Single Nucleotide Substitution In Exon Research Articles

A single nucleotide substitution in exon 5 generated the novel KIR2DL3*00112 allele.

The novel KIR2DL3*00112 allele differs from the closest allele KIR2DL3*00101 by a single same sense mutation.

Identification of the novel allele, HLA-A*30:01:22, in a Saudi individual.

A single nucleotide substitution in exon 5 of HLA-A*30:01:01:01 results in the novel HLA-A*30:01:22 allele.

A single nucleotide substitution in exon 4 produced the novel allele, HLA-C*07:1093.

Characterization of the novel HLA-C*07:1093 allele in a Russian female bone marrow donor.

Identification of the novel HLA-DQA1*01:138 allele by next-generation sequencing.

HLA-DQA1*01:138 is identical to HLA-DQA1*01:03 except for a single nucleotide substitution in exon 3.

A single nucleotide substitution in exon 5 produced the novel allele, HLA-B*40:01:83.

HLA-B*40:01:83, carrying a single nucleotide substitution in exon 5 is described.

Identification of the novel class II allele, HLA-DPA1*01:127.

HLA-DPA1*01:127 is identical to HLA-DPA1*01:03 except for a single nucleotide substitution in exon 3.

The novel HLA-B*51:01:83 allele was identified by next-generation sequencing.

HLA-B*51:01:83 differs from HLA-B*51:01:01:01 by one single nucleotide substitutions in exon 5.

Three novel variants in SOX10 gene: Waardenburg and PCWH syndromes

BackgroundWaardenburg syndrome (WS) is a rare genetic disorder characterized by musculoskeletal abnormalities, deafness and hypopigmentation of hair and skin. This article’s aim is to investigate clinical and genetic characteristics of WS in three unrelated Caucasian individuals.Case presentationThe first patient was a 25-year-old female with congenital bilateral hearing loss, bright-blue-eyes, hypopigmentation of hair and skin, megacolon, language retardation, tenosynovitis and neuromas. The second case was an infant symptomatic from birth, with dysphagia, Hirschsprung disease and neurological abnormalities. The third patient was a 14-year-old boy with congenital bilateral hearing loss and ileocolic Hirschsprung disease. In order to identify variants in potentially causal genes of the patients’ phenotype, genetical testing was conducted: targeted clinical exome, targeted exome and trio exome, respectively. We identified three novel variants spread throughout the coding sequence of SOX10. The c.395C>G variant identified de novo in patient 1 was a single nucleotide substitution in exon 2. The c.850G>T variant identified as heterozygous in patient 2 was a loss-of-function variant that generated a premature stop codon. The c.966dupT variant identified in patient 3 was a duplication that generated a premature stop codon. It had been identified in his father, arising a possible germinal mosaicism. According to in silico predictors the variant identified in patient 1 was considered as pathogenic, whereas the other two were classified as likely pathogenic.ConclusionsAn exact description of the mutations responsible for WS provides useful information to explain clinical features of WS and contributes to better genetic counselling of WS patients.

The novel HLA-DQB1*06:03:27 allele characterised by sequence-based typing in a European bone marrow donor.

A single nucleotide substitution in exon 3 of HLA-DQB1*06:03:01 results in a new allele, HLA-DQB1*06:03:27.

The novel allele, HLA‐A*32:148, identified by next generation sequencing in a Saudi individual

A single nucleotide substitution in exon 4 of HLA-A*32:01:01:01 results in novel HLA-A*32:148 allele.

The novel HLA-DPB1*571:01 allele characterized by SMRT DNA sequencing in an African Caribbean individual.

A single nucleotide substitution in exon 3 of HLA-DPB1*105:01 results in a new allele, HLA-DPB1*571:01.

HLA-C*08:01:25, a novel HLA allele, which has arisen by a silent mutation in codon 271.

HLA-C*08:01:25 differs from HLA-C*08:01:01 by a single-nucleotide substitution in exon 4.

Characterization of a novel HLA-C allele, HLA-C*04:288, in an Italian patient.

The novel HLA-C*04:288 differs from HLA-C*04:01:01:06 by a single nucleotide substitution in exon 2.

