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Статті в журналах з теми "Risk variants"

Автор: Grafiati

Опубліковано: 21 грудня 2024

Оновлено: 31 липня 2025

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1

Shah, Shrijal S., Herbert Lannon, Leny Dias, et al. "APOL1 Kidney Risk Variants Induce Cell Death via Mitochondrial Translocation and Opening of the Mitochondrial Permeability Transition Pore." Journal of the American Society of Nephrology 30, no. 12 (2019): 2355–68. http://dx.doi.org/10.1681/asn.2019020114.

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BackgroundGenetic Variants in Apolipoprotein L1 (APOL1) are associated with large increases in CKD rates among African Americans. Experiments in cell and mouse models suggest that these risk-related polymorphisms are toxic gain-of-function variants that cause kidney dysfunction, following a recessive mode of inheritance. Recent data in trypanosomes and in human cells indicate that such variants may cause toxicity through their effects on mitochondria.MethodsTo examine the molecular mechanisms underlying APOL1 risk variant–induced mitochondrial dysfunction, we generated tetracycline-inducible H

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2

Bayley, Jean Pierre, Birke Bausch, Johannes Adriaan Rijken, et al. "Variant type is associated with disease characteristics in SDHB, SDHC and SDHD-linked phaeochromocytoma–paraganglioma." Journal of Medical Genetics 57, no. 2 (2019): 96–103. http://dx.doi.org/10.1136/jmedgenet-2019-106214.

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BackgroundPathogenic germline variants in subunits of succinate dehydrogenase (SDHB, SDHC and SDHD) are broadly associated with disease subtypes of phaeochromocytoma–paraganglioma (PPGL) syndrome. Our objective was to investigate the role of variant type (ie, missense vs truncating) in determining tumour phenotype.MethodsThree independent datasets comprising 950 PPGL and head and neck paraganglioma (HNPGL) patients were analysed for associations of variant type with tumour type and age-related tumour risk. All patients were carriers of pathogenic germline variants in the SDHB, SDHC or SDHD gen

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3

Han, Shengtong. "Bayesian Rare Variant Analysis Identifies Novel Schizophrenia Putative Risk Genes." Journal of Personalized Medicine 14, no. 8 (2024): 822. http://dx.doi.org/10.3390/jpm14080822.

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The genetics of schizophrenia is so complex that it involves both common variants and rare variants. Rare variant association studies of schizophrenia are challenging because statistical methods for rare variant analysis are under-powered due to the rarity of rare variants. The recent Schizophrenia Exome meta-analysis (SCHEMA) consortium, the largest consortium in this field to date, has successfully identified 10 schizophrenia risk genes from ultra-rare variants by burden test, while more risk genes remain to be discovered by more powerful rare variant association test methods. In this study,

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4

Park, Jihye, Soo Youn Lee, Su Youn Baik, et al. "Gene-Wise Burden of Coding Variants Correlates to Noncoding Pharmacogenetic Risk Variants." International Journal of Molecular Sciences 21, no. 9 (2020): 3091. http://dx.doi.org/10.3390/ijms21093091.

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Genetic variability can modulate individual drug responses. A significant portion of pharmacogenetic variants reside in the noncoding genome yet it is unclear if the noncoding variants directly influence protein function and expression or are present on a haplotype including a functionally relevant genetic variation (synthetic association). Gene-wise variant burden (GVB) is a gene-level measure of deleteriousness, reflecting the cumulative effects of deleterious coding variants, predicted in silico. To test potential associations between noncoding and coding pharmacogenetic variants, we comput

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5

Barbirou, Mouadh, Amanda A. Miller, Amel Mezlini, Balkiss Bouhaouala-Zahar, and Peter J. Tonellato. "Variant Characterization of a Representative Large Pedigree Suggests “Variant Risk Clusters” Convey Varying Predisposition of Risk to Lynch Syndrome." Cancers 15, no. 16 (2023): 4074. http://dx.doi.org/10.3390/cancers15164074.

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Recently, worldwide incidences of young adult aggressive colorectal cancer (CRC) have rapidly increased. Of these incidences diagnosed as familial Lynch syndrome (LS) CRC, outcomes are extremely poor. In this study, we seek novel familial germline variants from a large pedigree Tunisian family with 12 LS-affected individuals to identify putative germline variants associated with varying risk of LS. Whole-genome sequencing analysis was performed to identify known and novel germline variants shared between affected and non-affected pedigree members. SNPs, indels, and structural variants (SVs) we

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6

Cannon-Albright, Lisa Anne, Craig Carl Teerlink, Jeff Stevens, et al. "A Rare Variant in ERF (rs144812092) Predisposes to Prostate and Bladder Cancers in an Extended Pedigree." Cancers 13, no. 10 (2021): 2399. http://dx.doi.org/10.3390/cancers13102399.

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Pairs of related bladder cancer cases who belong to pedigrees with an excess of bladder cancer were sequenced to identify rare, shared variants as candidate predisposition variants. Candidate variants were tested for association with bladder cancer risk. A validated variant was assayed for segregation to other related cancer cases, and the predicted protein structure of this variant was analyzed. This study of affected bladder cancer relative pairs from high-risk pedigrees identified 152 bladder cancer predisposition candidate variants. One variant in ERF (ETS Repressing Factor) was significan

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7

Bychkovsky, Brittany L., Nihat B. Agaoglu, Carolyn Horton, et al. "Double CHEK2 Pathogenic and Low-Risk Variants and Associated Cancer Phenotypes." JAMA Network Open 8, no. 1 (2025): e2451361. https://doi.org/10.1001/jamanetworkopen.2024.51361.

