Sequence Variants In Genes Research Articles

Identifying Sequence Variants of 18 Hereditary Ovarian Cancer-Associated Genes in Chinese Epithelial Ovarian Cancer Patients.

Objectives The causes of ovarian cancer (OC) have been confirmed to be closely related to genetic factors. Identifying sequence variants of hereditary ovarian cancer (HOC) susceptibility genes can increase clinical surveillance, facilitate early detection, and provide personalized treatment for patients. This study is aimed at investigating the variation frequency of HOC susceptibility genes in the Chinese population and providing information for the etiology and genetics of OC. Methods 118 epithelial OC patients were recruited in this clinical study. Variants of 18-gene panel were detected in blood samples by next-generation sequencing (NGS) technology. Results Overall, 36.44% (43/118) of patients carried at least one pathogenic variant. Among these, BRCA1 pathogenic variants were detected in 31 (26.27%) patients, and 5 (4.24%) patients carried pathogenic variants of BRCA2. Moreover, 27.12% (32/118) of patients carried variants of unknown significance (VUSs). Importantly, we detected eight variants that were not reported previously. Conclusions Our study enlarged the spectrum of HOC-associated gene sequence variants in the Chinese population and also proved the necessity of multigene testing in epithelial OC patients. The identification of patients with HOC will allow family members to undergo cascade testing where identification of unaffected carriers can facilitate early detection, risk reduction, or prevention of OC and ultimately improve long-term outcomes.

Multi-omics approach highlights differences between RLP classes in Arabidopsis thaliana

BackgroundThe Leucine rich-repeat (LRR) receptor-like protein (RLP) family is a complex gene family with 57 members in Arabidopsis thaliana. Some members of the RLP family are known to be involved in basal developmental processes, whereas others are involved in defence responses. However, functional data is currently only available for a small subset of RLPs, leaving the remaining ones classified as RLPs of unknown function.ResultsUsing publicly available datasets, we annotated RLPs of unknown function as either likely defence-related or likely fulfilling a more basal function in plants. Then, using these categories, we can identify important characteristics that differ between the RLP subclasses. We found that the two classes differ in abundance on both transcriptome and proteome level, physical clustering in the genome and putative interaction partners. However, the classes do not differ in the genetic di versity of their individual members in accessible pan-genome data.ConclusionsOur work has several implications for work related to functional studies on RLPs as well as for the understanding of RLP gene family evolution. Using our annotations, we can make suggestions on which RLPs can be identified as potential immune receptors using genetics tools and thereby complement disease studies. The lack of differences in nucleotide diversity between the two RLP subclasses further suggests that non-synonymous diversity of gene sequences alone cannot distinguish defence from developmental genes. By contrast, differences in transcript and protein abundance or clustering at genomic loci might also allow for functional annotations and characterisation in other plant species.

Transcriptome and genome re-sequencing analysis reveals differential expression patterns and sequence variation in pericarp wax metabolism-related genes in Ziziphus jujuba (Chinese jujube)

The fruit pericarp wax of jujube accessions with different cracking resistance show differences in morphology and wax chemical content. In this study, transcriptome and genome re-sequencing were used to analyze the differences in wax metabolism between jujube cultivars with different cracking resistance characteristics. The results showed that 431 differentially expressed genes were identified through transcriptome screening between the cracking-resistant cultivar ‘Linhuang No. 1’ and the cracking-susceptible cultivar ‘Muzao’ during the mature stage of fruit development. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis annotated three wax metabolism pathways (involving eight wax metabolism-related genes). Information on gene sequence variation in the eight genes was obtained from genome resequencing, with sequence variation between the two cultivars found in the promoter region of the LOC107415896 gene, which encodes the biotin carboxyl carrier protein of acetyl-CoA carboxylase 2, chloroplastic (BCCP2) protein, where 107 bases were inserted in ‘Linhuang No.1’. As a result, the fatty acid concentration in the wax of ‘Muzao’ was lower than that of ‘Linhuang No. 1’, with the proportion of fatty acids with fewer than 16 C atoms in ‘Muzao’ accounting for a greater proportion of the total fatty acids. This indicated that the expression of the ‘Muzao’ LOC107415896 gene was affected. Our research has laid the foundation for further analysis of the function of jujube wax metabolism in the cracking-resistant fruit phenomenon.

