Sorting Intolerant From Tolerant Research Articles

Insights into the structure–function relationship of missense mutations in the human TOP2A protein in ovarian cancer

Topoisomerase 2-alpha (TOP2A) is a nuclear protein that is responsible for the maintenance of the topological state of DNA. TOP2A is highly upregulated in ovarian cancer, and its copy number is an important prognosis factor. A large number of single-nucleotide polymorphism (SNP), insertion, and deletion mutations have been reported in TOP2A. Thus, a structural and functional study of missense SNPs was carried out to screen potentially damaging mutations. The 193 non-synonymous SNPs in the coding region of TOP2A in the dbSNP database were selected for in silico analysis. The deleterious SNPs were screened using sorting intolerant from tolerant (SIFT), PolyPhen-2, SNAP2, and SNPs&Go, and we obtained four possibly damaging SNPs at the end (Y481C, N7741, E922K, and R1514W). Mutants Y481C and E922K were predicted to be highly deleterious and showed decreased protein stability compared with native proteins, as predicted by I-Mutant 3. We used the SWISS-MODEL to model the structure of these two mutants, and the structural attributes of modeled mutants were studied using Hope Project, solvent accessibility-based protein–protein interface identification and recognition (SPPIDER), SRide, and HBAT, which predicted small variations from the native protein. Molecular dynamics simulation demonstrated a decrease in root mean square deviation (RMSD) and the radius of gyration of two mutants, which is relative to the native protein. The molecular docking of TOP2A with etoposide suggests that mutations may lead to resistance to TOP2A-targeted chemotherapy. In addition, the relative expression analysis performed by qRT-PCR also reveals that there is a three-fold increase in the expression levels of the TOP2A protein in ovarian adenoma cancer cell lines. Our analysis reveals that Y481C and E922K are highly damaging variants of TOP2A, which alter the protein dynamics and may be implicated in causing ovarian cancer.

Temporal analysis and comparative genomic study of SARS-CoV-2 variants across Uttar Pradesh, India: Insights from the first and second COVID-19 waves

The rapid emergence of genetic variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) after late 2020, lead to origin of the term “variant of concern” and became the prime issue for the health of the human populations across the globe. Genome surveillance provides the information about the functional consequences of the variants and their divergence. Presently, we report and compare the nucleotide sequences of the isolated SARS-CoV-2 genomes at two different time-frame i.e. first wave (June- September, 2020) and second wave (April-May, 2021) from Lucknow, Uttar Pradesh, India. We employed the Oxford Nanopore MINION system and ARTIC protocol for sequencing, achieving >90x genome coverage in approximately 90% of samples. Increased mutation density in viral spike proteins were the cause of higher transmission and infectivity of second wave. The second wave exhibited a higher mutation density in viral spike proteins, likely contributing to increased transmission and infectivity. Notable spike mutations included receptor-binding domain (RBD) mutations (L452R, T478K, D614G), N-terminal domain (NTD) mutations (T17R, G142D, Δ156–157, A222V), and furin cleavage site (FCS) mutations (P681R, D950N). The functional consequences of common and unique variants among the first and second wave were evaluated by Sorting Intolerant from Tolerant (SIFT) and Protein Variant Effect Analyser (PROVEAN). Furthermore, we extensively investigated phylogenetic clustering of the genome sequences by Nextstrain and identified the contrasting divergence between first and second wave. Different sub division of delta clade (21I, 21 A, 21 J) and 21 B (kappa) with mutations primarily in spike proteins and nucleocapsid proteins, were exclusive to the second wave. Our study identified changes in spike proteins and nucleocapsid potentially contributing to increased transmission and infectivity during the second wave. Loci specific variant map for different countries across the world suggested the appearance of large number of variants associated with ORF1a during the second wave in India. Overall, the data underscores the dynamic nature of viral evolution during different phases of an outbreak, highlighting the importance of continuous genomic surveillance to track and understand viral mutations and their implications for public health interventions.

Genotypic and phenotypic diversity in X-linked retinoschisis: Findings from a South Indian patient cohort.

