1
|
Zeng S, Zhou X, He R, Zhao Y, Liu Z, Xu Q, Guo J, Yan X, Li J, Tang B, Sun Q. Association Analysis of Essential Tremor-Associated Genetic Variants in Sporadic Late-Onset Parkinson's Disease. Tremor Other Hyperkinet Mov (N Y) 2024; 14:25. [PMID: 38737298 PMCID: PMC11086585 DOI: 10.5334/tohm.885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 04/25/2024] [Indexed: 05/14/2024] Open
Abstract
Background Parkinson's disease (PD) and Essential tremor (ET) are the two most common tremor diseases with recognized genetic pathogenesis. The overlapping clinical features suggest they may share genetic predispositions. Our previous study systematically investigated the association between rare coding variants in ET-associated genes and early-onset PD (EOPD), and found the suggestive association between teneurin transmembrane protein 4 (TENM4) and EOPD. In the current research, we explored the potential genetic interplay between ET-associated genetic loci/genes and sporadic late-onset PD (LOPD). Methods We performed whole-genome sequencing in the 1962 sporadic LOPD cases and 1279 controls from mainland China. We first used logistic regression analysis to test the top 16 SNPs identified by the ET genome-wide association study for the association between ET and LOPD. Then we applied the optimized sequence kernel association testing to explore the rare variant burden of 33 ET-associated genes in this cohort. Results We did not observe a significant association between the included SNPs with LOPD. We also did not discover a significant burden of rare deleterious variants of ET-associated genes in association with LOPD risk. Conclusion Our results do not support the role of ET-associated genetic loci and variants in LOPD. Highlights 1962 cases and 1279 controls were recruited to study the potential genetic interplay between ET-associated genetic loci/variants and sporadic LOPD.No significant association between the ET-associated SNPs and LOPD were observed.No significant burden of rare deleterious variants of ET-associated gene in LOPD risk were found.
Collapse
Affiliation(s)
- Sheng Zeng
- Department of Geriatrics, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan, 410008, China
| | - Xun Zhou
- Department of Geriatric Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Runcheng He
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Yuwen Zhao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Zhenhua Liu
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan, 410008, China
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Qian Xu
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan, 410008, China
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Jifeng Guo
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan, 410008, China
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Xinxiang Yan
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan, 410008, China
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Jinchen Li
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan, 410008, China
- Department of Geriatric Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Beisha Tang
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan, 410008, China
- Department of Geriatric Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, 410008, China
| | - Qiying Sun
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan, 410008, China
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, 410008, China
| |
Collapse
|
2
|
Yoshida T, Matsubara K, Ogata-Kawata H, Miyado M, Ishiwata K, Nakabayashi K, Hata K, Kageyama I, Tamaoka S, Shimada Y, Fukami M, Sasaki S. Variations in gender identity and sexual orientation of university students. Sex Med 2023; 11:qfad057. [PMID: 37965377 PMCID: PMC10642543 DOI: 10.1093/sexmed/qfad057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 09/28/2023] [Accepted: 10/05/2023] [Indexed: 11/16/2023] Open
Abstract
Background Previous studies have shown that a small percentage of people in the general population have atypical gender identity and/or sexual orientation. Aim This study aimed to explore variations in gender identity and sexual orientation in university students and determine genetic factors associated with these variations. Methods Deviations from complete gender congruence and exclusive heterosexual orientation in 736 Japanese university students were quantitatively assessed with self-assessment questionnaires. Next, we conducted genetic tests for 80 participants who showed relatively low gender identity scores and/or atypical sexual orientation. These genetic tests consisted of repeat number analysis of the androgen receptor gene (AR) and a SKAT-O: an optimal unified sequence kernel association test, which is an exome-based rare variant association study. The results of the genetic tests were compared with the Japanese reference data and the results of our 637 control samples. Outcomes We calculated the gender identity and sexual orientation scores of all participants and analyzed the molecular data of 80 selected participants. Results The gender identity scores of 736 participants were broadly distributed: only ~15% of natal males and ~5% of natal females had the maximum score that corresponds to complete gender congruence. The sexual orientation scores also varied: ~80% of natal males and ~60% of natal females showed exclusive heterosexual orientation. We found no association between gender characteristics and AR repeat numbers. The SKAT-O showed that rare damaging variants of TDRP and 3 other genes were more common in the 80 participants than in the control group. Clinical Implications Our data support the view that gender is a phenotypic continuum rather than a binary trait. Strength and Limitations This study quantitatively assessed the gender characteristics of a large cohort of university students. Moreover, we conducted systematic screening for genetic factors associated with gender variations. The weaknesses of the study were the limited analytic power of the questionnaires, the relatively small sample for molecular analyses, and incomplete clinical information and relatively advanced ages of the control group. Conclusion This study revealed significant variations in gender identity and sexual orientation in university students, which may be partly associated with variants in TDRP or other genes.