Evolution of the MLO gene families in octoploid strawberry (Fragaria \xd7ananassa) and progenitor diploid species identified potential genes for strawberry powdery mildew resistance

Powdery mildew (PM) caused by Podosphaera aphanis is a major fungal disease of cultivated strawberry. Mildew Resistance Locus O (MLO) is a gene family described for having conserved seven-transmembrane domains. Induced loss-of-function in specific MLO genes can confer durable and broad resistance against PM pathogens. However, the genomic structure and potential role of MLO genes for PM resistance have not been characterized yet in the octoploid cultivated strawberry. In the present study, MLO gene families were characterized in four diploid progenitor species (Fragaria vesca, F. iinumae, F. viridis, and F. nipponica) and octoploid cultivated (Fragaria ×ananassa) strawberry, and potential sources of MLO-mediated susceptibility were identified. Twenty MLO sequences were identified in F. vesca and 68 identified in F. ×ananassa. Phylogenetic analysis divided diploid and octoploid strawberry MLO genes into eight different clades, in which three FveMLO (MLO10, MLO17, and MLO20) and their twelve orthologs of FaMLO were grouped together with functionally characterized MLO genes conferring PM susceptibility. Copy number variations revealed differences in MLO composition among homoeologous chromosomes, supporting the distinct origin of each subgenome during the evolution of octoploid strawberry. Dissecting genomic sequence and structural variations in candidate FaMLO genes revealed their potential role associated with genetic controls and functionality in strawberry against PM pathogen. Furthermore, the gene expression profiling and RNAi silencing of putative FaMLO genes in response to the pathogen indicate the function in PM resistance. These results are a critical first step in understanding the function of strawberry MLO genes and will facilitate further genetic studies of PM resistance in cultivated strawberry.

Non-Driver Mutations and Gene Sequence Variants Identified By Targeted Deep Sequencing in Polycythemia Vera and Essential Thrombocythemia

