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Lee D, Baek JH, Kim Y, Lee BD, Cho EY, Joo EJ, Ahn YM, Kim SH, Chung YC, Rami FZ, Kim SJ, Kim SW, Myung W, Ha TH, Lee HJ, Oh H, Lee KY, Kim MJ, Kang CY, Jeon S, Jo A, Yu H, Jeong S, Ha K, Kim B, Shim I, Cho C, Huang H, Won HH, Hong KS. Genome-wide association study and polygenic risk score analysis for schizophrenia in a Korean population. Asian J Psychiatr 2024; 102:104203. [PMID: 39293130 DOI: 10.1016/j.ajp.2024.104203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 08/13/2024] [Accepted: 08/28/2024] [Indexed: 09/20/2024]
Abstract
Although large-scale genome-wide association studies (GWASs) have revealed the genetic architecture of schizophrenia, these studies have mainly focused on populations of European ancestry. This study aimed to identify common genetic variants associated with schizophrenia in the Korean population and evaluate the performance of polygenic risk scores (PRSs) derived from large-scale GWASs across ancestries. In the Korean psychiatric GWAS project (KPGP), seven academic institutes and their affiliated hospitals across South Korea recruited a cohort of 1670 patients with DSM-IV-defined schizophrenia and 2271 healthy controls. A total of 6690,822 SNPs were tested for association with schizophrenia. We identified one previously unreported genome-wide significant locus rs2423464 (P = 2.83 × 10-11; odds ratio = 1.65; 95 % confidence interval = 1.43-1.91, minor allele frequency = 0.126). This variant was also associated with increased lysosomal-associated membrane protein family member 5 (LAMP5) gene expression. The PRS derived from the meta-analysis results of East Asian and European GWASs explained a larger proportion of the phenotypic variance in the Korean schizophrenia sample than the PRS of an East Asian or European GWAS. (R2 = 0.073 for meta-analysis; 0.028 for East Asian GWAS; 0.037 for European GWAS). GWASs involving diverse ethnic groups will expand our understanding of the genetic architecture of schizophrenia.
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Affiliation(s)
- Dongbin Lee
- Department of Digital Health, Samsung Advanced Institute for Health Sciences and Technology (SAIHST), Sungkyunkwan University, Samsung Medical Center, Seoul, South Korea
| | - Ji Hyun Baek
- Department of Psychiatry, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Yujin Kim
- Department of Digital Health, Samsung Advanced Institute for Health Sciences and Technology (SAIHST), Sungkyunkwan University, Samsung Medical Center, Seoul, South Korea
| | - Byung Dae Lee
- Pusan National University Research Park, Busan, South Korea
| | - Eun-Young Cho
- Samsung Biomedical Research Institute, Seoul, South Korea
| | - Eun-Jeong Joo
- Department of Psychiatry, Euijeongbu Eulji University Hospital, Euijeongbu, South Korea; Department of Neuropsychiatry, Eulji University, School of Medicine, Daejeon, South Korea
| | - Yong Min Ahn
- Department of Psychiatry, Seoul National University, College of Medicine, Seoul, South Korea; Department of Neuropsychiatry, Seoul National University Hospital, Seoul, South Korea
| | - Se Hyun Kim
- Department of Psychiatry, Seoul National University, College of Medicine, Seoul, South Korea; Department of Neuropsychiatry, Seoul National University Hospital, Seoul, South Korea
| | - Young-Chul Chung
- Department of Psychiatry, Jeonbuk National University Medical School, Jeonju, South Korea; Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju, South Korea
| | - Fatima Zahra Rami
- Department of Psychiatry, Jeonbuk National University Medical School, Jeonju, South Korea; Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju, South Korea
| | - Se Joo Kim
- Department of Psychiatry and Institute of Behavioral Science in Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Sung-Wan Kim
- Department of Psychiatry, Chonnam National University Medical School, Gwangju, South Korea
| | - Woojae Myung
- Department of Psychiatry, Seoul National University, College of Medicine, Seoul, South Korea; Department of Neuropsychiatry, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Tae Hyon Ha
- Department of Psychiatry, Seoul National University, College of Medicine, Seoul, South Korea; Department of Neuropsychiatry, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Heon-Jeong Lee
- Department of Psychiatry, Korea University College of Medicine, Seoul, South Korea
| | - Hayoung Oh
- Pusan National University Research Park, Pusan, South Korea
| | - Kyu Young Lee
- Department of Neuropsychiatry, Eulji University, School of Medicine, Daejeon, South Korea; Department of Psychiatry, Nowon Eulji University Hospital, Seoul, South Korea
| | - Min Ji Kim
- Department of Psychiatry, Seoul National University, College of Medicine, Seoul, South Korea; Department of Neuropsychiatry, Seoul National University Hospital, Seoul, South Korea
| | - Chae Yeong Kang
- Department of Psychiatry, Jeonbuk National University Medical School, Jeonju, South Korea; Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju, South Korea
| | - Sumoa Jeon
- Institute of Behavioral Science in Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Anna Jo
- Department of Psychiatry, Chonnam National University Medical School, Gwangju, South Korea
| | - Hyeona Yu
- Department of Neuropsychiatry, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Seunghwa Jeong
- Department of Psychiatry, Korea University College of Medicine, Seoul, South Korea
| | - Kyooseob Ha
- Department of Psychiatry, University of British Columbia, Vancouver, British Columbia, Canada; Department of Psychiatry, Lions Gate Hospital - Vancouver Coastal Health Authority, British Columbia, Canada
| | - Beomsu Kim
- Department of Precision Medicine, Sungkyunkwan University, School of Medicine, Seoul, South Korea
| | - Injeong Shim
- Department of Digital Health, Samsung Advanced Institute for Health Sciences and Technology (SAIHST), Sungkyunkwan University, Samsung Medical Center, Seoul, South Korea
| | - Chamlee Cho
- Department of Digital Health, Samsung Advanced Institute for Health Sciences and Technology (SAIHST), Sungkyunkwan University, Samsung Medical Center, Seoul, South Korea
| | - Hailiang Huang
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
| | - Hong-Hee Won
- Department of Digital Health, Samsung Advanced Institute for Health Sciences and Technology (SAIHST), Sungkyunkwan University, Samsung Medical Center, Seoul, South Korea.
