Project description:POC1A encodes a WD repeat protein localizing to centrioles and spindle poles and associated with Short stature, onychodysplasia, facial dysmorphism and hypotrichosis (SOFT) syndrome (OMIM #614813). In our study, we reported on two patients with primordial dwarfism (PD) from the same family. We utilized Whole Exome Sequencing (WES) in the patients to screen all PD related genes and to define putative novel candidate genes. A novel homozygous p.T120A missense mutation was detected in POC1A, a known causative gene of SOFT syndrome, and confirmed using Sanger sequencing. To confirm the pathogenicity of the detected mutation, primary fibroblast cultures obtained from the patients and a control individual were used. Gene expression profiles of the fibroblast cultures were taken. We performed gene expression arrays on fibroblasts cultured from patients with SOFT syndrome and POC1A mutation and compared their expression profiles to that of control fibroblast cells.
Project description:To explore the genetic cause of a Chinese woman with fetal hydrocephalus X-linked hydrocephalus (XLH), a genetic disorder, has an incidence of 1/30,000 male births. The great proportion of XLH is ascribed to loss of function mutations of L1 cell adhesion molecule gene (L1CAM), but silent mutations in L1CAM with pathogenic potential were rare, and were usually ignored especially in WES detection. In the present study, we describe a novel silent L1CAM mutation in a Chinese pregnant woman reporting continuous five times pregnancies with fetal hydrocephalus. After fetal blood sampling, we found c.453G>T (p.Gly151=) in L1CAM gene of the fetus by whole exome sequencing (WES), RT-PCR of the mRNA from cord blood mononuclear cells and subsequent sequence analysis identified the mutation created a potential 5' splice site consensus sequence, which would result in an in-frame deletion of 72 bp from exon 5 and 24 amino acids of the L1CAM protein. Heterozygous mutations were confirmed in analyzing DNA and mRNA from peripheral blood mononuclear cells of the woman, and, a severe L1 syndrome was confirmed by fetal ultrasound scan and MRI. Our study first indicated c.453G>T (p.Gly151=) in L1CAM could be disease causing for hydrocephalus, which would aid in genetic counseling for the prenatal diagnosis of hydrocephalus. Meanwhile, it suggested some silent mutations detected in WES should not be ignored, splicing predictions of these mutations were necessary.
Project description:POC1A encodes a WD repeat protein localizing to centrioles and spindle poles and associated with Short stature, onychodysplasia, facial dysmorphism and hypotrichosis (SOFT) syndrome (OMIM #614813). In our study, we reported on two patients with primordial dwarfism (PD) from the same family. We utilized Whole Exome Sequencing (WES) in the patients to screen all PD related genes and to define putative novel candidate genes. A novel homozygous p.T120A missense mutation was detected in POC1A, a known causative gene of SOFT syndrome, and confirmed using Sanger sequencing. To confirm the pathogenicity of the detected mutation, primary fibroblast cultures obtained from the patients and a control individual were used. Gene expression profiles of the fibroblast cultures were taken.
Project description:Fourteen LGSOC cell lines were interrogated using whole exome sequencing, RNA sequencing, and mass spectrometry-based proteomics. Somatic mutation, copy-number aberrations, gene and protein expression were analyzed and integrated using different computational approaches. LGSOC cell line data was compared to publicly available LGSOC tumor data (AACR GENIE cohort), and also used for predictive biomarker identification of MEK inhibitor (MEKi) efficacy. Protein interaction databases were evaluated to identify novel therapeutic targets.
Project description:In this study, we analyze DNA whole-exome sequencing (WES) data from 3 patients with m.14487T>C mutation to detect rare candidate SNVs.
Project description:SMARCB1 encodes a core subunit of the SWI/SNF chromatin remodeling complex, which plays a crucial role in the regulation of gene expression. Germline mutations in the SMARCB1 gene have been linked to early childhood Coffin-Siris syndrome type 3 (CSS3), a rare congenital malformation syndrome characterized by severe developmental delay and intellectual disability. In this study, we report two adult CSS3 patients with novel missense SMARCB1 mutation (c.1091A>C, p.Lys364Thr) identified through whole exome sequencing (WES). Both two patients exhibited selective difficulties in verbal learning and language delay. Additionally, the development of meningioma was confirmed in one of the patients. Mechanistic studies indicate that this missense mutation may abnormally activates the expression of MAPK14, a gene implicated in the pathogenesis of tumor progression and neurodevelopmental disorders. This is the first reported case of a germline mutation in SMARCB1 gene associated with both CSS3 and meningioma, thereby expanding the phenotypic spectrum of SMARCB1-related neurodevelopmental disorders.
Project description:This study reports two unrelated patients with a combined immunodeficiency. Whole-exome sequencing of both patients, their healthy parents and siblings identified in both families a /de novo/ missense variant in /ITPR3/ (NM_002224.3:c.7570C>T, p.Arg2524Cys). While the mRNA level in patients remained the same as in healthy siblings and controls, the level of protein expression was diminished. It was also shown that the ITPR3 heterozygous p.Arg2524Cys mutation impairs calcium flux function in dermal fibroblast of one patient and in a knock-in Jurkat T cell line.
Project description:Whole Exome sequencing of two patients with Cardiac angiosarcoma in Li-Fraumeni-like families discovers that a mutation in the pot1 gene is responsible for cardiac angiosarcoma in tp53-negative li-fraumeni-like families
Project description:Current methods for detection of copy number aberrations (CNA) from whole-exome sequencing (WES) data are based on the read counts of the captured exons only. However, accurate CNA determination is complicated by the non-uniform read depth and uneven distribution of exons. Therefore, we developed ENCODER (ENhanced COpy number Detection from Exome Reads), which eludes these problems. By exploiting the ‘off-target’ sequence reads, it allows for creation of robust copy number profiles from WES. The accuracy of ENCODER compares to approaches specifically designed for copy number detection, and outperforms current exon-based WES methods, particularly in samples of low quality. Current methods for detection of copy number aberrations (CNA) from whole-exome sequencing (WES) data are based on the read counts of the captured exons only. However, accurate CNA determination is complicated by the non-uniform read depth and uneven distribution of exons. Therefore, we developed ENCODER (ENhanced COpy number Detection from Exome Reads), which eludes these problems. By exploiting the ‘off-target’ sequence reads, it allows for creation of robust copy number profiles from WES. The accuracy of ENCODER compares to approaches specifically designed for copy number detection, and outperforms current exon-based WES methods, particularly in samples of low quality. Current methods for detection of copy number aberrations (CNA) from whole-exome sequencing (WES) data are based on the read counts of the captured exons only. However, accurate CNA determination is complicated by the non-uniform read depth and uneven distribution of exons. Therefore, we developed ENCODER (ENhanced COpy number Detection from Exome Reads), which eludes these problems. By exploiting the ‘off-target’ sequence reads, it allows for creation of robust copy number profiles from WES. The accuracy of ENCODER compares to approaches specifically designed for copy number detection, and outperforms current exon-based WES methods, particularly in samples of low quality. DNA copy number profiles generated with a new tool, ENCODER, were compared to DNA copy number profiles from SNP6, NimbleGen and low-coverage Whole Genome Sequencing.