Location Of Exons Research Articles

Systematic identification of regulatory elements in Leukemia.

Background: Leukemia is a type of cancer that originates from the bone marrow's blood-forming stem cells. Cancer cells don't follow the usual cellular differentiation and function pathway, so they supersede the healthy cells. Depending on the population and maturity level of abnormal cells, leukemia can be classified as Acute or Chronic. Methodology: We mapped defined leukemia mutations from the COSMIC- The Catalogue of Somatic Mutations to perspective regulatory elements. GeneCards - Human Genes Database and Factorbook were utilized in this work to extract data to analyze gene-centric data related to AML and CML. The chromosomal location, Ensembl version, GRCh37 coordinates, and detailed examination of exons, introns, promoter binding regions, and enhancers were used to investigate co-expressed and differentially expressed genes. Downloaded from Factorbook, the expression levels of healthy and sick genes were compared to known transcription factor binding patterns. Results: When translational control genes become mutated, they begin performing their function excessively, leading to uncontrolled cell proliferation and an accumulation of immature cells in the blood that are unable to perform any function on the one hand and interfering with healthy cells' ability to function optimally due to overpopulation and growth on the other. There is a group of genes whose expression level declines as they are affected by the gene, suggesting that these genes should function as insulators or silencers under normal circumstances. The data for Myc and Max genes were extracted from the Human Genome database and sorted using different techniques to find the common regulatory regions (CRRs). These CRRs were then divided into distinct categories based on the degree to which they co-expressed or their level of expression. Conclusion: Regulatory elements have been identified depending on the values of their expression level and how they are changing concerning the control group. This work will help in understanding the guidelines of blood malignancy at the cellular level by recognizing administrative destinations and are, in this manner, possible focuses for the treatment plans and precession accuracy medication.

Advanced variant classification framework reduces the false positive rate of predicted loss-of-function variants in population sequencing data

Predicted loss of function (pLoF) variants are often highly deleterious and play an important role in disease biology, but many pLoF variants may not result in loss of function (LoF). Here we present a framework that advances interpretation of pLoF variants in research and clinical settings by considering three categories of LoF evasion: (1) predicted rescue by secondary sequence properties, (2) uncertain biological relevance, and (3) potential technical artifacts. We also provide recommendations on adjustments to ACMG/AMP guidelines' PVS1 criterion. Applying this framework to all high-confidence pLoF variants in 22 genes associated with autosomal-recessive disease from the Genome Aggregation Database (gnomAD v.2.1.1) revealed predicted LoF evasion or potential artifacts in 27.3% (304/1,113) of variants. The major reasons were location in the last exon, in a homopolymer repeat, in a low proportion expressed across transcripts (pext) scored region, or the presence of cryptic in-frame splice rescues. Variants predicted to evade LoF or to be potential artifacts were enriched for ClinVar benign variants. PVS1 was downgraded in 99.4% (162/163) of pLoF variants predicted as likely not LoF/not LoF, with 17.2% (28/163) downgraded as a result of our framework, adding to previous guidelines. Variant pathogenicity was affected (mostly from likely pathogenic to VUS) in 20 (71.4%) of these 28 variants. This framework guides assessment of pLoF variants beyond standard annotation pipelines and substantially reduces false positive rates, which is key to ensure accurate LoF variant prediction in both a research and clinical setting.

KRAS Mutation Status in Bulgarian Patients with Advanced and Metastatic Colorectal Cancer.

RAS somatic variants are predictors of resistance to anti-EGFR therapy for colorectal cancer (CRC) and affect the outcome of the disease. Our study aimed to evaluate the frequency of RAS, with a focus on KRAS variants, and their association with tumor location and some clinicopathological characteristics in Bulgarian CRC patients. We prospectively investigated 236 patients with advanced and metastatic CRC. Genomic DNA was extracted from FFPE tumor tissue samples, and commercially available kits were used to detect RAS gene somatic mutations via real-time PCR. A total of 115 (48.73%) patients tested positive for RAS mutations, with 106 (44.92%) testing positive for KRAS mutations. The most common mutation in exon 2 was c.35G>T p.Gly12Val (32.56%). We did not find a significant difference in KRAS mutation frequency according to tumor location. However, patients with a mutation in exon 4 of KRAS were 3.23 times more likely to have a tumor in the rectum than in other locations (95% CI: 1.19-8.72, p = 0.021). Studying the link between tumor location and KRAS mutations in exon 4 is crucial for better characterizing CRC patients. Further research with larger cohorts, especially in rectal cancer patients, could provide valuable insights for patient follow-up and treatment selection.

