Genotyping Of Variants Research Articles

Role of Oral Retinoids in Treatment of Acne Vulgaris With a Bioinformatics-Based Perspective of Personalized Medicine.

Acne vulgaris is a skin condition characterized by the inflammation or hyperactivity of sebaceous glands on the skin, which results in the creation of comedones, lesions, nodules, and perifollicular hyperkeratinization. Increased sebum production, follicular blockage, and bacterial colonization may contribute to the disease etiology. Environmental factors, hormonal imbalance, and genetic predisposition can alter the severity of the disease. Its mental and monetary effects can be problematic for the society. In this study, we examined the role of isotretinoin in the treatment of acne vulgaris based on evidence from prior research. This review literature study compiled publications on the treatment of acne vulgaris from 1985 to 2022 based on PubMed and Google Scholar publications. Additional bioinformatics analyses were accompanied by GeneCards, STRING model, and DrugBank databases. These complementary analyses were designed to obtain a better perspective of personalized medicine which is highly required for dose-precise administrations of acne vulgaris treatment. Isotretinoin has been recognized as an effective treatment for acne vulgaris, particularly in cases that have been resistant to previous medications or have resulted in scarring, according to gathered data. Oral isotretinoin inhibits the proliferation of Propionibacterium acne, a critical factor in the development of acne lesions; also, it has been shown to be effective in reducing the number of Propionibacterium-resistant patients and regulating sebum production and reducing sebaceous gland size more effectively than other treatment options resulting in general improvements in skin clarity and acne severity and reduce inflammatory in 90% of patients. In addition to its efficacy, the majority of patients have shown that oral isotretinoin is well tolerated. This review highlights the use of oral retinoids, particularly isotretinoin, as an effective and well-tolerated treatment option for acne vulgaris. It has been proven that oral isotretinoin is useful for achieving long-lasting remission in patients with severe or resistant instances. Despite the fact that oral isotretinoin is related to a number of potential harmful effects, skin dryness was the most common side effect reported by patients that can be managed with the aid of suitable monitoring and drug administration against specific genes identified by genotyping of the susceptible variants of genes involved in TGFβ signaling pathway.

Aligning distant sequences to graphs using long seed sketches.

Sequence-to-graph alignment is crucial for applications such as variant genotyping, read error correction, and genome assembly. We propose a novel seeding approach that relies on long inexact matches rather than short exact matches, and show that it yields a better time-accuracy trade-off in settings with up to a [Formula: see text] mutation rate. We use sketches of a subset of graph nodes, which are more robust to indels, and store them in a k-nearest neighbor index to avoid the curse of dimensionality. Our approach contrasts with existing methods and highlights the important role that sketching into vector space can play in bioinformatics applications. We show that our method scales to graphs with 1 billion nodes and has quasi-logarithmic query time for queries with an edit distance of [Formula: see text] For such queries, longer sketch-based seeds yield a [Formula: see text] increase in recall compared with exact seeds. Our approach can be incorporated into other aligners, providing a novel direction for sequence-to-graph alignment.

The relationship between liver lipase gene polymorphism and the development of endothelial dysfunction in military personnel in extreme climatic conditions