Collapse
Affiliation(s)
- Tomoko Yoshida
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, 157-8535, Japan
| | - Keiko Matsubara
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, 157-8535, Japan
| | - Hiroko Ogata-Kawata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, 157-8535, Japan
| | - Mami Miyado
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, 157-8535, Japan
| | - Keisuke Ishiwata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, 157-8535, Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, 157-8535, Japan
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, 157-8535, Japan
| | - Ikuko Kageyama
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, 157-8535, Japan
| | - Satoshi Tamaoka
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, 157-8535, Japan
| | - Yukiko Shimada
- Department of Child Studies, Faculty of Human Development, Kokugakuin University, Kanagawa, 225-0003, Japan
| | - Maki Fukami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, 157-8535, Japan
| | - Shoko Sasaki
- Graduate School of Arts and Letters, Meiji University, Tokyo ,101-0064, Japan
| |
Collapse
|
3
|
Minnai F, Noci S, Mangano N, De Cecco L, Meazza C, Terenziani M, Massimino M, Colombo F. A pilot exome sequencing study suggests that germline variants influence methotrexate-induced toxicities in pediatric patients with localized osteosarcoma. Pediatr Blood Cancer 2023:e30501. [PMID: 37338505 DOI: 10.1002/pbc.30501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/30/2023] [Accepted: 06/05/2023] [Indexed: 06/21/2023]
Abstract
INTRODUCTION Osteosarcoma (OS) is a rare pediatric cancer for which therapeutic approaches, including chemotherapy and surgery, show a wide interindividual variability in patient response, both in terms of adverse events and therapy efficacy. There is growing evidence that this individual variable response to therapies is also influenced by inherited genetic variations. However, the results obtained to date in these pediatric cancers have been contradictory and often lack validation in independent series. Additionally, these studies frequently focused only on a limited number of polymorphisms in candidate genes. METHODS In order to identify germline coding variations associated with individual differences in adverse events occurrence in pediatric patients affected by localized OS, we carried out an exome-wide association study in 24 OS patients treated with methotrexate, cisplatin, and doxorubicin, using the SNP-Set (Sequence) Kernel Association Test (SKAT), optimized for small sample size. RESULTS Gene sets significantly associated (FDR < .05) with neutropenia and hepatotoxicity induced by methotrexate were identified. Some of the identified genes map in loci previously associated with similar phenotypes (e.g., leukocyte count, alkaline phosphatase levels). CONCLUSION Further studies in larger series and with functional characterization of the identified associations are needed; nonetheless, this pilot study prompts the relevance of broadly investigating variants along the whole genome, to identify new potential pharmacogenes, beyond drug metabolism, transport, and receptor candidate genes.
Collapse
Affiliation(s)
- Francesca Minnai
- Institute for Biomedical Technologies, National Research Council, Segrate (MI), Italy
- Department of Medical Biotechnology and Translational Medicine (BioMeTra), Università degli Studi di Milano, Milan, Italy
| | - Sara Noci
- Genetic Epidemiology and Pharmacogenomics, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Nunzia Mangano
- Genetic Epidemiology and Pharmacogenomics, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Loris De Cecco
- Integrated Biology of Rare Tumors Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Cristina Meazza
- Pediatric Oncology Unit, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Monica Terenziani
- Pediatric Oncology Unit, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Maura Massimino
- Pediatric Oncology Unit, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Francesca Colombo
- Institute for Biomedical Technologies, National Research Council, Segrate (MI), Italy
- Genetic Epidemiology and Pharmacogenomics, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| |
Collapse
|
4
|
Zeng Q, Pan H, Zhao Y, Wang Y, Xu Q, Tan J, Yan X, Li J, Tang B, Guo J. Evaluation of common and rare variants of Alzheimer's disease-causal genes in Parkinson's disease. Parkinsonism Relat Disord 2022; 97:8-14. [PMID: 35276586 DOI: 10.1016/j.parkreldis.2022.02.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 02/14/2022] [Accepted: 02/22/2022] [Indexed: 11/17/2022]
Abstract
INTRODUCTION Parkinson's disease (PD) and Alzheimer's disease (AD) are the most common neurodegenerative diseases in the elderly. Recently, some variants of AD-causal genes (APP, PSEN1, PSEN2) have been reported in PD. In this study, we investigated the association between coding variants of AD-causal genes and PD in a large Chinese population cohort. METHODS We performed whole-exome sequencing (WES) on 1,917 patients with early-onset or familial PD and 1,652 controls, and whole-genome sequencing (WGS) on 1,962 sporadic late-onset PD and 1,279 controls. Genetic and phenotypic data were analyzed with regression analyses and the optimized sequence kernel association test. Further validation study was performed by Fisher's exact test. RESULTS We found that rs75733498 in the PSEN2 gene was significantly associated with early-onset or familial PD; however, no significant relationship was discovered between rs75733498 and sporadic late-onset PD. The result of the validation study still revealed a significant association between rs75733498 and PD. We observed a suggestive association with APP gene in early-onset or familial PD when considering damaging missense variants alone (p = 0.018) or combined with loss-of-function variants (p = 0.029). Further phenotypic analysis did not demonstrate any significant associations. CONCLUSION Our results support a possible genetic contribution of AD-causal genes to PD. These findings warrant further genetic and functional confirmation, and more powerful association studies will better decipher the mechanisms of PD.
Collapse
Affiliation(s)
- Qian Zeng
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Hongxu Pan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Yuwen Zhao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Yige Wang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Qian Xu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Jieqiong Tan
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China
| | - Xinxiang Yan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Jinchen Li
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China; Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China; Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, China
| | - Beisha Tang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China; Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China; Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Jifeng Guo
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China; Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China; Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China; Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic Diseases, Changsha, China.
| |
Collapse
|
5
|
Guan Z, Shen R, Begg CB. Exome-Wide Pan-Cancer Analysis of Germline Variants in 8,719 Individuals Finds Little Evidence of Rare Variant Associations. Hum Hered 2021; 86:34-44. [PMID: 34718237 DOI: 10.1159/000519355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 08/30/2021] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Many cancer types show considerable heritability, and extensive research has been done to identify germline susceptibility variants. Linkage studies have discovered many rare high-risk variants, and genome-wide association studies (GWAS) have discovered many common low-risk variants. However, it is believed that a considerable proportion of the heritability of cancer remains unexplained by known susceptibility variants. The "rare variant hypothesis" proposes that much of the missing heritability lies in rare variants that cannot reliably be detected by linkage analysis or GWAS. Until recently, high sequencing costs have precluded extensive surveys of rare variants, but technological advances have now made it possible to analyze rare variants on a much greater scale. OBJECTIVES In this study, we investigated associations between rare variants and 14 cancer types. METHODS We ran association tests using whole-exome sequencing data from The Cancer Genome Atlas (TCGA) and validated the findings using data from the Pan-Cancer Analysis of Whole Genomes Consortium (PCAWG). RESULTS We identified four significant associations in TCGA, only one of which was replicated in PCAWG (BRCA1 and ovarian cancer). CONCLUSIONS Our results provide little evidence in favor of the rare variant hypothesis. Much larger sample sizes may be needed to detect undiscovered rare cancer variants.
Collapse
Affiliation(s)
- Zoe Guan
- Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, New York, USA
| | - Ronglai Shen
- Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, New York, USA
| | - Colin B Begg
- Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, New York, USA
| |
Collapse
|
6
|
De Vilder EYG, Martin L, Lefthériotis G, Coucke P, Van Nieuwerburgh F, Vanakker OM. Rare Modifier Variants Alter the Severity of Cardiovascular Disease in Pseudoxanthoma Elasticum: Identification of Novel Candidate Modifier Genes and Disease Pathways Through Mixture of Effects Analysis. Front Cell Dev Biol 2021; 9:612581. [PMID: 34169069 PMCID: PMC8218811 DOI: 10.3389/fcell.2021.612581] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 05/11/2021] [Indexed: 12/30/2022] Open
Abstract
Introduction: Pseudoxanthoma elasticum (PXE), an ectopic mineralization disorder caused by pathogenic ABCC6 variants, is characterized by skin, ocular and cardiovascular (CV) symptoms. Due to striking phenotypic variability without genotype-phenotype correlations, modifier genes are thought to play a role in disease variability. In this study, we evaluated the collective modifying effect of rare variants on the cardiovascular phenotype of PXE. Materials and Methods: Mixed effects of rare variants were assessed by Whole Exome Sequencing in 11 PXE patients with an extreme CV phenotype (mild/severe). Statistical analysis (SKAT-O and C-alpha testing) was performed to identify new modifier genes for the CV PXE phenotype and enrichment analysis for genes significantly associated with the severe cohort was used to evaluate pathway and gene ontology features. Results Respectively 16 (SKAT-O) and 74 (C-alpha) genes were significantly associated to the severe cohort. Top significant genes could be stratified in 3 groups–calcium homeostasis, association with vascular disease and induction of apoptosis. Comparative analysis of both analyses led to prioritization of four genes (NLRP1, SELE, TRPV1, and CSF1R), all signaling through IL-1B. Conclusion This study explored for the first time the cumulative effect of rare variants on the severity of cardiovascular disease in PXE, leading to a panel of novel candidate modifier genes and disease pathways. Though further validation is essential, this panel may aid in risk stratification and genetic counseling of PXE patients and will help to gain new insights in the PXE pathophysiology.
Collapse
Affiliation(s)
- Eva Y G De Vilder
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.,The Research Foundation - Flanders, Ghent, Belgium.,Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium
| | - Ludovic Martin
- Department of Dermatology, Angers University Hospital, Angers, France
| | - Georges Lefthériotis
- Department of Vascular Physiology and Sports Medicine, Angers University, Angers, France
| | - Paul Coucke
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Filip Van Nieuwerburgh
- Department of Pharmaceutics, Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
| | - Olivier M Vanakker
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| |
Collapse
|
7
|
Patel D, Zhang X, Farrell JJ, Lunetta KL, Farrer LA. Set-Based Rare Variant Expression Quantitative Trait Loci in Blood and Brain from Alzheimer Disease Study Participants. Genes (Basel) 2021; 12:419. [PMID: 33804025 PMCID: PMC7999141 DOI: 10.3390/genes12030419] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/04/2021] [Accepted: 03/10/2021] [Indexed: 12/12/2022] Open
Abstract
Because studies of rare variant effects on gene expression have limited power, we investigated set-based methods to identify rare expression quantitative trait loci (eQTL) related to Alzheimer disease (AD). Gene-level and pathway-level cis rare-eQTL mapping was performed genome-wide using gene expression data derived from blood donated by 713 Alzheimer's Disease Neuroimaging Initiative participants and from brain tissues donated by 475 Religious Orders Study/Memory and Aging Project participants. The association of gene or pathway expression with a set of all cis potentially regulatory low-frequency and rare variants within 1 Mb of genes was evaluated using SKAT-O. A total of 65 genes expressed in the brain were significant targets for rare expression single nucleotide polymorphisms (eSNPs) among which 17% (11/65) included established AD genes HLA-DRB1 and HLA-DRB5. In the blood, 307 genes were significant targets for rare eSNPs. In the blood and the brain, GNMT, LDHC, RBPMS2, DUS2, and HP were targets for significant eSNPs. Pathway enrichment analysis revealed significant pathways in the brain (n = 9) and blood (n = 16). Pathways for apoptosis signaling, cholecystokinin receptor (CCKR) signaling, and inflammation mediated by chemokine and cytokine signaling were common to both tissues. Significant rare eQTLs in inflammation pathways included five genes in the blood (ALOX5AP, CXCR2, FPR2, GRB2, IFNAR1) that were previously linked to AD. This study identified several significant gene- and pathway-level rare eQTLs, which further confirmed the importance of the immune system and inflammation in AD and highlighted the advantages of using a set-based eQTL approach for evaluating the effect of low-frequency and rare variants on gene expression.
Collapse
Affiliation(s)
- Devanshi Patel
- Bioinformatics Graduate Program, Boston University, Boston, MA 02215, USA;
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA 02118, USA; (X.Z.); (J.J.F.)
| | - Xiaoling Zhang
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA 02118, USA; (X.Z.); (J.J.F.)
| | - John J. Farrell
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA 02118, USA; (X.Z.); (J.J.F.)
| | - Kathryn L. Lunetta
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA;
| | - Lindsay A. Farrer
- Bioinformatics Graduate Program, Boston University, Boston, MA 02215, USA;
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA 02118, USA; (X.Z.); (J.J.F.)
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA;
- Department of Ophthalmology, Boston University School of Medicine, Boston, MA 02118, USA
- Department of Neurology, Boston University School of Medicine, Boston, MA 02118, USA
- Department of Epidemiology, Boston University School of Public Health, Boston, MA 02118, USA
| |
Collapse
|
8
|
Saini P, Rudakou U, Yu E, Ruskey JA, Asayesh F, Laurent SB, Spiegelman D, Fahn S, Waters C, Monchi O, Dauvilliers Y, Dupré N, Greenbaum L, Hassin-Baer S, Espay AJ, Rouleau GA, Alcalay RN, Fon EA, Postuma RB, Gan-Or Z. Association study of DNAJC13, UCHL1, HTRA2, GIGYF2, and EIF4G1 with Parkinson's disease. Neurobiol Aging 2020; 100:119.e7-119.e13. [PMID: 33239198 DOI: 10.1016/j.neurobiolaging.2020.10.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 10/05/2020] [Accepted: 10/17/2020] [Indexed: 12/13/2022]
Abstract
Rare mutations in genes originally discovered in multigenerational families have been associated with increased risk of Parkinson's disease (PD). The involvement of rare variants in DNAJC13, UCHL1, HTRA2, GIGYF2, and EIF4G1 loci has been poorly studied or has produced conflicting results across cohorts. However, they are still being often referred to as "PD genes" and used in different models. To further elucidate the role of these 5 genes in PD, we fully sequenced them using molecular inversion probes in 2408 patients with PD and 3444 controls from 3 different cohorts. A total of 788 rare variants were identified across the 5 genes and 3 cohorts. Burden analyses and optimized sequence Kernel association tests revealed no significant association between any of the genes and PD after correction for multiple comparisons. Our results do not support an association of the 5 tested genes with PD. Combined with previous studies, it is unlikely that any of these genes plays an important role in PD. Their designation as "PARK" genes should be reconsidered.
Collapse
Affiliation(s)
- Prabhjyot Saini
- Montreal Neurological Institute, McGill University, Montréal, Quebec, Canada; Department of Human Genetics, McGill University, Montréal, Quebec, Canada
| | - Uladzislau Rudakou
- Montreal Neurological Institute, McGill University, Montréal, Quebec, Canada; Department of Human Genetics, McGill University, Montréal, Quebec, Canada
| | - Eric Yu
- Montreal Neurological Institute, McGill University, Montréal, Quebec, Canada; Department of Human Genetics, McGill University, Montréal, Quebec, Canada
| | - Jennifer A Ruskey
- Montreal Neurological Institute, McGill University, Montréal, Quebec, Canada; Department of Neurology and neurosurgery, McGill University, Montréal, Quebec, Canada
| | - Farnaz Asayesh
- Montreal Neurological Institute, McGill University, Montréal, Quebec, Canada; Department of Neurology and neurosurgery, McGill University, Montréal, Quebec, Canada
| | - Sandra B Laurent
- Montreal Neurological Institute, McGill University, Montréal, Quebec, Canada; Department of Human Genetics, McGill University, Montréal, Quebec, Canada
| | - Dan Spiegelman
- Montreal Neurological Institute, McGill University, Montréal, Quebec, Canada; Department of Neurology and neurosurgery, McGill University, Montréal, Quebec, Canada
| | - Stanley Fahn
- Department of Neurology, College of Physicians and Surgeons, Columbia University Medical Center, New York, NY, USA
| | - Cheryl Waters
- Department of Neurology, College of Physicians and Surgeons, Columbia University Medical Center, New York, NY, USA
| | - Oury Monchi
- Department of Clinical Neurosciences and Department of Radiology, University of Calgary, Calgary, Alberta, Canada; Cumming School of Medicine, Hotchkiss Brain Institute, Calgary, Alberta, Canada
| | - Yves Dauvilliers
- Department of Neurology, National Reference Center for Narcolepsy, Sleep Unit, Gui-de-Chauliac Hospital, CHU Montpellier, University of Montpellier, Inserm U1061, Montpellier, France
| | - Nicolas Dupré
- Division of Neurosciences, CHU de Québec, Université Laval, Quebec City, Quebec, Canada; Department of Medicine, Faculty of Medicine, Université Laval, Québec, Quebec, Canada
| | - Lior Greenbaum
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel; The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Israel
| | - Sharon Hassin-Baer
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Department of Neurology, The Movement Disorders Institute, Sheba Medical Center, Tel Hashomer, Israel
| | - Alberto J Espay
- Department of Neurology, Gardner Family Center for Parkinson's Disease and Movement Disorders, University of Cincinnati, Cincinnati, OH, USA
| | - Guy A Rouleau
- Montreal Neurological Institute, McGill University, Montréal, Quebec, Canada; Department of Human Genetics, McGill University, Montréal, Quebec, Canada; Department of Neurology and neurosurgery, McGill University, Montréal, Quebec, Canada
| | - Roy N Alcalay
- Department of Neurology, College of Physicians and Surgeons, Columbia University Medical Center, New York, NY, USA; Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University Medical Center, New York, NY, USA
| | - Edward A Fon
- Montreal Neurological Institute, McGill University, Montréal, Quebec, Canada; Department of Neurology and neurosurgery, McGill University, Montréal, Quebec, Canada
| | - Ronald B Postuma
- Montreal Neurological Institute, McGill University, Montréal, Quebec, Canada; Department of Neurology and neurosurgery, McGill University, Montréal, Quebec, Canada
| | - Ziv Gan-Or
- Montreal Neurological Institute, McGill University, Montréal, Quebec, Canada; Department of Human Genetics, McGill University, Montréal, Quebec, Canada; Department of Neurology and neurosurgery, McGill University, Montréal, Quebec, Canada.
| |
Collapse
|
9
|
Scannell Bryan M, Argos M, Andrulis IL, Hopper JL, Chang-Claude J, Malone K, John EM, Gammon MD, Daly M, Terry MB, Buys SS, Huo D, Olopade O, Genkinger JM, Jasmine F, Kibriya MG, Chen L, Ahsan H. Limited influence of germline genetic variation on all-cause mortality in women with early onset breast cancer: evidence from gene-based tests, single-marker regression, and whole-genome prediction. Breast Cancer Res Treat 2017; 164:707-717. [PMID: 28503721 PMCID: PMC5510603 DOI: 10.1007/s10549-017-4287-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 05/08/2017] [Indexed: 11/30/2022]
Abstract
PURPOSE Women diagnosed with breast cancer have heterogeneous survival outcomes that cannot be fully explained by known prognostic factors, and germline variation is a plausible but unconfirmed risk factor. METHODS We used three approaches to test the hypothesis that germline variation drives some differences in survival: mortality loci identification, tumor aggressiveness loci identification, and whole-genome prediction. The 2954 study participants were women diagnosed with breast cancer before age 50, with a median follow-up of 15 years who were genotyped on an exome array. We first searched for loci in gene regions that were associated with all-cause mortality. We next searched for loci in gene regions associated with five histopathological characteristics related to tumor aggressiveness. Last, we also predicted 10-year all-cause mortality on a subset of 1903 participants (3,245,343 variants after imputation) using whole-genome prediction methods. RESULTS No risk loci for mortality or tumor aggressiveness were identified. This null result persisted when restricting to women with estrogen receptor-positive tumors, when examining suggestive loci in an independent study, and when restricting to previously published risk loci. Additionally, the whole-genome prediction model also found no evidence to support an association. CONCLUSION Despite multiple complementary approaches, our study found no evidence that mortality in women with early onset breast cancer is influenced by germline variation.
Collapse
Affiliation(s)
- Molly Scannell Bryan
- University of Chicago, Chicago, IL, USA.
- University of Illinois at Chicago, Chicago, IL, 60608-1264, USA.
| | - Maria Argos
- University of Illinois at Chicago, Chicago, IL, 60608-1264, USA
| | - Irene L Andrulis
- Lunefeld-Tanenbaum Research Institute, Sinai Health System and Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | | | - Jenny Chang-Claude
- Deutsches Krebsforschungszentrum in der Helmholtz-Gemeinshaft, Hamburg, Germany
- University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Esther M John
- Cancer Prevention Institute of California, Fremont, CA, USA
- Stanford University School of Medicine, Stanford, CA, USA
| | - Marilie D Gammon
- University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Mary Daly
- Fox Chase Cancer Center, Philadelphia, PA, USA
| | | | | | | | | | | | | | | | - Lin Chen
- University of Chicago, Chicago, IL, USA
| | | |
Collapse
|
10
|
Giri A, Mok KY, Jansen I, Sharma M, Tesson C, Mangone G, Lesage S, Bras JM, Shulman JM, Sheerin UM, Díez-Fairen M, Pastor P, Martí MJ, Ezquerra M, Tolosa E, Correia-Guedes L, Ferreira J, Amin N, van Duijn CM, van Rooij J, Uitterlinden AG, Kraaij R, Nalls M, Simón-Sánchez J. Lack of evidence for a role of genetic variation in TMEM230 in the risk for Parkinson's disease in the Caucasian population. Neurobiol Aging 2016; 50:167.e11-167.e13. [PMID: 27818000 DOI: 10.1016/j.neurobiolaging.2016.10.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 10/02/2016] [Indexed: 01/03/2023]
Abstract
Mutations in TMEM230 have recently been associated to Parkinson's disease (PD). To further understand the role of this gene in the Caucasian population, we interrogated our large repository of next generation sequencing data from unrelated PD cases and controls, as well as multiplex families with autosomal dominant PD. We identified 2 heterozygous missense variants in 2 unrelated PD cases and not in our control database (p.Y106H and p.I162V), and a heterozygous missense variant in 2 PD cases from the same family (p.A163T). However, data presented herein is not sufficient to support the role of any of these variants in PD pathology. A series of unified sequence kernel association tests also failed to show a cumulative effect of rare variation in this gene on the risk of PD in the general Caucasian population. Further evaluation of genetic data from different populations is needed to understand the genetic role of TMEM230 in PD etiology.