Retinoschisis is a distinctive condition characterized by intraretinal layer clefts, primarily associated with X-linked recessive inheritance due to RS1 gene mutations. This study aims to uncover the RS1 mutation spectrum in a cohort of 22 X-linked retinoschisis cases from South India and emphasizes the genotypic and phenotypic associations within patients harboring only RS1 mutations. A total of 22 probands were suspected of having X-linked retinoschisis. All study subjects underwent ophthalmic investigations, including assessments of visual acuity, fundus examination, optical coherence tomography (OCT), and electroretinogram (ERG). RS1 gene screening was conducted using Sanger sequencing, and the pathogenicity of the variants was assessed through Sorting Intolerant from Tolerant (SIFT) and PolyPhen-2 in silico tools. The study found that the probands had an average visual acuity of 0.79 ± 0.39 log of minimum angle of resolution (logMAR), ranging from 0.17 to 1.77. During fundus examination, the probands exhibited a characteristic spoke wheel-like pattern in the macular region. Furthermore, OCT analysis revealed distinct alterations in the inner retinal microstructure, and ERG results consistently showed a reduction in b-wave amplitude. Eventually, Sanger sequencing results showed hemizygous mutations in the RS1 gene in only 12 probands, including a novel missense mutation in the RS1 gene's signal sequence. This study provides valuable insights into the spectrum of RS1 mutations in X-linked retinoschisis probands from South India. It reveals distinct genotypic-phenotypic associations and highlights the clinical manifestations associated with the disease pathogenesis.

Augmenting tomato functional genomics with a genome-wide induced genetic variation resource.

Induced mutations accelerate crop improvement by providing novel disease resistance and yield alleles. However, the alleles with no perceptible phenotype but have an altered function remain hidden in mutagenized plants. The whole-genome sequencing (WGS) of mutagenized individuals uncovers the complete spectrum of mutations in the genome. Genome-wide induced mutation resources can improve the targeted breeding of tomatoes and facilitate functional genomics. In this study, we sequenced 132 doubly ethyl methanesulfonate (EMS)-mutagenized lines of tomato and detected approximately 41 million novel mutations and 5.5 million short InDels not present in the parental cultivar. Approximately 97% of the genome had mutations, including the genes, promoters, UTRs, and introns. More than one-third of genes in the mutagenized population had one or more deleterious mutations predicted by Sorting Intolerant From Tolerant (SIFT). Nearly one-fourth of deleterious genes mapped on tomato metabolic pathways modulate multiple pathway steps. In addition to the reported GC>AT transition bias for EMS, our population also had a substantial number of AT>GC transitions. Comparing mutation frequency among synonymous codons revealed that the most preferred codon is the least mutagenic toward EMS. The validation of a potato leaf-like mutation, reduction in carotenoids in ζ-carotene isomerase mutant fruits, and chloroplast relocation loss in phototropin1 mutant validated the mutation discovery pipeline. Our database makes a large repertoire of mutations accessible to functional genomics studies and breeding of tomatoes.

Identification of Pathogenic Missense Mutations in the CHRNA5 Gene: A Computational Approach.

Aim TheCHRNA5/A3/B4gene locus is closely related to nicotine dependence and other smoking-related disorders. Coupling genetic and clinical studies of nicotine dependence and smoking behaviors may open new avenues for medication development. The aim of this study is to investigate the functional missense mutations in the CHRNA5 gene. Methodology The Ensembl database was used to gather data on missense mutations of the human CHRNA5 gene. Computational tools viz. SIFT (Sorting Intolerant From Tolerant), PolyPhen (Polymorphism Phenotyping),PROVEAN (Protein Variation Effect Analyzer), I-Mutant, and MutPred were used to uncover the pathogenic mutations in the gene under investigation. Results Among 161 missense variants reported inthe CHRNA5 gene, 94 variants were found to be highly pathogenic. Moreover, 20 were pathogenic and 4 were not pathogenic. Conclusion The computational analysis disclosed harmful mutations intheCHRNA5 gene which could be potentiallyassociated with smoking-related traits.

