Search results for: Szymon M. Kiełbasa

Items from 1 to 12 out of 12 results

article

Statistical method for modeling sequencing data from different technologies in longitudinal studies with application to Huntington disease

Angga M. Fuady, Willeke M. C. van Roon‐Mom, Szymon M. Kiełbasa, Hae‐Won Uh, more

Biometrical Journal > 63 > 4 > 745 - 760

Advancement of gene expression measurements in longitudinal studies enables the identification of genes associated with disease severity over time. However, problems arise when the technology used to measure gene expression differs between time points. Observed differences between the results obtained at different time points can be caused by technical differences. Modeling the two measurements jointly...

article

Templated insertions at VD and DJ junctions create unique B‐cell receptors in the healthy B‐cell repertoire

Marvyn T. Koning, Esther M. Vletter, Rik Rademaker, Rochelle D. Vergroesen, more

European Journal of Immunology > 50 > 12 > 2099 - 2101

RAG complexes recognise (cryptic) RSS sites both in and outside immunoglobulin sites. Excision circles may be reinserted into V(D)J rearrangements as long templated insertions to diversify the adaptive immune repertoire. We show that such VDJ with templated insertions are incidentally found in the repertoire of healthy donors.

article

RNA-Seq in 296 phased trios provides a high-resolution map of genomic imprinting

Bharati Jadhav, Ramin Monajemi, Kristina K. Gagalova, Daniel Ho, more

BMC Biology > 2019 > 17 > 1 > 1-20

Background Identification of imprinted genes, demonstrating a consistent preference towards the paternal or maternal allelic expression, is important for the understanding of gene expression regulation during embryonic development and of the molecular basis of developmental disorders with a parent-of-origin effect. Combining allelic analysis of RNA-Seq data with phased genotypes in family trios provides...

article

Integrating omics datasets with the OmicsPLS package

Said el Bouhaddani, Hae-Won Uh, Geurt Jongbloed, Caroline Hayward, more

BMC Bioinformatics > 2018 > 19 > 1 > 1-9

Background With the exponential growth in available biomedical data, there is a need for data integration methods that can extract information about relationships between the data sets. However, these data sets might have very different characteristics. For interpretable results, data-specific variation needs to be quantified. For this task, Two-way Orthogonal Partial Least Squares (O2PLS) has been...

article

RNA‐seq analysis of Lgr6⁺ stem cells and identification of an Lgr6 isoform

Gerline C. Glind, Armando N. Bastidas Torres, Willem H. Zoutman, Sander A. J. Zeeuw, more

Experimental Dermatology > 27 > 10 > 1172 - 1175

We studied Lgr6⁺ stem cells in experimental UV carcinogenesis in hairless mice. For further characterization through RNA‐seq, these stem cells were isolated by FACS from transgenic hairless mice bearing an EGFP‐Ires‐CreERT2 reporter cassette inserted into exon 1 of the Lgr6 gene (purity confirmed by human ERT2 expression). Between Lgr6/EGFP⁺ and Lgr6/EGFP⁻ basal cells (Tg/wt), 682 RNAs were differentially...

article

Transcriptional profiling and biomarker identification reveal tissue specific effects of expanded ataxin-3 in a spinocerebellar ataxia type 3 mouse model

Lodewijk J. A. Toonen, Maurice Overzier, Melvin M. Evers, Leticia G. Leon, more

Molecular Neurodegeneration > 2018 > 13 > 1 > 1-18

Background Spinocerebellar ataxia type 3 (SCA3) is a progressive neurodegenerative disorder caused by expansion of the polyglutamine repeat in the ataxin-3 protein. Expression of mutant ataxin-3 is known to result in transcriptional dysregulation, which can contribute to the cellular toxicity and neurodegeneration. Since the exact causative mechanisms underlying this process have not been fully elucidated,...

article

DNA Methylation Analysis Identifies Loci for Blood Pressure Regulation

Melissa A. Richard, Tianxiao Huan, Symen Ligthart, Rahul Gondalia, more

The American Journal of Human Genetics > 2017 > 101 > 6 > 888-902

Genome-wide association studies have identified hundreds of genetic variants associated with blood pressure (BP), but sequence variation accounts for a small fraction of the phenotypic variance. Epigenetic changes may alter the expression of genes involved in BP regulation and explain part of the missing heritability. We therefore conducted a two-stage meta-analysis of the cross-sectional associations...

article

ARTISAN PCR: rapid identification of full‐length immunoglobulin rearrangements without primer binding bias

Marvyn T. Koning, Szymon M. Kiełbasa, Vesna Boersma, Henk P. J. Buermans, more

British Journal of Haematology > 178 > 6 > 983 - 986

article

Selection patterns of B‐cell receptors and the natural history of follicular lymphoma

Florian Scherer, Marlon Burgt, Szymon M. Kiełbasa, Cristina Bertinetti‐Lapatki, more

British Journal of Haematology > 175 > 5 > 972 - 975

article

Refined mapping of autoimmune disease associated genetic variants with gene expression suggests an important role for non-coding RNAs

Isis Ricaño-Ponce, Daria V. Zhernakova, Patrick Deelen, Oscar Luo, more

Journal of Autoimmunity > 2016 > 68 > C > 62-74

Genome-wide association and fine-mapping studies in 14 autoimmune diseases (AID) have implicated more than 250 loci in one or more of these diseases. As more than 90% of AID-associated SNPs are intergenic or intronic, pinpointing the causal genes is challenging. We performed a systematic analysis to link 460 SNPs that are associated with 14 AID to causal genes using transcriptomic data from 629 blood...

article

Improving Phenotypic Prediction by Combining Genetic and Epigenetic Associations

Sonia Shah, Marc J. Bonder, Riccardo E. Marioni, Zhihong Zhu, more

The American Journal of Human Genetics > 2015 > 97 > 1 > 75-85

We tested whether DNA-methylation profiles account for inter-individual variation in body mass index (BMI) and height and whether they predict these phenotypes over and above genetic factors. Genetic predictors were derived from published summary results from the largest genome-wide association studies on BMI (n ∼ 350,000) and height (n ∼ 250,000) to date. We derived methylation predictors by estimating...

article

Methylation and deamination of CpGs generate p53-binding sites on a genomic scale

Tomasz Zemojtel, Szymon M. Kielbasa, Peter F. Arndt, Ho-Ryun Chung, more

Trends in Genetics > 2009 > 25 > 2 > 63-66

The formation of transcription-factor-binding sites is an important evolutionary process. Here, we show that methylation and deamination of CpG dinucleotides generate in vivo p53-binding sites in numerous Alu elements and in non-repetitive DNA in a species-specific manner. In light of this, we propose that the deamination of methylated CpGs constitutes a universal mechanism for de novo generation...

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Search results for: Szymon M. Kiełbasa

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