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ImportanceCHEK2 pathogenic and likely pathogenic variants (PVs) are common, and low-risk (LR) variants, p.I157T, p.S428F, and p.T476M, are even more common. Biallelic CHEK2 PVs are associated with specific cancer phenotypes, including early age at onset of breast cancers. Whether biallelic LR variants are associated with cancer predisposition is unknown.ObjectiveTo characterize the cancer phenotype among individuals with biallelic CHEK2 variants, specifically those that have been associated with lower cancer risk in the heterozygous state.Design, Setting, and ParticipantsThis retrospective obs

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8

Cornelis, Stéphanie S., and Frans P. M. Cremers. "Improving personalised genetic counselling for ABCA4 -associated retinopathy: Updated recurrence risk estimates." Medizinische Genetik 37, no. 1 (2025): 19–25. https://doi.org/10.1515/medgen-2024-2065.

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Abstract Stargardt disease type 1 (STGD1) is caused by biallelic pathogenic variants in ABCA4. These variants vary in their effect on the resulting protein and the disease phenotype. Not all variant combinations cause disease, which complicates the determination of the recurrence risk of STGD1. Previously, the recurrence risk of STGD1 was estimated by analyzing variants in patient data and using their population variant frequencies in which white patients are overrepresented. Furthermore, assuming that variant effects are independent of genetic ancestry, estimates were made for each gnomAD pop

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9

Boddicker, Nicholas J., Raphael Mwangi, Dennis P. Robinson, et al. "Abstract 5233: Germline CHEK2 variants and risk of lymphoma." Cancer Research 83, no. 7_Supplement (2023): 5233. http://dx.doi.org/10.1158/1538-7445.am2023-5233.

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Abstract Lymphoma is the sixth most commonly diagnosed cancer in the US. Genome-wide association studies have identified common variants associated with risk of specific lymphoma subtypes, but less is known about the contribution of rare inherited variants in the genetic architecture of lymphoma risk. CHEK2 is important to DNA repair and 2 small studies have found evidence of an association between CHEK2 variants and risk of lymphoma. Here, we investigated loss of function (LoF) variants in CHEK2 with risk of lymphoma (overall and subtypes). The study population included newly diagnosed lympho

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10

Tu, J. J., L. Kuhn, L. Denny, K. J. Beattie, A. Lorincz, and T. C. Wright. "Molecular variants of human papillomavirus type 16 and risk for cervical neoplasia in South Africa." International Journal of Gynecologic Cancer 16, no. 2 (2006): 736–42. http://dx.doi.org/10.1136/ijgc-00009577-200603000-00043.

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Non-European variants of human papillomavirus (HPV) type 16 are generally associated with a greater risk of cervical neoplasia than European prototype variants. We investigated whether this association would persist in a population in which non-European HPV 16 variants were more common. We sequenced HPV 16 isolates in cervical samples collected from 93 Black South African women enrolled in a cervical cancer screening study and examined associations between cervical neoplasia identified though colposcopy with cervical biopsy and the specific HPV 16 variant identified. The European prototype var

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11

Ament, Seth A., Szabolcs Szelinger, Gustavo Glusman, et al. "Rare variants in neuronal excitability genes influence risk for bipolar disorder." Proceedings of the National Academy of Sciences 112, no. 11 (2015): 3576–81. http://dx.doi.org/10.1073/pnas.1424958112.

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We sequenced the genomes of 200 individuals from 41 families multiply affected with bipolar disorder (BD) to identify contributions of rare variants to genetic risk. We initially focused on 3,087 candidate genes with known synaptic functions or prior evidence from genome-wide association studies. BD pedigrees had an increased burden of rare variants in genes encoding neuronal ion channels, including subunits of GABAA receptors and voltage-gated calcium channels. Four uncommon coding and regulatory variants also showed significant association, including a missense variant in GABRA6. Targeted se

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12

Vargas-Neri, Jessica L., Bruce Carleton, Colin J. Ross, Mara Medeiros, Gilberto Castañeda-Hernández, and Patricia Clark. "Pharmacogenomic study of anthracycline-induced cardiotoxicity in Mexican pediatric patients." Pharmacogenomics 23, no. 5 (2022): 291–301. http://dx.doi.org/10.2217/pgs-2021-0144.

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Background: The aim of this study was to evaluate the association between well-defined genetic risk variants in SLC28A3, RARG and UGT1A6 and anthracycline-induced cardiotoxicity in Mexican pediatric patients. Methods: We tested a cohort of 79 children treated with anthracyclines for the presence of SLC28A3-rs7853758, RARG-rs2229774 and UGT1A6-rs17863783. Results: The SLC28A3-rs7853758 variant was more frequent in this cohort, while the UGT1A6-rs17863783 and RARG-rs2229774 variants were present at lower frequencies. A clinically important decrease of fractional shortening was associated with SL

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13

Reková, Petra, Gabriela Dostálová, David Kemlink, et al. "Detailed Phenotype of GLA Variants Identified by the Nationwide Neurological Screening of Stroke Patients in the Czech Republic." Journal of Clinical Medicine 10, no. 16 (2021): 3543. http://dx.doi.org/10.3390/jcm10163543.