New frontiers in linguistic research: Eliminating the challenges of understanding the genetics of language through bioinformatics

Abstract The contemporary research in linguistics aims to forge an understanding of consilience by evading the stereotypic semantic studies in linguistics. Modern linguistics calls for understanding language evolution, language production, and language disorders in association with neuro-genetic studies. To undertake genetic trials, language scholars from the humanities and social sciences disciplines have constraints like funding, inaccessibility to genetic labs, and ethical issues over biological bodies. To resolve the constraints and to enhance extensive knowledge on the genetic association with language, this article employs bioinformatics tools, namely the Basic Local Alignment Search Tool (BLAST) and the Sorting Intolerant From Tolerant (SIFT). Through the BLAST tool, the article aids the language researcher to understand language evolution, and through the application of SIFT, the article highlights mutation points in the gene of a severe speech disorder. Finally, the article emphasizes the inclusion of bioinformatics in the field of humanities and social sciences with respect to language studies

Pregnancy-related type citrullinemia type 1: A case report and literature review

Citrullinemia type 1 (CTLN1) is a rare autosomal recessive urea cycle disorder, without functional argininosuccinate synthase 1 (ASS1), mostly occurring in newborns and infants, but it has been reported as having an adult-onset in carriers of the pathogenic gene, and even more rarely, the onset of the disease is pregnancy related. Only 12 reported cases of onset during pregnancy and puerperium were reported since 1980. We herein report a case of gestational onset that resulted in patient death with a reported pathogenic mutation, c.421-2A>G, resulting in an amino acid change, splicing mutation, on exon7, in ASS1 gene, and a novel mutation, c.1046T>G, resulting in an amino acid change p.V349G, predicted by sorting intolerant from tolerant (SIFT), PolyPhen-2, Mutation Taster, Genomic Evolutionary Rate Profiling 2 (GERP++) and Rare Exome Variant Ensemble Learner (REVEL). This article provides an overview of the relationship between CTLN1 and pregnancy and discusses the possible mechanisms, clinical manifestations, and genetic characteristics of pregnancy-related onset.

Genomic health is dependent on long-term population demographic history.

Current genetic methods of population assessment in conservation biology have been challenged by genome-scale analyses due to their quantitatively novel insights. These analyses include assessments of runs-of-homozygosity (ROH), genomic evolutionary rate profiling (GERP), and mutational load. Here, we aim to elucidate the relationships between these measures using three divergent ungulates: white-tailed deer, caribou, and mountain goat. The white-tailed deer is currently expanding, while caribou are in the midst of a significant decline. Mountain goats remain stable, having suffered a large historical bottleneck. We assessed genome-wide signatures of inbreeding using the inbreeding coefficient F and %ROH (FROH ) and identified evolutionarily constrained regions with GERP. Mutational load was estimated by identifying mutations in highly constrained elements (CEs) and sorting intolerant from tolerant (SIFT) mutations. Our results showed that F and FROH are higher in mountain goats than in caribou and white-tailed deer. Given the extended bottleneck and low Ne of the mountain goat, this supports the idea that the genome-wide effects of demographic change take time to accrue. Similarly, we found that mountain goats possess more highly constrained CEs and the lowest dN/dS values, both of which are indicative of greater purifying selection; this is also reflected by fewer mutations in CEs and deleterious mutations identified by SIFT. In contrast, white-tailed deer presented the highest mutational load with both metrics, in addition to dN/dS, while caribou were intermediate. Our results demonstrate that extended bottlenecks may lead to reduced diversity and increased FROH in ungulates, but not necessarily an increase in mutational load, probably due to the purging of deleterious alleles in small populations.

Novel Mutations of PAX6 and WFS1 Associated With Congenital Cataract in a Chinese Family.

