1
|
Baltazar-Soares M, Karell P, Wright D, Nilsson JÅ, Brommer JE. Genomic basis of melanin-associated phenotypes suggests colour-specific environmental adaptations in tawny owls. Mol Ecol 2024; 33:e17247. [PMID: 38173194 DOI: 10.1111/mec.17247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 11/24/2023] [Indexed: 01/05/2024]
Abstract
Feathers comprise a series of evolutionary innovations but also harbour colour, a key biological trait known to co-vary with life history or complex traits. Those relationships are particularly true in melanin-based pigmentation species due to known pleiotropic effects of the melanocortin pathway - originating from melanin-associated phenotypes. Here, we explore the molecular basis of melanin colouration and expected co-variation at the molecular level in the melanin-based, colour polymorphic system of the tawny owl (Strix aluco). An extensive body of literature has revealed that grey and brown tawny owl colour morphs differ in a series of life history and behavioural traits. Thus, it is plausible to expect co-variation also at molecular level between colour morphs. To investigate this possibility, we assembled the first draft genome of the species against which we mapped ddRADseq reads from 220 grey and 150 brown morphs - representing 10 years of pedigree data from a population in Southern Finland - and explored genome-wide associations with colour phenotype. Our results revealed putative molecular signatures of cold adaptation strongly associated with the grey phenotype, namely, a non-synonymous substitution in MCHR1, plus 2 substitutions in non-coding regions of FTCD and FAM135A whose genotype combinations obtained a predictive power of up to 100% (predicting grey colour). These suggest a molecular basis of cold environment adaptations predicted to be grey-morph specific. Our results potentially reveal part of the molecular machinery of melanin-associated phenotypes and provide novel insights towards understanding the functional genomics of colour polymorphism in melanin-based pigmented species.
Collapse
Affiliation(s)
| | - Patrik Karell
- Department of Biology, Section of Evolutionary Ecology, Lund University, Lund, Sweden
- Department of Ecology and Genetics, University of Uppsala, Uppsala, Sweden
- Department of Bioeconomy, Novia University of Applied Sciences, Ekenäs, Finland
| | | | - Jan-Åke Nilsson
- Department of Biology, Section of Evolutionary Ecology, Lund University, Lund, Sweden
| | - Jon E Brommer
- Department of Biology, University of Turku, Turku, Finland
| |
Collapse
|
2
|
Sun R, Weng H, Wang MH. W-Test for Genetic Epistasis Testing. Methods Mol Biol 2021; 2212:45-53. [PMID: 33733349 DOI: 10.1007/978-1-0716-0947-7_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The genetic epistasis effect has been widely acknowledged as an essential contributor to genetic variation in complex diseases. In this chapter, we introduce a powerful and efficient statistical method, called W-test, for genetic epistasis testing. A wtest R package is developed for the implementation of the W-test method, which provides various functions to measure the main effect, pairwise interaction, higher-order interaction, and cis-regulation of SNP-CpG pairs in genetic and epigenetic data. It allows flexible stagewise and exhaustive association testing as well as diagnostic checking on the probability distributions in a user-friendly interface. The wtest package is available in CRAN at https://CRAN.R-project.org/package=wtest .
Collapse
Affiliation(s)
- Rui Sun
- The Chinese University of Hong Kong, Hong Kong, China
| | - Haoyi Weng
- The Chinese University of Hong Kong, Hong Kong, China
| | | |
Collapse
|
3
|
Li JK, Li L, Li W, Wang Z, Gao F, Hu FY, Zhang S, Qu SF, Huang J, Wang LS, Wu JH, Chen F. Panel-based targeted exome sequencing reveals novel candidate susceptibility loci for age-related cataracts in Chinese Cohort. Mol Genet Genomic Med 2020; 8:e1218. [PMID: 32337810 PMCID: PMC7336732 DOI: 10.1002/mgg3.1218] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 02/05/2020] [Accepted: 02/25/2020] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Age-related cataracts (ARC) is the most common blinding eye disease worldwide, and its incidence tend to become younger. However, the relationship between genetic factors and mechanisms is not fully understood. The aim of the study was to further clarify the relationship between ARC and genetic mechanisms in East Asian populations and to elucidate the pathogenesis. METHODS The study collected 191 sporadic cataracts and 208 healthy people from the eastern provinces of China, with an average age of about 60 years. All participants were subjected to a comprehensive ophthalmic clinical examination and peripheral blood samples were collected and their genomic DNA was extracted. Mutations were screened among 792 candidate genes to enhance understanding of the disease through targeted capture and high-throughput sequencing. RESULTS We identified novel candidate susceptibility gene, which may serve as a potential susceptibility factor leading to an increase in the incidence of age-related cataracts. Three novel loci are associated with age-related cataracts significant significance: rs129882 in DBH (p = 5.27E-07, odds ratio = 3.9), rs1800280 in DMD (p = 2.85E-06, odds ratio = 1.4) and rs2871776 in ATP13A2 (p = 4.18E-05, odds ratio = 0.04). Gene-gene interaction analysis revealed that the most significant interactions between genes include the interaction between DBH and TUB (rs17847537 in TUB, rs129882 in DBH, p-value = 2.12E-14), and the interaction between DBH and DMD (rs1800280 in DMD, rs129882 in DBH, p-value = 2.12E-14). Pathway analysis shows that the most significant processes are concentrated in response to light stimulation (adjusted p-Value = 5.56E-03), response to radiation (adjusted P-Value = 5.56E-03), abiotic stimulus (adjusted p-Value = 5.56E-03). eQTL analysis shows that DBH rs129882 could regulate the expression of DBH mRNA in various tissues including retina. CONCLUSION Our study indicates rs129882 and rs1800280 loci are associated with age-related cataracts, which enlarge the gene map of age-related cataracts.
