scholarly journals Characteristics of the mutation spectrum identified by comprehensive investigation of the CFTR gene in the Russian patients

2019 ◽  
Vol 47 (1) ◽  
pp. 38-46
Author(s):  
N. V. Petrova ◽  
A. Yu. Marakhonov ◽  
T. A. Vasilyeva ◽  
N. Yu. Kashirskaya ◽  
E. I. Kondratyeva ◽  
...  

Rationale: Cystic fibrosis (CF; OMIM 219700) is a  common hereditary disease caused by mutations in the CFTR gene (OMIM 602421). The distribution and frequencies of the CFTR gene mutations vary considerably between countries and ethnic groups. By now about 11%  alleles of the CFTR gene remain unidentified after testing for frequent mutations in the Russian patients. A full determination of the mutation spectrum in the CFTR gene is necessary to optimize medical and genetic assistance to the population and to implement the achievements of targeted therapy in the treatment of CF patients.Materials and methods: The sample included 121 Russian CF patients, in whom testing for 34 routinely analyzed mutations did not identify one (n = 107) or both (n = 14) mutant alleles. Assessment of the coding sequence of the CFTR gene, including the regions of exon-intron junctions, 5’- and 3’-untranslated regions was performed by the Sanger sequencing method; in addition, the search for large rearrangements was conducted by the multiplex ligation-dependent probe amplification (MLPA) method.Results: In addition to the previously identified, 88  more variants were determined, including 28  missense mutations, 15  nonsense mutations, 18 frameshift mutations (14 deletions, 4  insertions), 14  splicing mutations, 1  in-frame insertion, 1  in-frame deletion, 1  in/del mutation, and 10  large rearrangements (7  deletions, 3  duplications). Twenty three (23) novel variants were sequenced. Four (4) complex mutant alleles were found. Sixty (60) variants are found once each. One hundred and thirty four (134) of 135 tested mutant alleles were identified.Conclusion: Consequent use of the sequencing and MLPA methods has allowed for identification of a high proportion of the tested mutant alleles in CF patients from Russia (134/135, > 99%), to detect a  significant diversity of the CFTR mutation spectrum (88  additional variants, 32  of them novel), a  number of repeated mutations (c.2353C>T, c.1240_1244delCAAAA, c.1766+1G>A and c.3929G>A) encountered in 5 or more unrelated patients, which could be included in the panel of routinely analyzed variants in the Russian CF patients; and a high proportion of large rearrangements of the CFTR gene. 

2021 ◽  
pp. bjophthalmol-2021-319084
Author(s):  
Zexu Chen ◽  
Tianhui Chen ◽  
Min Zhang ◽  
Jiahui Chen ◽  
Michael Deng ◽  
...  

AimsTo identify the mutation spectrum and genotype–phenotype correlations of fibrillin-1 (FBN1) mutations in a Chinese cohort with congenital ectopia lentis (EL).MethodsPatients clinically suspected of congenital zonulopathy were screened using panel-based next-generation sequencing followed by multiplex ligation-dependent probe amplification. All the probands were subjected to thorough ocular examinations. Molecular and clinical data were integrated in pursuit of genotype–phenotype correlation.ResultsA total of 131 probands of FBN1 mutations from unrelated families were recruited. Around 65% of the probands were children younger than 9 years old. Overall, 110 distinct FBN1 mutations were identified, including 39 novel ones. The most at-risk regions were exons 13, 2, 6, 15, 24 and 33 in descending order of mutation frequency. The most prevalent mutation was c.184C>T (seven, 5.34%) in the coding sequence and c.5788+5G>A (three, 2.29%) in introns. Missense mutations were the most frequent type (103, 78.63%); half of which were distributed in the N-terminal regions (53, 51.46%). The majority of missense mutations were detected in one of the calcium-binding epidermal growth factor-like domains (62, 60.19%), and 39 (62.90%) of them were substitutions of conserved cysteine residues. Microspherophakia (MSP) was found in 15 patients (11.45%). Mutations in the middle region (exons 22–42), especially exon 26, had higher risks of combined MSP (OR, 5.51 (95% CI 1.364 to 22.274), p=0.017).ConclusionsThis study extended the knowledge of the FBN1 mutation spectrum and provided novel insights into its clinical correlation regarding EL and MSP in the Chinese population.


Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 3211-3211
Author(s):  
Giuseppe Tagariello ◽  
Roberta Salviato ◽  
Donata Belvini ◽  
Paolo Radossi ◽  
Ezio Zanon ◽  
...  

Abstract Introduction: Immune tolerance therapy (ITT), consists of administration of daily high doses of factor VIII concentrates by intravenous infusions. It can induce tolerance to the exogenous protein and eradicate the antibody response to FVIII, which still represents the main complication of replacement therapy in haemophilia A (HA) severe cases. Methods: We have investigated 71 HA patients with inhibitors (sixty-nine severe, one moderate and one mild cases). We screened the patients for the causative mutations in the F8 gene using Long Range PCR for the intron22 inversion, multiplex-PCR for intron1 inversion or conformation sensitive gel electrophoresis (CSGE) followed by DNA sequencing for other mutation types. Results: Diverse genetic defects were detected in the severe cases, with a predominance of gross mutations: F8 gene inversions, large deletions and nonsense mutations account for 68% of the mutations, whereas in the two non severe patients specific missense mutations were identified. ITT has been attempted in 16 HR patients of this cohort but failed in 5 cases. Conclusion: We confirmed that the presence of inhibitors correlates well with the presence of null mutations, as reported by Schwaab et al (Thromb Haemost 1995). Several predictive factors for ITT outcome have been so far taken into consideration but no correlation has been made between F8 gene defect and ITT response. In our cohort 2 large deletions, 2 intron22 inversions and 1 nonsense mutations failed to respond. For the remaining 2 large deletions no ITT were attempted so no information are available. Large deletions appear to be a high risk genetic factor both for inhibitor development and for long term inhibitor persistence and ITT unresponsiveness. The identification of these patients at very high risk of inhibitor development and ITT unresponsiveness by mutation analysis should therefore be strongly recommended soon after the diagnosis, even because of the high cost of the therapy.


Dermatology ◽  
2020 ◽  
pp. 1-7
Author(s):  
Zhongshuai Wang ◽  
Yan Yan ◽  
Baoxi Wang

<b><i>Background:</i></b> Acne inversa/hidradenitis suppurativa (HS) is a chronic, recurrent inflammatory disease of the skin that can significantly affect patients’ quality of life. The etiology and pathogenesis of HS are unclear and gene mutations might play a role. <b><i>Summary:</i></b> The primary focus of the review is on aggregating the gene mutations reported, summarizing the structure of γ-secretase and analyzing and speculating about the mechanism and the underlying relations between gene mutation and functional changes of protein. The systematic literature review was done by searching the PubMed, Embase, and Web of Science databases. γ-Secretase is an intramembrane protease complex responsible for the intramembranous cleavage of more than 30 type-1 transmembrane proteins including amyloid precursor protein and Notch receptors. The protein complex consists of four hydrophobic proteins: presenilin, presenilin enhancer-2 (PSENEN), nicastrin, and anterior pharynx defective 1 (APH1). To date, 57 mutations of γ-secretase genes have been reported in 70 patients or families worldwide, including 39 in NCSTN, 14 in PSENEN, and 4 in PSEN1, of which 17 are frameshifts, 15 result in nonsense mutations, 13 in missense mutations, and 12 are splice site mutations. Given the structure of γ-secretase and analysis of related mutation loci of NCSTN, PSENEN, and PSEN1, mutations in γ-secretase genes could affect activation of presenilin, prevent substrate binding, and hinder intramembrane cleavage of select proteins.


2021 ◽  
Author(s):  
Hu yuan xiang ◽  
Li wei hao ◽  
Kang ning lin ◽  
Ma li yan ◽  
Teng qing ◽  
...  

Abstract BACKGROUND: Acute intermittent porphyria (AIP) is an autosomal dominant hereditary disease caused by mutations to the hydroxymethylbilane synthase (HMBS) gene in the heme biosynthesis pathway. AIP is a rare disease that is thought to display incomplete penetrance. Studies on the characteristics of HMBS mutations in people from Britain, France, Russia, and Sweden have been performed. RESULT: In this study, a total of 45 different gene mutations were found, 17 of which were novel mutations that have not been previously reported. The 45 HMBS mutations included 19 missense, 11 splicing, and 4 nonsense mutations; 9 small deletions, 1 repeat insertion, and 1 complex deletion-insertion mutation. One mutation (c.673C>T) was found in the gene sequence of 8 unrelated patients, making it the most common mutation, and another mutation (c.517C>T) was found in 7 unrelated patients, making it the next most common mutation found in this study. To study the expression level of mutant HMBSs, Western blot and immunofluorescence staining were performed with four novel mutants (c.653G>A, c.597dupC, c.673_674del, c.1045_1046delAA), and the crystal structure changes were compared through homologous modeling to indicate the possible pathogenic mechanism.CONCLUSIONS: In this study, the characteristics of HMBS gene mutation in Chinese were studied, which laid a foundation for further research in the future.