BACKGROUND:The analysis of the association of polymorphism of hepatic lipase gene with vascular wall stiffness in extreme climatic conditions, the development of criteria for the selection and effectiveness of military service in the Arctic zone, depending on the characteristics of the genotype is one of the main tasks of military medicine.
 AIM:The aim is to evaluate the relationship of the polymorphism of theLIPCrs2043085andrs1532085genes with vascular wall stiffness in military personnel in extreme climatic conditions.
 MATERIALS AND METHODS:295 contract servicemen undergoing military service in various climatic and geographical conditions were examined. Participants are divided into three groups: 1stgroup 100 people serving in the Arctic climate zone; 2ndgroup 100 people serving in the temperate climate zone; 3rdgroup 95 people serving in the conditions of the midmountain subtropical zone. The average age of military personnel in all groups was approximately 34 years. All the examined patients were examined, blood pressure and heart rate were measured, regional blood circulation was assessed using the AngioScan-01P device based on the study of the shape of the volumetric pulse wave by a photoplethysmographic sensor, and a molecular genetic study was performed. Genotyping of single-nucleotide variants of theLIPCrs2043085andrs1532085genes was performed using a polymerase chain reaction in real time on an amplifier (RT-PCR) DT-Prime (GC DNA Technology, Russia) using a set of reagents manufactured by the company Syntol (Moscow).
 RESULTS:In servicemen undergoing military service in the Arctic zone, a significant increase in systolic blood pressure, increased vascular stiffness, arterial wall stiffness, and average arterial wall stiffness were revealed. In military personnel undergoing military service in the conditions of the mid-mountain subtropical zone, a significant increase in the stiffness of the artery wall was revealed. On the contrary, high elasticity of the arterial wall has been established in servicemen undergoing military service in a temperate zone. Statistically significant differences in the frequency of occurrence of theLIPSgene (rs2043085) were found in servicemen undergoing military service in various climatic and geographical zones: in the Arctic zone mainly persons with the T/T genotype (up to 53%), in the temperate zone the T/C genotype prevails (up to 43%), in the subtropical zone genotype C/C (up to 40%). The association of the T/T genotype of theLIPSgene (rs2043085) with the stiffness of the vascular wall was established, which corresponds to an excess of the average passport age of the subjects by 67 years, and in the same genotype, according to the type of pulse wave, there is a tendency to increase the stiffness of the artery wall in servicemen aged 34 years with an average military service of 13 years, serving in the Arctic zone for more than 10 years.
 CONCLUSIONS:In the conditions of the Arctic belt, with prolonged exposure (more than 10 years) to adverse environmental factors, the cardiovascular system is depleted, physiological functions are involuted and the body prematurely ages in the form of hypertonic vascular reactions with the progression of excessive vascular stiffness, especially in individuals with theLIPSgene genotype T/T (rs2043085).

Genotyping, characterization, and imputation of known and novel CYP2A6 structural variants using SNP array data.

CYP2A6 metabolically inactivates nicotine. Faster CYP2A6 activity is associated with heavier smoking and higher lung cancer risk. The CYP2A6 gene is polymorphic, including functional structural variants (SV) such as gene deletions (CYP2A6*4), duplications (CYP2A6*1 × 2), and hybrids with the CYP2A7 pseudogene (CYP2A6*12, CYP2A6*34). SVs are challenging to genotype due to their complex genetic architecture. Our aims were to develop a reliable protocol for SV genotyping, functionally phenotype known and novel SVs, and investigate the feasibility of CYP2A6 SV imputation from SNP array data in two ancestry populations. European- (EUR; n = 935) and African- (AFR; n = 964) ancestry individuals from smoking cessation trials were genotyped for SNPs using an Illumina array and for CYP2A6 SVs using Taqman copy number (CN) assays. SV-specific PCR amplification and Sanger sequencing was used to characterize a novel SV. Individuals with SVs were phenotyped using the nicotine metabolite ratio, a biomarker of CYP2A6 activity. SV diplotype and SNP array data were integrated and phased to generate ancestry-specific SV reference panels. Leave-one-out cross-validation was used to investigate the feasibility of CYP2A6 SV imputation. A minimal protocol requiring three Taqman CN assays for CYP2A6 SV genotyping was developed and known SV associations with activity were replicated. The first domain swap CYP2A6-CYP2A7 hybrid SV, CYP2A6*53, was identified, sequenced, and associated with lower CYP2A6 activity. In both EURs and AFRs, most SV alleles were identified using imputation (>70% and >60%, respectively); importantly, false positive rates were <1%. These results confirm that CYP2A6 SV imputation can identify most SV alleles, including a novel SV.

Abstract 1024: Improved cfDNA methylation profiling through correction of misrepaired jagged-ends

