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Familial Thrombocytosis germline exome sequencing

ABSTRACT: Agilent whole exome hybridisation capture will be performed on genomic DNA derived from 3 relatives from a family with multiple affected familial thrombocytosis (FT) patients. Germline DNA from 2-4 patients affected with FT will be used to prepare libraries and sequenced in one lane of HiSeq sequencing, mapped to build 37 of the human reference genome to facilitate the identification of novel cancer genes.

PROVIDER: EGAS00001000088 | EGA |

REPOSITORIES: EGA

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Transcriptomic Genes Identified in Familial Eosinophilic Esophagitis

Project description:Background and Aims: Evidence for a genetic contribution to eosinophilic esophagitis (EoE) exists from family and genome-wide association studies. Extensive investigation into rare variants contributing to EoE has not been performed. The Aim is to evaluate families with multiple cases of EoE by genomic and transcriptomic sequencing to identify genes predisposing to EoE. Methods: We whole exome sequenced (WES) distant relative pairs (e.g., cousins) in extended EoE pedigrees and other affected relatives to identify rare, shared, potentially pathologic variants. Whole-transcriptome sequencing by RNA-Seq was performed in nuclear families with multiple EoE cases. We compared the overlap of genes from DNA and RNA sequencing for relevance to disease manifestations. Results: WES was performed in 50 familial cases in 21 EoE extended pedigrees. We observed 219 rare, candidate predisposition variants in 210 genes with complete sharing among all affected family members. Transcriptome sequencing was performed for 43 EoE cases in 18 nuclear kindreds, including 6 relatives without EoE. We observed 10,070 total differentially expressed genes compared to controls. We identified three genes (MUC16, ADGRE1, and TENM3) with evidence of rare variant sharing and differential gene expression among all affected family members. We identified 43 other genes with partial sharing of rare variants among affected family members and with differential gene expression. Several genes identified as prominent in EoE were also differentially expressed in unaffected relatives. Conclusions: Multiple genes related to immune response, barrier dysfunction, and cell adhesion were identified in familial EoE cases and unaffected family members supporting a genetic familial predisposition and a possible multi-hit background to disease pathophysiology.

2025-01-24 | GSE250595 | GEO

A familial disorder of altered DNA-methylation

2014-07-01 | GSE47879 | GEO

A familial disorder of altered DNA-methylation

Project description:In a subset of imprinting disorders caused by epimutations, multiple imprinted loci are affected. We have investigated the clinical and molecular features of a familial DNA methylation disorder. Bisulphite converted DNA from the 60 samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip

2014-07-01 | E-GEOD-47879 | biostudies-arrayexpress

Transcriptional profiles of familial cases of myeloproliferative neoplams

Project description:Familial cases of MPN are usually transmitted by autosomal inheritance with incomplete penetrance, appear in adulthood, and demonstrate acquired genetic abnormalities that are similar to those identified in sporadic cases such as JAK2V617F and TET2 mutations. Linkage and segregation analyses indicate that genetic predisposition to MPN cannot be related to a common alteration and rather involves a number of susceptibility loci responsible for independent familial aggregations. Identification of these susceptibility loci may improve our understanding of the mechanisms of predisposition, which may result either in the induction of a genetic instability, favoring the acquisition of oncogenic mutations or corresponds to a fertile ground for selection of somatic mutations. Here, we describe a newly identified germline copy number variation (CNV) that predisposes to essential thrombocythemia (ET) which rapidly progress to myelofibrosis (MF) and MDS/AML. Using induced pluripotent stem and primary cells to explore hematopoietic differentiation, we demonstrate that overexpressed ATG2B and GSKIP enhance hematopoietic progenitor differentiation, including megakaryocytic through increasing their sensitivity to TPO. To evaluate the overexpression of ATG2B and GSKIP in patients and their role in hematopoiesis, we generated EBV cell lines from peripheral blood of patients or relatives. These cell lines were cultured in RPMI with 20% FBS. The present study concerns gene expression of EBV cell lines from patients and controls after RNA extraction (qiagen kit). Gene expression was performed in single color on Agilent8x60K v2 Human whole genome (design 039494) in replicates 15 cell lines from affected patients and 9 non affected controls).

2015-08-17 | E-MTAB-3570 | biostudies-arrayexpress

Rare germline variations in familial melanoma

Project description:Rare germline variations in familial melanoma

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A large germline alteration affecting MAX and FUT8, causing familial bilateral malignant pheochromocytoma and renal oncocytoma

Project description:Familial pheochromocytoma (PCC) has been associated with germline mutations in 14 genes. Here we investigated three siblings, who presented with (metastatic) bilateral pheochromocytomas, renal oncocytoma, and erythrocytosis. By SNP-array on one patient’s germline DNA a large complex genomic alteration was identified encompassing the intragenic and promoter regions of Myc-Associated Factor X (MAX) and alpha-(1,6)-fucosyltransferase (FUT8). The alteration was confirmed in all patients, as well as loss of the wild type MAX and FUT8 alleles and corresponding loss of protein expression. Uniparental disomy of chromosome 14q, previously demonstrated as a hallmark for MAX-related PCC, was also shown in the index patient by SNP-array. Our results indicate that large genomic deletions of MAX should be considered in familial and bilateral PCC with prior negative testing for gene mutations. In addition, MAX appears to be a new tumor suppressor gene for renal oncocytomas. SNP array was performed for 2 samples: 1 tumor DNA sample and 1 corresponding germline DNA sample

2015-05-13 | E-GEOD-68794 | biostudies-arrayexpress

DNA methylation analysis in familial adenomatous polyposis

Project description:DNA methylation of 23 familial adenomatous polyposis tumors. Infinium HumanMethylation450 BeadChip was used to obtain DNA methylation profiles across 485,577 CpG sites.

2019-01-15 | GSE109507 | GEO

A large germline alteration affecting MAX and FUT8, causing familial bilateral malignant pheochromocytoma and renal oncocytoma

2015-05-13 | GSE68794 | GEO

High-resolution array CGH profiling identifies Na-K transporting ATPase interacting 2 - NKAIN2- as a predisposing candidate gene in neuroblastoma

Project description:We studied an Italian family with three NB patients, two siblings and one of their cousins carrying the R1192P mutation in the ALK gene (that has been found mutated in a fraction of familial NBs). However, because some individuals harboring mutations in this gene do not develop this tumor, additional genetic alterations appear to be required for NB pathogenesis. In this family, a comparison between somatic and germline DNA copy number changes in the two affected siblings and their relatives by an high resolution array-based Comparative Genomic Hybridization (CGH) technique was performed.

2013-08-02 | E-MEXP-3948 | biostudies-arrayexpress

Familial resemblances in human whole blood transcriptome

Project description:The objective is to quantify the contribution of genetic and common environmental effects in the familial resemblances of whole blood genome-wide gene expression levels. We also make comparisons with familial resemblances in blood leukocytes genome-wide DNA methylation levels in the same cohort in order to further investigate biological mechanims.

2018-05-18 | GSE114620 | GEO

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