Overrepresentation Of Rare Variants Research Articles

Clinical and genetic characteristics of ALS patients with variants in genes regulating DNA methylation.

Aberrant DNA methylation alterations are implicated in amyotrophic lateral sclerosis (ALS). Nevertheless, the influence of genetic variants in genes regulating DNA methylation on ALS patients is not well understood. Therefore, we aim to provide a comprehensive variant profile of genes related to DNA methylation (DNMT1, DNMT3A, DNMT3B, DNMT3L) and demethylation (TET1, TET2, TET3, TDG) and to investigate the association of these variants with ALS. Variants were screened in a cohort of 2240 ALS patients from Southwest China, using controls from the Genome Aggregation Database (n = 9976) and the China Metabolic Analytics Project (n = 10,588). The over-representation of rare variants and their association with ALS risk were evaluated using Fisher's exact test with Bonferroni correction at both allele and gene levels. Kaplan-Meier analysis and Cox regression analysis were employed to explore the relationship between variants and survival. A total of 210 variants meeting the criteria were identified. Gene-based burden analysis identified a significant increase in ALS risk associated with rare variants in the TET2 gene (OR = 1.95, 95% CI = 1.29-2.88, P = 0.001). Survival analysis demonstrated that patients carrying variants in demethylation-related genes had a higher risk of death compared to those with methylation-related gene variants (HR = 1.29, 95% CI = 1.03-1.86, P = 0.039). This study provides a genetic variant profile of genes involved in DNA methylation and demethylation regulation, along with the clinical characteristics of ALS patients carrying these variants. The findings offer genetic evidence implicating disrupted DNA methylation dynamics in ALS.

Mutation screening of AOPEP variants in a large dystonia cohort.

Recently, AOPEP has been identified to be a novel causative gene of autosomal-recessive dystonia. However, no large cohort study has been conducted to confirm the association. We aimed to systematically evaluate the genetic associations of AOPEP with dystonia in a large Chinese dystonia cohort. We analyzed rare variants of AOPEP in 878 dystonia patients with whole-exome sequencing. The over-representation of rare variants in patients was examined with Fisher's exact test at allele and gene levels. Among the 878 patients with dystonia, we found two patients with biallelic likely pathogenic variants in the AOPEP gene. One patient carried putative compound heterozygous variants (p.A212D and p.G216R) and presented with childhood-onset segmental dystonia involving the upper limbs and craniocervical muscles accompanied by myoclonus of the dystonia affected areas. One patient carried homozygote of p.M291Nfs*68 and presented with adult-onset isolated cervical dystonia. Another 15 patients were identified to carry heterozygous rare variants in AOPEP, including 2 loss-of-function variants (p.M291Nfs*68 and p.R493X) and 6 missense variants. One loss-of-function variant (p.R493X) was the same as previously reported. Nearly, all of the 15 patients carrying heterozygous variants in AOPEP presented with isolated dystonia with only craniocervical muscles affected, except for one patient who carried the p.R493X variant presented with segmental dystonia affecting the neck and right upper limb combined with parkinsonism. Gene-based burden analysis detected enrichment of rare variants and rare damaging variants of AOPEP in dystonia. Our study supplemented the evidence on the role of AOPEP in autosomal-recessive dystonia in Chinese population, and expanded the genotypic and phenotypic spectrum of AOPEP.

Mutation Screening of MED27 in a Large Dystonia Cohort

Objectives. Recently, biallelic variants in MED27 have been identified to correlate with complex dystonia. However, no replicative study has been conducted in larger dystonia cohorts. In this study, we aimed to systematically evaluate the genetic associations of MED27 with dystonia in a large dystonia cohort. Materials and Methods. We analyzed rare variants (minor allele frequency < 0.01 ) of MED27 in a large Chinese dystonia cohort with whole exome sequencing. The overrepresentation of rare variants in patients was examined with Fisher’s exact test at allele and gene levels. Results. A total of 688 patients with dystonia were included in the study, including 483 isolated dystonia, 133 combined dystonia, and 72 complex dystonia. The average age at onset (SD) was 34.3 (19.1) years old. After applying filtering criteria, five rare variants, namely, p.R247H, p.P174A, p.P123A, p.L120F, and p.F56C, were identified in six individuals. All of them carried the variant in the heterozygous form, and no patients with compound heterozygous or homozygous alleles were identified. At allele level, no variant was associated with risk of dystonia. Gene-based burden analysis did not detect enrichment of rare variants of MED27 in dystonia either. Conclusion. Variants of MED27 were rare in Chinese dystonia patients, probably because that mutations in MED27 are more associated with more complex neurodevelopmental disorders that can also include dystonia among the various neurological features. Further studies are needed to confirm the role of MED27 in dystonia and other neurological disorders.

Rare variants in IMPDH2 cause autosomal dominant dystonia in Chinese population.

Recently, IMPDH2 has been linked to dystonia. However, no replication study from other cohorts has been conducted to confirm the association. We aimed to systematically evaluate the genetic associations of IMPDH2 with dystonia in a large dystonia cohort. We analyzed rare variants (minor allele frequency < 0.01) of IMPDH2 in 688 Chinese dystonia patients with whole exome sequencing. The over-representation of rare variants in patients was examined with Fisher's exact test at allele and gene levels. Four rare variants were detected in IMPDH2 in four patients with dystonia in our cohort, including three missense variants (p.Ser508Leu, p.Ala396Thr, and p.Phe24Val) and one splice acceptor variant (c.1296-1G>T). Two of them (c.1296-1G>T and p.Ser508Leu) were co-segregated in the family co-segregation analysis and were classified as pathogenic and likely pathogenic variant according to the American College of Medical Genetics and Genomics (ACMG) guidelines, respectively. Gene burden analysis revealed enrichment of rare variants in IMPDH2 in dystonia. Our work supplemented the evidence on the role of IMPDH2 in autosomal dominant dystonia in Chinese population, and expanded the genetic and phenotypic spectrum of IMPDH2, paving way for future studies.