| | - Kyung Sue Hong
- Department of Psychiatry, University of British Columbia, Vancouver, British Columbia, Canada; Department of Psychiatry, Lions Gate Hospital - Vancouver Coastal Health Authority, British Columbia, Canada.
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Ohi K, Tanaka Y, Otowa T, Shimada M, Kaiya H, Nishimura F, Sasaki T, Tanii H, Shioiri T, Hara T. Discrimination between healthy participants and people with panic disorder based on polygenic scores for psychiatric disorders and for intermediate phenotypes using machine learning. Aust N Z J Psychiatry 2024; 58:603-614. [PMID: 38581251 DOI: 10.1177/00048674241242936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/08/2024]
Abstract
OBJECTIVE Panic disorder is a modestly heritable condition. Currently, diagnosis is based only on clinical symptoms; identifying objective biomarkers and a more reliable diagnostic procedure is desirable. We investigated whether people with panic disorder can be reliably diagnosed utilizing combinations of multiple polygenic scores for psychiatric disorders and their intermediate phenotypes, compared with single polygenic score approaches, by applying specific machine learning techniques. METHODS Polygenic scores for 48 psychiatric disorders and intermediate phenotypes based on large-scale genome-wide association studies (n = 7556-1,131,881) were calculated for people with panic disorder (n = 718) and healthy controls (n = 1717). Discrimination between people with panic disorder and healthy controls was based on the 48 polygenic scores using five methods for classification: logistic regression, neural networks, quadratic discriminant analysis, random forests and a support vector machine. Differences in discrimination accuracy (area under the curve) due to an increased number of polygenic score combinations and differences in the accuracy across five classifiers were investigated. RESULTS All five classifiers performed relatively well for distinguishing people with panic disorder from healthy controls by increasing the number of polygenic scores. Of the 48 polygenic scores, the polygenic score for anxiety UK Biobank was the most useful for discrimination by the classifiers. In combinations of two or three polygenic scores, the polygenic score for anxiety UK Biobank was included as one of polygenic scores in all classifiers. When all 48 polygenic scores were used in combination, the greatest areas under the curve significantly differed among the five classifiers. Support vector machine and logistic regression had higher accuracy than quadratic discriminant analysis and random forests. For each classifier, the greatest area under the curve was 0.600 ± 0.030 for logistic regression (polygenic score combinations N = 14), 0.591 ± 0.039 for neural networks (N = 9), 0.603 ± 0.033 for quadratic discriminant analysis (N = 10), 0.572 ± 0.039 for random forests (N = 25) and 0.617 ± 0.041 for support vector machine (N = 11). The greatest areas under the curve at the best polygenic score combination significantly differed among the five classifiers. Random forests had the lowest accuracy among classifiers. Support vector machine had higher accuracy than neural networks. CONCLUSIONS These findings suggest that increasing the number of polygenic score combinations up to approximately 10 effectively improved the discrimination accuracy and that support vector machine exhibited greater accuracy among classifiers. However, the discrimination accuracy for panic disorder, when based solely on polygenic score combinations, was found to be modest.