Abstract Background: cfDNA methylation profiling allows early cancer detection and tissue-of-origin classification. Recent studies show that end repair (ER) process during double strand library preparation (dsLibP) introduces differential methylation signals between original and repaired sequences. We hypothesized that algorithmic correction of cfDNA jagged-ends could allow superior cfDNA methylation profiling performance, and better preserve double-stranded cfDNA molecules. Methods: We introduce JEEPERS (Jagged-End Error Polishing of Enzymatically misRepaired Sequences), a novel approach for correction of such errors in dsLibP methylation data. Specifically, JEEPERS is not only able to detect and quantify ER-induced errors at JEs, but also to correct them in silico. When using double-stranded unique molecular identifiers, JEEPERS leverages support from 2 sources to identify/correct errors at JEs: 1) complementary strands from individual DNA duplexes, and 2) sibling reads from other, non-jagged cfDNA families. JEEPERS relies on the 5’&amp;gt;3’ polarity of ER-associated errors and JE length profiles to correct R2 for longer fragments and both R1/2 for shorter ones. Results: We quantified the prevalence of such errors at JEs of double-stranded cfDNA molecules in plasma of 2 healthy subjects. We compared library preparations on single- (SPLAT-Seq) vs double-stranded DNA (EM-Seq), and strikingly found ~40% of CpGs to be involved in jagged cfDNA ends and impacted by misrepair during enzymatic ER of dsDNA. This resulted in an artifactual 13.1-16.3% lower global methylation across the genome, an effect that was exaggerated in hypermethylated (hyper) regions (~69% of genome). While ER-associated misrepair resulted in ~10.2% lower CpG methylation within the first 110bp of cfDNA fragments (R1 AUC=0.95, R2 AUC=0.81), when comparing R1/R2, the final 30bp showed even larger biases (13.8-77.4%). Remarkably, JEEPERS could accurately detect and correct these biases and produce highly uniform R1/R2 profiles in EM-Seq on par with SPLAT-Seq, even when considering short cfDNA fragments (&amp;lt;141bp) with substantial JE fractions. We also compared JEEPERS performance with other methods, including simple JE trimming or reliance on R1 alone, finding superior performance by JEEPERS for methylation quantification. Conclusions: ER distorts a large fraction of CpGs across the genome clustering at cfDNA fragment ends, resulting in substantially decreased methylation levels in cfDNA. JEEPERS accurately recovers methylation levels distorted by such misrepair. This not only enables more accurate methylation levels, but also retains cfDNA fragmentation features and duplex information. These advantages allow not only superior cfDNA genotyping of germline and somatic variants, but also enable better identification of allele-specific methylation, hemi-methylation, and gene expression inferences, as relevant for cancer detection. Citation Format: Rui Wang, Emily G. Hamilton, Angela Hui, Diego Almanza, Mohammad S. Esfahani, Maximilian Diehn, Ash A. Alizadeh. Improved cfDNA methylation profiling through correction of misrepaired jagged-ends [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1024.

Cue: a deep-learning framework for structural variant discovery and genotyping.

Structural variants (SVs) are a major driver of genetic diversity and disease in the human genome and their discovery is imperative to advances in precision medicine. Existing SV callers rely on hand-engineered features and heuristics to model SVs, which cannot scale to the vast diversity of SVs nor fully harness the information available in sequencing datasets. Here we propose an extensible deep-learning framework, Cue, to call and genotype SVs that can learn complex SV abstractions directly from the data. At a high level, Cue converts alignments to images that encode SV-informative signals and uses a stacked hourglass convolutional neural network to predict the type, genotype and genomic locus of the SVs captured in each image. We show that Cue outperforms the state of the art in the detection of several classes of SVs on synthetic and real short-read data and that it can be easily extended to other sequencing platforms, while achieving competitive performance.

MiR-122 dysregulation is associated with type 2 diabetes mellitus-induced dyslipidemia and hyperglycemia independently of its rs17669 variant

miR-122 is a liver specific micro-RNA that participates in the regulation of carbohydrate and lipid metabolism. The rs17669 variant of miR-122 is positioned at the flanking region of miR-122 and may affect its stability and maturation. Therefore, this study was aimed to investigate the association of the rs17669 polymorphism with the miR-122 circulating level, risk of type 2 diabetes mellitus (T2DM) development, and biochemical parameters in T2DM patients and matched healthy controls. This study involved 295 subjects (controls: n = 145 and T2DM: n = 150). The rs17669 variant genotyping was done by ARMS-PCR. Serum biochemical parameters including lipid profile, small-dense low density lipoprotein (sdLDL) and glucose were measured by colorimetric kits. Insulin and Glycated hemoglobin (HbA1c) were assayed using ELISA and capillary electrophoresis methods, respectively. miR-122 expression was measured by real-time PCR. There was no significant difference between study groups in terms of allele and genotype distribution (P > 0.05). The rs17669 variant did not have any significant association with miR-122 gene expression and biochemical parameters (P > 0.05). miR-122 expression level in T2DM patients was significantly higher than that in control subjects (5.7 ± 2.4 vs. 1.4 ± 0.78) (P < 0.001). Furthermore, miR-122 fold change had a positive and significant correlation with low-density lipoprotein cholesterol (LDL-C), sdLDL, fasting blood sugar (FBS), and insulin resistance (P < 0.05). It can be concluded that the rs17669 variant of miR-122 is not associated with the miR-122 expression and T2DM-associated serum parameters. Furthermore, it can be suggested that miR-122 dysregulation is involved in T2DM development through inducing dyslipidemia, hyperglycemia, and resistance to insulin.

