, leading to systemic changes in regulation of metabolic genes. To address this, we acquire genome-wide DNA methylation profiles from saliva DNA in a unique cohort of 17 monozygotic monochorionic female twins very discordant for birth weight. We examine if adverse prenatal growth conditions experienced by the smaller co-twins lead to long-lasting DNA methylation changes. RESULTS: Overall, co-twins show very similar genome-wide DNA methylation profiles. Since observed differences are almost exclusively caused by variable cellular composition, an original marker-based adjustment strategy was developed to eliminate such variation at affected CpGs. Among adjusted and unchanged CpGs 3153 are differentially methylated between the heavy and light co-twins at nominal significance, of which 45 show sensible absolute mean beta-value differences. Deep bisulfite sequencing of eight such loci reveals that differences remained in the range of technical variation, arguing against a reproducible biological effect. Analysis of methylation in repetitive elements using methylation-dependent primer extension assays also indicates no significant intra-pair differences. CONCLUSIONS: Severe intra-uterine growth differences observed within these monozygotic twins are not associated with long-lasting DNA methylation differences in cells composing saliva, detectable with up-to-date technologies. Additionally, our results indicate that uneven cell type composition can lead to spurious results and should be addressed in epigenomic studies. ispartof: Genome biology vol:14 issue:5 ispartof: location:England status: published
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- 2013
4. Assisted reproductive technologies do not enhance the variability of DNA methylation imprints in human
- Author
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Eberhard Schwinger, Jörn Walter, Heribert Kentenich, Christina LoPorto, Marco Groth, Georg Griesinger, Gabriele Gillessen-Kaesbach, Karl Sperling, Pavlo Lutsik, Sascha Tierling, Isabelle Utz-Billing, N Y Souren, Jasmin Gries, Heidemarie Neitzel, Complexe Genetica, RS: NUTRIM - R4 - Gene-environment interaction, and Genetica & Celbiologie
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Male ,medicine.medical_specialty ,RNA, Untranslated ,Reproductive Techniques, Assisted ,medicine.medical_treatment ,GRB10 Adaptor Protein ,Reproductive technology ,Umbilical cord ,Intracytoplasmic sperm injection ,Genomic Instability ,snRNP Core Proteins ,Pregnancy ,Internal medicine ,Genetics ,medicine ,GNAS complex locus ,Chromogranins ,GTP-Binding Protein alpha Subunits, Gs ,Humans ,Amnion ,Genetics (clinical) ,In vitro fertilisation ,biology ,Genome, Human ,Calcium-Binding Proteins ,Infant, Newborn ,Membrane Proteins ,Proteins ,Methylation ,Chorion ,DNA ,Sequence Analysis, DNA ,DNA Methylation ,Fetal Blood ,medicine.anatomical_structure ,Differentially methylated regions ,Endocrinology ,Potassium Channels, Voltage-Gated ,DNA methylation ,embryonic structures ,biology.protein ,Intercellular Signaling Peptides and Proteins ,Female ,RNA, Long Noncoding - Abstract
BACKGROUND Assisted reproductive technologies (ART) such as in vitro fertilisation (IVF) and intracytoplasmic sperm injection (ICSI) are believed to destabilise genomic imprints. An increased frequency of Beckwith-Wiedemann syndrome in children born after ART has been reported. Other, mostly epidemiological, studies argue against this finding. OBJECTIVE To examine the effect of ART on the stability of DNA methylation imprints, DNA was extracted from maternal peripheral blood (MPB), umbilical cord blood (UCB) and amnion/chorion tissue (ACT) of 185 phenotypically normal children (77 ICSI, 35 IVF, and 73 spontaneous conceptions). Using bisulfite based technologies 10 differentially methylated regions (DMRs) were analysed, including KvDMR1, H19, SNRPN, MEST, GRB10, DLK1/MEG3 IG-DMR, GNAS NESP55, GNAS NESPas, GNAS XL-alpha-s and GNAS Exon1A. RESULTS Methylation indices (MI) do not reveal any significant differences at nine DMRs among the conception groups in neither MPB, UCB nor in ACT. The only slightly variable DMR was that of MEST. Here the mean MI was higher in UCB and MPB of IVF cases (mean MI+/-SD: 0.41+/-0.03 (UCB) and 0.40+/-0.03 (MPB)) compared to the ICSI (0.38+/-0.03, p=0.003 (UCB); 0.37+/-0.04, p=0.0007 (MPB)) or spontaneous cases (0.38+/-0.03, p=0.003 (UCB); 0.38+/-0.04, p=0.02 (MPB)). Weak but suggestive correlations between DMRs were, however, found between MPB, UCB and ACT. CONCLUSION This study supports the notion that children conceived by ART do not show a higher degree of imprint variability and hence do not have an a priori higher risk for imprinting disorders.
- Published
- 2010
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