The rate of weight gain and productivity of a chicken broiler cross with various polymorphic types of the myostatin gene

The search for single nucleotide polymorphisms (SNPs) in the myostatin gene is a promising direction of research as this gene is involved in the development of important biological and productive traits in chickens. Using polymerase chain reaction (PCR-RFLP), allele and genotype frequencies were analyzed in the Cornish chicken breed, line G5, cross Smena-8. Two pairs of primers allowing the PCR product to be obtained in the myostatin gene were used. Two single nucleotide substitutions in exon 1 of the myostatin gene were considered: G/A in position MST2109 and G/С in position MST2244. A significant predominance of deoxynucleotide G over C in MST2244 and deoxynucleotide A over G in MST2109 was observed. No differences in the productive traits between genotypes for MST2109 were detected. The analysis of the allelic variability for locus MST2244 showed statistically significant differences in the weight of live chicken at the age of seven days between the CC and G2G2 genotypes (p < 0.01) and CG2 and G2G2 (p < 0.05). G2G2 individuals (203.52 g) were significantly heavier than the CC (179.5 g) and CG2 (193.95 g) chickens at the age of sevendays. Statistically significant differences between the CC and G2G2 genotypes in live weight at the age of 33 days were revealed (p < 0.05). Thus, this research made it possible to estimate allele frequencies in the myostatin gene in line G5 of the Cornish breed. The results obtained will allow taking into account particular chicken genotypes for the myostatin gene for accelerating the breeding process in the broiler poultry industry.

Notch1 Signaling in NOTCH1-Mutated Mantle Cell Lymphoma Depends on DLL4 and Is a Potential Target for Specific Antibody Therapy

Mantle cell lymphoma (MCL) is a rare B-cell-neoplasm with an aggressive clinical course characterized by the hallmark translocation t(11;14)(q13;q32) resulting in overexpression of cyclin D1. Furthermore, genomic profiling revealed numerous secondary genetic alterations and recurrent mutations contributing to MCL pathogenesis. Among them, mutations in the NOTCH1 gene have been described with a frequency of ~10% and are associated with significantly shorter survival rates. Therefore, further investigation of the biological impact of this mutation in MCL and its potential as a target for a specific inhibitory antibody therapy is of great interest.Here we investigated the role of the Notch receptor ligands Jagged1 (JAG1), Jagged2 (JAG2), Delta-like canonical Notch ligand 1 (DLL1) and Delta-like canonical Notch ligand 4 (DLL4) in activating the Notch1-signaling pathway in NOTCH1-mutated Mino and NOTCH1-wt Jeko1 MCL cell lines and evaluated the effects of the novel and specific monoclonal Notch1-antibody OMP-52M51.Mino cells are characterized by a single nucleotide substitution in exon 34 of the NOTCH1 gene, leading to truncation of the C-terminal PEST-domain. These mutations are known to remove the recognition site from the ubiquitin ligase degradation complex, resulting in increased stability and transcriptional activity of Notch1 upon ligand-stimulation. We confirmed the predicted truncation of Notch1 in Mino cell lysates and demonstrated that the expression of cleaved Notch1 was potently stimulated by recombinant DLL4 protein. In contrast, in the NOTCH1-wt cell line Jeko1, no stable overexpression of cleaved Notch1 could be observed upon any ligand-stimulation. Treatment of the NOTCH1-mutated cells with OMP-52M51 effectively prevented DLL4-dependent activation of Notch1 and suppressed transcriptional induction of well-known Notch1-target genes HES1 (hairy and enhancer of-split 1), DTX1 (deltex E3 ubiquitin ligase 1) and c-MYC as observed by real-time quantitative PCR. Gene expression profiling furthermore revealed that OMP-52M51 significantly impeded DLL4-induced upregulation of numerous genes involved in lymphoid biology and lymphomagenesis, as well as genes related to the cell cycle and the MAP-Kinase signaling pathway. Western blot analysis confirmed Notch1-antibody-mediated abrogation of enhanced expression of p-ERK and p-MEK upon DLL4-ligand-stimulation. Further investigations of functional effects revealed inhibitory effects of OMP-52M51 on enhanced tumor cell migration of DLL4-stimulated cells. As the DLL4-Notch-axis is known to be involved in regulating angiogenesis, we investigated the impact of activating NOTCH1-mutations in MCL on HUVEC tube formation and observed increased vessel sprouting upon DLL4-stimulation that could be abolished by treatment with OMP-52M51. Importantly, all these effects were specific for NOTCH1-mutated cells and did not occur in the NOTCH1-wt cell line Jeko1.In conclusion, we demonstrate for the first time that DLL4 is the most important ligand to activate Notch1 in MCL harbouring NOTCH1-mutations in the PEST-domain. Our findings indicate that enhanced Notch1 activity promotes a more aggressive behavior of the disease and specific antibody-inhibition of the Notch1-signaling pathway might provide an interesting therapeutic alternative for a subset of MCL patients, warranting further investigation. DisclosuresNo relevant conflicts of interest to declare.