Congenital cataract is a common cause of blindness in childhood. About half of the cases have a genetic etiology, and more than 100 genes have been associated with congenital cataracts. This study reports the clinical and genetic findings of a two-generation Chinese family affected by congenital cataract. Ophthalmologic examinations were performed for clinical evaluation of the cataract patients. Whole exome sequencing (WES) and Sanger sequencing were used to identify potentially relevant mutations. The online programsProtein Variation Effect Analyzer (PROVEAN) and Sorting Intolerant from Tolerant (SIFT) were employed to predict the impact of variation on protein function. Both the proband and her mother were blind because of bilateral nuclear cataracts, and the elder brother of the proband also manifested obvious bilateral cataracts. Sanger sequencing confirmed the mutations in the proband as well as in her mother. The elder brother simply carried the PAX6 c.221G>A variation. The WFS1 c.2070_2079del variation potentially generates a loss-of-function mutant. The novel PAX6mutation (c.221G>A) is associated with congenital cataract, and the WFS1 mutation (c.2070_2079del) may interactively aggravates this process. These findings may increase our understanding of the genetic etiology of congenital cataract.

Comprehensive in vitro and in silico assessments of metabolic capabilities of 24 genomic variants of CYP2C19 using two different substrates.

Introduction: Most hepatically cleared drugs are metabolized by cytochromes P450 (CYPs), and Clinical Pharmacogenetics Implementation Consortium (CPIC) guidelines provide curated clinical references for CYPs to apply individual genome data for optimized drug therapy. However, incorporating novel pharmacogenetic variants into guidelines takes considerable time. Methods: We comprehensively assessed the drug metabolizing capabilities of CYP2C19 variants discovered through population sequencing of two substrates, S-mephenytoin and omeprazole. Results: Based on established functional assays, 75% (18/24) of the variants not yet described in Pharmacogene Variation (PharmVar) had significantly altered drug metabolizing capabilities. Of them, seven variants with inappreciable protein expression were evaluated as protein damaging by all three in silico prediction algorithms, Sorting intolerant from tolerant (SIFT), Polymorphism Phenotyping v2 (PolyPhen-2), and Combined annotation dependent depletion (CADD). The five variants with decreased metabolic capability (<50%) of wild type for either substrates were evaluated as protein damaging by all three in silico prediction algorithms, except CADD exact score of NM_000769.4:c.593T>C that was 19.68 (<20.0). In the crystal structure of the five polymorphic proteins, each altered residue of all those proteins was observed to affect the key structures of drug binding specificity. We also identified polymorphic proteins indicating different tendencies of metabolic capability between the two substrates (5/24). Discussion: Therefore, we propose a methodology that combines in silico prediction algorithms and functional assays on polymorphic CYPs with multiple substrates to evaluate the changes in the metabolism of all possible genomic variants in CYP genes. The approach would reinforce existing guidelines and provide information for prescribing appropriate medicines for individual patients.

Comparison of In Vitro and In Silico Assessments of Human Galactose-1-Phosphate Uridylyltransferase Coding Variants.

Introduction Human pathogenic coding variations of the galactose-1-phosphate uridylyltransferase (GALT) gene cause classic galactosemia, a recessive disease of galactose metabolism. Unfortunately, there are many variants of uncertain significance (VUS) that need to be characterized in order to be able to predict the likelihood of classic galactosemia for all possible genotypes.There are many bioinformatic resources available that attempt to predict the pathogenicity of a human variant, but it is unclear if these methods realistically predict the consequence of these variants. To determine the clinical application of these resources, we compared the results of in vitro enzymatic assays with in silico predictive models. Methods In all assays, we compared the activity of the three human GALT VUS (Alanine81Threonine, Histidine47Aspartate, Glutamate58Lysine) to native GALT (nGALT) and to a variant of known pathogenic clinical significance (Glutamine188Arginine). The enzymatic activities of VUS recombinant proteins were compared to the results of in silico analytical methods. The in silico methods included the comparison of molecular dynamic simulation root-mean-square deviation (RMSD) results and the results from predictive programs PredictSNP, evolutionary model of variant effect (EVE), ConSurf, and sorting intolerant from tolerant (SIFT). Results The enzymatic assays showed that the variants tested had diminished Vmax relative to the native protein. The VUS RMSD data for both the whole protein and individual residues in the molecular dynamics simulations were not significantly different when compared to nGALT. The other predictive programs had mixed results for each VUS and were not consistent with the enzyme activity or simulation results. Conclusions Our experiments indicated a statistically significant decrease in enzymatic activity of the VUS when compared to nGALT. These experiments also demonstrated significant differences between in silico predictions and in vitro results. These results suggest that the in silico tools used may not be beneficial in determining the pathogenicity of GALT VUS.

Uncovering Ethnic Genomic Disparities Associated with Inferior Outcome in African Americans Diagnosed with Acute Myelogenous Leukemia

Background: African Americans (AA) have higher cancer-associated mortality than other ethnicities. AA with AML exhibit inferior overall survival (OS) to non-AA subgroups (OS=162 d vs 709 d, respectively, p=0.0001, HR=7.8) Fig 1A. In other cancers, higher genomic instability (GI) and differential oncogenic addiction contribute to AA worse outcomes; however, in AML, genetic causes of inferior outcomes are uncharacterized. In this study, we seek to investigate differential AML mut and other factors that contribute to inferior AA OS. Methods: After IRB approval, 92/250 (36.8%) available AML patients (pt) had next generation sequencing (NGS) data and were included. Mut frequencies were annotated by ethnicity [White (W) vs AA vs Hispanic (H) vs Asians (A)] and prioritized by European Leukemia Network (ELN) 2017 classification. Numeric chromosomic alterations (NCA) were extracted from metaphase karyotyping at diagnosis. Deleteriousness of mutations to protein function was calculated with sorting intolerant from tolerant (SIFT) prediction method. Chi-square and t-test evaluated differences in categorical and continuous variables respectively. Logistic binary regression was used to detect predictors for racial induced survival. SAS software was used. Results: Whites (W), AA, Hispanics (H) and Asians (A) represented 57/91 (62%), 14/91 (15%), 20/91 and (22%), 5/91 (5.4%) of the cohort, respectively. Median age was 63 (W) , 57.5 (AA) , 53 (H), 62 (A), p=NS. 60/92 (65%) were male. Median number of mut were 2.04 (W), 1.8 (AA), 2.2 (H) and 1.8 (A), p=NS. Distribution for adverse ELN-2017 defects were equivalent among AA vs non-AA except RUNX1, p=0.05. Lack of favorable mut was observed among AA. Only AA demonstrated CUX1, previously associated with DNA repair defects, and FBXW7 mut. A non-significant trend for higher NCA in AA (2.7 [W], 6.4 [AA], 3 [H] and 0.8 [A], p=0.09) was observed. Age correlated with NCA and number of mut in AML genome, p=0.02 and p=0.004. Interestingly, correlation effect was mostly driven only by AA, p=0.02 and p=0.003, respectively. SIFT score was 0.01 (W), 0.09 (AA), 0.02 (H), and 0.01 (A). These SIFT results suggest that AA mut are functionally tolerated. After adjusting for multiple factors, only canonical ELN-2017 mut, p=0.02 (OR 0.37, CI 0.16-0.8), and AA race, p=0.005 (OR 0.25, CI 0.1-0.67) increased risk of death (c-statistics=0.66) Fig.1B. Conclusions: In AA, frequency of Adverse ELN-2017 mut is similar to other races, but favorable mutations were lacking. NCA and number of AML genome mut strongly correlate with aging in AA, but not other ethnic groups. Surprisingly, SIFT score failed to demonstrate functional deleteriousness for AA mut, which suggests alternative genomic defects as a culprit for poor outcome. Acknowledging the small number of mut in our cohort, our study advances our understanding of racial disparity in AML survival. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Genotype and phenotype analysis of epilepsy caused by ADGRV1 mutations in Chinese children