Background:Driver mutations in myeloproliferative neoplasms involve mutations in the JAK2, MPL, and CALR genes. However, incorporation of next generation sequencing (NGS) testing into routine clinical practice may identify for mutations or variants in additional hematologic malignancy-associated genes, the roles of which have not been extensively elucidated in patients with polycythemia vera (PV) or essential thrombocythemia (ET). The purpose of this study is to characterize the clinical characteristics of ET/PV patients harboring additional non-driver mutations or gene variants.Methods:Eligible cases included patients with PV/ET diagnosed and treated at MD Anderson Cancer Center from January 2012 to January 2017. NGS sequencing of 28 genes known to be mutated in hematologic malignancies was performed on samples from 240 ET/PV patients. Non-driver mutations detected by the NGS platform were classified based on the allele frequency recorded in our database in conjunction with currently available and periodically updated public reference databases of somatic mutations or variants of unclear significance.Results:A total of 110 ET and 130 PV cases had NGS performed on samples collected at the time of initial referral. Among them, 21 (19%) ET cases and 28 (21.5%) PV cases had ≥1 non-driver somatic mutation detected. The distribution of non-driver somatic mutations in ET and PV are shown in Figure 1A. On grouping non-driver genes into functional pathways, the most frequent mutational targets were in genes associated with epigenetic regulation (PV, 22; ET, 25), mainly DNA methylation (PV, 18; ET, 20) followed by epigenetic modifier (PV, 4; ET, 5). In subjects with PV, TET2 (n = 12) was the most frequently mutated gene, followed by DNMT3A (n = 7), IDH1/2 (n = 5), and ASXL1 (n = 4). A similar pattern was noted in ET, with TET2 mutations (n = 8) being most frequent followed by DNMT3A (n = 7), and ASXL1 (n = 5). Older patients were more likely to display non-driver mutations in both ET (p < 0.001) and PV (p = 0.02). The combined prevalence of non-driver somatic mutations was 27% and 32% in PV and ET, respectively. Over a short median follow up of 3.9 (range, 1.0-37.1) months among PV patients with non-driver somatic mutations, no leukemic transformations occurred. Similarly, no leukemic transformations were observed in ET patients with additional non-driver somatic mutations over a median follow up of 3.8 (range, 1.1-36) months. Overall survival (OS) was significantly longer in patients without additional mutations in epigenetic modifiers (Figure 1C). The prognostic relevance of non-driver somatic mutations on OS was not determined due the small sample size and limited follow up duration. Of 13 (12%) triple-negative ET patients without non-driver somatic mutations, nine had non-synonymous gene sequence variants; the most common being in DNA methylation genes namely TET2 &IDH1/2 genes (Figure 1B).Conclusion:The spectrum of non-driver somatic mutations in our ET and PV study cohorts was dominated by mutations in the TET2, DNMT3A, ASXL1 genes, and were correlated with age (Buscarlet Blood, 2017). A larger sample size and longer follow-up is needed to determine the impact of non-driver somatic mutations on transformation-free and overall survival. Germline TET2 variants or their combinations with other variants/non-driver mutations may constitute low penetrance predisposition factors for myeloid neoplasms and their functional relevance warrants further exploration. [Display omitted] DisclosuresBose:Incyte Corporation: Honoraria. Kantarjian:Amgen: Research Funding; Novartis: Research Funding; Bristol-Meyers Squibb: Research Funding; ARIAD: Research Funding; Pfizer: Research Funding; Delta-Fly Pharma: Research Funding. Verstovsek:Astrazeneca: Research Funding; Roche: Research Funding; NS Pharma: Research Funding; Roche: Research Funding; Blueprint Medicines Corp: Research Funding; Galena BioPharma: Research Funding; Genentech: Research Funding; Galena BioPharma: Research Funding; Promedior: Research Funding; Genentech: Research Funding; Blueprint Medicines Corp: Research Funding; Lilly Oncology: Research Funding; Incyte: Research Funding; Pfizer: Research Funding; Bristol Myers Squibb: Research Funding; Lilly Oncology: Research Funding; CTI BioPharma Corp: Research Funding; Pfizer: Research Funding; NS Pharma: Research Funding; Celgene: Research Funding; CTI BioPharma Corp: Research Funding; Bristol Myers Squibb: Research Funding; Astrazeneca: Research Funding; Gilead: Research Funding; Celgene: Research Funding; Promedior: Research Funding; Gilead: Research Funding; Seattle Genetics: Research Funding; Seattle Genetics: Research Funding; Incyte: Research Funding.

Mutational analysis of CYP1B1 gene in Iranian pedigrees with glaucoma reveals known and novel mutations.

Primary congenital glaucoma (PCG) (OMIM#231,300) can be caused by pathogenic sequence variations in CYP1B1, LTBP2, MYOC and PXDN genes. The purpose of this study was to investigate mutations in the CYP1B1 gene in families affected with primary congenital glaucoma (PCG) using linkage analysis and Sanger sequencing. A total number of four families with nine affected PCG patients during six months were included in this study. The mutations were identified by homozygosity mapping to find the linked loci and then direct sequencing of all coding exons, the exon-intron boundaries and the 5' untranslated region of CYP1B1 using genomic DNA obtained from affected family members and their parents. Moreover, bioinformatic tools were applied to study mutation effect on protein structure and function. A total of four mutations were identified, and three of these were novel. Two were missense mutations: One was truncating mutation, and the other was an in-frame deletion. Mutations in CYP1B1 could fully explain the PCG phenotype in all of the patients. Also, the bioinformatic study of the mutations showed the structure of the protein is affected, and it is well conserved among similar species. In this study, we identified 4 CYP1B1 mutations, 3 of which were novel. In silico analysis of identified mutations confirmed their molecular pathogenicity. A similar analysis will help understand the biological role of CYP1B1 and the effect of mutations on the regulatory and enzymatic functions of CYP1B1 that result in PCG. Not relevant.

Molecular characterization and population genetics of Theileria parva in Burundi's unvaccinated cattle: Towards the introduction of East Coast fever vaccine.

Theileria parva (T. parva) is a protozoan parasite that causes East Coast fever (ECF). The disease is endemic in Burundi and is a major constraint to livestock development. In this study, the parasite prevalence in cattle in six regions namely; Northern, Southern, Eastern, Western, Central and North Eastern was estimated. Furthermore, the sequence diversity of p67, Tp1 and Tp2 genes was assessed coupled with the population genetic structure of T. parva using five satellite markers. The prevalence of ECF was 30% (332/1109) on microscopy, 60% (860/1431) on ELISA and 79% (158/200) on p104 gene PCR. Phylogenetic analysis of p67 gene revealed that only allele 1 was present in the field samples. Furthermore, phylogenetic analysis of Tp1 and Tp2 showed that the majority of samples clustered with Muguga, Kiambu and Serengeti and shared similar epitopes. On the other hand, genetic analysis revealed that field samples shared only two alleles with Muguga Cocktail. The populations from the different regions indicated low genetic differentiation (FST = 0.047) coupled with linkage disequilibrium and non-panmixia. A low to moderate genetic differentiation (FST = 0.065) was also observed between samples and Muguga cocktail. In conclusion, the data presented revealed the presence of a parasite population that shared similar epitopes with Muguga Cocktail and was moderately genetically differentiated from it. Thus, use of Muguga Cocktail vaccine in Burundi is likely to confer protection against T. parva in field challenge trials.

A common classification framework for histone sequence alterations in tumours: an expert consensus proposal.

The description of genetic alterations in tumours is of increasing importance. In human genetics, and in pathology reports, sequence alterations are given using the human genome variation society (HGVS) guidelines for the description of such variants. However, there is less adherence to these guidelines for sequence variations in histone genes. Due to early cleavage of the N-terminal methionine in most histones, the description of histone sequence alterations follows their own nomenclature and differs from the HGVS-compliant numbering by omitting this first amino acid. Next generation sequencing reports, however, follow the HGVS guidelines and as a result, an unambiguous description of sequence variants in histones cannot be provided. The coexistence of these two nomenclatures leads to confusions for pathologists, oncologists, and researchers. This review provides an overview of tumour entities with sequence alterations of the H3-3A gene (HGNC ID = HGNC:4764), highlights the problems associated with the coexistence of these two nomenclatures, and proposes a standard for the reporting of histone sequence variants that allows an unambiguous description of these variants according to HGVS principles. We hope that scientific journals will adopt the new notation, and that both geneticists and pathologists will include it in their reports. © 2021 The Authors. The Journal of Pathology published by John Wiley & Sons, Ltd. on behalf of The Pathological Society of Great Britain and Ireland.

A hypomorphic mutation in the mouse Csn1s1 gene generated by CRISPR/Cas9 pronuclear microinjection.

Caseins are major milk proteins that have an evolutionarily conserved role in nutrition. Sequence variations in the casein genes affect milk composition in livestock species. Regulatory elements of the casein genes could be used to direct the expression of desired transgenes into the milk of transgenic animals. Dozens of casein alleles have been identified for goats, cows, sheep, camels and horses, and these sequence variants are associated with altered gene expression and milk protein content. Most of the known mutations affecting casein genes’ expression are located in the promoter and 3’-untranslated regions. We performed pronuclear microinjections with Cas9 mRNA and sgRNA against the first coding exon of the mouse Csn1s1 gene to introduce random mutations in the α-casein (Csn1s1) signal peptide sequence at the beginning of the mouse gene. Sanger sequencing of the founder mice identified 40 mutations. As expected, mutations clustered around the sgRNA cut site (3 bp from PAM). Most of the mutations represented small deletions (1–10 bp), but we detected several larger deletions as well (100–300 bp). Functionally most mutations led to gene knockout due to a frameshift or a start codon loss. Some of the mutations represented in-frame indels in the first coding exon. Of these, we describe a novel hypomorphic Csn1s1 (Csn1s1c.4-5insTCC) allele. We measured Csn1s1 protein levels and confirmed that the mutation has a negative effect on milk composition, which shows a 50 % reduction in gene expression and a 40–80 % decrease in Csn1s1 protein amount, compared to the wild-type allele. We assumed that mutation affected transcript stability or splicing by an unknown mechanism. This mutation can potentially serve as a genetic marker for low Csn1s1 expression.

Hidden by the name: A new fluorescent pumpkin toadlet from the Brachycephalus ephippium group (Anura: Brachycephalidae).

Species of Brachycephalus has been having taxonomical issues due its morphological similarity and genetic conservatism. Herein, we describe a new species of Brachycephalus from the south Mantiqueira mountain range and semidecidual forests in the municipalities of Mogi das Cruzes, Campinas and Jundiaí, state of São Paulo, Brazil, based on an integrative approach. It can be distinguished from all species of the B. ephippium species group based on morphological characters (especially osteology and head shape), advertisement call and divergence in partial mitochondrial DNA gene sequences (16S). The new species is genetically similar to B. margaritatus and morphologically similar to B. ephippium. It can be differentiated from B. ephippium by the presence of dark faded spots on skull and post-cranial plates, presence of black connective tissue connective tissue scattered over dorsal musculature, parotic plate morphology, smaller snout-vent length (adult SVL: males 13.46–15.92 mm; females 16.04–17.69 mm) and 3% genetic distance. We also present natural history data and discuss the robustness of the integrative approach, geographic distribution, genetic data, behaviour, fluorescence in ontogeny, and conservation status.

Phenotypic and Phylogenetic Characterization of Cu Homeostasis among Xylella fastidiosa Strains.

Xylella fastidiosa is a bacterial pathogen causing severe diseases and asymptomatic colonization in more than 600 plants worldwide. Copper (Cu) is a widely used antimicrobial treatment for various plant diseases, including those affecting X. fastidiosa hosts. Cu homeostasis among X. fastidiosa strains from different geographical locations and host species has not been characterized. Here, we assessed minimum inhibitory concentration (MIC) of Cu for 54 X. fastidiosa strains. We observed strain-level variation in MIC values within each subspecies. We hypothesized that these differences could be explained by sequence variation in Cu homeostasis genes. Phylogenies based on copA, copB, copL, and cutC were created using 74 genomes (including 43 strains used in vitro) of X. fastidiosa, showing that the phylogenetic clustering of Cu homeostasis associated with clustering was based on core genome phylogenies, rather than on pattern of MIC. No association was found among Cu MIC, subspecies classification, and host and location of isolation, probably due to uneven and limited group of strains whose genomes are available. Further analysis focused on a subgroup of isolates from Georgia’s vineyards that shared similar Cu-related phenotypes. Further research is needed to better understand the distribution of Cu homeostasis for this pathogen.

Analysis of Genetic Variations in Poly Gene Sequences in Dengue Virus 2 Using In-Silico RFLP

Dengue hemorrhagic fever (DHF) is a disease caused by Dengue virus transmitted to humans through infected Aedes aegypti and Ae. Albopictus . Dengue virus classified into 4 serotypes, including DEN-1, DEN-2, DEN-3, and DEN-4. The genomes of the four dengue viruses share about 65% similarities, the rest is a genetic variation that differentiates between serotypes. Genetic variations also occur even within one serotype. This study aimed to analyse genetic variation in envelope protein E ( POLY ) gene sequences in Dengue Virus 2 NCBI PopSet 1760494694 using in-silico RFLP by free bioinformatic tools on internet. The restriction enzymes used were Afe I and Apa LI. The results of the in-silico RFLP in this study showed that there were genetic variations in the recognition site of the AfeI enzymes (A1 allele and A2 allele) and ApaLI (B1 allele and B2 allele) in 18 DNA sequences of the POLY gene for Dengue 2 virus NCBI PopSet 1760494694.

DNA barcoding of lamp shells (Brachiopoda: Lingula anatina) from Probolinggo, East Java, Indonesia

Abstract. Ambarwati R, Rahayu DA, Rachmadiarti F, Khaleyla F. 2021. DNA barcoding of lamp shells (Brachiopoda: Lingula anatina) from Probolinggo, East Java, Indonesia. Biodiversitas 22: 1764-1774. Lingula anatina is one of brachiopods found in tropical regions, however, the reports on this species from South East Asia is currently limited. This study, therefore, aims to identify the Cytochrome Oxidase subunit I (COI) sequence and phylogenetic of lamp shells from Probolinggo, Indonesia. A total of five samples of lamp shells were collected from Probolinggo, Indonesia, then identified based on morphological characters, and the identification was confirmed using molecular data. Subsequently, molecular characterization and identification were conducted based on 657 bp of COI gene similarity, sequence variation, genetic distance, phylogenetic topology, and BOLD System. According to the results, the Lingula species found in Probolinggo Indonesia was Lingula anatina. The median-joining network and Automatic Barcode Gap Discovery (ABGD) analysis showed this Lingula anatina population from Probolinggo had relatives of 22 haplotypes and divided into six haplogroups. Furthermore, the population belonged to the same haplogroup but had different haplotypes. Thus, this study provides more information for Lingula anatina phylogenetic and haplotype studies.

Targeted Sequencing Approach to Identifying Rare Genetic Variants Associated with Atrial Fibrillation

Purpose Atrial fibrillation (AF) is the most common cardiac arrhythmia in clinical practice and is associated with considerable morbidity and mortality. Multiple genes and genetic loci affecting AF susceptibility have been identified using positional cloning and candidate gene approaches The extent to which such polymorphisms contribute to AF is unknown. The aim of this study was to determine the spectrum and prevalence of rare amino acid coding (AAC) variants in candidate AF genes in a cohort of unrelated AF patients from Kazakhstan. Methods We sequenced 96 candidate genes in 102 Kazakhstani patients with AF using customized targeted gene panel (Haloplex, Agilent Technologies). Variants detected were compared with variants observed in the Exome Sequencing Project (ESP) to identify very rare (minor allele frequency 0.04%) AAC variants. ACMG/AMP guidelines were applied for variant interpretation of clinical significance - pathogenic (P), possibly pathogenic (PP), variant of uncertain significance (VUS), possibly benign (PB), benign (B). The ClinVar, Varsome and HGMD databases were also used. Results Median age at AF onset was 47.0 years, and 31.3% had a family history of AF. Totally 456 variants were identified in 74 genes for the overall study group. Variants included one in/del variant, four splice-site variants and 451 single-nucleotide variants (SNV) within the coding exonic regions. 168 HGMD mutations (61 unique) were observed in 37 genes. Classification of 456 variants according to ACMG guidelines showed that 13(2.9%) variants were classified as pathogenic, 13(2.9%) - likely pathogenic, 145 (31.9%) - uncertain significance, 109 (23.8%) likely benign and 175 (38.4%) benign. 31 rare AAC variants were identified in 20 of 102 AF patients. Among them three pathogenic variants KCNQ1 c.477+1G>A, KCNJ2 R218Q and KCNE2 T10K C29A (PP) were identified. Conclusion Our study shows that individuals presenting with AF carry rare mutations and potentially pathogenetic sequence variants in classical cardiac risk genes in almost 20%. No very rare AAC variants were identified in 80% of AF patients. Potential reasons for the lack of very rare AAC variants include a complex pattern of inheritance, variants in as yet unidentified AF genes or in noncoding regions, and environmental factors.

The role of new technologies in myeloproliferative neoplasms: Application of next-generation sequencing in myelofibrosis.

Driver mutations in Philadelphia chromosome-negative myeloproliferative neoplasms are well known. In the past, whole-genome sequencing identified nondriver mutations in other genes, potentially contributing to evolution of malignant clones. Next-generation sequencing was used to assess the presence of any mutations in 14 candidate genes at the point of diagnosis and the resultant impact on the clinical course of the disease. The study analysed 63 patients with myelofibrosis (MF). Nondriver mutations were detected in 44% of them. The most frequently affected genes were ASXL1 (27%), TET2 (11%) and SF3B1 (6%). The frequency of such mutations was highest in primary MF (59%) and lowest in the prefibrotic phase of primary MF (21%). Patients with prognostically unfavourable sequence variants in genes had significantly worse overall survival (53 vs 71months; HR=2.77; 95% CI 1.17-6.56; P=.017). In our study, multivariate analysis proved DIPSS to be the only significant factor to predict patient survival. DIPSS contains all of the important clinical and laboratory factors except genetic changes. Stratification of patients according to DIPSS is still beneficial although there are newer and improved scoring systems like GIPSS or MIPSS70. Assessing subclonal mutations in candidate genes during diagnosis may aid in the identification of high-risk MF patients and is therefore relevant for making a prediction for overall survival more accurate.

Gene Sequence Variation and Genetic Differentiation of Mitochondrial COI in Genus Saperda (Coleoptera:Cerambycidae:Lamiinae)

Gene Sequence Variation and Genetic Differentiation of Mitochondrial COI in Genus Saperda (Coleoptera:Cerambycidae:Lamiinae)

Interpreting Sequence Variation in PDAC-Predisposing Genes Using a Multi-Tier Annotation Approach Performed at the Gene, Patient, and Cohort Level.

We investigated germline variation in pancreatic ductal adenocarcinoma (PDAC) predisposition genes in 535 patients, using a custom-built panel and a new complementary bioinformatic approach. Our panel assessed genes belonging to DNA repair, cell cycle checkpoints, migration, and preneoplastic pancreatic conditions. Our bioinformatics approach integrated annotations of variants by using data derived from both germline and somatic references. This integrated approach with expanded evidence enabled us to consider patterns even among private mutations, supporting a functional role for certain alleles, which we believe enhances individualized medicine beyond classic gene-centric approaches. Concurrent evaluation of three levels of evidence, at the gene, sample, and cohort level, has not been previously done. Overall, we identified in PDAC patient germline samples, 12% with mutations previously observed in pancreatic cancers, 23% with mutations previously discovered by sequencing other human tumors, and 46% with mutations with germline associations to cancer. Non-polymorphic protein-coding pathogenic variants were found in 18.4% of patient samples. Moreover, among patients with metastatic PDAC, 16% carried at least one pathogenic variant, and this subgroup was found to have an improved overall survival (22.0 months versus 9.8; p=0.008) despite a higher pre-treatment CA19-9 level (p=0.02). Genetic alterations in DNA damage repair genes were associated with longer overall survival among patients who underwent resection surgery (92 months vs. 46; p=0.06). ATM alterations were associated with more frequent metastatic stage (p = 0.04) while patients with BRCA1 or BRCA2 alterations had improved overall survival (79 months vs. 39; p=0.05). We found that mutations in genes associated with chronic pancreatitis were more common in non-white patients (p<0.001) and associated with longer overall survival (52 months vs. 26; p=0.004), indicating the need for greater study of the relationship among these factors. More than 90% of patients were found to have variants of uncertain significance, which is higher than previously reported. Furthermore, we generated 3D models for selected mutant proteins, which suggested distinct mechanisms underlying their dysfunction, likely caused by genetic alterations. Notably, this type of information is not predictable from sequence alone, underscoring the value of structural bioinformatics to improve genomic interpretation. In conclusion, the variation in PDAC predisposition genes appears to be more extensive than anticipated. This information adds to the growing body of literature on the genomic landscape of PDAC and brings us closer to a more widespread use of precision medicine for this challenging disease.

The Utility of Otx1B Gene Sequence in Evaluating Some Epinephelus species Evolutionary Variations Compared with Other Ray-finned Fishes

Background: The application of molecular methods for evaluating the Epinephelus species evolutionary variations is considered the backbone for the conservation process for these biological resources. Methods: In this study, the utility of the Otx1B gene sequence variations was evaluated for the identification of some Red Sea Epinephelus species (E. areolatus, E. malabaricus, E. summana, E. radiatus and E. chlorostigma) compared with other ray-finned fishes. Some Otx1B gene fragments were isolated, purified, sequenced, analyzed (663 bp) and submitted to NCBI. Result: A total of 140 single nucleotide polymorphisms were identified among the evaluated fishes. The phylogenetic relations among the evaluated fishes were reconstructed using the Maximum Likelihood and Neighbor-Joining methods. The genus Epinephelus was distantly related to the group formed by genera Chlorurus, Scarus and Oxycheilinus. The DNA polymorphism and sequence conservation values were calculated. The estimated Otx1B gene fragment sequences have proven their ability to detect speciation in each studied fish genera.

Whole-Exome Sequencing in Patients Affected by Stevens-Johnson Syndrome and Toxic Epidermal Necrolysis Reveals New Variants Potentially Contributing to the Phenotype.