Collapse
Affiliation(s)
- Jian-Kang Li
- Dept of Computer ScienceCity University of Hong KongKowloonHong Kong
- BGI‐ShenzhenShenzhenChina
- Guangdong Provincial Key Laboratory of Human Disease Genomics Shenzhen Key Laboratory of GenomicsBGI-ShenzhenShanghaiChina
| | - Li‐Li Li
- National Institutes of food and drug Control (NIFDC)BeijingP. R. China
| | - Wei Li
- BGI‐ShenzhenShenzhenChina
- Guangdong Provincial Key Laboratory of Human Disease Genomics Shenzhen Key Laboratory of GenomicsBGI-ShenzhenShanghaiChina
- BGI Education CenterUniversity of Chinese Academy of SciencesShenzhenChina
| | - Zi‐Wei Wang
- BGI‐ShenzhenShenzhenChina
- BGI Education CenterUniversity of Chinese Academy of SciencesShenzhenChina
| | - Feng‐Juan Gao
- Eye Institute, Eye and ENT HospitalCollege of MedicineFudan UniversityShanghaiChina
- Shanghai Key Laboratory of Visual Impairment and Restoration, Science and Technology Commission of Shanghai MunicipalityShanghaiChina
- Key Laboratory of MyopiaMinistry of HealthShanghaiChina
| | - Fang-Yuan Hu
- Eye Institute, Eye and ENT HospitalCollege of MedicineFudan UniversityShanghaiChina
- Shanghai Key Laboratory of Visual Impairment and Restoration, Science and Technology Commission of Shanghai MunicipalityShanghaiChina
- Key Laboratory of MyopiaMinistry of HealthShanghaiChina
| | - Sheng‐Hai Zhang
- Eye Institute, Eye and ENT HospitalCollege of MedicineFudan UniversityShanghaiChina
- Shanghai Key Laboratory of Visual Impairment and Restoration, Science and Technology Commission of Shanghai MunicipalityShanghaiChina
- Key Laboratory of MyopiaMinistry of HealthShanghaiChina
| | - Shou-Fang Qu
- National Institutes of food and drug Control (NIFDC)BeijingP. R. China
| | - Jie Huang
- National Institutes of food and drug Control (NIFDC)BeijingP. R. China
| | - Lu-Sheng Wang
- Dept of Computer ScienceCity University of Hong KongKowloonHong Kong
- BGI‐ShenzhenShenzhenChina
| | - Ji-Hong Wu
- Eye Institute, Eye and ENT HospitalCollege of MedicineFudan UniversityShanghaiChina
- Shanghai Key Laboratory of Visual Impairment and Restoration, Science and Technology Commission of Shanghai MunicipalityShanghaiChina
- Key Laboratory of MyopiaMinistry of HealthShanghaiChina
| | - Fang Chen
- BGI‐ShenzhenShenzhenChina
- Guangdong Provincial Key Laboratory of Human Disease Genomics Shenzhen Key Laboratory of GenomicsBGI-ShenzhenShanghaiChina
| |
Collapse
|
4
|
Sun R, Xia X, Chong KC, Zee BCY, Wu WKK, Wang MH. wtest: an integrated R package for genetic epistasis testing. BMC Med Genomics 2019; 12:180. [PMID: 31874630 PMCID: PMC6929460 DOI: 10.1186/s12920-019-0638-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 11/26/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND With the increasing amount of high-throughput genomic sequencing data, there is a growing demand for a robust and flexible tool to perform interaction analysis. The identification of SNP-SNP, SNP-CpG, and higher order interactions helps explain the genetic etiology of human diseases, yet genome-wide analysis for interactions has been very challenging, due to the computational burden and a lack of statistical power in most datasets. RESULTS The wtest R package performs association testing for main effects, pairwise and high order interactions in genome-wide association study data, and cis-regulation of SNP and CpG sites in genome-wide and epigenome-wide data. The software includes a number of post-test diagnostic and analysis functions and offers an integrated toolset for genetic epistasis testing. CONCLUSIONS The wtest is an efficient and powerful statistical tool for integrated genetic epistasis testing. The package is available in CRAN: https://CRAN.R-project.org/package=wtest.