Collapse
Affiliation(s)
- Anamika Giri
- Department for Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany; German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Kin Y Mok
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Iris Jansen
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany; Department of Clinical Genetics, VU University Medical Center, Amsterdam, the Netherlands
| | - Manu Sharma
- Department for Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany; Centre for Genetic Epidemiology, Institute for Clinical Epidemiology and Applied Biometry, University of Tübingen, Tübingen, Germany
| | - Christelle Tesson
- Institut du Cerveau et de la Moelle épinière, ICM, Inserm U 1127, CNRS, UMR 7225, Sorbonne Universités, UPMC University Paris 06, UMR S 1127, AP-HP, Pitié-Salpêtrière Hospital, Paris, France
| | - Graziella Mangone
- Institut du Cerveau et de la Moelle épinière, ICM, Inserm U 1127, CNRS, UMR 7225, Sorbonne Universités, UPMC University Paris 06, UMR S 1127, AP-HP, Pitié-Salpêtrière Hospital, Paris, France
| | - Suzanne Lesage
- Institut du Cerveau et de la Moelle épinière, ICM, Inserm U 1127, CNRS, UMR 7225, Sorbonne Universités, UPMC University Paris 06, UMR S 1127, AP-HP, Pitié-Salpêtrière Hospital, Paris, France
| | - José M Bras
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Joshua M Shulman
- Departments of Neurology and Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Una-Marie Sheerin
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Mónica Díez-Fairen
- Movement Disorders Unit, Department of Neurology, Hospital Universitari Mutua de Terrassa, Barcelona, Spain
| | - Pau Pastor
- Movement Disorders Unit, Department of Neurology, Hospital Universitari Mutua de Terrassa, Barcelona, Spain
| | - María José Martí
- Movement Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, Barcelona, Spain; Institute of Biomedical Research August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Barcelona, Spain
| | - Mario Ezquerra
- Movement Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, Barcelona, Spain; Institute of Biomedical Research August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Barcelona, Spain
| | - Eduardo Tolosa
- Movement Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, Barcelona, Spain; Institute of Biomedical Research August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Barcelona, Spain
| | - Leonor Correia-Guedes
- Department of Neurosciences, Hospital de Santa Maria, Centro Hospitalar Lisboa Norte, Lisbon, Portugal
| | - Joaquim Ferreira
- Instituto de Medicina Molecular, Faculty of Medicine, University of Lisbon, Lisbon, Portugal
| | - Najaf Amin
- Department of Epidemiology, Erasmus MC, Rotterdam, the Netherlands
| | | | - Jeroen van Rooij
- Department of Internal Medicine, Erasmus MC, Rotterdam, the Netherlands; Netherlands Consortium for Healthy Ageing (NCHA), Rotterdam, the Netherlands
| | - André G Uitterlinden
- Department of Neurosciences, Hospital de Santa Maria, Centro Hospitalar Lisboa Norte, Lisbon, Portugal; Department of Epidemiology, Erasmus MC, Rotterdam, the Netherlands; Department of Internal Medicine, Erasmus MC, Rotterdam, the Netherlands; Netherlands Consortium for Healthy Ageing (NCHA), Rotterdam, the Netherlands
| | - Robert Kraaij
- Department of Epidemiology, Erasmus MC, Rotterdam, the Netherlands; Department of Internal Medicine, Erasmus MC, Rotterdam, the Netherlands; Netherlands Consortium for Healthy Ageing (NCHA), Rotterdam, the Netherlands
| | - Michael Nalls
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
| | - Javier Simón-Sánchez
- Department for Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany; German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany.
| |
Collapse
|
11
|
Wu B, Guan W, Pankow JS. On Efficient and Accurate Calculation of Significance P-Values for Sequence Kernel Association Testing of Variant Set. Ann Hum Genet 2016; 80:123-35. [PMID: 26757198 DOI: 10.1111/ahg.12144] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 11/12/2015] [Indexed: 01/04/2023]
Abstract
The objective of this paper is to discuss and develop alternative computational methods to accurately and efficiently calculate significance P-values for the commonly used sequence kernel association test (SKAT) and adaptive sum of SKAT and burden test (SKAT-O) for variant set association. We show that the existing software can lead to either conservative or inflated type I errors. We develop alternative and efficient computational algorithms that quickly compute the SKAT P-value and have well-controlled type I errors. In addition, we derive an alternative and simplified formula for calculating the significance P-value of SKAT-O, which sheds light on the development of efficient and accurate numerical algorithms. We implement the proposed methods in the publicly available R package that can be readily used or adapted to large-scale sequencing studies. Given that more and more large-scale exome and whole genome sequencing or re-sequencing studies are being conducted, the proposed methods are practically very important. We conduct extensive numerical studies to investigate the performance of the proposed methods. We further illustrate their usefulness with application to associations between rare exonic variants and fasting glucose levels in the Atherosclerosis Risk in Communities (ARIC) study.
Collapse
Affiliation(s)
- Baolin Wu
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Weihua Guan
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - James S Pankow
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| |
Collapse
|