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Fabry disease (FD) is a rare X-linked disorder of glycosphingolipid metabolism caused by pathogenic variants within the alpha-galactosidase A (GLA) gene, often leading to neurological manifestations including stroke. Multiple screening programs seeking GLA variants among stroke survivors lacked detailed phenotype description, making the interpretation of the detected variant’s pathogenicity difficult. Here, we describe detailed clinical characteristics of GLA variant carriers identified by a nationwide stroke screening program in the Czech Republic. A total of 23 individuals with 8 different G

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14

Iwaki, Hirotaka, Cornelis Blauwendraat, Hampton L. Leonard, et al. "Genetic risk of Parkinson disease and progression:." Neurology Genetics 5, no. 4 (2019): e348. http://dx.doi.org/10.1212/nxg.0000000000000348.

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ObjectiveTo determine if any association between previously identified alleles that confer risk for Parkinson disease and variables measuring disease progression.MethodsWe evaluated the association between 31 risk variants and variables measuring disease progression. A total of 23,423 visits by 4,307 patients of European ancestry from 13 longitudinal cohorts in Europe, North America, and Australia were analyzed.ResultsWe confirmed the importance of GBA on phenotypes. GBA variants were associated with the development of daytime sleepiness (p.N370S: hazard ratio [HR] 3.28 [1.69–6.34]) and possib

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15

Gibson, Summer B., Jonathan M. Downie, Spyridoula Tsetsou, et al. "The evolving genetic risk for sporadic ALS." Neurology 89, no. 3 (2017): 226–33. http://dx.doi.org/10.1212/wnl.0000000000004109.

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Objective:To estimate the genetic risk conferred by known amyotrophic lateral sclerosis (ALS)–associated genes to the pathogenesis of sporadic ALS (SALS) using variant allele frequencies combined with predicted variant pathogenicity.Methods:Whole exome sequencing and repeat expansion PCR of C9orf72 and ATXN2 were performed on 87 patients of European ancestry with SALS seen at the University of Utah. DNA variants that change the protein coding sequence of 31 ALS-associated genes were annotated to determine which were rare and deleterious as predicted by MetaSVM. The percentage of patients with

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16

Vogan, Kyle. "Bladder exstrophy risk variants." Nature Genetics 47, no. 5 (2015): 429. http://dx.doi.org/10.1038/ng.3298.

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17

Durward-Akhurst, Sian, Joy Stock, Freya Stein, Christopher Stauthammer, and Samuel Dudley. "451 Identification of candidate sudden arrhythmic death -causing variants in a spontaneous animal model." Journal of Clinical and Translational Science 8, s1 (2024): 134. http://dx.doi.org/10.1017/cts.2024.386.

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OBJECTIVES/GOALS: 1. Identify candidate AN-SAD-causing variants. 2. Estimate the variant effect size of and genotypic relative risk for arrhythmias and AN-SAD. METHODS/STUDY POPULATION: We performed whole genome sequencing (WGS) on 59 Thoroughbred AN-SAD cases and 58 controls. WGS was mapped and variants identified using a modified version of the Genome Analysis Toolkit best practices. Variants will be selected based on case-control analysis using SnpSift and presence in candidate genes. The top 400 candidate AN-SAD-causing variants will be selected based on being common in cases and rare or a

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18

Cannon-Albright, Lisa A., Jeff Stevens, Julio C. Facelli, Craig C. Teerlink, Kristina Allen-Brady, and Neeraj Agarwal. "High-Risk Pedigree Study Identifies LRBA (rs62346982) as a Likely Predisposition Variant for Prostate Cancer." Cancers 15, no. 7 (2023): 2085. http://dx.doi.org/10.3390/cancers15072085.

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There is evidence for contribution of inherited factors to prostate cancer, and more specifically to lethal prostate cancer, but few responsible genes/variants have been identified. We examined genetic sequence data for 51 affected cousin pairs who each died from prostate cancer and who were members of high-risk prostate cancer pedigrees in order to identify rare variants shared by the cousins as candidate predisposition variants. Candidate variants were tested for association with prostate cancer risk in UK Biobank data. Candidate variants were also assayed in 1195 additional sampled Utah pro

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19

Nomura, Akihiro, Connor A. Emdin, Hong Hee Won, et al. "Heterozygous ABCG5 Gene Deficiency and Risk of Coronary Artery Disease." Circulation: Genomic and Precision Medicine 13, no. 5 (2020): 417–23. http://dx.doi.org/10.1161/circgen.119.002871.

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Background: Familial sitosterolemia is a rare Mendelian disorder characterized by hyperabsorption and decreased biliary excretion of dietary sterols. Affected individuals typically have complete genetic deficiency—homozygous loss-of-function (LoF) variants—in the ABCG5 or ABCG8 genes and have substantially elevated plasma sitosterol and LDL (low-density lipoprotein) cholesterol (LDL-C) levels. The impact of partial genetic deficiency of ABCG5 or ABCG8 —as occurs in heterozygous carriers of LoF variants—on LDL-C and risk of coronary artery disease (CAD) has remained uncertain. Methods: We first

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20

Oliverio, Andreina, Eleonora Bruno, Mara Colombo, et al. "BRCA1/2 Variants and Metabolic Factors: Results From a Cohort of Italian Female Carriers." Cancers 12, no. 12 (2020): 3584. http://dx.doi.org/10.3390/cancers12123584.

