Dataset Information

The mutation spectrum in familial versus sporadic congenital cataract based on next-generation sequencing.

ABSTRACT: BACKGROUND:Congenital cataract (CC) is a significant cause of lifelong visual loss, and its genetic diagnosis is challenging due to marked genetic heterogeneity. The purpose of this article is to report the genetic findings in sporadic and familial CC patients. METHODS:Patients (n?=?53) who were clinically diagnosed with CC and their parents were recruited. Blood samples were collected in our hospital. Mutations were detected by panel-based next-generation DNA sequencing (NGS) targeting 792 genes frequently involved in common inherited eye diseases. RESULTS:We identified variants in 10/37 cases (27.02%) of sporadic CC and 14/16 cases (87.5%) of familial CC, which indicated a significant difference (P?=?0.000). Of the 13 variants identified in sporadic cases, nine were previously reported mutations, and three were novel mutations, including one de novo mutation (CRYBB2 c.487C?>?T). The most frequent variants in our cohort were in crystallins and cytoskeletal genes (5/27, 18.52%), followed by proteins associated with X-linked syndromic conditions (14.81%) and transcriptional factors (11.11%). Additional information on the possibility of complications with inherited ocular or systemic diseases other than CC was provided in 17/27 (62.96%) variants. CONCLUSIONS:These results contribute to expanding the mutation spectrum and frequency of genes responsible for CC. Targeted NGS in CC provided significant diagnostic information and enabled more accurate genetic counselling. This study reports the different distributions of mutation genes in familial and sporadic CC cases.

SUBMITTER: Fan F

PROVIDER: S-EPMC7469093 | biostudies-literature | 2020 Sep

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

The mutation spectrum in familial versus sporadic congenital cataract based on next-generation sequencing.

Fan Fan F Luo Yi Y Wu Jihong J Gao Chao C Liu Xin X Mei Hengjun H Zhou Xiyue X

BMC ophthalmology 20200903 1

<h4>Background</h4>Congenital cataract (CC) is a significant cause of lifelong visual loss, and its genetic diagnosis is challenging due to marked genetic heterogeneity. The purpose of this article is to report the genetic findings in sporadic and familial CC patients.<h4>Methods</h4>Patients (n = 53) who were clinically diagnosed with CC and their parents were recruited. Blood samples were collected in our hospital. Mutations were detected by panel-based next-generation DNA sequencing (NGS) tar ...[more]

PMID: 32883240

Similar Datasets

Project description:Dilated cardiomyopathy (DCM) is a complex myocardial disease of multifactorial etiologies, including enlarged cardiac chambers and contractile dysfunction. It has been suggested that the inheritance of DCM‑associated mutations predominates its onset. Therefore, the present study investigated the pathogenesis of DCM via pedigree analysis and genetic diagnosis by massive whole‑exome screening, and targeted exon capture. To study the familial gene‑phenotype association, the exon and splice sites of 325 hereditary disease‑associated genes in the proband with familial dilated cardiomyopathy (FDC), including 61 cardiac disease‑associated genes, such as the lamins A/C (LMNA), were analyzed by ultra‑high multiplex polymerase chain reaction and the Ion AmpliSeq™ Inherited Disease Panel. The present study also conducted Sanger DNA Sequencing for family members with global minor allele frequencies <1% to verify potential pathogenic mutation sites. A total of three rare missense mutations were detected, including heterozygous c.244G>A in LMNA, c.546C>G in potassium voltage‑gated channel subfamily KQT (KCNQ4) and c.1276G>A in EYA transcriptional coactivator and phosphatase 1 (EYA1), indicating a glutamic acid to lysine substitution at amino acid 82 (p.E82K) in LMNA, a p.F182L in KCNQ4 (a mutation associated with pathogenic deafness) and p.G426S in EYA1 (associated with Branchiootorenal syndrome 1 and Branchiootic syndrome 1 pathogenesis). In the present study, a carrier with slight hearing impairment was detected in the family analyzed; however, no patients with deafness or branchiootorenal syndrome were observed. LMNA p.E82K revealed SIFT and PolyPhen‑2 scores of 0 and 1, respectively. In the second generation, 3 patients with DCM underwent permanent pacemaker implantation due to sick sinus syndrome, atrioventricular block and unstable cardiac electrophysiology. The present study suggested that LMNA p.E82K may contribute to the pathogenesis of FDC and concomitant atrioventricular block. At present, only three families with DCM resulting from similar mutations have been reported. The present study demonstrated the strong pathogenic effects of LMNA p.E82K on DCM.