Exome-based new allele-specific PCR markers and transferability for sodicity tolerance in bread wheat (Triticum aestivum L.).

Targeted exome-based genotype by sequencing (t-GBS), a sequencing technology that tags SNPs and haplotypes in gene-rich regions was used in previous genome-wide association studies (GWAS) for sodicity tolerance in bread wheat. Thirty-nine novel SNPs including 18 haplotypes for yield and yield-components were identified. The present study aimed at developing SNP-derived markers by precisely locating new SNPs on ~180 bp allelic sequence of t-GBS, marker validation, and SNP functional characterization based on its exonic location. We identified unknown locations of significant SNPs/haplotypes by aligning allelic sequences on to IWGSC RefSeqv1.0 on respective chromosomes. Eighteen out of the target 39 SNP locations fulfilled the criteria for producing PCR markers, among which only eight produced polymorphic signals. These eight markers associated with yield, plants m-2, heads m-2, and harvest index, including a pleiotropic marker for yield, harvest index, and grains/head were validated for its amplification efficiency and phenotypic effects in focused identification germplasm strategy (FIGS) wheat set and a doubled haploid (DH) population (Scepter/IG107116). The phenotypic variation explained by these markers are in the range of 4.1-37.6 in the FIGS population. High throughput PCR-based genotyping using new markers and association with phenotypes in FIGS wheat set and DH population validated the effect of functional SNP on closely associated genes-calcineurin B-like- and dirigent protein, basic helix-loop-helix (BHLH-), plant homeodomain (PHD-) and helix-turn-helix myeloblastosis (HTH myb) type -transcription factor. Further, genome-wide SNP annotation using SnpEff tool confirmed that these SNPs are in gene regulatory regions (upstream, 3'-UTR, and intron) modifying gene expression and protein-coding. This integrated approach of marker design for t-GBS alleles, SNP functional annotation, and high-throughput genotyping of functional SNP offers translation solutions across crops and complex traits in crop improvement programs.

Identification of exon locations in DNA sequences using a fractional digital anti-notch filter

Identification of protein coding region (exon) locations in DNA sequences is a fundamental initial step in genomic signal processing (GSP). Several techniques have already been applied to achieve this challenging task. However, improvements are still needed. Transforms-based methods and digital filtering are among those techniques that have been widely used. These techniques exploit the period-3 property of protein coding regions. This paper proposes the application of a narrowband bandpass fractional digital filter to extract more selectively the single frequency component corresponding to the frequency f=1/3 from DNA sequences. The ideal fractional digital anti-notch filter has an infinite amplitude at the central frequency and two tuning parameters which may be used to independently adjust the central frequency and the amplitude frequency response. The ideal filter has been approximated and implemented efficiently as an infinite impulse response (IIR) filter. The effectiveness of the proposed method has been assessed in terms of common performance evaluation metrics computed from the results obtained using DNA sequences taken from the National Center for Biotechnology Information (NCBI) and HMR195 datasets using different numerical transformations including Voss mapping and electron–ion potential (EIIP) representation. In addition to overcome the problem of sliding window size encountered in transform-based methods, comparison with existing state-of-the-art methods for exon location identification has demonstrated superiority of the proposed method on benchmark datasets.

Molecular Divergence upon EGFR-TKI Resistance Could Be Dependent on the Exon Location of the Original EGFR-Sensitizing Mutation.