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Women carriers of pathogenic variants (mutations) in the BRCA1/2 genes face a high lifetime risk of developing breast cancer (BC) and/or ovarian cancer (OC). However, metabolic factors may influence BRCA penetrance. We studied the association of metabolic factors with BRCA1/2 variants and the risk effect of metabolic exposures in relation to the position of the mutations within the BRCA1/2. Overall, 438 women carriers of BRCA1/2 mutations, aged 18–70, with or without a previous diagnosis of BC/OC and without metastases, who joined our randomized dietary trial, were included in the study. The p

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21

Kent, Jason, and Michael C. Heinrich. "Novel models for the functional characterization of SDHA germline variants to predict cancer risk." Journal of Clinical Oncology 42, no. 16_suppl (2024): 11532. http://dx.doi.org/10.1200/jco.2024.42.16_suppl.11532.

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11532 Background: SDHA mutations are the most common cause of SDH-deficient GIST. More than 80% of SDHA-mutant GIST are associated with heterozygous germline mutations. Enhanced cancer surveillance of individuals carrying a known pathogenic germline SDHA mutation has the potential to detect early-stage tumors, allowing for curative surgery. However, of the > 1000 SDHA missense variants listed in ClinVar, > 95% are VUS. We must improve our ability to interpret the significance of SDHA variants before genetic sequencing can be utilized to its fullest potential for assessing cancer risk. Me

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22

Asanomi, Yuya, Daichi Shigemizu, Shintaro Akiyama, et al. "A functional variant of SHARPIN confers increased risk of late-onset Alzheimer’s disease." Journal of Human Genetics 67, no. 4 (2021): 203–8. http://dx.doi.org/10.1038/s10038-021-00987-x.

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AbstractLate-onset Alzheimer’s disease (LOAD) is the most common form of dementia, and its pathogenesis is multifactorial. We previously reported a rare functional variant of SHARPIN (rs572750141, NP_112236.3:p.Gly186Arg) that was significantly associated with LOAD. In addition, several recent studies have suggested the potential role of SHARPIN in AD pathogenesis. In this study, we sought to identify additional functional variants of SHARPIN in Japanese population. Six highly deleterious variants of SHARPIN, comprising four missense variants, one frameshift variant, and one stop-gain variant

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23

Wickland, Daniel P., Yingxue Ren, Jason P. Sinnwell, et al. "Impact of variant-level batch effects on identification of genetic risk factors in large sequencing studies." PLOS ONE 16, no. 4 (2021): e0249305. http://dx.doi.org/10.1371/journal.pone.0249305.

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Genetic studies have shifted to sequencing-based rare variants discovery after decades of success in identifying common disease variants by Genome-Wide Association Studies using Single Nucleotide Polymorphism chips. Sequencing-based studies require large sample sizes for statistical power and therefore often inadvertently introduce batch effects because samples are typically collected, processed, and sequenced at multiple centers. Conventionally, batch effects are first detected and visualized using Principal Components Analysis and then controlled by including batch covariates in the disease

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24

Bobbili, Dheeraj Reddy, Peter Banda, Rejko Krüger, and Patrick May. "Excess of singleton loss-of-function variants in Parkinson’s disease contributes to genetic risk." Journal of Medical Genetics 57, no. 9 (2020): 617–23. http://dx.doi.org/10.1136/jmedgenet-2019-106316.

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BackgroundParkinson’s disease (PD) is a neurodegenerative disorder with complex genetic architecture. Besides rare mutations in high-risk genes related to monogenic familial forms of PD, multiple variants associated with sporadic PD were discovered via association studies.MethodsWe studied the whole-exome sequencing data of 340 PD cases and 146 ethnically matched controls from the Parkinson’s Progression Markers Initiative (PPMI) and performed burden analysis for different rare variant classes. Disease prediction models were built based on clinical, non-clinical and genetic features, including

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25

Lewandowski, Laura, Linda Hiraki, Christiaan Scott, et al. "Next generation sequencing analysis reveals complex genetic architecture of childhood-onset systemic lupus erythematosus." Lupus Science & Medicine 12, no. 1 (2025): e001475. https://doi.org/10.1136/lupus-2024-001475.

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ObjectivesOur current understanding of the genetic architecture of childhood-onset SLE (cSLE) is limited by a dearth of comprehensive genomic studies in cSLE. We have quantified the number of known rare and common SLE risk variants in a diverse cSLE cohort. We characterised type I interferon (IFN) gene expression scores along with genomic data.MethodsWe performed whole genome sequencing on 83 patients with cSLE and 109 unaffected parents and analysed sequences for known common and rare SLE-associated risk variants. Type I IFN gene expression was quantified on a subset of patients. We investiga

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26

Ratajczak, Wiktoria, Angus G. Jones, Sarah D. Atkinson, and Catriona Kelly. "Type 1 Diabetes Risk Variants Reduce Beta Cell Function." Genes 16, no. 2 (2025): 172. https://doi.org/10.3390/genes16020172.

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Introduction: The variants rs10517086 and rs1534422 are predictive of type 1 diabetes mellitus (T1DM) development and poor residual β cell function within the first year of diagnosis. However, the mechanism by which risk is conferred is unknown. We explored the impact of both variants on β cell function in vitro and assessed their relationship with C-peptide in people with T1DM and type 2 diabetes mellitus (T2DM). Methods: Using CRISPR/Cas9, the variants were introduced into a β cell line (BRIN-BD11) and a T cell line (Jurkat cells) from which the conditioned media was applied to otherwise hea

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27

Pramukarso, Dodik Tugasworo, Herlina Suryawati, Soetedjo Soetedjo, et al. "The Association Between Variants of Angiotensin Converting Enzyme (ACE) Gene With Risk Factors in Patients with Ischemic Stroke at Dr. Kariadi Semarang." Medica Hospitalia : Journal of Clinical Medicine 8, no. 3 (2021): 297–303. http://dx.doi.org/10.36408/mhjcm.v8i3.565.

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BACKGROUND : Stroke is the leading cause of death and disability in the world. The occurrence of ischemic stroke is indicated by genetic factors, environmental factors and the interaction between it. Angiotensin Converting Enzyme (ACE) genetic variant is associated with various characteristics of risk factors for ischemic stroke. OBJECTIVE : Identifying genetic variants of Angiotensin Converting Enzyme (ACE) with the Polymerase Chain Reaction (PCR) method and to find it’s correlation beetwen risk factor in patients with Ischemic Stroke at Dr. Kariadi Semarang METHOD : The subjects

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Krohn, Lynne, Jennifer A. Ruskey, Uladzislau Rudakou, et al. "GBA variants in REM sleep behavior disorder." Neurology 95, no. 8 (2020): e1008-e1016. http://dx.doi.org/10.1212/wnl.0000000000010042.

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ObjectiveTo study the role of GBA variants in the risk for isolated REM sleep behavior disorder (iRBD) and conversion to overt neurodegeneration.MethodsA total of 4,147 individuals were included: 1,061 patients with iRBD and 3,086 controls. GBA was fully sequenced using molecular inversion probes and Sanger sequencing. We analyzed the effects of GBA variants on the risk of iRBD, age at onset (AAO), and conversion rates.ResultsGBA variants were found in 9.5% of patients with iRBD compared to 4.1% of controls (odds ratio, 2.45; 95% confidence interval [CI], 1.87–3.22; p = 1 × 10−10). The estimat

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Waller, Rosalie G., Karen Curtin, Djordje Atanackovic, Guido J. Tricot, Steven M. Lipkin, and Nicola J. Camp. "Exome Sequencing in Myeloma Pedigrees Implicates RAS1 and NOTCH Signaling Are Involved in Inherited Myeloma Risk." Blood 126, no. 23 (2015): 2976. http://dx.doi.org/10.1182/blood.v126.23.2976.2976.

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Abstract Multiple Myeloma (MM) is a cancer of plasma cells with poor prognosis. Although, MM has been shown to be highly heritable in genealogy studies, no inherited risk-alleles have been identified. We hypothesize MM heritability is in part due to rare, germline variation that can be discovered in high-risk pedigrees. High-risk MM pedigrees were identified using the Utah Population Database which contains both genealogical and state cancer records. High-risk pedigrees were defined to have statistical excess of MM (p < 0.05). In this study we whole-exome sequenced germline DNA from 42 MM c

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Acharya, Ratna, and Kiran Upadhyay. "Early recurrence of focal segmental glomerulosclerosis in a kidney transplant recipient withAPOL1one risk variant." BMJ Case Reports 16, no. 5 (2023): e254593. http://dx.doi.org/10.1136/bcr-2023-254593.

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Apolipoprotein 1(APOL1) risk variants (G1 and G2) are associated with focal segmental glomerulosclerosis (FSGS) in patients of African ancestry. The prevalence ofAPOL1two risk variants is lower in Hispanics and very rare in European and Asian populations.APOL1two risk variants in donor kidneys is associated with recipient kidney graft loss, however the effect of recipient risk variant in the kidney transplant outcome is unclear. Here, we present a late adolescent male with FSGS and end stage renal disease with oneAPOL1risk variant (G2) who had immediate recurrence of FSGS in the post-KT period

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Karantanos, Theodoros, Shruti Chaturvedi, Christopher D. Gocke, Donna Marie Williams, Alison R. Moliterno, and Evan M. Braunstein. "ATM Germline Variant Increases the Risk of MPN Progression." Blood 134, Supplement_1 (2019): 835. http://dx.doi.org/10.1182/blood-2019-125362.

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Introduction: Chronic myeloproliferative neoplasms (MPN) share the same driver mutations but their disease course and prognosis varies significantly. Deficiency of DNA damage repair (DDR) due to germline mutation is known to predispose to certain cancer types and has been implicated in the biology of MPN. The aim of our study was to evaluate the impact of germline variants in DDR genes in the natural history and outcomes of MPN patients. Patients and Methods: 76 individuals who were diagnosed with MPN (essential thrombocytosis (ET), polycythemia vera (PV) and primary myelofibrosis (PMF)) at Jo

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Li, Qingqin S., Chao Tian, David Hinds, and Guy R. Seabrook. "The association of clinical phenotypes to known AD/FTD genetic risk loci and their inter-relationship." PLOS ONE 15, no. 11 (2020): e0241552. http://dx.doi.org/10.1371/journal.pone.0241552.