Project description:The present study aimed to determine genomic changes in sporadic intracranial hemangioblastoma (HBL), and the mutation patterns were analyzed using next-generation DNA sequencing (NGS). In this NGS analysis of the HBL tumor, 67 variants of 41 genes were identified. Of these, 64 were single-nucleotide variants (SNVs), two were exonic insertions and deletions (INDEL), and one was an intronic INDEL. In total, 15 were missense exonic variants, including an insertion variant in the NRAS gene, c.1_2insA, and a deletion variant, c.745delT, in the HNF1A gene, both of these mutations produced a termination codon. Other exonic missense variants found in the tumor were CTNNB1, FGFR3, KDR, SMO, HRAS, RAI1, and a TP53 variant (c.430C>G). Moreover, the results of the present study revealed a novel variant, c.430C>G, in TP53 and two missense variants of SND1 (c.1810G>C and c.1814G>C), which were also novel. ALK (rs760315884) and FGFR2 (rs1042522) missense variants were reported previously. Notably, a total of 10 previously reported single-nucleotide polymorphisms (SNPs) were found in this tumor in genes including MLH1 (rs769364808), FGFR3 (rs769364808), two variants (rs1873778 and rs2228230) in PDGFRA, KIT (rs55986963), APC (rs41115), and RET (rs1800861). The results of this study revealed a synonymous mutation (SNP) in c.1104 G>T; p. (Ser368Ser) in the MLH1 gene. In this amino acid (AA) codon, two other variants are also known to cause missense substitutions, c.1103C>G; p. (Ser368Trp); COSM6986674) and c.1103C>T; p.(Ser368Leu; COSM3915870), were found in hematopoietic and urinary tract tissue, respectively. However, three SNPs found in genes such as ALK, KDR, and ABL1 in the HBL tumor in this study were not reported in UCSC, COSMIC, and ClinVar databases. Additionally, 19 intronic variants were identified in this tumor. One intronic SNV was present in each of the following genes: EGFR, ERBB4, KDR, SMO, CDKN2B, PTEN, PTPN11, RB1, AKT1, and ERBB2. In PIK3CA and FBXL18 genes, two intronic variants were present, and in the SND1 gene, three intronic variants were detected in the HBL tumor presented in this study. Notably, only one of these was reported in the catalog of somatic mutations in cancer. Only one 3'-untranslated region (UTR) insertion variant in the NRAS gene (c.*2010T>AT) was detected in the tumor of the present study, and this was a splice site acceptor. A TP53 intronic mutation (c.782+1G>T) was the only pathogenic splice_donor_variant found in this HBL tumor. The frequency of variants and Phred scores were markedly high, and the p-values were significant for all of the aforementioned mutations. In summary, a total of 15 missense, 10 synonymous, and 19 intronic variants were identified in the HBL tumor. Results of the present study detected one novel insertion in NRAS and one novel deletion in HNF1A genes, a novel missense variant in the TP53 gene, and two novel missense variants of SND1. Hotspot mutations in other cancer driver genes, such as PTEN, ATM, SMAD4, SMARCB1, STK11, NPM1, CDKN2A, and EGFR, which are frequently affected in gliomas, were not found in the tumor of the present study. Future studies should aim to validate oncogenic mutations that may act as novel targets for the treatment of these tumors.

Dataset Information

The mutation spectrum in familial versus sporadic congenital cataract based on next-generation sequencing.

Publications

The mutation spectrum in familial versus sporadic congenital cataract based on next-generation sequencing.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets