Association between SNCA Intron and genetic predisposition to sporadic Parkinson's disease: a meta-analysis based on 49576 individuals

Background The aetiology of Parkinson's disease (PD) is indistinct, but previous studies of different ethnicities have shown that genetic variations in synuclein alpha (SNCA) have an essential character in the risk of PD. The relation between SNCA intronic single nucleotide polymorphisms (SNPs) and the risk of PD is unclear. Based on the general population and five ethnic groups, this article managed a meta-analysis about the connection of SNCA intronic SNPs with the PD genetic predisposition. Methods This study was implemented according to the 24-step guideline, with strict criteria. The analysis was performed using Stata 16.0 software. Five genetic models were used to analyze the strength of the association, which was quantified by OR value and 95% CI. Results We included 15433 cases and 34143 controls from 31 articles. 6 SNPs in the intron region were screened, and 5 SNPs were statistically significant. Three variants augmented the PD susceptibility (rs2736990, rs3822086, and rs3857059), and two SNPs decreased the risk (rs356186 and rs7684318). Subgroup analysis showed that rs2736990 and rs3822086 carriers added the PD genetic predisposition in the East Asian group. European and Latin group carrying rs3857059 and rs2736990 is the high-risk populations of PD. Conclusions This study finally found 5 SNCA intronic SNPs related to the risk of PD. And racial factors should not be ignored.

Intronic TP53 Polymorphisms Are Associated with Increased Δ133TP53 Transcript, Immune Infiltration and Cancer Risk

We investigated the influence of selected TP53 SNPs in exon 4 and intron 4 on cancer risk, clinicopathological features and expression of TP53 isoforms. The intron 4 SNPs were significantly over-represented in cohorts of mixed cancers compared to three ethnically matched controls, suggesting they confer increased cancer risk. Further analysis showed that heterozygosity at rs1042522(GC) and either of the two intronic SNPs rs9895829(TC) and rs2909430(AG) confer a 2.34–5.35-fold greater risk of developing cancer. These SNP combinations were found to be associated with shorter patient survival for glioblastoma and prostate cancer. Additionally, these SNPs were associated with tumor-promoting inflammation as evidenced by high levels of infiltrating immune cells and expression of the Δ133TP53 and TP53β transcripts. We propose that these SNP combinations allow increased expression of the Δ133p53 isoforms to promote the recruitment of immune cells that create an immunosuppressive environment leading to cancer progression.

P898Association of acroparesthesias and angiokeratomas with the alpha-galactosidase A gene polymorphisms in females with hypertrophic cardiomyopathy

Introduction Clinical implications of different single nucleotide polymorphisms (SNPs) in the alpha-galactosidase A gene (α-GLA) as potential cause of symptoms and organ manifestations similarly to those seen in Fabry disease (FD) remain unclear. Purpose To study the prevalence of FD among patients with hypertrophic cardiomyopathy (HCM), as well as to evaluate the impact of polymorphic variants of the α-GLA gene on extracardiac manifestations in females with HCM. Methods The study included 321 patients with left ventricular hypertrophy ≥15 mm. 24 of the 321 patients (males (n=15) and females (n=9)) presented with HCM phenotype and extracardiac features suggestive of FD: acroparesthesias and pain in hands and feet, stroke at a young age, angiokeratomas, kidney damage (microalbuminuria, proteinuria, decreased glomerular filtration rate), suspicion for X-linked inheritance. This patients carried out screening for FD. A combined enzymatic and genetic strategy was used, measuring the activity of α-D-galactosidase A by tandem mass spectrometry (ESI-MS/MS) and genotyping the α-GLA (in females) in dried filter-paper blood spot samples. Results We haven't identified any pathogenic genetic variants in the α-GLA gene. However, in three patients with HCM, the two intronic SNPs within the α-GAL gene (c.640–16A>G [rs2071397] and c.1000–22C>T [rs2071228]) were identified. Patient no. 1, a 64-year-old female, was admitted to our clinic for the diagnosis of obstructive HCM. She also had a transient 2:1 second degree atrioventricular block, an Adams-Stokes attack, angiokeratomas and left median cerebral artery lacunar stroke in middle age. In case no. 2, a 75-year-old female, were verified obstructive HCM, a 1st degree atrioventricular block, paroxysms of nonsustained ventricular tachycardia, acroparesthesia, pain in hands and angiokeratomas. In patient no. 3, a 41-year-old female, were established combined phenotypes (nonobstructive hypertrophic + restrictive), acroparesthesia, pain in hands and angiokeratomas. Conclusions In females with HCM, the intronic SNPs (rs2071397 and rs2071228) in the α-GLA gene can be associated with angiokeratomas and acroparesthesias.