Tumor molecular profiling upon disease progression enables investigations of the tumor evolution. Next-generation sequencing (NGS) of liquid biopsies constitutes a noninvasive readily available source of tumor molecular information. In this study, 124 plasma samples from advanced EGFR-positive NSCLC patients, treated with a first-line EGFR tyrosine kinase inhibitor (EGFR-TKI) were collected upon disease progression. The circulating cell-free DNA (cfDNA) was sequenced using the Oncomine Pan-Cancer Cell-Free Assay™. Excluding EGFR mutations, the most frequently mutated gene was TP53 (57.3%), followed by APC (11.3%), FGFR3 (7.3%), and KRAS (5.6%). Different molecular alterations were observed upon disease progression depending on the location of the original EGFR-sensitizing mutation. Specifically, the detection of the p.T790M mutation was significantly associated with the presence of exon 19 mutations in EGFR (Fisher p-value: 0.028). All KRAS activating mutations (n = 8) were detected in tumors with EGFR mutations in exons 18 and 21 (Fisher p-value < 0.001). Similarly, mutations in NRAS and HRAS were more frequently detected in samples from tumors harboring mutations in exons 18 or 21 (Fisher p-value: 0.050 and Fisher p-value: 0.099, respectively). In conclusion, our data suggest that the mechanisms underlying EGFR-TKI resistance could be dependent on the exon location of the original EGFR-sensitizing mutation.

Shared and Distinct Functional Effects of Patient-Specific Tbr1 Mutations on Cortical Development.

T-Box Brain Transcription Factor 1 (TBR1) plays essential roles in brain development, mediating neuronal migration, fate specification, and axon tract formation. While heterozygous loss-of-function and missense TBR1 mutations are associated with neurodevelopmental conditions, the effects of these heterogeneous mutations on brain development have yet to be fully explored. We characterized multiple mouse lines carrying Tbr1 mutations differing by type and exonic location, including the previously generated Tbr1 exon 2-3 knock-out (KO) line, and we analyzed male and female mice at neonatal and adult stages. The frameshift patient mutation A136PfsX80 (A136fs) caused reduced TBR1 protein in cortex similar to Tbr1 KO, while the missense patient mutation K228E caused significant TBR1 upregulation. Analysis of cortical layer formation found similar defects between KO and A136fs homozygotes in their CUX1+ and CTIP2+ layer positions, while K228E homozygosity produced layering defects distinct from these mutants. Meanwhile, the examination of cortical apoptosis found extensive cell death in KO homozygotes but limited cell death in A136fs or K228E homozygotes. Despite their discordant cortical phenotypes, these Tbr1 mutations produced several congruent phenotypes, including anterior commissure reduction in heterozygotes, which was previously observed in humans with TBR1 mutations. These results indicate that patient-specific Tbr1 mutant mice will be valuable translational models for pinpointing shared and distinct etiologies among patients with TBR1-related developmental conditions.SIGNIFICANCE STATEMENT Mutations of the TBR1 gene increase the likelihood of neurodevelopmental conditions such as intellectual disability and autism. Therefore, the study of TBR1 can offer insights into the biological mechanisms underlying these conditions, which affect millions worldwide. To improve the modeling of TBR1-related conditions over current Tbr1 knock-out mice, we created mouse lines carrying Tbr1 mutations identical to those found in human patients. Mice with one mutant Tbr1 copy show reduced amygdalar connections regardless of mutation type, suggesting a core biomarker for TBR1-related disorders. In mice with two mutant Tbr1 copies, brain phenotypes diverge by mutation type, suggesting differences in Tbr1 gene functionality in different patients. These mouse models will serve as valuable tools for understanding genotype-phenotype relationships among patients with neurodevelopmental conditions.

Discovery of Novel Variants on the CHD7 Gene: A Case Series of CHARGE Syndrome.

Background: CHARGE syndrome (CS) is a single-gene genetic disorder with multiple organ malformations caused by a variant of the chromodomain helicase DNA-binding protein 7 (CHD7) gene on chromosome 8q12.1. In this study, we aimed to investigate new variants that have emerged in these cases compared with typical CS and the relationship between the genes and phenotypes. Methods: Patients with suspected genetic diseases were subjected to Whole Exome Sequencing (WES) at a genetics laboratory in Guangzhou. The average sequencing coverage depth was >200 ×, and 96% was >20 ×. The variant interpretation was manipulated according to the American College of Medical Genetics (ACMG) guidelines. Molecular data on databases for ClinVar and CHD7 were also collected and collated. We reviewed the currently described CHD7 variants and analyzed the genetic variation and phenotypic heterogeneity. Results: Data of 12 patients with CS from four hospitals in China were collected. According to gestational age, most of them (8/12) were near-term babies with a lower birth weight than their peers, averaging 2.62 kg. In this study, the most common phenotypes were respiratory tract malformations (11/12), heart malformations (10/12), and central nervous system malformations (9/12). Two fetuses were confirmed to have brain or heart abnormalities during prenatal testing, while 10/12 were found to have abnormalities during prenatal testing. The maximum Acute Physiology and Chronic Health Evaluation (APACHE II) score at admission was 19, and the average was 11.58. Five variants in the CHD7 gene c.7012C > T (p.Q2338*), c.7868delC (p.P2623Rfs*16), c.5405-3C > G, c.6936 + 2T > C, and c.8077-2A > G) were novel and were located in exons 33, 36, and introns 25, 32, and 37, respectively. There may be a positive correlation between exon location and phenotype. Conclusion: Five novel variants were discovered. These expanded the mutational spectrum of the CHD7 gene and the phenotype of CS. There may be a correlation between the new mutation sites and the phenotype, which has some reference value for the evaluation of mutation sites.

