Targeted sequencing of SMZL patients
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina NovaSeq X
ORGANISM(S): Homo sapiens
SUBMITTER: Helen Parker
PROVIDER: E-MTAB-16810 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Targeted non-coding and coding sequencing of patients with SMZL to identify disease relevant mutations
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Project description:Targeted sequencing of SMZL patients
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Project description:Array-based comparative genomic hybridization comparing splenic marginal zone lymphoma (SMZL) specimens with control DNA A custom high-definition oligonucleotide microarray (4x44K, Agilent) was designed for aCGH from the online application tool eArray (version 5.3) and HD-CGH probe library (sequence source UCSC hg18 / NCBI Build 36). This custom microarray combines the capability to scan human genome-wide with an average resolution of approximately 100 Kb and to focus on regions of interest for highest resolution tiling (11 Kb-resolution for either chromosomes 3q and 7q). The array contains about 8,500 and 9,000 oligonucleotides spanning 97 Mb and 105 Mb of the 7q and the 3q chromosomes respectively. Twenty-seven SMZL specimens (9 males, 18 females) were analyzed using a dye-swap methodology to confirm the copy number variations. Two samples (one male, one female, namely M-CTRL and F-CTRL) collected from healthy volunteers blood from national Etablissement FranM-CM-'ais du Sang were used as DNA reference for aCGH experiments.
2014-01-01 | E-GEOD-34768 | biostudies-arrayexpress
Project description:A custom high density tiling path was designed to a 1.5Mb region of the canFam2.0 reference genome with probes tiled at 6bp or 26bp offsets. 60mer oligonucleotides were synthesized in situ to one 8 x 60K Agilent microarray and hybridized with canine genomic DNA. A single-channel hybridization protocol was employed using eight canine samples.
2013-03-07 | E-MEXP-3860 | biostudies-arrayexpress
Project description:Methylation Profiling of Splenic Marginal Zone Lymphomas to characterise epi(genetically) distinct subgroups
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Project description:Splenic marginal zone lymphomas (SMZL) are an uncommon type of B-cell non-Hodgkin’s lymphoma (NHL-B) in which no specific chromosomal translocations have been described. In contrast, the most frequent cytogenetic abnormality is the loss of the long arm of chromosome 7 (7q). Previous reports have located this loss in the 7q32 region. In order to better characterize the genomic imbalances in SMZL, molecular studies were carried out in 73 patients with SMZL. To gain insight into the mapping at 7q a tiling array was also used. Our results confirmed the presence of a new region of loss on chromosome 7 in these NHL.
2011-10-11 | GSE31203 | GEO
Project description:Background DNA methylation has been recognized as a key mechanism in cell differentiation. Various studies have compared tissues to characterize epigenetically regulated genomic regions, but due to differences in study design and focus there still is no consensus as to the annotation of genomic regions predominantly involved in tissue-specific methylation. We used a new algorithm to identify and annotate tissue-specific Differentially Methylated Regions (tDMRs) in Illumina 450k chip data on four peripheral (blood, saliva, buccal swab and hair follicles) and six internal tissues (liver, muscle, pancreas, subcutaneous fat, omentum, spleen with matched blood samples). Results The majority of tDMRs, in both relative and absolute terms, occurred in CpG-poor regions. Further analysis revealed that these regions were associated with alternative transcription events (alternative first exons, mutually exclusive exons and cassette exons). Only a minority of tDMRs mapped to gene-body CpG islands (13%) or CpG islands shores (25%) suggesting a less prominent role for these regions than indicated previously. Implementation of ENCODE annotations showed enrichment of tDMRs in DNase hypersensitive sites and transcription factor binding sites. Despite the predominance of tissue differences, inter-individual differences in DNA methylation in internal tissues were correlated with that in blood for a subset of CpG sites in a locus and tissue-specific manner. Conclusions We conclude that tDMRs preferentially occur in CpG-poor regions and are associated with alternative transcription. Furthermore, our data suggest the utility of creating an atlas cataloguing variably methylated regions in internal tissues that are marked by DNA methylation measured in easy accessible peripheral tissues. Comparison of four peripheral (blood, saliva, buccal swab and hair follicles in n=5) and six internal tissues (liver, muscle, pancreas, subcutaneous fat, omentum, spleen with matched blood samples in n=6).
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Project description:Splenic marginal zone lymphoma (SMZL) is an indolent B-cell lymphoproliferative disorder characterised by 7q32 deletion, but the target genes of this deletion remain unknown. In order to elucidate the genetic target of this deletion, we performed an integrative analysis of the genetic, epigenetic, transcriptomic and miRNomic data. High resolution array comparative genomic hybridization of 56 cases of SMZL delineated a minimally deleted region (2.8Mb) at 7q32, but showed no evidence of any cryptic homozygous deletion or recurrent breakpoint in this region. Integrative transcriptomic analysis confirmed significant under-expression of a number of genes in this region in cases of SMZL with deletion, several of which showed hypermethylation. In addition, a cluster of 8 miRNA in this region showed under-expression in cases with the deletion, and three (miR-182/96/183) were also significantly under-expressed (P <0.05) in SMZL relative to other lymphomas. Genomic sequencing of these miRNA and IRF5, a strong candidate gene, did not show any evidence of somatic mutation in SMZL.
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Project description:We performed whole genome SNP profiling on DNA samples from 236 patients with NF1, 123 with glimoa tumors and 113 without; 117 females and 119 males, together with 29 control samples. To identify polymorphisms in human adenylate cyclase 8 (AC8) which correlate with glioma risk in NF1 in a sex-specific manner, Ac8 SNP were extracted and further analyzed for their sex-specific NF1-associated glioma risk. Three SNPs on ADCY8 were found signficant while other SNPs on CXCR7 and ADCYAP1 were promising. Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from blood samples or saliva samples in three separate sets with one processed in Washington University and two in University of Utah. The data included 29 control samples and 236 NF1 patient samples (123 with and 113 without GBM) with 153 blood specimen and 97 saliva specimen.
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