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To elucidate how variants in genetic risk loci previously implicated in Alzheimer’s Disease (AD) and/or frontotemporal dementia (FTD) contribute to expression of disease phenotypes, a phenome-wide association study was performed in two waves. In the first wave, we explored clinical traits associated with thirteen genetic variants previously reported to be linked to disease risk using both the 23andMe and UKB cohorts. We tested 30 additional AD variants in UKB cohort only in the second wave. APOE variants defining ε2/ε3/ε4 alleles and rs646776 were identified to be significantly associated with

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Arning, Astrid, Astrid Jeibmann, Stephan Köhnemann, et al. "ADAMTS genes and the risk of cerebral aneurysm." Journal of Neurosurgery 125, no. 2 (2016): 269–74. http://dx.doi.org/10.3171/2015.7.jns154.

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OBJECTIVE Cerebral aneurysms (CAs) affect 2%–5% of the population, and familial predisposition plays a significant role in CA pathogenesis. Several lines of evidence suggest that genetic variations in matrix metalloproteinase genes (MMP) are involved in the etiopathology of CAs. The authors performed a case-control study to investigate the effect of 4 MMP variants from the ADAMTS family on the pathogenesis of CAs. METHODS To identify susceptible genetic variants, the authors investigated 8 single nucleotide polymorphisms (SNPs) in 4 genes from the ADAMTS family (ADAMTS2, -7, -12, and -13) know

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Veyrat-Durebex, Charlotte, Nathalie Bouzamondo, Morgane Le Mao, et al. "Metabolomics signatures of a subset of RET variants according to their oncogenic risk level." Endocrine-Related Cancer 26, no. 3 (2019): 379–89. http://dx.doi.org/10.1530/erc-18-0314.

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Thirty percent of medullary thyroid carcinomas (MTCs) are related to dominant germline pathogenic variants in the RET proto-oncogene. According to their aggressiveness, these pathogenic variants are classified in three risk levels: ‘moderate’, ‘high’ and ‘highest’. The present study compares the metabolomics profiles of five pathogenic variants, whether already classified or not. We have generated six stable murine fibroblast cell lines (NIH3T3) expressing the WT allele or variants of the human RET gene, with different levels of pathogenicity, including the M918V variant that is yet to be accu

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Nguyen-Dumont, Tú, James G. Dowty, Jason A. Steen, et al. "Population-Based Estimates of the Age-Specific Cumulative Risk of Breast Cancer for Pathogenic Variants in CHEK2: Findings from the Australian Breast Cancer Family Registry." Cancers 13, no. 6 (2021): 1378. http://dx.doi.org/10.3390/cancers13061378.

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Case-control studies of breast cancer have consistently shown that pathogenic variants in CHEK2 are associated with about a 3-fold increased risk of breast cancer. Information about the recurrent protein-truncating variant CHEK2 c.1100delC dominates this estimate. There have been no formal estimates of age-specific cumulative risk of breast cancer for all CHEK2 pathogenic (including likely pathogenic) variants combined. We conducted a population-based case-control-family study of pathogenic CHEK2 variants (26 families, 1071 relatives) and estimated the age-specific cumulative risk of breast ca

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Foley, Georgea R., James R. Marthick, Sionne E. Lucas, et al. "Germline Sequencing of DNA Damage Repair Genes in Two Hereditary Prostate Cancer Cohorts Reveals New Disease Risk-Associated Gene Variants." Cancers 16, no. 13 (2024): 2482. http://dx.doi.org/10.3390/cancers16132482.

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Rare, inherited variants in DNA damage repair (DDR) genes have a recognised role in prostate cancer (PrCa) susceptibility. In addition, these genes are therapeutically targetable. While rare variants are informing clinical management in other common cancers, defining the rare disease-associated variants in PrCa has been challenging. Here, whole-genome and -exome sequencing data from two independent, high-risk Australian and North American familial PrCa datasets were interrogated for novel DDR risk variants. Rare DDR gene variants (predicted to be damaging and present in two or more family memb

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Nurmi, Anna K., Maija Suvanto, Joe Dennis, Kristiina Aittomäki, Carl Blomqvist, and Heli Nevanlinna. "Pathogenic Variant Spectrum in Breast Cancer Risk Genes in Finnish Patients." Cancers 14, no. 24 (2022): 6158. http://dx.doi.org/10.3390/cancers14246158.

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Recurrent pathogenic variants have been detected in several breast and ovarian cancer (BC/OC) risk genes in the Finnish population. We conducted a gene-panel sequencing and copy number variant (CNV) analysis to define a more comprehensive spectrum of pathogenic variants in BRCA1, BRCA2, PALB2, CHEK2, ATM, BARD1, RAD51C, RAD51D, BRIP1, and FANCM genes in Finnish BC patients. The combined frequency of pathogenic variants in the BRCA1/2 genes was 1.8% in 1356 unselected patients, whereas variants in the other genes were detected altogether in 8.3% of 1356 unselected patients and in 12.9% of 699 f

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Olabisi, Opeyemi A., Jia-Yue Zhang, Lynn VerPlank, et al. "APOL1 kidney disease risk variants cause cytotoxicity by depleting cellular potassium and inducing stress-activated protein kinases." Proceedings of the National Academy of Sciences 113, no. 4 (2015): 830–37. http://dx.doi.org/10.1073/pnas.1522913113.