Location of EGFR exon 20 insertions matters

EGFR exon 20 insertions represent a subgroup of NSCLC patients posed with a therapy dilemma. In this issue of Cancer Cell, Elamin and colleagues demonstrate that only insertions localized in the near loop respond to poziotinib. Pharmacological inhibition of spindle assembly checkpoint components inhibits tumor growth in poziotinib-resistant exon 20 insertions.

P-264 The molecular-metabolic interplay in metastatic gastrointestinal stromal tumors (GISTs): The predictive role of body mass index

KIT exon 11 Pathogenic Variants (PVs) are the most frequent mutations in Gastrointestinal Stromal Tumors (GISTs). These patients represent a heterogeneous subgroup in terms of biological and clinical behavior: despite most GISTs with KIT exon 11 mutations are highly sensitive to front-line imatinib, the Progression Free Survival (PFS) may vary greatly. We investigated the predictive role of Body Mass Index (BMI), Neutrophil–Lymphocyte Ratio (NLR), and type and codon location of KIT exon 11 mutations in metastatic GIST patients treated with first-line imatinib 400 mg/die. Clinico-pathological characteristics, mutational status, BMI and NLR, were analyzed from a GIST System database prospectively collected. The primary outcome investigated was the Time to Treatment Failure (TTF). We classified the patients in 2 groups: i) KIT Exon 11 deletion or insertion/deletion in codons 557 and/or 558 (named “D-557/8”); ii) other than D-557/8 mutations (named “No-D-557/8”). The NLR was recorded from the routinely performed blood cell count as the absolute count of neutrophils divided by the absolute count of lymphocytes from peripheral blood samples collected at baseline. Sixty (60) KIT exon 11 mutated patients were included in the study: 25 (31.3%) showed exon 11 deletion or delins involving 557 and/or 558 codons (D-557/8 group), and 35 patients (43.7%) had a deletion in codons other than 557/558 or other PV types (duplication, insertion or SNV)(No-D-557/8 group). A total of 41 events (progression or death) were observed (68.3%): 18 events in the D-557/8 group of 25 patients (72%); 23 events in the No-D-557/8 group of 35 patients (65.7%). Overall median TTF was 37 months (95% confidence interval [CI]: 26.8-47.1). Median TTF was 24 months (95% CI: 21.3, 26.7) for the D-557/8 Group, and 49 months (95% CI: 39.4, 58.6) for the No-D-557/8 Group (p 25 (median TTF: 57.4 months (range 32-92) vs 24.2 months (range 3-45); p=0.001). In the KIT exon 11 mutated patients, who are the most common molecular-based subgroup of advanced GIST patients, our results reveal the important impact of BMI on TTF. These data support the functional cross-talk between metabolic and molecular features also in GISTs, paradigmatic model of oncogene addiction, and represent the rationale to better investigate whether factors of metabolic interest, such as BMI, could have a further impact on response to treatment.

Genome-Wide Investigation of G6PDH Gene in Strawberry: Evolution and Expression Analysis during Development and Stress.