ObjectiveTo investigate the genotype and phenotype of epilepsy caused by ADGRV1 variants in Chinese children. MethodsA total of 625 patients with epilepsy who had undergone whole-exon gene sequencing or epilepsy and related paroxysmal disease gene panel sequencing were recruited. Variants were evaluated for susceptibility pathogenicity based on their frequency in the Genome Aggregation Database (≤ 0.001). We used six algorithms (sorting intolerant from tolerant (SIFT), PolyPhen-2, Mutation Taster, CADD, REVEL and Splice AI) that predicted that the ADGRV1 variant would have a harmful impact on the function of genes and gene products. We retrospectively reviewed the clinical information of patients with susceptible pathogenic ADGRV1 variants. The relationship between the genotype and phenotype was also analyzed. ResultsEighteen patients with epilepsy were found to have likely pathogenic variants in ADGRV1. The rate of ADGRV1 variants in patients with epilepsy in this cohort was 2.88%. A total of 19 ADGRV1 variants were found, of which 13 were novel and 6 had been previously reported. Eleven out of the 18 children (61.1%) had febrile and afebrile seizures (FS and AS), two children had only FS, one child had infantile spasms, and the other four children had only AS that occurred during sleep (Rolandic epilepsy or atypical Rolandic epilepsy). SignificanceOur study showed a statistically significant association between ADGRV1 variants and FS and AS (p < 0.05), supporting the hypothesis that ADGRV1 is a susceptibility gene for Rolandic epilepsy and infantile spasms. Most epilepsy cases caused by ADGRV1 variants have a good prognosis.

Association of Palm gene mutations with structure and function of paralemmin proteins in Lori-Bakhtiari and Zel sheep Breeds

The aim of current study was to survey genetic variability of PALM gene’s exon 3 and 4 by PCR-SSCP and DNA sequencing in Zel and Lori Bakhtiari sheep breeds. The SIFT (Sorting Intolerant from Tolerant) and PHyre2 program were used to predict the possible impact of amino acid substitutions on performance and structure of the paralemmin protein. A total of 140 animal's from 2 Iranian sheep breeds with different fat metabolisms, Lori-Bakhtiari and Zel sheep breeds were considered. The results showed that there are two polymorphic sites including a nonsynonymous substitution and an insertion mutation (49bp). Non-synonymous mutation deduced Thr20Ala amino acid exchange and ensuing two different structures for paralemmin protein that could be potentially affect protein structure and function during the interaction with glutamate in the cytosolic surface of plasma membrane. PALM gene, according to evolutionary path, is classified into two separate categories. In first covey, Gallus gallus and in second one, other species in several branches, so that the sequence of cow and sheep is placed in a sub-branch which forms a clade beside goat. Comparison of illustrated coding region sequences, PALM gene among different species, is of orthologous which are derived from a common ancestor.

Identification of a novel missense mutation in non-syndromic familial multiple supernumerary teeth

ObjectiveThis study intended to evaluate the involvement of genetic factors in the etiology of non-syndromic multiple supernumerary teeth. DesignWe filtered the single nucleotide polymorphisms (SNPs) of the proband and his mother with similar phenotypes through whole-genome sequencing (WGS). By integrating multiple databases related to human genome mutations and disease information for mutation annotation, we excluded the SNPs of people without supernumerary teeth. Subsequently, the bioinformatics analysis tools (Sorting Intolerant From Tolerant (SIFT) < 0.05, Polymorphism Phenotyping (PolyPhen) > 0.90) were used to screen out the most correlated SNPs of the disease, besides, Gene Ontology (GO) analysis (P<0.05, FDR<0.05) and Sanger sequencing was applied to further verify the candidate pathogenic mutation point. ResultsA novel heterozygous variant in fer-1 like family member 6 (FER1L6) gene likely denoted pathogenicity in non-syndromic familial multiple supernumerary teeth. We identified a cohort of 3499 non-synonymous SNPs (nsSNPs), and only 142 nsSNPs with the score of SIFT < 0.05 and PolyPhen > 0.90 were retained. Then we got 54 nsSNPs from 31 candidate genes through GO analysis. Sanger sequencing revealed a missense variant in exon 31 of the FER1L6 gene, causing a transition from guanine to adenine in position 1447 of protein kinase C conserved region 2. ConclusionsWe identified a novel heterozygous chromosome 8q24.13 mutation of FER1L6, which was a new mutation site identified in non-syndromic familial multiple supernumerary teeth through genetic analysis of a Chinese family.