Liver phenotypes in PCOS: Analysis of exogenous and inherited risk factors for liver injury in two European cohorts.

Fatty liver disease (FLD) is common in women with polycystic ovary syndrome (PCOS). Here, we use non-invasive tests to quantify liver injury in women with PCOS and analyse whether FLD-associated genetic variants contribute to liver phenotypes in PCOS. Prospectively, we recruited women with PCOS and controls at two university centres in Germany and Poland. Alcohol abuse was regarded as an exclusion criterion. Genotyping of variants associated with FLD was performed using TaqMan assays. Liver stiffness measurements (LSM), controlled attenuation parameters (CAP) and non-invasive HSI, FLI, FIB-4 scores were determined to assess hepatic steatosis and fibrosis. A total of 42 German (age range 18-53 years) and 143 Polish (age range 18-40 years) women with PCOS, as well as 245 German and 289 Polish controlswere recruited. In contrast to Polish patients, Germans were older, presented with more severe metabolic profiles and had significantly higher LSM (median 5.9 kPa vs. 3.8 kPa). In the German cohort, carriers of the PNPLA3 p.I148M risk variant had an increased LSM (p=.01). In the Polish cohort, the minor MTARC1 allele was linked with significantly lower serum aminotransferases activities, whereas the HSD17B13 polymorphism was associated with lower concentrations of 17-OH progesterone, total testosterone, and androstenedione (all p < .05). FLD is common in women with PCOS. Its extent is modulated by both genetic and metabolic risk factors. Genotyping of variants associated with FLD might help to stratify the risk of liver disease progression in women suffering from PCOS.

HLA and Non-HLA gene polymorphisms in autoimmune hepatitis patients of North Indian adults.

Autoimmune hepatitis (AIH) is a chronic and progressive disease of the liver. This is a multifactorial autoimmune disease with both environmental factors and genetic factors playing a role in its pathogenesis. Certain environmental agents like viruses, drugs, etc., can trigger the disease in a genetically susceptible individual. The present study was aimed to explore the distribution of human leukocyte antigen (HLA)-DRB1, Protein tyrosine phosphatase non-receptor type 22 (PTPN22) and Cytotoxic T-Lymphocyte-associated protein 4 (CTLA-4) polymorphisms in North Indian adult AIH patients and their associations with clinical and pathological characteristics associated with the disease. A total of 147 subjects with 47 cases and 100 healthy controls were enrolled. Diagnosis of AIH was made by Revised International Autoimmune Hepatitis Group scoring system. HLA-DRB1 Typing was done by Luminex-based reverse Sequence-Specific Oligonucleotide Probing (SSOP). Single nucleotide variant (SNV) genotyping for CTLA-4 and PTPN22 was done by simple probe-based SNP arrays. Results indicated SLA positive AIH patients are poor responders to therapy. A significant predispositional association of HLA-DRB1*03 was observed in AIH patients from the North Indian population (p= 0.0001, OR=4.83 (2.30-10.15). The frequency of the GG genotype of CTLA-4 CT 60 was significantly increased in AIH patients compared to controls. Multinomial analysis showed that CTLA-4 CT 60 is an independent predictor for cases.

Influence of glutathione-related genetic variants on the oxidative stress profile of Mexican patients with psychotic disorders.

The clinical trajectories of patients with psychotic disorders have divergent outcomes, which may result in part from glutathione (GSH)-related high-risk genotypes. We aimed to determine pharmacokinetics of clozapine, GSH levels, GSH peroxidase (GPx) activity, gene variants involved in the synthesis and metabolism of GSH, and their association with psychotic disorders in Mexican patients on clozapine monotherapy and controls. The sample included 75 patients with psychotic disorders on clozapine therapy and 40 paired healthy controls. Plasma clozapine/N-desmethylclozapine, GSH concentrations, and GPx activity were determined, along with genotyping of GCLC and GSTP1 variants and copy number variations of GSTP1, GSTT1, and GSTM1. Clinical, molecular and biochemical data were analyzed with a logistic regression model. GSH levels were significantly reduced and, conversely, GPx activity was higher in PD patients compared to controls. GCLC_GAG-7/9 genotype (OR=4.3, CI95=1.40-14.31, p=0.019) and hetero-/homozygous genotypes of GCLC_rs761142 (OR=6.09, CI95=1.93-22.59, p=0.003) were found as risk factors for psychosis. The genetic variants were not related to clozapine/N-desmethylclozapine levels or to metabolic ratio. GCLC variants were associated with the oxidative stress profile of PD patients raising opportunities for intervention to improve their antioxidant defenses. Further studies with larger samples should explore this proposal.