Rare variant screening and burden analysis of PLXNA1 in Parkinson's disease.

Recently, p.Glu1121Ter in PLXNA1 was identified as a potential cause of parkinsonism. However, no further replication has been conducted in a wider range of Parkinson's disease (PD) cohorts. We aimed to evaluate the genetic role of PLXNA1 in PD. We systematically analyzed the rare protein-coding variants (minor allele frequency [MAF] &lt; 0.01) in 1080 patients and 1051 healthy controls. Fisher's exact test was used to analyze the associations between each variant and risk of PD, while, at gene level, over-representation of rare variants in patients was examined using the optimized sequence kernel association test (SKAT-O). In total, 43 rare variants were identified in PD. No variant was significantly associated with risk of PD. Burden analysis showed enrichment of ultra-rare variants (MAF &lt; 0.001) of PLXNA1 in PD. One patient carried a variant (p.E1121D) in the same amino acid as that in the original study. Both patients showed worsened motor symptoms, and developed dyskinesia during follow-up. Our study explored the rare variant of PLXNA1 in PD, and paves the way for future research on the genetic role of PLXNA1 in PD.

ANXA1 and the risk for early-onset Parkinson's disease

Recently, homozygous missense variants in ANXA1 were identified to cause parkinsonism by segregation analysis in a consanguineous family. However, no further replication has been conducted in a wider range of Parkinson's disease (PD) populations. To investigate the involvement of ANXA1 mutations in PD, we analyzed the rare variants in 743 Chinese early-onset PD (EOPD) patients (age at onset <50) using whole exome sequencing. The over-representation of rare variants in patients was examined with Fisher's exact test at allele and gene levels. We did not find the disease-causing variant described in the original study, and no patient carried other homozygous or compound heterozygous variants of ANXA1. Six rare missense mutations in ANXA1 were identified (minor allele frequency <0.01). No significant association was found between ANXA1 variants and PD at allele and gene levels. Genetic screening of ANXA1 mutations suggested rare variants of ANXA1 were rare in EOPD in the Asian ethnic background. Further explorations with larger sample size were warranted to better understand the role of ANXA1 in PD.

Evaluating the Role of SNCA, LRRK2, and GBA in Chinese Patients With Early-Onset Parkinson's Disease.

Defects in the α-synuclein, leucine-rich repeat kinase 2, or glucocerebrosidase genes have been regarded as essential contributors to PD. However, genetic variability of these genes with respect to early-onset PD remains poorly defined for the Chinese demographic. We aim to systematically characterize the clinical and genetic architecture of α-synuclein, leucine-rich repeat kinase 2, and glucocerebrosidase in Chinese early-onset PD patients. Whole-exome sequencing and Sanger sequencing were used to identify variants of α-synuclein, leucine-rich repeat kinase 2, and glucocerebrosidase in 662 Chinese early-onset PD patients. Haplotype and burden analyses were conducted to investigate the role of rare variants of these three genes in early-onset PD. Sixty rare variants, including 23 novel variants, were identified in 73 patients (11.0%). Frequencies of patients with rare pathogenic/likely pathogenic variants of α-synuclein, leucine-rich repeat kinase 2, and glucocerebrosidase were 0.6%, 3.0%, and 5.4%, respectively. Evidences of two founder events exclusive to Asians were identified in 2 patients with leucine-rich repeat kinase 2 p.R1441C and 3 patients with α-synuclein p.A53V. Gene-based burden analysis supported glucocerebrosidase as a strong risk factor for early-onset PD, but argued against over-representation of rare variants in α-synuclein or leucine-rich repeat kinase 2 in early-onset PD. Clinically, no differences in motor or nonmotor symptoms were found between glucocerebrosidase variants carriers, and noncarriers or between leucine-rich repeat kinase 2 carriers and noncarriers. Patients with α-synuclein variants showed both rapid progression and worse cognitive impairment. Our study provides a better understanding of the clinical and genetic correlations of α-synuclein, leucine-rich repeat kinase 2, and glucocerebrosidase in early-onset PD, which may be beneficial for drafting genetic scanning strategies and evaluating disease progression. © 2020 International Parkinson and Movement Disorder Society.

Overrepresentation of rare variants in a specific ethnic group may confuse interpretation of association analyses

Rare sequence variants may be important in understanding the biology of common diseases, but clearly establishing their association with disease is often difficult. Association studies of such variants are becoming increasingly common as large-scale sequence analysis of candidate genes has become feasible. A recent report suggested SLITRK1 (Slit and Trk-like 1) as a candidate gene for Tourette Syndrome (TS). The statistical evidence for this suggestion came from association analyses of a rare 3'-UTR variant, var321, which was observed in two patients but not observed in more than 2000 controls. We genotyped 307 Costa Rican and 515 Ashkenazi individuals (TS probands and their parents) and observed var321 in five independent Ashkenazi parents, two of whom did not transmit this variant to their affected child. Furthermore, we identified var321 in one subject from an Ashkenazi control sample. Our findings do not support the previously reported association and suggest that var321 is overrepresented among Ashkenazi Jews compared with other populations of European origin. The results further suggest that overrepresentation of rare variants in a specific ethnic group may complicate the interpretation of association analyses of such variants, highlighting the particular importance of precisely matching case and control populations for association analyses of rare variants.