Detection of Common and Less Frequent EGFR Mutations in Cytological Samples of Lung Cancer

Objective: Lung cancer represents the leading cause of cancer death. EGFR mutations, detected in 10-40% of lung adenocarcinomas, are an essential key to therapeutic management. EGFR-activated mutations comprise mainly deletions in exon 19 and point mutations in exon 21. Although histology is the traditional method of detection, we investigated the role of cytology in EGFR mutations. Study Design: A total of 774 lung cancers were studied for EGFR mutations (676 histological and 98 cytological samples), including 424 adenocarcinomas, 326 non-small cell lung carcinomas not otherwise specified, and 24 squamous cell carcinomas. Results: We had a total of 164 (21.2%) cases of mutations. Common mutations were short in-frame deletions in exon 19 (53.7%) and single-nucleotide substitutions in exon 21 (34.1%); less frequent mutations included single-nucleotide substitutions in exon 18 (3.7%) and in-frame insertions/deletions in exon 20 (8.5%). Histologically, EGFR mutations in exons 19 and 21 occurred in 19.4% and in exons 18 and 20 in 2.2%, while the rates cytologically were 13.3% for exons 19 and 21 and 5.1% for exons 18 and 20. Conclusions: The sensitivity for the detection of EGFR mutations in cytological samples overlaps histology, so the use of cytological material constitutes an adequate approach for treatment selection in patients with locally advanced or metastatic lung cancer.

Detection of a new HLA-A allele, designatedHLA-A*32:53

The novel allele A*32:53 differs from A*32:01 by a single nucleotide substitution in exon 4 (position 649G>A).

Trichorhinophalangeal syndrome with low expression of TRPS1 on epidermal and hair follicle epithelial cells

Trichorhinophalangeal syndrome (TRPS) is an autosomal-dominant congenital hair loss disease characterized by sparse and slow-growing scalp hair, craniofacial and skeletal abnormalities, pear-shaped nose, thin upper lip, brittle and thin toenails, and bilateral brachydactyly of the big toes. We report a case of TRPS1 exhibiting these clinical features with a novel heterozygous single nucleotide substitution in exon 3 of the TRPS1 gene. By immunohistochemical analysis of a biopsied specimen of the patient's alopecia lesion, we found for the first time that the expression level of TRPS1 was markedly reduced in the epidermis and the outer root sheath of hair follicles as compared to a normal subject. In addition, higher expression of phospho-Stat3 was found consequent to the loss of TRPS1 in the outer root sheath.

Full-length sequence of a novel HLA-B*15:220 allele identified in an individual from Guadeloupe

The new HLA-B*15:220 allele shows a single-nucleotide substitution in exon 1 at position 47 (C>T) when compared to its closest allele HLA-B*15:03:01, resulting in an amino acid substitution from Ala to Val in the signal peptide at codon -9.

Variation in the Yak Dectin-1 Gene (CLEC7A)

C-type lectin domain family 7, member A (CLEC7A, dectin-1) plays an important role in antifungal immunity and belongs to the family of C-type lectin receptors. Variation in the extended exon 4-6 region of the yak dectin-1 gene (CLEC7A), which encodes the β-glucan recognition domain, was investigated using polymerase chain reaction-single strand conformational polymorphism (PCR-SSCP). Three and two variant sequences were identified in exons 4 and 5, respectively, and no variation was found in exon 6. The variation included two single-nucleotide substitutions in exon 4 and one single-nucleotide polymorphism in exon 5, and two of these substitutions would nominally cause amino acid substitutions (p.I158T and p.S197G) in yak dectin-1. This is the first report identifying the yak dectin-1 gene, revealing that it is polymorphic and this polymorphism might affect the structure and function of this gene in yak.