β‐glucosidase, driven by porcine transthyretin promoter, specific expression in the liver of transgenic mice

AbstractUnder the background of food security, using non‐grain feed instead of corn–soybean‐based feed is an effective measure to alleviate the food‐feed competition. While, non‐grain feeds are often rich in fiber, which cannot be digested by non‐ruminants. Producing heterologous enzymes in non‐ruminants to improve cellulose utilization rate is a new research strategy by transgenic technology. In this study, porcine transthyretin (TTR) promoter, signal peptide‐coding sequence (CDS), Saccharomycopsis fibuligera β‐glucosidase gene (BGL1)‐CDS, 6×His sequences fragments were fused into pGL3‐control vector to generate transgenic vector. Then, transgenic mice were generated by pronuclear microinjection of the linearized expression vectors. Transgenic mice and their offspring were examined by PCR‐based genotyping and copy number variation. Results showed that BGL1 was successfully integrated into the mouse genome and transmitted stably. Furthermore, reverse transcription‐polymerase chain reaction (RT‐PCR), Western blotting, and β‐glucosidase activity assay demonstrated that BGL1 was specifically expressed in the liver, and β‐glucosidase activity significantly increased. In addition, liver weight index, cellular morphology, and collagen fiber content of the liver showed that exogenous gene insertion did not cause any lesions to live. Taken together, our findings suggest that β‐glucosidase driven by TTR promoter was specifically expressed in the liver of transgenic mice.

Exome Array Analysis of 9721 Ischemic Stroke Cases from the SiGN Consortium.

Recent genome wide association studies have identified 89 common genetic variants robustly associated with ischemic stroke and primarily located in non-coding regions. To evaluate the contribution of coding variants, which are mostly rare, we performed an exome array analysis on 106,101 SNPs for 9721 ischemic stroke cases from the SiGN Consortium, and 12,345 subjects with no history of stroke from the Health Retirement Study and SiGN consortium. We identified 15 coding variants significantly associated with all ischemic stroke at array-wide threshold (i.e., p < 4.7 × 10-7), including two common SNPs in ABO that have previously been associated with stroke. Twelve of the remaining 13 variants were extremely rare in European Caucasians (MAF < 0.1%) and the associations were driven by African American samples. There was no evidence for replication of these associations in either TOPMed Stroke samples (n = 5613 cases) or UK Biobank (n = 5874 stroke cases), although power to replicate was very low given the low allele frequencies of the associated variants and a shortage of samples from diverse ancestries. Our study highlights the need for acquiring large, well-powered diverse cohorts to study rare variants, and the technical challenges using array-based genotyping technologies for rare variant genotyping.

Diagnostic and Prognostic Risk Assessment of Heat Shock Protein HSPA1B rs2763979 Gene Variant in Asthma.

Given the significant role the heat shock protein Hsp70 plays in modulating cellular homeostasis in several chronic inflammatory disorders, the genetic variation of the inducible HSP70 (HSPA1B) gene may impact protein expression and disease phenotype. The HSPA1B rs2763979 variant has been associated with multiple inflammatory scenarios, but no previous studies have explored its association with asthma. In this sense, this cross-sectional study enrolled 90 children with asthma and 218 age-/sex-matched healthy volunteers for rs2763979 variant genotyping by TaqMan allelic discrimination analysis. The results were investigated under several genetic models and associated with disease susceptibility and clinicolaboratory data. Overall analysis, including the 308 participants, revealed a higher C allele frequency among patients relative to controls (43.0% vs. 33%, p = 0.006). Furthermore, patients with the C variant initially had a higher risk of asthma under heterozygous (OR = 2.75, 95%CI = 1.46-5.18, p = 0.003), homozygous (OR = 3.35, 95%CI = 1.19-9.39, p = 0.008), dominant (OR = 2.83, 95%CI = 1.52-5.25, p < 0.001), and overdominant (OR = 2.12, 95%CI = 1.20-3.74, p = 0.008) models. However, after employing a 1:1 nearest propensity matching analysis, the studied variant showed only borderline significance with asthma under the dominant model in 71 matched cohorts. Interestingly, patients who carry the rs2763979 CC genotype showed favorable spirometric parameters in terms of better (mean ± SD) forced vital capacity (86.3 ± 7.4 vs. 77.7 ± 6.1 and 75.7 ± 7.2 for CT and TT, respectively, p = 0.021), forced expiratory volume in one second before bronchodilation (60.7 ± 12.9 vs. 54.9 ± 7.6 and 56.1 ± 7.5 for CT and TT, respectively, p = 0.021), and an improvement in peak expiratory flow rate after inhaled salbutamol bronchodilator (p = 0.044) relative to the counterpart genotypes. In conclusion, the HSPA1B rs2763979 variant might have prognostic utility as a genetic marker for asthma in our population. Further larger studies on different ethnicities are recommended to validate the results.

