Improving Care After Inherited Cancer Testing
Ontology highlight
ABSTRACT:
DISEASE(S): Endometrial Cancer,Colorectal Cancer,Inherited Cancer Syndrome,Prostate Cancer,Endometrial Neoplasms,Breast Cancer,Neoplastic Syndromes, Hereditary
PROVIDER: 2368091 | ecrin-mdr-crc |
REPOSITORIES: ECRIN MDR
Similar Datasets
Project description:Over 400 million people worldwide are living with a rare disease, with genetic variants determining 80% of cases. Next Generation Sequencing identifies potential disease causative genetic variants, however many of these are classified as variants of uncertain significance (VUS). Each VUS requires functional validation as pathogenic or benign in disease pathology in specialist laboratories creating major delays in patient diagnosis. In this study we test a rapid genetic variant assessment pipeline using an EHMT1 (Euchromatin histone methyltransferase 1; EHMT1 p.Gln1144Ter) genetic variant that is pathogenic for Kleefstra Syndrome. Precise CRISPR homology directed (HDR) gene editing introduced the single nucleotide genetic variant in iPS cells and EHMT1_SNV cell clones were rapidly identified with amplicon sequencing. Induction of neural differentiation and RNA sequencing determined differences in differentiation at the gene and transcription factor level. The applied CRISPR HDR methodology was rapid and reliable for the introduction of SNVs in iPSCs for subsequent neuronal cell differentiation. Key features of Kleefstra Syndrome were identified, with involvement of key transcription factors REST and SP1 in disease mechanisms. This study indicates that precise iPSC gene editing and changes in disease modelling pathways can contribute to disease diagnosis and understanding of mechanisms.
2021-06-23 | GSE178646 | GEO
Project description:Autism spectrum disorder (ASD) is a complex heterogeneous developmental disease with a significant genetic background that is frequently caused by rare copy number variants (CNV). The aim of the study was to identify new candidate genes for ASD in the studied cohort of ASD-diagnosed patients. We used chromosomal microarray analysis (CMA) - a Cytoscan HD (Affymetrix, Santa Clara, CA, USA) to detect CNV in 87 ASD patients and their relatives and evaluated their clinical significance. Pathogenic and likely pathogenic mutations were identified by CMA in 8 and 9 ASD patients, respectively. CMA revealed 89 rare CNV: 8 pathogenic, 12 designated VOUS - likely pathogenic, 12 VOUS - uncertain, and 57 VOUS - likely benign or benign. CNV (pathogenic/VOUS-likely pathogenic/VOUS - uncertain) overlapping the same gene in more than one patient were observed in DOCK8 gene and PARK2 gene. This work presents new evidence about the possible roles of PARK2 and DOCK8 in the etiology of ASD, and suggests CTNNA2 as a candidate gene for ASD risk.
2018-05-25 | GSE114870 | GEO
Project description:Delineating functionally normal variants from functionally abnormal variants in tumor suppressor proteins is critical for cancer surveillance, prognosis, and treatment options. BRCA1 is a protein that has many variants of uncertain significance which are not yet classified as functionally normal or abnormal. In vitro functional assays can be used to identify the functional impact of a variant when the variant has not yet been categorized through clinical observation. Here we employ a homology-directed repair (HDR) reporter assay to evaluate over 300 missense and nonsense BRCA1 variants between amino acid residues 1280 and 1576, which encompasses the coiled-coil and serine cluster domains. Functionally abnormal variants tended to cluster in residues known to interact with PALB2, which is critical for homology-directed repair. Multiplexed results were confirmed by singleton assay and by ClinVar database variant interpretations. Comparison of multiplexed results to designated benign or likely benign or pathogenic or likely pathogenic variants in the ClinVar database yielded 100% specificity and 100% sensitivity of the multiplexed assay. Clinicians can reference the results of this functional assay for help in guiding cancer treatment and surveillance options. These results are the first to evaluate this domain of BRCA1 using a multiplexed approach and indicate the importance of this domain in the DNA repair process.
2023-10-13 | GSE237142 | GEO
Project description:Over 400 million people worldwide live with a rare disease. Whole exome and whole genome sequencing often identifies potential disease causative genetic variants that are novel, which must be classified as variants of uncertain significance (VUS). Functional laboratory assays must be performed to prove disease causation, creating major delays in patient diagnostics. Here we investigate a GATA4 (p.Arg283Cys) VUS in a with congenital heart disease. The variant was CRISPR gene edited into inducible pluripotent stem cells, followed by cardio-myocyte differentiation. Genetic variant and healthy cells were similar at the level of cardiomy-ocyte cell marker expression of troponin T (cTNNT), and GATA4 protein expression. Strik-ingly, transcriptomics profiling identified differences in differentiation consistent with the pa-tient’s disease characteristics, and elucidated changes in calcium signaling and adrenergic sig-naling in cardiomyocytes. Altered action potential changes in GATA4,p.Arg283Cys (GA-TA4_HDR) cardiomyocytes were indicative of cardiac abnormalities. Our work provides strong molecular evidence for classifying the GATA4 p.Arg283Cys variant as pathogenic. Furthermore, we demonstrate the combined utility of iPSCs, CRISPR gene edit-ing and differentiation into cardiomyocytes in assessing variants associated with cardiac pheno-types.