As one of the key enzymes in the pentose phosphate pathway (PPP), glucose-6-phosphate dehydrogenase (G6PDH) provides NADPH and plays an important role in plant development and stress responses. However, little information was available about the G6PDH genes in strawberry (Fragaria × ananassa). The recent release of the whole-genome sequence of strawberry allowed us to perform a genome-wide investigation into the organization and expression profiling of strawberry G6PDH genes. In the present study, 19 strawberry G6PDH genes (FaG6PDHs) were identified from the strawberry genome database. They were designated as FaG6PDH1 to FaG6PDH19, respectively, according to the conserved domain of each subfamily and multiple sequence alignment with Arabidopsis. According to their structural and phylogenetic features, the 19 FaG6PDHs were further classified into five types: Cy, P1, P1.1, P2 and PO. The number and location of exons and introns are similar, suggesting that genes of the same type are very similar and are alleles. A cis-element analysis inferred that FaG6PDHs possessed at least one stress-responsive cis-acting element. Expression profiles derived from transcriptome data analysis exhibited distinct expression patterns of FaG6PDHs genes in different developmental stages. Real-time quantitative PCR was used to detect the expression level of five types FaG6PDHs genes and demonstrated that the genes were expressed and responded to multiple abiotic stress and hormonal treatments.

Genotype\u2013phenotype correlations for COL4A3\u2013COL4A5 variants resulting in Gly substitutions in Alport syndrome

Alport syndrome is the commonest inherited kidney disease and nearly half the pathogenic variants in the COL4A3–COL4A5 genes that cause Alport syndrome result in Gly substitutions. This study examined the molecular characteristics of Gly substitutions that determine the severity of clinical features. Pathogenic COL4A5 variants affecting Gly in the Leiden Open Variation Database in males with X-linked Alport syndrome were correlated with age at kidney failure (n = 157) and hearing loss diagnosis (n = 80). Heterozygous pathogenic COL4A3 and COL4A4 variants affecting Gly (n = 304) in autosomal dominant Alport syndrome were correlated with the risk of haematuria in the UK 100,000 Genomes Project. Gly substitutions were stratified by exon location (1 to 20 or 21 to carboxyl terminus), being adjacent to a non-collagenous region (interruption or terminus), and the degree of instability caused by the replacement residue. Pathogenic COL4A5 variants that resulted in a Gly substitution with a highly destabilising residue reduced the median age at kidney failure by 7 years (p = 0.002), and age at hearing loss diagnosis by 21 years (p = 0.004). Substitutions adjacent to a non-collagenous region delayed kidney failure by 19 years (p = 0.014). Heterozygous pathogenic COL4A3 and COL4A4 variants that resulted in a Gly substitution with a highly destabilising residue (Arg, Val, Glu, Asp, Trp) were associated with an increased risk of haematuria (p = 0.018), and those adjacent to a non-collagenous region were associated with a reduced risk (p = 0.046). Exon location had no effect. In addition, COL4A5 variants adjacent to non-collagenous regions were over-represented in the normal population in gnomAD (p < 0.001). The nature of the substitution and of nearby residues determine the risk of haematuria, early onset kidney failure and hearing loss for Gly substitutions in X-linked and autosomal dominant Alport syndrome.

Mutations of p53 Gene in Canine Sweat Gland Carcinomas Probably Associated with UV Radiation.

IntroductionApocrine sweat gland carcinomas (ASGCs) are rare malignant skin tumours in dogs and humans. The literature published so far focuses mostly on the clinico-epidemiological aspect of these tumours, but little is known about their pathogenesis. In this study we aimed to determine whether the p53 gene is involved in the carcinogenesis of the apocrine sweat gland in dogs and whether ultraviolet radiation (UV) is related to it.Material and MethodsForty canine ASGCs were submitted to laser capture microdissection to isolate neoplastic cells, from which DNA was subsequently extracted. PCR amplification and sequencing of p53 exons 2–8 was then performed, followed by computer analysis of the obtained sequences.ResultsSixteen mutations within the p53 gene were found in 13 tumours. The mutations involved C → T, T → C, G → A, and CC → TT transitions, C → G transversion and adenine deletion, which are gene alteration types known to be related to UV radiation in the process of skin carcinogenesis in humans. Six of the thirteen tumour cases displayed the C → T transitions in the same location in exon 4 and three of the thirteen cases displayed T → C in the same location in exon 5.ConclusionThe results of the present study indicate both the participation of the p53 gene and the influence of UV radiation in the formation of ASGCs in dogs.

The architecture of the simian varicella virus transcriptome.