Cloud-native distributed genomic pileup operations.

Pileup analysis is a building block of many bioinformatics pipelines, including variant calling and genotyping. This step tends to become a bottleneck of the entire assay since the straightforward pileup implementations involve processing of all base calls from all alignments sequentially. On the other hand, a distributed version of the algorithm faces the intrinsic challenge of splitting reads-oriented file formats into self-contained partitions to avoid costly data exchange between computational nodes. Here, we present a scalable, distributed, and efficient implementation of a pileup algorithm that is suitable for deploying in cloud computing environments. In particular, we implemented: (i) our custom data-partitioning algorithm optimized to work with the alignment reads, (ii) a novel and unique approach to process alignment events from sequencing reads using the MD tags, (iii) the source code micro-optimizations for recurrent operations, and (iv) a modular structure of the algorithm. We have proven that our novel approach consistently and significantly outperforms other state-of-the-art distributed tools in terms of execution time (up to 6.5x faster) and memory usage (up to 2x less), resulting in a substantial cloud cost reduction. SeQuiLa is a cloud-native solution that can be easily deployed using any managed Kubernetes and Hadoop services available in public clouds, like Microsoft Azure Cloud, Google Cloud Platform or Amazon Web Services. Together with the already implemented distributed range joins and coverage calculations, our package provides end-users with an unified SQL interface for convenient analyzing of population-scale genomic data in an interactive way. https://biodatageeks.github.io/sequila/. Supplementary data are available at Bioinformatics online.

Systems genomics in age-related macular degeneration.

Genomic studies in age-related macular degeneration (AMD) have identified genetic variants that account for the majority of AMD risk. An important next step is to understand the functional consequences and downstream effects of the identified AMD-associated genetic variants. Instrumental for this next step are 'omics' technologies, which enable high-throughput characterization and quantification of biological molecules, and subsequent integration of genomics with these omics datasets, a field referred to as systems genomics. Single cell sequencing studies of the retina and choroid demonstrated that the majority of candidate AMD genes identified through genomic studies are expressed in non-neuronal cells, such as the retinal pigment epithelium (RPE), glia, myeloid and choroidal cells, highlighting that many different retinal and choroidal cell types contribute to the pathogenesis of AMD. Expression quantitative trait locus (eQTL) studies in retinal tissue have identified putative causal genes by demonstrating a genetic overlap between gene regulation and AMD risk. Linking genetic data to complement measurements in the systemic circulation has aided in understanding the effect of AMD-associated genetic variants in the complement system, and supports that protein QTL (pQTL) studies in plasma or serum samples may aid in understanding the effect of genetic variants and pinpointing causal genes in AMD. A recent epigenomic study fine-mapped AMD causal variants by determing regulatory regions in RPE cells differentiated from induced pluripotent stem cells (iPSC-RPE). Another approach that is being employed to pinpoint causal AMD genes is to produce synthetic DNA assemblons representing risk and protective haplotypes, which are then delivered to cellular or animal model systems. Pinpointing causal genes and understanding disease mechanisms is crucial for the next step towards clinical translation. Clinical trials targeting proteins encoded by the AMD-associated genomic loci C3, CFB, CFI, CFH, and ARMS2/HTRA1 are currently ongoing, and a phase III clinical trial for C3 inhibition recently showed a modest reduction of lesion growth in geographic atrophy. The EYERISK consortium recently developed a genetic test for AMD that allows genotyping of common and rare variants in AMD-associated genes. Polygenic risk scores (PRS) were applied to quantify AMD genetic risk, and may aid in predicting AMD progression. In conclusion, genomic studies represent a turning point in our exploration of AMD. The results of those studies now serve as a driving force for several clinical trials. Expanding to omics and systems genomics will further decipher function and causality from the associations that have been reported, and will enable the development of therapies that will lessen the burden of AMD.