2023-11-23 | GSE229879 | GEO
Project description:This experiment seeks to ascertain the transcriptional changes in the adult mouse hippocampus (CA1 subregion) that occur following viral knockdown of the histone variant H2A.Z. We are especially interested in understanding the role of this histone variant in memory formation and memory maintenance in the adult central nervous system.
2014-09-09 | GSE58797 | GEO
Project description:Human nontransformed retinal pigment epithelia RPE-PPM1D-T2 cells carrying a truncating mutation in exon 6 of the PPM1D were exposed to ionising radiation (3 Gy) and subsequently were grown in semisolid media for 8 weeks. Six spheroid clones (RPE-PPM1D-T2-SA clones 1-6) were recovered and then were cultivated in adherent conditions. RNA was isolated from asynchronically growing parental RPE-PPM1D-T2 and transformed RPE-PPM1D-T2-SA-1 to 6 cells and was subjected to whole exome sequencing. RNA sequencing libraries were prepared using KAPA RNA HyperPrep Kit (Roche) and were sequenced on the NovaSeq 6000 system using NovaSeq S1 Reagent Kit v1.5, 200 cycles (Illumina) with mean coverage >120 for RNA samples, respectively. RNA fastq files were mapped to the hg19 reference using Novoalign (novoalign_2.08.03). PCR duplicates were removed from the BAM files using Picard Tools (picard-tools 1.129), and variant calling was performed using GATK HaplotypeCaller (3.8). RNA fastq files were mapped to the hg19 reference using STAR (STAR-2.5.2b). The PCR duplicates were removed using Picard Tools (picard-tools 1.129). All parts of RNAseq data analysis were conducted in R, version 4.3.2. and RNAseq read counts were normalized using R package DESeq2. Fold change (FC) and log2FC were calculated from normalized reads, nontransformed RPE-PPM1D-T1 cells were considered a reference. Significance of differential expression for each gene was evaluated by Fisher's t-test with simulated p-values and Holm's p-value correction for multiple comparisons.
2024-04-05 | E-MTAB-13933 | biostudies-arrayexpress
Project description:Gene expression profiling of CD138 purified bone marrow plasma cells of previoulsy untreated multiple myeloma patients and individuals with monoclonal gammopathy of uncertain significance (MGUS)
2010-09-08 | E-MTAB-372 | biostudies-arrayexpress
Project description:NGS-based multiple gene panel resequencing in combination with a high resolution CGH-array was used to identify genetic risk factors for hereditary breast and/or ovarian cancer in 237 high risk patients who were previously tested negative for pathogenic BRCA1/2 variants. All patients were screened for pathogenic variants in 94 different cancer predisposing genes. We identified 32 pathogenic variants in 14 different genes (ATM, BLM, BRCA1, CDH1, CHEK2, FANCG, FANCM, FH, HRAS, PALB2, PMS2, PTEN, RAD51C and NBN) in 30 patients (12.7%). Two pathogenic BRCA1 variants that were previously undetected due to less comprehensive and sensitive methods were found. Five pathogenic variants are novel, three of which occur in genes yet unrelated to hereditary breast and/or ovarian cancer (FANCG, FH and HRAS). In our cohort we discovered a remarkably high frequency of truncating variants in FANCM (2.1%), which has recently been suggested as a susceptibility gene for hereditary breast cancer. Two patients of our cohort carried two different pathogenic variants each and ten other patients in whom a pathogenic variant was confirmed also harbored a variant of unknown significance in a breast and ovarian cancer susceptibility gene. We were able to identify pathogenic variants predisposing for tumor formation in 12.3% of BRCA1/2 negative breast and/or ovarian cancer patients.
2018-10-31 | GSE121968 | GEO
Project description:Chromatin alterations during the epididymal maturation of mouse sperm refine the paternally inherited epigenome
| PRJNA769954 | ENA
Project description:Single nucleotide variants are the most frequent type of sequence changes detected in the genome and these are frequently variants of uncertain significance (VUS). VUS are changes in DNA for which disease risk association is unknown. Thus, methods that classify the functional impact of a VUS can be used as evidence for variant interpretation. In the case of the breast and ovarian cancer specific tumor suppressor protein, BRCA1, pathogenic missense variants frequently score as loss of function in an assay for homology-directed repair (HDR) of DNA double-strand breaks. We previously published functional results using a multiplexed assay for 1056 amino acid substitutions residues 2-192 in the amino terminus of BRCA1. In this study, we have re-assessed the data from this multiplexed assay using an improved analysis pipeline. These new analysis methods yield functional scores for more variants in the first 192 amino acids of BRCA1, plus we report new results for BRCA1 amino acid residues 193-302. We now present the functional classification of 2172 BRCA1 variants in BRCA1 residues 2-302 using the multiplexed HDR assay. Comparison of the functional determinations of the missense variants with clinically known benign or pathogenic variants indicated 93% sensitivity and 100% specificity for this assay. The results from BRCA1 variants tested in this assay are a resource for clinical geneticists for evidence to evaluate VUS in BRCA1.
2023-06-12 | GSE234482 | GEO