Primary infection with varicella-zoster virus (VZV) causes varicella and the establishment of lifelong latency in sensory ganglion neurons. In one-third of infected individuals VZV reactivates from latency to cause herpes zoster, often complicated by difficult-to-treat chronic pain. Experimental infection of non-human primates with simian varicella virus (SVV) recapitulates most features of human VZV disease, thereby providing the opportunity to study the pathogenesis of varicella and herpes zoster in vivo. However, compared to VZV, the transcriptome and the full coding potential of SVV remains incompletely understood. Here, we performed nanopore direct RNA sequencing to annotate the SVV transcriptome in lytically SVV-infected African green monkey (AGM) and rhesus macaque (RM) kidney epithelial cells. We refined structures of canonical SVV transcripts and uncovered numerous RNA isoforms, splicing events, fusion transcripts and non-coding RNAs, mostly unique to SVV. We verified the expression of canonical and newly identified SVV transcripts in vivo, using lung samples from acutely SVV-infected cynomolgus macaques. Expression of selected transcript isoforms, including those located in the unique left-end of the SVV genome, was confirmed by reverse transcription PCR. Finally, we performed detailed characterization of the SVV homologue of the VZV latency-associated transcript (VLT), located antisense to ORF61. Analogous to VZV VLT, SVV VLT is multiply spliced and numerous isoforms are generated using alternative transcription start sites and extensive splicing. Conversely, low level expression of a single spliced SVV VLT isoform defines in vivo latency. Notably, the genomic location of VLT core exons is highly conserved between SVV and VZV. This work thus highlights the complexity of lytic SVV gene expression and provides new insights into the molecular biology underlying lytic and latent SVV infection. The identification of the SVV VLT homolog further underlines the value of the SVV non-human primate model to develop new strategies for prevention of herpes zoster.

Phenotypic implications of pathogenic variant types in Pompe disease.

Newborn screening and therapies for Pompe disease (glycogen storage disease type II, acid maltase deficiency) will continue to expand in the future. It is thus important to determine whether enzyme activity or type of pathogenic genetic variant in GAA can best predict phenotypic severity, particularly the presence of infantile-onset Pompe disease (IOPD) versus late-onset Pompe disease (LOPD). We performed a retrospective analysis of 23 participants with genetically-confirmed cases of Pompe disease. The following data were collected: clinical details including presence or absence of cardiomyopathy, enzyme activity levels, and features of GAA variants including exon versus intron location and splice site versus non-splice site. Several combinations of GAA variant types for individual participants had significant associations with disease subtype, cardiomyopathy, age at diagnosis, gross motor function scale (GMFS), and stability of body weight. The presence of at least one splice site variant (c.546 G > C/p.T182 = , c.1076-22 T > G, c.2646 + 2 T > A, and the classic c.-32-13T > G variant) was associated with LOPD, while the presence of non-splice site variants on both alleles was associated with IOPD. Enzyme activity levels in isolation were not sufficient to predict disease subtype or other major clinical features. To extend the findings of prior studies, we found that multiple types of splice site variants beyond the classic c.-32-13T > G variant are often associated with a milder phenotype. Enzyme activity levels continue to have utility for supporting the diagnosis when the genetic variants are ambiguous. It is important for newly diagnosed patients with Pompe disease to have complete genetic, cardiac, and neurological evaluations.

The Worldwide Landscape of Variants in the Androgen Receptor Gene Related to Androgen Insensitivity Syndrome: An Integrative Analysis

Androgen Insensitivity Syndrome (AIS) is an X-linked genetic disease and it is the most common cause of 46,XY DSD. It is divided into 3 phenotypes: complete (CAIS), partial (PAIS), and mild (MAIS). To analyse the landscape of AR variants in AIS we collected all AR variants reported among AIS in the literature (Pubmed, EMBASE, Medline) and websites (ensemble, HGMD, ClinVar). They were analyzed according to phenotype, exon location, domain, amino acid (aa) conservation, sex assignment, external genitalia virilization (EMS score), molecular and functional studies. Conservation analysis of the AR were performed using CONSURF plataform. To test our hypothesis that non-synonymous AR variants could also impact on splicing, we used both ESEfinder and Human Splicing Finder 3.1. We founded 901 individuals with AIS: CAIS = 565 (62.7%); PAIS = 282 (31.3%); and MAIS = 54 (6%). They had 465 different AR variants: CAIS = 290 (62.3%); PAIS = 135 (29.1%); and MAIS = 40 (8.6%). Among MAIS and PAIS, most variants were at LDB domain (22 out 40 = 55% and 84 out 135 = 62.2%, respectively) whereas they were at NTD domain among CAIS (129 out 290 = 44.5%). Most were missense (81%). However, small indels (11%), nonsense (3%), splicing sites (4%) and large deletions (1%) were all reported. Non-synonymous AR variants accounting for 60%, 96%, and 100% of CAIS, PAIS, and MAIS, respectively. Synonymous AR variants were rarely found (n=3). In 81% only the AR sequencing was performed. The remaining was detected by WES (18%) or WGS (1%). Deep intronic variant was detected in PAIS (n=1) while variants in the 5’UTR of the AR gene in both PAIS and CAIS (n=2). Most AR variants were located at conserved aa (78%), but AR variants at non-conserved aa were more frequently indels (p<.01). Functional studies were found in 38%, mostly showing reduced AR expression. Among PAIS, 48% (n=134) were assigned as male at birth. The median EMS was 5 (95% CI, 5-7) in those assigned as male while it was 3.2 (95% CI, 2-6) in those assigned as female (p<.01). The median of EMS score was lower in variants at NTD domain (2.8, 95% CI, 0-7). We identified 34 AR variants causing more than one AIS phenotype (mostly CAIS and PAIS) and 6 AR variants causing all of three AIS phenotypes. In silico analysis suggests potential to disrupt normal AR splicing in 18 (53%) by creating new acceptor or donor splicing sites (n=11) or exonic splicing signals (n=7). More severe AR variants are related to CAIS. Most AR variants were reported only based on AR sequencing. Therefore, the functional pathogenicity of these variants remains unclear. Further studies including WGS could help to expand the molecular diagnosis of AIS. There is phenotype variability in AIS. So, sex assignment of patients with PAIS cannot be based on a specific identified AR gene mutation. There is potential to alter splicing among non-synonymous AR variants, which could be an explanation for phenotype variability in AIS.

A Novel Approach For Identification Of Exon Locations In DNA Sequences Using GLC Window

The application of signal processing techniques for identification of exons in Deoxyribonucleic acid (DNA) sequence is a challenging task. The objective of this paper is to introduce a combinational window approach for locating exons in DNA sequence. In contrast to the traditional single window function for evaluation of short time Fourier transform (STFT), this work proposes a novel method for evaluating STFT coefficients using a combinational window function comprising of Gaussian, Lanczos and Chebyshev (GLC) windows. The chosen combinational window GLC has the highest relative side lobe attenuation values compared to other window functions introduced by various researchers. The proposed algorithm incorporates GLC window function for evaluating STFT coefficients and in the design of FIR bandpass filter. Simulation results revealed its effectiveness in improving the evaluation parameters like Sensitivity, Specificity, Accuracy, Area under curve (AUC), Discrimination Measure (DM). Furthermore, the proposed algorithm has been applied successfully to some universal benchmark datasets like C. elegans, Homosapiens, etc., The proposed method has shown to be an efficient approach for the prediction of protein coding regions compared to other existing methods. All the simulations are done using the MATLAB 2016a.

Type and Gene Location of KIT Mutations Predict Progression-Free Survival to First-Line Imatinib in Gastrointestinal Stromal Tumors: A Look into the Exon.