Development of pyrosequencing-based assay for genotyping of different coronavirus variants

BACKGROUND: The rapid spread of SARS-CoV-2 virus, which caused the COVID-19 pandemic, and the emergence of new co-circulating antigenic variants require the development and update of subtyping kits and protocols. Pyrosequencing-based protocols are promising approach for detection of single nucleotide polymorphisms.&#x0D; AIM: In this study we designed the assays for genotyping Variants of Concern of the SARS-CoV-2 coronavirus using polymerase chain reaction, followed by determination of the virus variant in the sample by pyrosequencing.&#x0D; MATERIALS AND METHODS: Pyrosequencing assays were designed based on alignment of SARS-CoV-2 sequences. Testing was performed using RNA of SARS-CoV-2 viruses of different lineages (alpha, beta, gamma, delta, and omicron). Pyrosequencing was performed using the PyroMark Q24 system.&#x0D; RESULTS: The protocols of sample preparation and pyrosequencing were developed and tested for sequencing of regions encoding substitutions in amino acid positions: L18F, T19R, T20N; A67V, 69-70; G142D, 143-145; 156-157, R158G; 242-244; K417N/T; L452R; S477N, T478K, E484A/K/Q; H655Y; N679K, P681H/R. The specificity of the system was also evaluated in reactions with a negative control sample (RNA isolated from human nasal swab).&#x0D; CONCLUSIONS: In this study, we developed and initially tested protocol for detecting coronavirus variants (alpha, beta, gamma, delta, and omicron) from samples collected from cell culture, based on the PCR technique, followed by genotyping of the variants by pyrosequencing with PyroMark Q24. The developed protocols may be adjusted to the current epidemiological situation by increasing the number of detectable sites.

Origin and timing of de novo variants implicated in type 2 von Willebrand disease.

Very few studies have shown the real origin and timing of de novo variants (DNV) implicated in von Willebrand disease (VWD). We investigated four families with type 2 VWD. First, we conducted linkage analysis using single nucleotide variant genotyping to recognize the possible provenance of DNV. Second, we performed amplification refractory mutation system-quantitative polymerase chain reaction to confirm the real origin of variant (~0% mutant cells) or presence of a genetic mosaic variant (0%-50% mutant cells) in three embryonic germ layer-derived tissues and sperm cells. Then, three possible timings of DNV were categorized based on the relative likelihood of occurrence according to the number of cell divisions during embryogenesis. Two each with type 2B VWD (proband 1 p.Arg1308Cys, proband 4 p.Arg1306Trp) and type 2A VWD (proband 2 p.Leu1276Arg, proband 3 p.Ser1506Leu) were identified. Variant origins were identified for families 1, 2 and 3 and confirmed to originate from the mother, father and father, respectively. However, the father of family 4 was confirmed to have isolated germline mosaicism with 2.2% mutant sperm cells. Further investigation confirmed the paternal grandfather to be the origin of variant. Thus, we proposed that DNV originating from the two fathers most likely occurred at the single sperm cell, the one originating from the mother occurred at the zygote during the first few cellular divisions; alternatively, in family 4, the DNV most likely occurred at the early postzygotic development in the father. Our findings are essential for understanding genetic pathogenesis and providing accurate genetic counselling.

MMP16 as NSCL ± P Susceptible Gene in Western Han Chinese.