Whole-Genome Sequencing Identified KCNJ12 and SLC25A5 Mutations in Port-Wine Stains.

Port-wine stains (PWSs) are a congenital capillary malformed disorder and are caused by a number of somatic mutations that disrupt vascular development. However, the underlying genetic mutations in the pathogenesis of PWS have not yet been fully elucidated. To understand PWS genetic variations and investigate novel genetic mutations, we extracted genomic DNA from four sporadic PWS patients and then performed whole-genome sequencing (WGS). Using Sorting Intolerant from Tolerant (SIFT), PolyPhen2, Mutation Assessor, MetaSVM to identify candidate genetic mutations and whole-exome sequencing (WES) to confirm the identified variants. We found a previously reported G protein subunit alpha q (GNAQ) mutation c.548G > A, p.Arg183Gln in one case, whereas no such mutation was found in the other three samples. Moreover, six novel somatic mutations in three genes, including KCNJ12, SLC25A5, POTEE, were found in these four samples. Importantly, WES also verified the KCNJ12 (c.433G > A, p.Gly145Ser) and SLC25A5 (c.413G > A, p.Arg138His) mutations in other five sporadic PWS patients, with the frequency of 60% (3 of 5) and 40% (2 of 5), respectively. Thus, we reveal in this study two novel somatic mutations, KCNJ12 and SLC25A5, in the sporadic PWS patients for the first time. These findings highlight the genetic polymorphism of PWS and provide potential clinical prediction targets for this disease.

Mutational load and deleterious mutations in goat genome from Kenya

Different domestication processes such as selection and effective population size are among other factors responsible for the accumulation of mutations in an animal. This study investigated the mutation load and accumulation of deleterious mutations in Kenyan goat populations using Single Nucleotide Polymorphism (SNP) data obtained from local (Galla = 12) and exotic (Saanen = 24, Alpine = 28, and Toggenburg = 30) goat genotypes. The SNP annotation was done on the ENSEMBLE goat (Capra hircus) using the Variant Effect Predictor (VEP). Sorting Intolerant from Tolerant (SIFT) was done on the annotated file using a score of > 0.01 to describe highly deleterious mutations. Biomart tool in the ENSEMBL goat C. hircus was used for Gene Ontology (GO) for the genes identified from highly deleterious mutations. The analysis disclosed no differences in mutation load among the studied genotypes. Overall, the synonymous mutations were in abundance compared to missense mutations, totaling 693 and 258 representing 1.01% and 0.37%, respectively. The calculated mutation load was similar (0.37) suggesting exposure of goats to similar domestication processes that are creating similar effects on the animal’s genome. Further analysis of the missense variants revealed 126 deleterious mutations and 132 tolerated mutations. A total of 111 genes were identified from the deleterious mutations and only 5 were among the highly deleterious mutations (SIFT score > 0.01) which include PROS1, EHBP1, LTN1, LRRN4, and FNDC3A. Gene Ontology describes these genes as responsible for different functions associated with animal reproduction, diseases, and memory. This study's results have confirmed the levels of mutation load and the presence of deleterious mutations in Kenyan goats. This can be used as a base to predict the future rate of mutation load to ensure better implementation of conservation programs to avoid an accumulation of deleterious mutations.

Case Report: Novel Mutation of F5 With Maternal Uniparental Disomy Causes Severe Congenital Factor V Deficiency