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Two specific genetic variants of the apolipoprotein L1 (APOL1) gene are responsible for the high rate of kidney disease in people of recent African ancestry. Expression in cultured cells of these APOL1 risk variants, commonly referred to as G1 and G2, results in significant cytotoxicity. The underlying mechanism of this cytotoxicity is poorly understood. We hypothesized that this cytotoxicity is mediated by APOL1 risk variant-induced dysregulation of intracellular signaling relevant for cell survival. To test this hypothesis, we conditionally expressed WT human APOL1 (G0), the APOL1 G1 variant

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Soufir, N., L. Bagait Miss, C. Oudin Miss, et al. "MC1R variants and melanoma risk: First study on Melan-Cohort." Journal of Clinical Oncology 25, no. 18_suppl (2007): 10524. http://dx.doi.org/10.1200/jco.2007.25.18_suppl.10524.

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10524 Background: The presence of functional variants of MC1R, has been shown to be associated with melanoma (MM) risk in different populations worldwide. We had previously shown in a first case - control pilot study that MC1R variants were associated the risk of melanoma (MM) in France. Methods: In order to confirm and precise these results on a larger sample, we performed a case-control study with patients from Melan-Cohort, a prospective cohort from the Paris’ region. After signature of informed consents and extraction of blood DNAs, MC1R variants were sought by automatic sequencing in 270

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Hawkins, Gregory A., David J. Friedman, Lingyi Lu, et al. "Re-Sequencing of the APOL1-APOL4 and MYH9 Gene Regions in African Americans Does Not Identify Additional Risks for CKD Progression." American Journal of Nephrology 42, no. 2 (2015): 99–106. http://dx.doi.org/10.1159/000439448.

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Background: In African Americans (AAs), APOL1 G1 and G2 nephropathy risk variants are associated with non-diabetic end-stage kidney disease (ESKD) in an autosomal recessive pattern. Additional risk and protective genetic variants may be present near the APOL1 loci, since earlier age ESKD is observed in some AAs with one APOL1 renal-risk variant, and because the adjacent gene MYH9 is associated with nephropathy in populations lacking G1 and G2 variants. Methods: Re-sequencing was performed across a ∼275 kb region encompassing the APOL1-APOL4 and MYH9 genes in 154 AA cases with non-diabetic ESKD

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Reilly, Christopher R., Mikko Myllymäki, Robert Redd, et al. "The clinical and functional effects of TERT variants in myelodysplastic syndrome." Blood 138, no. 10 (2021): 898–911. http://dx.doi.org/10.1182/blood.2021011075.

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Abstract Germline pathogenic TERT variants are associated with short telomeres and an increased risk of developing myelodysplastic syndrome (MDS) among patients with a telomere biology disorder. We identified TERT rare variants in 41 of 1514 MDS patients (2.7%) without a clinical diagnosis of a telomere biology disorder who underwent allogeneic transplantation. Patients with a TERT rare variant had shorter telomere length (P &lt; .001) and younger age at MDS diagnosis (52 vs 59 years, P = .03) than patients without a TERT rare variant. In multivariable models, TERT rare variants were assoc

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Zenteno, Juan C., Oscar F. Chacón-Camacho, Vianey Ordoñez-Labastida, et al. "Identification of Genetic Variants for Diabetic Retinopathy Risk Applying Exome Sequencing in Extreme Phenotypes." BioMed Research International 2024 (January 13, 2024): 1–8. http://dx.doi.org/10.1155/2024/2052766.

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Background. Diabetic retinopathy (DR) risk has been shown to vary depending on ethnic backgrounds, and thus, it is worthy that underrepresented populations are analyzed for the potential identification of DR-associated genetic variants. We conducted a case-control study for the identification of DR-risk variants in Mexican population. Methods. We ascertained 60 type 2 diabetes mellitus (T2DM) patients. Cases (n=30) were patients with advanced proliferative DR (PDR) with less than 15 years after a T2DM diagnosis while controls (n=30) were patients with no DR 15 years after the diagnosis of T2DM

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Zavaleta, Elizabeth, Nelly Solis, Maria Isabel Palacios, et al. "Genetic Characterization in High-Risk Individuals from a Low-Resource City of Peru." Cancers 14, no. 22 (2022): 5603. http://dx.doi.org/10.3390/cancers14225603.

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Background: Genetic testing for hereditary cancers is inconsistently applied within the healthcare systems in Latin America. In Peru, the prevalence and spectrum of cancer-predisposing germline variants is thus poorly characterized. Purpose: To determine the spectrum and prevalence of cancer-predisposing germline variants and variants of uncertain significance (VUS) in high-risk individuals located in a Peruvian low-resource setting city. Methods: Individuals presenting clinical criteria for hereditary cancer syndromes or being unaffected with familial history of cancer were included in the st

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Bryant, Nicole, Nicole Malpeli, Julia Ziaee, Cornelis Blauwendraat, Zhiyong Liu, and Andrew B. West. "Identification of LRRK2 missense variants in the accelerating medicines partnership Parkinson’s disease cohort." Human Molecular Genetics 30, no. 6 (2021): 454–66. http://dx.doi.org/10.1093/hmg/ddab058.

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Abstract Pathogenic missense variants in the leucine-rich repeat kinase 2 (LRRK2) gene have been identified through linkage analysis in familial Parkinson disease (PD). Subsequently, other missense variants with lower effect sizes on PD risk have emerged, as well as non-coding polymorphisms (e.g. rs76904798) enriched in PD cases in genome-wide association studies. Here we leverage recent whole-genome sequences from the Accelerating Medicines Partnership-Parkinson’s Disease (AMP-PD) and the Genome Aggregation (gnomAD) databases to characterize novel missense variants in LRRK2 and explore their

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Hostetler, Ellen M., Ellen S. Regalado, Dong-Chuan Guo, et al. "SMAD3 pathogenic variants: risk for thoracic aortic disease and associated complications from the Montalcino Aortic Consortium." Journal of Medical Genetics 56, no. 4 (2019): 252–60. http://dx.doi.org/10.1136/jmedgenet-2018-105583.