The role of MMP16 in lip development is unclear. This study aimed to identify nonsyndromic cleft lip with or without palate (NSCL ± P) susceptible loci of MMP16 in western Han Chinese. We performed targeted sequencing around MMP16 combined with a 2-phase association analysis on common variants. Phase 2 association analysis was performed with NSCL ± P specific subphenotypes (NSCL and NSCLP). Then we used rare variants burden analysis and genotyping, accompanied by motif analysis. This study was completed in a tertiary medical center. Phase 1 targeted sequencing included 159 patients with NSCL ± P and 542 normal controls; phase 2 included 1626 patients with NSCL ± P (1047 NSCL and 579 NSCLP) and 2255 normal controls. Venous blood samples were collected from patients and used to extract DNA. After Bonferroni correction, phase 1 significant threshold of p-value was 4.28 × 10-5 (0.05/1167 single nucleotide polymorphisms [SNPs]), and phase 2 was .00025 (0.05/200 SNPs). Burden analysis significant threshold p-value was .05. Common variants phase 1 association analysis identified 11 statistically significant SNPs (lowest p = 1.90 × 10-9, odds ratio (OR) = 0.27, 95% CI: 0.17-0.44), phase 2 replication identified 16 SNPs in NSCL ± P (lowest p = 6.26 × 10-6, OR = 0.77, 95% CI: 0.69-0.86) and 9 in NSCL (lowest p = 8.44 × 10-5, OR = 0.76, 95% CI: 0.66-0.87). Rare variants burden analysis showed no significant results, genotyping results showed they were maternally inherited. Our study identified MMP16 susceptible SNPs in NSCL ± P and NSCL, emphasizing its potential role in lip development. Our study also highlighted the importance to perform association analysis with subphenotypes divided.

Detection of Indiscriminate Genetic Manipulation in Thoroughbred Racehorses by Targeted Resequencing for Gene-Doping Control.

The creation of genetically modified horses is prohibited in horse racing as it falls under the banner of gene doping. In this study, we developed a test to detect gene editing based on amplicon sequencing using next-generation sequencing (NGS). We designed 1012 amplicons to target 52 genes (481 exons) and 147 single-nucleotide variants (SNVs). NGS analyses showed that 97.7% of the targeted exons were sequenced to sufficient coverage (depth > 50) for calling variants. The targets of artificial editing were defined as homozygous alternative (HomoALT) and compound heterozygous alternative (ALT1/ALT2) insertion/deletion (INDEL) mutations in this study. Four models of gene editing (three homoALT with 1-bp insertions, one REF/ALT with 77-bp deletion) were constructed by editing the myostatin gene in horse fibroblasts using CRISPR/Cas9. The edited cells and 101 samples from thoroughbred horses were screened using the developed test, which was capable of identifying the three homoALT cells containing 1-bp insertions. Furthermore, 147 SNVs were investigated for their utility in confirming biological parentage. Of these, 120 SNVs were amenable to consistent and accurate genotyping. Surrogate (nonbiological) dams were excluded by 9.8 SNVs on average, indicating that the 120 SNV could be used to detect foals that have been produced by somatic cloning or embryo transfer, two practices that are prohibited in thoroughbred racing and breeding. These results indicate that gene-editing tests that include variant calling and SNV genotyping are useful to identify genetically modified racehorses.

The S267F variant of sodium taurocholate co-transporting polypeptide is strongly associated with resistance to chronic hepatitis B and high level of serum total bile acids

Background and aimsThe sodium taurocholate co-transporting polypeptide (NTCP) is a functional receptor for the hepatitis B virus (HBV), and it is critical for bile acid homeostasis. Previous studies of the association between the S267F variant and chronic hepatitis B (CHB) have generated conflicting results. This study analyzed the correlation between the NTCP S267F variant and CHB susceptibility by using a large sample of participants classified by gender and age, and this study also analyzed the relationship between this variant and the level of serum total bile acids. MethodsIn total, 543 patients with CHB and 429 control subjects underwent S267F variant genotyping using SNaPshot technology. Logistic regression was utilized to evaluate any association of the NTCP S267F variant with CHB susceptibility. ResultsThe S267F variant was inversely correlated with the risk of chronic HBV infection in both the dominant model (GG genotype vs. AG genotype: odds ratio (OR) = 0.46, 95% confidence interval (CI) 0.30–0.71, P < 0.001) and the allele model (G allele vs. A allele: OR = 0.50, 95% CI 0.33–0.76, P = 0.001), and this correlation was not affected by gender and age stratification. The carriers of the heterozygous NTCP variant exhibited higher total bile acids levels than the carriers of wild-type NTCP, regardless of whether they were control subjects or patients with CHB. Heterozygous carriers exhibited reduced hepatitis B e antigen (HBeAg)-positivity rates and had lower ALT, AST, and lg DNA concentrations compared with wild-type carriers in patients with CHB. ConclusionsThe S267F variant of NTCP is a protective factor that reduces the risk of chronic HBV infection and exhibits a higher total bile acids level. Patients with CHB who carry this variant may have a better prognosis than those carrying wild-type NTCP.