2000 ◽  
Vol 37 (3) ◽  
pp. 248-253 ◽  
Author(s):  
T. Muto ◽  
S. Wakui ◽  
H. Takahashi ◽  
S. Maekawa ◽  
T. Masaoka ◽  
...  

Sixty-three cases of benign and malignant canine mammary tumors were analyzed to define the alteration of exons 5–8 for the p53 tumor suppressor gene using polymerase chain reaction direct sequence analysis with paraffin-embedded tissues. Four missense mutations were found in 38 benign mammary tumors (11%), and five missense (one tumor had two missense mutations) and one nonsense mutations were found in 25 mammary carcinomas (20%). These data suggest that the p53 gene alterations might be initiated at an early stage of canine mammary carcinogenesis and p53 mutations might be associated with malignancy. However, there was no evidence of any relationship between the p53 alterations and the histologic types of tumors or breeds of dogs.


Blood ◽  
2014 ◽  
Vol 124 (21) ◽  
pp. 1527-1527
Author(s):  
Anna Pavlova ◽  
Irina Matytsina ◽  
Morio Arai ◽  
Johannes Oldenburg

Abstract Introduction: Factor (F) VIII genotype has been shown to be a risk factor for inhibitor development, where different mutation types are associated with different degrees of risk (Oldenburg J, et al.Haemophilia 2006;12 Suppl 6:15–22). However, it is not clear why some patients with a specific mutation develop inhibitors while others with the same mutation do not, including those with high-risk defects such as null mutations. Patients with severe hemophilia A (HA) with low-risk mutations are thought to produce some functional or non-functional FVIII that is sufficient to induce immune tolerance (Oldenburg J, et al.Haemophilia 2002;8 Suppl 2:23–29). In the present study, the distribution of F8 gene mutations in 81 patients fully exposed to FVIII with severe HA and no inhibitors is compared to data on mutation distribution among severe HA patients with/without inhibitors. Materials & Methods: Turoctocog alfa (NovoEight®) is a new recombinant FVIII product with a truncated B-domain. Previously treated patients (PTPs) with severe HA participated in the pivotal trials guardian™1 (n=150; 12–65 yrs) or guardian™3 (n=63; <12 yrs), in which they received turoctocog alfa as prophylaxis and to treat bleeds. The majority continued in an ongoing extension trial, guardian™2. All patients ≥12 yrs had a history of ≥150 exposure days (EDs) to FVIII products and patients <12 yrs had ≥50 EDs. No patients had inhibitors prior to or after turoctocog alfa treatment. Distribution of mutation types has previously been reported in populations with HA that consisted of or included patients with inhibitors (Salviato R, et al. Haemophilia 2007;13:361–372; Gouw SC, et al.Blood 2012;119:2922–2934). Here we report mutation distribution in a sample of guardian™ patients with severe HA who had long been previously treated with FVIII protein and remained inhibitor free, and compared this distribution with that from 2 published studies (Oldenburg J, et al. 2006; Salviato R, et al. 2007). Results: Eighty-one patients enrolled in the guardian™ trials had F8 gene mutation analyzed. For 52 patients <12 yrs old, genotype was analyzed during guardian™3. For 29 patients ≥12 yrs old, genotype analysis was done prior to enrollment and obtained from medical records. In 77/81 patients, the F8 gene defect was identifiable. Distribution of gene mutations in guardian™, in a population with severe HA with inhibitors, and in a population with severe HA with/without inhibitors are compared in table 1. It is interesting that the overall distribution of mutations among the populations appears quite similar, pointing toward the multifactorial nature of inhibitor development. Null mutations (inversions, nonsense mutations, and large deletions) were present in 66% and 75% of patients with severe HA and severe HA with inhibitors, respectively (table 1). In guardian™, 57% (46/81) of patients had null mutations despite never having developed an inhibitor. The difference in distribution of null mutations in the 3 populations is mainly accounted for by large deletions and nonsense mutations, while distribution of inversions was similar. It should be noted that in guardian™, 10/11 patients with missense mutations had these located outside the C1/C2 domain, which reportedly has a lower frequency of inhibitors compared with missense mutations at the C1/C2 domain (Oldenburg J, et al. 2006). Conclusions: Eighty-one patients in the guardian™ trial with severe hemophilia A had their genotype analyzed and all of them were inhibitor-free over their lifetime. Interestingly, the prevalence of high-risk mutation types does not seem to differ markedly from previously published data in patients with inhibitors, probably indicating the relevance of other factors in inhibitor development. Table 1. Distribution of F8 gene mutation types guardian™ Additional studies guardian™ patients (N) Distribution (%) in guardian™ patients (severe HA without inhibitors) Distribution (%) in patients with severe HA and inhibitors (Salviato R, et al. 2007)* Distribution (%) in patients with severe HA with/without inhibitors (Oldenburg J, et al. 2006) Total, N 81 81 76 753 Intron 22 inversion 33 40.7 44.7 45.0 Intron 1 inversion 3 3.7 1.3 2.5 Nonsense 8 9.9 18.4 13.5 Large deletion 2 2.5 10.5 5.0 Missense 11 13.6 5.2 14.5 Small del/ins/dupl 16 19.8 10.5 16.0 Splice site 4 4.9 5.2 3.5 Unidentified/ not enough information 4 4.9 3.9 0.0 Total 81 100.0 100.0 100.0 *Only patients with severe HA included. Disclosures Matytsina: Novo Nordisk A/S: Employment. Arai:Novo Nordisk Pharma, Ltd: Employment. Oldenburg:Baxter, Bayer, Biogen Idec, Biotest, CSL-Behring, Grifols, Novo Nordisk, Octapharma, Swedish Orphan Biovitrum and Pfizer: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding.