We summarized two cases of congenital factor V deficiency (FVD) associated with a novel F5 mutation, and analyzed the relationship of the clinical features and genetic characteristics in congenital FVD. Case 1 was a female newborn infant with remarkable bleeding who died of severe intracranial hemorrhage on day 42 after birth. She had significant prolongation of prothrombin time (PT) and activated partial thromboplastin time (APTT). The percentage activity of FV (PFV) was lower than 3% in case 1. The mother of case 1 showed no tendency to bleed. She had mild prolongation of PT and APTT. The PFV was only 43%. Both cases were found to have the same novel mutation in F5, which was c.5419G>A (p.Ala1807Thr) in exon 16. The variant in case 1 was inherited from the mother of case 1. Whole-exome sequencing (WES) also found a splice site mutation: a 103 Mb maternal uniparental disomy (UPD) of 1q21.1-qter in case 1, in which the F5 gene is located in this segment. So case 1 was homozygote and the mother of case 1 was heterozygote. The novel mutation of F5 was predicted to be harmful by bioinformatics software including Sorting Intolerant From Tolerant (SIFT), Polyphen2, LRT, and Mutation Taster. In summary, c.5419G>A (p.Ala1807Thr) in exon 16 of F5 is a pathogenic mutation, which causes severe congenital FVD in homozygote patients.

Whole exome sequencing applied to 42 Han Chinese patients with posterior hypospadias

Hypospadias, a malformation of male external genitalia, is characterized by an aberrant opening of the urethra on the ventral side of the penis. It is considered a complex disorder with both environmental and genetic factors involved in its pathogenesis. To identify the genetic abnormality involved in the pathogenesis of hypospadias, we performed whole exome sequencing (WES) analysis in 42 hypospadias patients with karyotype 46, XY in the Nanhai Meternity&Child Health Hospital of Foshan. All the likely pathogenic variants were confirmed by Sanger sequencing and assessed by Sorting Intolerant from Tolerant (SIFT), PROVEAN, PolyPhen2, ClinPred, LRT, Mutation Assessor, FATHMM, and GERP software. We discovered 27 gene mutations in 20 patients, including eight cases of the SRD5A2 gene, 4 cases of the AR gene, 3 cases of the CYP17A1 gene, 1 case of the WT1 gene, 1 case of the ANOS1 gene, 1 case of the NR5A1 gene, 1 case of the FGFR1 gene, and one case of the DHX37 gene. Our study is the first to describe six novel missense mutations, AR(c.302G > A, c.2593G > T, and c.1705G > T), CYP17A1(c.1298 T > C), FGFR1 (c.995C > T) and DHX37(c.923G > A). In summary, genetic defect detection was useful for early diagnosis of severe hypospadias in the Han Chinese population. Nevertheless, most cases remain unexplained, and the exact pathogenesis of hypospadias still needs further study.

Splice-disrupt genomic variants in prostate cancer

BackgroundSplice-disrupt genomic variants are one of the causes of cancer-causing errors in gene expression. Little is known about splice-disrupt genomic variants.Methods and resultsHere, pattern of splice-disrupt variants was investigated using 21,842,764 genomic variants in different types of prostate cancer. A particular attention was paid to genomic locations of splice-disrupt variants on target genes. HLA-A in prostate cancer, MSR1 in familial prostate cancer, and EGFR in both castration-resistant prostate cancer and metastatic castration-resistant had the highest allele frequencies of splice-disrupt variations. Some splice-disrupt variants, located on coding sequences of NCOR2, PTPRC, and CRP, were solely present in the advanced metastatic castration-resistant prostate cancer. High-risk splice-disrupt variants were identified based on computationally calculated Polymorphism Phenotyping (PolyPhen), Sorting Intolerant From Tolerant (SIFT), and Genomic Evolutionary Rate Profiling (GERP) + + scores as well as the recorded clinical significance in dbSNP database of NCBI. Functional annotation of damaging splice-disrupt variants highlighted important cancer-associated functions, including endocrine resistance, lipid metabolic process, steroid metabolic process, regulation of mitotic cell cycle, and regulation of metabolic process. This is the first study that profiles the splice-disrupt genomic variants and their target genes in prostate cancer. Literature mining based variant analysis highlighted the importance of rs1800716 variant, located on the CYP2D6 gene, involved in a range of important functions, such as RNA spicing, drug interaction, death, and urotoxicity.ConclusionsThis is the first study that profiles the splice-disrupt genomic variants and their target genes in different types of prostate cancer. Unravelling alternative splicing opens a new avenue towards the establishment of new diagnostic and prognostic markers for prostate cancer progression and metastasis.