Simple SummaryAlthough effective in the majority of patients, the progression-free survival (PFS) to imatinib treatment can vary widely in effectiveness. Based on the known predictive role of tyrosine kinase (KIT) and platelet-derived growth factor receptor α (PDGRA) tumor genotypes, the differential clinical response to first-line imatinib treatment might be related to the different types and gene locations of the mutations. In our study, metastatic patients with gastrointestinal stromal tumors (GIST)-carrying KIT exon 11 deletion or a deletion/insertion involving codons 557/558 showed significantly shorter PFS to imatinib compared with those with deletion in codons other than 557/558 and patients with exon 11 duplication, insertion or single nucleotide variants (SNVs). Conversely, the latter subgroup showed the longest PFS first-line to imatinib. These results highlight the predictive role of pathogenic variant (PV) type and codon location in GIST, and can support stratification via mutational status in future clinical trials.In previous studies on localized GISTs, KIT exon 11 deletions and mutations involving codons 557/558 showed an adverse prognostic influence on recurrence-free survival. In the metastatic setting, there are limited data on how mutation type and codon location might contribute to progression-free survival (PFS) variability to first-line imatinib treatment. We analyzed the type and gene location of KIT and PDGFRA mutations for 206 patients from a GIST System database prospectively collected at an Italian reference center between January 2005 and September 2020. By describing the mutational landscape, we focused on clinicopathological characteristics according to the critical mutations and investigated the predictive role of type and gene location of the KIT exon 11 mutations in metastatic patients treated with first-line imatinib. Our data showed a predictive impact of KIT exon 11 pathogenic variant on PFS to imatinib treatment: patients with deletion or insertion/deletion (delins) in 557/558 codons had a shorter PFS (median PFS: 24 months) compared to the patients with a deletion in other codons, or duplication/insertion/SNV (median PFS: 43 and 49 months, respectively) (p < 0.001). These results reached an independent value in the multivariate model, which showed that the absence of exon 11 deletions or delins 557/558, the female gender, primitive tumor diameter (≤5 cm) and polymorphonuclear leucocytosis (>7.5 109/L) were significant prognostic factors for longer PFS. Analysis of the predictive role of PDGFRA PVs showed no significant results. Our results also confirm the aggressive biology of 557/558 deletions/delins in the metastatic setting and allow for prediction at the baseline which GIST patients would develop resistance to first-line imatinib treatment earlier.

Dissecting the contribution of single nucleotide polymorphisms in CCR9 and CCL25 genomic regions to the celiac disease phenotype

Purpose and objectivesGiven their role in homing immune cells to the intestine, CC motif chemokine receptor 9 (CCR9) and its specific ligand CC motif chemokine ligand 25 (CCL25) are interesting candidate genes for celiac disease. These genes are located in regions previously shown to be associated with or linked to celiac disease, but no investigations on their association with various celiac disease phenotypes have so far been conducted. Here we studied such associations of both genotyped and imputed single nucleotide polymorphisms (SNPs) with either regulatory function or exonic location of the CCR9 and CCL25 loci. ResultsExploiting a carefully phenotyped cohort of 625 celiac disease patients and 1817 non-celiac controls, we identified that multiple SNPs with predicted regulatory function (RegulomeDB score ≤3a and/or eQTL effect) located between 100 kB upstream and downstream of CCR9 and CCL25 are associated with celiac disease and/or selected phenotypes. Of the genotyped SNPs in the CCR9 loci, rs213360 with an eQTL effect on CCR9 expression in blood was associated with celiac disease and all investigated phenotypes except high HLA risk. Rs1545985 with an eQTL on CCR9 expression and rs7652331 and rs12493471, both with RegulomeDB score ≤3a, were all associated with gastrointestinal symptoms and malabsorption and the latter additionally with anemia. The genotyped CCL25 SNPs rs952444 and rs882951, with RegulomeDB scores 1d and 1f respectively and eQTL effect on CCL25 expression in small intestine, were associated with gastrointestinal symptoms and malabsorption. The CCL25 SNP rs2303165 identified in sequencing followed by imputation was associated with partial villous atrophy. However, the association did not pass the permutation based multiple testing correction (PEMP2 > 0.05). ConclusionsWe conclude that SNPs in the region of CCR9 and CCL25 with predicted functional effect or exonic localization likely contribute only modestly to various celiac disease phenotypes.

Genes containing hexanucleotide repeats resembling C9ORF72 and expressed in the central nervous system are frequent in the human genome

More than 40 human diseases, mainly diseases affecting the central nervous system, are caused by the expansion of unstable nucleotide repeats. Repeats of sequences like (CAG)n present in different genes can be responsible for various diseases of the central nervous system. An expanded hexanucleotide repeat (GGGGCC)n in the C9ORF72 gene has been characterized as the most frequent genetic cause of amyotrophic lateral sclerosis and frontotemporal lobar dementia. In this study, we performed a genome-wide analysis in the human genome and identified 74 genes containing this precise hexanucleotide repeat, with a preference for a location in exon 1 or intron 1, similar to the C9ORF72 gene. A total of 36 of these 74 genes may be of interest as candidates in neurodevelopmental or neurodegenerative diseases, based on their function.