BackgroundAdverse drug reactions (ADRs) are frequent occurring events that can essentially be defined as harmful or unpleasant symptoms secondary to the use of a medicinal product. ADRs involve a wide spectrum of clinical manifestations ranging from minor itching and rash to life-threatening reactions. Stevens-Johnson syndrome (SJS) and toxic epidermal necrolysis (TEN) are rare ADRs. SJS-TEN may be considered a polygenic pathology due to additive/epistatic effects caused by sequence variants in numerous genes. Next-generation sequencing (NGS) represents a potentially interesting exploration tool in such scenario as it facilitates the simultaneous analysis of large genomic regions and genes at affordable cost.MethodsThe present study has involved using whole-exome sequencing (WES) for the first time on SJS-TEN patients. It involved robust and innovative multistep bioinformatics analysis focusing on 313 candidate genes potentially participating in the disease’s aetiology, specific drugs’ metabolism and gene regulation.ResultsWe identified combinations of frequently occurring and rare variants that may contribute to the disease’s pathogenesis. Depending on the specific drug being taken, different variants (and alleles) in NAT2, CYP2D8, CYP2B6, ABCC2, UGT2B7 and TCF3 were identified as coherent candidates representing potential future markers for SJS-TEN.ConclusionThe present study proposed and has described (for the first time) a large-scale genomic analysis of patients affected by SJS-TEN. The genes and variants identified represent relevant candidates potentially participating in the disease’s pathogenesis. Corroborating that proposed by others, we found that complex combinations of frequently occurring and rare variants participating in particular drug metabolism molecular cascades could be associated with the phenotype. TCF3 TF may be considered a coherent candidate for SJS-TEN that should be analysed in new cohorts of patients having ADRs.

Worldwide genetic variations in high-risk human papillomaviruses capsid L1 gene and their impact on vaccine efficiency.

Human papillomavirus is the most common sexually transmitted infection. It is associated with different cancers, mainly cervical cancer, which remains the fourth most frequent cancer among women worldwide; it is also related to anogenital (anus, vulvar, vagina, and penis) and oropharyngeal cancers. Vaccination against HPV infection is the major way of prevention, and it has demonstrated impressive efficacy in reducing cervical cancer incidence. Nowadays, all the licensed HPV recombinant vaccines were designed based on HPV major capsid L1 protein. However, some variations in the HPV L1 gene sequence may induce structural changes within the L1 protein, which may alter the affinity and interaction of monoclonal antibodies (MAbs) with L1 protein epitopes, and influence host immune response and recognition. Hence, the importance of accuracy in delineating epitopes relevant to vaccine design and defining genetic variations within antigenic regions in the L1 gene to predict its impact on prophylactic vaccine efficiency. The present review reports the sequence variations in HR-HPV L1 gene isolates from different countries around the world, which may help to understand the effect of HPV L1 gene variations on vaccine efficiency. Research studies were retrieved from PubMed, Google Scholar, Science direct, and the National Center for Biotechnology Information (NCBI) database. A total of 31 articles describing genetic variations within the major capsid L1 gene and conducted in Africa, Europe, America and Asia were found. Only 26 studies conducted on HPV16, 18, 31, 33, 58, 45 and 52 which are the targets of HPV prophylactic vaccines, and which reported genetic variations within the L1 gene, were selected and evaluated in this review. We found a total of 87, 49, 11, 7, 22, 3, and 17 non-synonymous single nucleotide polymorphisms (SNPs) within HPV16, HPV18, HPV31, HPV58, HPV45, and HPV52 L1 gene, respectively. Four mutations were frequently observed in HPV16 L1 sequences: T353P in the HI loop, H228D in the EF loop, T266A in the FG loop, and T292A in the FG loop. Two mutations in HPV58 L1 sequences: T375N in the HI loop and L150F in the DE loop. Three mutations in HPV33 L1 sequences: T56N in the BC loop, G133S in the DE loop, T266K in the FG loop. Other mutations were found in HPV18, HPV45, and HPV52 L1 sequences. Some were found in different countries, and others were specific to a given population. Furthermore, some variations were located on peptide binding epitopes and lead to a modification of epitopes, which may influence MAbs interactions. Others need further investigations due to the lack of studies. This study investigated the major capsid L1 genetic diversity of HPV16, 18, 31, 33, 58, 45, and 52 circulating in different populations around the world. Further investigations should be conducted to confirm their effect on immunogenicity and prophylactic vaccine efficiency.