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Aysun Urhan ◽  
Thomas Abeel

AbstractCoronavirus disease 2019 (COVID-19) has emerged in December 2019 when the first case was reported in Wuhan, China and turned into a pandemic with 27 million (September 9th) cases. Currently, there are over 95,000 complete genome sequences of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus causing COVID-19, in public databases, accompanying a growing number of studies. Nevertheless, there is still much to learn about the viral population variation when the virus is evolving as it continues to spread. We have analyzed SARS-CoV-2 genomes to identify the most variant sites, as well as the stable, conserved ones in samples collected in the Netherlands until June 2020. We identified the most frequent mutations in different geographies. We also performed a phylogenetic study focused on the Netherlands to detect novel variants emerging in the late stages of the pandemic and forming local clusters. We investigated the S and N proteins on SARS-CoV-2 genomes in the Netherlands and found the most variant and stable sites to guide development of diagnostics assays and vaccines. We observed that while the SARS-CoV-2 genome has accumulated mutations, diverging from reference sequence, the variation landscape is dominated by four mutations globally, suggesting the current reference does not represent the virus samples circulating currently. In addition, we detected novel variants of SARS-CoV-2 almost unique to the Netherlands that form localized clusters and region-specific sub-populations indicating community spread. We explored SARS-CoV-2 variants in the Netherlands until June 2020 within a global context; our results provide insight into the viral population diversity for localized efforts in tracking the transmission of COVID-19, as well as sequenced-based approaches in diagnostics and therapeutics. We emphasize that little diversity is observed globally in recent samples despite the increased number of mutations relative to the established reference sequence. We suggest sequence-based analyses should opt for a consensus representation to adequately cover the genomic variation observed to speed up diagnostics and vaccine design.


2021 ◽  
Vol 22 (8) ◽  
pp. 4009
Author(s):  
Maik Liedtke ◽  
Christin Völkner ◽  
Alexandra V. Jürs ◽  
Franziska Peter ◽  
Michael Rabenstein ◽  
...  

Niemann-Pick type C2 (NP-C2) disease is a rare hereditary disease caused by mutations in the NPC2 gene. NPC2 is a small, soluble protein consisting of 151 amino acids, primarily expressed in late endosomes and lysosomes (LE/LY). Together with NPC1, a transmembrane protein found in these organelles, NPC2 accomplishes the exclusion of cholesterol; thus, both proteins are essential to maintain cellular cholesterol homeostasis. Consequently, mutations in the NPC2 or NPC1 gene result in pathophysiological accumulation of cholesterol and sphingolipids in LE/LY. The vast majority of Niemann-Pick type C disease patients, 95%, suffer from a mutation of NPC1, and only 5% display a mutation of NPC2. The biochemical phenotype of NP-C1 and NP-C2 appears to be indistinguishable, and both diseases share several commonalities in the clinical manifestation. Studies of the pathological mechanisms underlying NP-C2 are mostly based on NP-C2 animal models and NP-C2 patient-derived fibroblasts. Recently, we established induced pluripotent stem cells (iPSCs), derived from a donor carrying the NPC2 mutations c.58G>T/c.140G>T. Here, we present a profile of pathophysiological in vitro features, shared by NP-C1 and NP-C2, of neural differentiated cells obtained from the patient specific iPSCs. Profiling comprised a determination of the NPC2 protein level, detection of cholesterol accumulation by filipin staining, analysis of oxidative stress, and determination of autophagy. As expected, the NPC2-deficient cells displayed a significantly reduced amount of NPC2 protein, and, accordingly, we observed a significantly increased amount of cholesterol. Most notably, NPC2-deficient cells displayed only a slight increase of reactive oxygen species (ROS), suggesting that they do not suffer from oxidative stress and express catalase at a high level. As a site note, comparable NPC1-deficient cells suffer from a lack of catalase and display an increased level of ROS. In summary, this cell line provides a valuable tool to gain deeper understanding, not only of the pathogenic mechanism of NP-C2, but also of NP-C1.


2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Xiang Zhang ◽  
Xuewu Zhang ◽  
Xia Li ◽  
Yunfei Lv ◽  
Yanan Zhu ◽  
...  

Abstract IKZF1 belongs to the IKAROS family of transcription factors, and its deletion/mutation frequently affects acute lymphoblastic leukemia. In acute myeloid leukemia, IKZF1 deletion has been demonstrated recurrent, but whether IKZF1 mutation also exists in AML remained largely unknown. Herein, we analyzed the IKZF1 mutation in AML. In our cohort, the frequency of IKZF1 mutation was 2.6% (5/193), and 5 frameshift/nonsense mutations as well as 2 missense mutations were identified in total. Molecularly, IKZF1 mutation was absent in fusion gene-positive AML, but it was demonstrated as the significant concomitant genetic alteration with SF3B1 or bi-alleleCEBPA mutation in AML. Clinically, two IKZF1, PTPN11 and SF3B1-mutated AML patients exhibited one aggressive clinical course and showed primary resistant to chemotherapy. Furthermore, we confirmed the recurrent IKZF1 mutation in AML with cBioPortal tool from OHSU, TCGA and TARGET studies. Interestingly, OHSU study also showed that SF3B1 mutation was the significant concomitant genetic alteration with IKZF1 mutation, indicating their strong synergy in leukemogenesis. In conclusion, IKZF1 mutation recurrently affected AML.


2005 ◽  
Vol 152 (2) ◽  
pp. 193-198 ◽  
Author(s):  
Carina Rodrigues ◽  
Paula Jorge ◽  
José Pires Soares ◽  
Isaura Santos ◽  
Regina Salomão ◽  
...  

Objective: Defects in the human thyroid peroxidase (TPO) gene are reported to be one of the causes of congenital hypothyroidism (CH) due to a total iodide organification defect. The aim of the present study was to determine the nature and frequency of TPO gene mutations in patients with CH, characterised by elevated TSH levels and orthotopic thyroid gland, identified in the Portuguese National Neonatal Screening Programme. Subjects and methods: The sample comprised 55 patients, from 53 unrelated families, with follow-up in the endocrinology clinics of the treatment centres of Porto and Lisbon. Mutation screening in the TPO gene (exons 1–17) was performed by single-strand conformational analysis followed by sequencing of fragments with abnormal migration patterns. Results: Eight different mutations were detected in 13 patients (seven homozygotes and six compound heterozygotes). Novel mutations included three missense mutations, namely 391T > C (S131P), 1274A > G (N425S) and 2512T > A (C838S), as well as the predictable splice mutation 2748G > A (Q916Q/spl?). The undocumented polymorphism 180-47A > C was also detected. Conclusion: The results are in accordance with previous observations confirming the genetic heterogeneity of TPO defects. The proportion of patients in which the aetiology was determined justifies the implementation of this molecular testing in our CH patients with dyshormonogenesis.


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