Complete RHD next-generation sequencing: establishment of reference RHD alleles

The Rh blood group system (ISBT004) is the second most important blood group after ABO and is the most polymorphic one, with 55 antigens encoded by 2 genes, RHD and RHCE. This research uses next-generation sequencing (NGS) to sequence the complete RHD gene by amplifying the whole gene using overlapping long-range polymerase chain reaction (LR-PCR) amplicons. The aim was to study different RHD alleles present in the population to establish reference RHD allele sequences by using the analysis of intronic single-nucleotide polymorphisms (SNPs) and their correlation to a specific Rh haplotype. Genomic DNA samples (n = 69) from blood donors of different serologically predicted genotypes including R1R1 (DCe/DCe), R2R2 (DcE/DcE), R1R2 (DCe/DcE), R2RZ (DcE/DCE), R1r (DCe/dce), R2r (DcE/dce), and R0r (Dce/dce) were sequenced and data were then mapped to the human genome reference sequence hg38. We focused on the analysis of hemizygous samples, as these by definition will only have a single copy of RHD. For the 69 samples sequenced, different exonic SNPs were detected that correlate with known variants. Multiple intronic SNPs were found in all samples: 21 intronic SNPs were present in all samples indicating their specificity to the RHD*DAU0 (RHD*10.00) haplotype which the hg38 reference sequence encodes. Twenty-three intronic SNPs were found to be R2 haplotype specific, and 15 were linked to R1, R0, and RZ haplotypes. In conclusion, intronic SNPs may represent a novel diagnostic approach to investigate known and novel variants of the RHD and RHCE genes, while being a useful approach to establish reference RHD allele sequences.

Detection of GBA missense mutations and other variants using the Oxford Nanopore MinION

PurposeMutations in GBA cause Gaucher disease when biallelic, and are strong risk factors for Parkinson’s disease when heterozygous. GBA analysis is complicated by the nearby pseudogene. We aimed to design and validate a method for sequencing GBA on the Oxford Nanopore MinION.MethodsWe sequenced an 8.9 kb amplicon from DNA samples of 17 individuals, including patients with Parkinson’s and Gaucher disease, on older and current (R9.4) flow cells. These included samples with known mutations, assessed in a blinded fashion on the R9.4 data. We used NanoOK for quality metrics, two different aligners (Graphmap and NGMLR), Nanopolish and Sniffles to call variants, and Whatshap for phasing.ResultsWe detected all known mutations, including the common p.N409S (N370S) and p.L483P (L444P), and three rarer ones, at the correct zygosity, as well as intronic SNPs. In a sample with the complex RecNciI allele, we detected an additional coding mutation, and a 55-base pair deletion. We confirmed compound heterozygosity where relevant. False positives were easily identified.ConclusionThe Oxford Nanopore MinION can detect missense mutations and an exonic deletion in this difficult gene, with the added advantage of phasing and intronic analysis. It can be used as an efficient diagnostic tool.

Influence of single nucleotide polymorphisms in factor VIII and von Willebrand factor genes on plasma factor VIII activity: the ARIC Study

Factor VIII (FVIII) functions as a cofactor for factor IXa in the contact coagulation pathway and circulates in a protective complex with von Willebrand factor (VWF). Plasma FVIII activity is strongly influenced by environmental and genetic factors through VWF-dependent and -independent mechanisms. Single nucleotide polymorphisms (SNPs) of the coding and promoter sequence in the FVIII gene have been extensively studied for effects on FVIII synthesis, secretion, and activity, but impacts of non–disease-causing intronic SNPs remain largely unknown. We analyzed FVIII SNPs and FVIII activity in 10 434 healthy Americans of European (EA) or African (AA) descent in the Atherosclerosis Risk in Communities (ARIC) study. Among covariates, age, race, diabetes, and ABO contributed 2.2%, 3.5%, 4%, and 10.7% to FVIII intersubject variation, respectively. Four intronic FVIII SNPs associated with FVIII activity and 8 with FVIII-VWF ratio in a sex- and race-dependent manner. The FVIII haplotypes AT and GCTTTT also associated with FVIII activity. Seven VWF SNPs were associated with FVIII activity in EA subjects, but no FVIII SNPs were associated with VWF Ag. These data demonstrate that intronic SNPs could directly or indirectly influence intersubject variation of FVIII activity. Further investigation may reveal novel mechanisms of regulating FVIII expression and activity.