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Affiliation(s)
- Kazutaka Ohi
- Department of Psychiatry, Gifu University Graduate School of Medicine, Gifu, Japan
- Department of General Internal Medicine, Kanazawa Medical University, Ishikawa, Japan
| | - Yuta Tanaka
- Department of Intelligence Science and Engineering, Gifu University Graduate School of Natural Science and Technology, Gifu, Japan
| | - Takeshi Otowa
- Department of Psychiatry, East Medical Center, Nagoya City University, Nagoya, Japan
| | - Mihoko Shimada
- Genome Medical Science Project (Toyama), National Center for Global Health and Medicine (NCGM), Tokyo, Japan
| | - Hisanobu Kaiya
- Panic Disorder Research Center, Warakukai Medical Corporation, Tokyo, Japan
| | - Fumichika Nishimura
- Center for Research on Counseling and Support Services, The University of Tokyo, Tokyo, Japan
| | - Tsukasa Sasaki
- Department of Physical and Health Education, Graduate School of Education, The University of Tokyo, Tokyo, Japan
| | - Hisashi Tanii
- Center for Physical and Mental Health, Mie University, Mie, Japan
- Graduate School of Medicine, Department of Health Promotion and Disease Prevention, Mie University, Mie, Japan
| | - Toshiki Shioiri
- Department of Psychiatry, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Takeshi Hara
- Department of Intelligence Science and Engineering, Gifu University Graduate School of Natural Science and Technology, Gifu, Japan
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Ohi K, Nishizawa D, Sugiyama S, Takai K, Fujikane D, Kuramitsu A, Hasegawa J, Soda M, Kitaichi K, Hashimoto R, Ikeda K, Shioiri T. Cognitive performances across individuals at high genetic risk for schizophrenia, high genetic risk for bipolar disorder, and low genetic risks: a combined polygenic risk score approach. Psychol Med 2023; 53:4454-4463. [PMID: 35971752 DOI: 10.1017/s0033291722001271] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
BACKGROUND Individuals with schizophrenia (SCZ) and bipolar disorder (BD) display cognitive impairments, but the impairments in those with SCZ are more prominent, supported by genetic overlap between SCZ and cognitive impairments. However, it remains unclear whether cognitive performances differ between individuals at high and low genetic risks for SCZ or BD. METHODS Using the latest Psychiatric Genomics Consortium (PGC) data, we calculated PGC3 SCZ-, PGC3 BD-, and SCZ v. BD polygenic risk scores (PRSs) in 173 SCZ patients, 70 unaffected first-degree relatives (FRs) and 196 healthy controls (HCs). Based on combinations of three PRS deciles, individuals in the genetic SCZ, genetic BD and low genetic risk groups were extracted. Cognitive performance was assessed by the Brief Assessment of Cognition in Schizophrenia. RESULTS SCZ-, BD-, SCZ v. BD-PRSs were associated with case-control status (R2 = 0.020-0.061), and SCZ-PRS was associated with relative-control status (R2 = 0.023). Furthermore, individuals in the highest decile for SCZ PRSs had elevated BD-PRSs [odds ratio (OR) = 6.33] and SCZ v. BD-PRSs (OR = 1.86) compared with those in the lowest decile. Of the three genetic risk groups, the low genetic risk group contained more HCs, whereas the genetic BD and SCZ groups contained more SCZ patients (p < 0.05). SCZ patients had widespread cognitive impairments, and FRs had cognitive impairments that were between those of SCZ patients and HCs (p < 0.05). Cognitive differences between HCs in the low genetic risk group and SCZ patients in the genetic BD or genetic SCZ groups were more prominent (Cohen's d > -0.20) than those between HCs and SCZ patients in the no genetic risk group. Furthermore, SCZ patients in the genetic SCZ group displayed lower scores in verbal fluency and attention than those in the genetic BD group (d > -0.20). CONCLUSIONS Our findings suggest that cognitive impairments in SCZ are partially mediated through genetic loadings for SCZ but not BD.
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Affiliation(s)
- Kazutaka Ohi
- Department of Psychiatry, Gifu University Graduate School of Medicine, Gifu, Japan
- Department of General Internal Medicine, Kanazawa Medical University, Ishikawa, Japan
| | - Daisuke Nishizawa
- Addictive Substance Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Shunsuke Sugiyama
- Department of Psychiatry, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Kentaro Takai
- Department of Psychiatry, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Daisuke Fujikane
- Department of Psychiatry, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Ayumi Kuramitsu
- Department of Psychiatry, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Junko Hasegawa
- Addictive Substance Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Midori Soda
- Laboratory of Pharmaceutics, Department of Biomedical Pharmaceutics, Gifu Pharmaceutical University, Gifu, Japan
| | - Kiyoyuki Kitaichi
- Laboratory of Pharmaceutics, Department of Biomedical Pharmaceutics, Gifu Pharmaceutical University, Gifu, Japan
| | - Ryota Hashimoto
- Department of Pathology of Mental Diseases, National Institute of Mental Health, National Center of Neurology and Psychiatry, Kodaira, Tokyo, Japan
| | - Kazutaka Ikeda
- Addictive Substance Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Toshiki Shioiri
- Department of Psychiatry, Gifu University Graduate School of Medicine, Gifu, Japan
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