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BackgroundPathogenic variants in SMAD3 cause thoracic aortic aneurysms and dissections, along with aneurysms and rupture of other arteries. Here, we examined differences in clinical presentation of aortic events (dissection or surgical repair of an aneurysm) with respect to age and variant type in an international cohort of individuals with SMAD3 variants.MethodsAortic status and events, vital status and clinical features were abstracted through retrospective review of medical records of 212 individuals with 51 unique SMAD3 variants, including haploinsufficiency (HI) and missense substitutions

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Trottier, Amy M., Lawrence J. Druhan, Ira L. Kraft, et al. "Heterozygous germ line CSF3R variants as risk alleles for development of hematologic malignancies." Blood Advances 4, no. 20 (2020): 5269–84. http://dx.doi.org/10.1182/bloodadvances.2020002013.

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Abstract Colony-stimulating factor 3 receptor (CSF3R) encodes the receptor for granulocyte colony-stimulating factor (G-CSF), a cytokine vital for granulocyte proliferation and differentiation. Acquired activating heterozygous variants in CSF3R are the main cause of chronic neutrophilic leukemia, a hyperproliferative disorder. In contrast, biallelic germ line hypomorphic variants in CSF3R are a rare cause of severe congenital neutropenia, a hypoproliferative condition. The impact of heterozygous germ line CSF3R variants, however, is unknown. We identified CSF3R as a new germ line hematologic m

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AI-Ghalayini, Kamal W., Mohammed A. Salama, Hadia Bassam Al Mahdi, et al. "Identification of Genetic Variants Associated With Myocardial Infarction in Saudi Arabia." Heart Surgery Forum 23, no. 4 (2020): E517—E523. http://dx.doi.org/10.1532/hsf.2955.

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The genetic variants associated with various genetic disorders have not been identified decisively in Saudi Arabia. Among these variants, six known for their association with coronary artery disease or myocardial infarction (MI) were studied on Saudi patients. Reference single nucleotide polymorphisms (SNPs) of these variants are rs5174, rs11591147, rs2259816, rs111245230, rs3782886 and rs2259820, referring to genes LRP8, PCSK9, HNF1A, SVEP1, BRAP and HNF1A, respectively. The analysis employed polymerase chain reaction panel coupled with mini-sequencing (SNapShot multiplex system) in order to

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Reiner, Anne S., Mark E. Robson, Lene Mellemkjær, et al. "Radiation Treatment, ATM, BRCA1/2, and CHEK2*1100delC Pathogenic Variants and Risk of Contralateral Breast Cancer." JNCI: Journal of the National Cancer Institute 112, no. 12 (2020): 1275–79. http://dx.doi.org/10.1093/jnci/djaa031.

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Abstract Whether radiation therapy (RT) affects contralateral breast cancer (CBC) risk in women with pathogenic germline variants in moderate- to high-penetrance breast cancer–associated genes is unknown. In a population-based case-control study, we examined the association between RT; variants in ATM, BRCA1/2, or CHEK2*1100delC; and CBC risk. We analyzed 708 cases of women with CBC and 1399 controls with unilateral breast cancer, all diagnosed with first invasive breast cancer between 1985 and 2000 and aged younger than 55 years at diagnosis and screened for variants in breast cancer–associat

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Zhou, Xiaopu, Yu Chen, Kin Y. Mok, et al. "Identification of genetic risk factors in the Chinese population implicates a role of immune system in Alzheimer’s disease pathogenesis." Proceedings of the National Academy of Sciences 115, no. 8 (2018): 1697–706. http://dx.doi.org/10.1073/pnas.1715554115.

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Alzheimer’s disease (AD) is a leading cause of mortality among the elderly. We performed a whole-genome sequencing study of AD in the Chinese population. In addition to the variants identified in or around the APOE locus (sentinel variant rs73052335, P = 1.44 × 10−14), two common variants, GCH1 (rs72713460, P = 4.36 × 10−5) and KCNJ15 (rs928771, P = 3.60 × 10−6), were identified and further verified for their possible risk effects for AD in three small non-Asian AD cohorts. Genotype–phenotype analysis showed that KCNJ15 variant rs928771 affects the onset age of AD, with earlier disease onset i

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Dinur, Tama, Michal Becker-Cohen, Shoshana Revel-Vilk, Ari Zimran, and David Arkadir. "Parkinson’s Clustering in Families of Non-Neuronopathic N370S GBA Mutation Carriers Indicates the Presence of Genetic Modifiers." Journal of Parkinson's Disease 11, no. 2 (2021): 615–18. http://dx.doi.org/10.3233/jpd-202422.

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Low penetrance of Parkinson’s disease (PD) associated with GBA pathogenic variants indicates the presence of modifiers genes. Clusters of PD cases in certain families with GBA variants would serve as a strong evidence for the clinical relevance of such modifiers. We studied eight family trees of non-Parkinsonian, GBA-N370S homozygote, Gaucher probands, with multiple cases of PD. Differences in PD risk associated with different GBA variants were balanced by variant homozygosity. In these families, all PD cases stemmed from only one of the proband’s parents. This observation provides a direct ep

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