Collapse
Affiliation(s)
- Rui Sun
- Division of Biostatistics and Centre for Clinical Research and Biostatistics(CCRB), JC School of Public Health and Primary Care, the Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, China.,Centre for Clinical Trials and Biostatistics, CUHK Shenzhen Research Institute, Shenzhen, China
| | - Xiaoxuan Xia
- Division of Biostatistics and Centre for Clinical Research and Biostatistics(CCRB), JC School of Public Health and Primary Care, the Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, China.,Centre for Clinical Trials and Biostatistics, CUHK Shenzhen Research Institute, Shenzhen, China
| | - Ka Chun Chong
- Division of Biostatistics and Centre for Clinical Research and Biostatistics(CCRB), JC School of Public Health and Primary Care, the Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, China.,Centre for Clinical Trials and Biostatistics, CUHK Shenzhen Research Institute, Shenzhen, China
| | - Benny Chung-Ying Zee
- Division of Biostatistics and Centre for Clinical Research and Biostatistics(CCRB), JC School of Public Health and Primary Care, the Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, China.,Centre for Clinical Trials and Biostatistics, CUHK Shenzhen Research Institute, Shenzhen, China
| | - William Ka Kei Wu
- Institute of Digestive Diseases and Department of Medicine & Therapeutics, State Key Laboratory of Digestive Diseases, LKS Institute of Health Sciences, CUHK Shenzhen Research Institute, Shenzhen, China.,Department of Anesthesia, the Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, China
| | - Maggie Haitian Wang
- Division of Biostatistics and Centre for Clinical Research and Biostatistics(CCRB), JC School of Public Health and Primary Care, the Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, China. .,Centre for Clinical Trials and Biostatistics, CUHK Shenzhen Research Institute, Shenzhen, China.
| |
Collapse
|
5
|
Van Steen K, Moore JH. How to increase our belief in discovered statistical interactions via large-scale association studies? Hum Genet 2019; 138:293-305. [PMID: 30840129 PMCID: PMC6483943 DOI: 10.1007/s00439-019-01987-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 02/20/2019] [Indexed: 12/31/2022]
Abstract
The understanding that differences in biological epistasis may impact disease risk, diagnosis, or disease management stands in wide contrast to the unavailability of widely accepted large-scale epistasis analysis protocols. Several choices in the analysis workflow will impact false-positive and false-negative rates. One of these choices relates to the exploitation of particular modelling or testing strategies. The strengths and limitations of these need to be well understood, as well as the contexts in which these hold. This will contribute to determining the potentially complementary value of epistasis detection workflows and is expected to increase replication success with biological relevance. In this contribution, we take a recently introduced regression-based epistasis detection tool as a leading example to review the key elements that need to be considered to fully appreciate the value of analytical epistasis detection performance assessments. We point out unresolved hurdles and give our perspectives towards overcoming these.
Collapse
Affiliation(s)
- K Van Steen
- WELBIO, GIGA-R Medical Genomics-BIO3, University of Liège, Liege, Belgium.
- Department of Human Genetics, University of Leuven, Leuven, Belgium.
| | - J H Moore
- Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, USA
| |
Collapse
|
6
|
Statistical methods for genome-wide association studies. Semin Cancer Biol 2019; 55:53-60. [DOI: 10.1016/j.semcancer.2018.04.008] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Revised: 04/27/2018] [Accepted: 04/28/2018] [Indexed: 12/12/2022]
|
7
|
Wu M, Ma S. Robust genetic interaction analysis. Brief Bioinform 2019; 20:624-637. [PMID: 29897421 PMCID: PMC6556899 DOI: 10.1093/bib/bby033] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 03/22/2018] [Indexed: 01/17/2023] Open
Abstract
For the risk, progression, and response to treatment of many complex diseases, it has been increasingly recognized that genetic interactions (including gene-gene and gene-environment interactions) play important roles beyond the main genetic and environmental effects. In practical genetic interaction analyses, model mis-specification and outliers/contaminations in response variables and covariates are not uncommon, and demand robust analysis methods. Compared with their nonrobust counterparts, robust genetic interaction analysis methods are significantly less popular but are gaining attention fast. In this article, we provide a comprehensive review of robust genetic interaction analysis methods, on their methodologies and applications, for both marginal and joint analysis, and for addressing model mis-specification as well as outliers/contaminations in response variables and covariates.
Collapse
Affiliation(s)
- Mengyun Wu
- Mengyun Wu and Shuangge Ma, School of Statistics and Management, Shanghai University of Finance and Economics, Shanghai 200433, China and Yale School of Public Health, New Haven, CT 06520, USA
| | - Shuangge Ma
- Mengyun Wu and Shuangge Ma, School of Statistics and Management, Shanghai University of Finance and Economics, Shanghai 200433, China and Yale School of Public Health, New Haven, CT 06520, USA
| |
Collapse
|
8
|
Uppu S, Krishna A. A deep hybrid model to detect multi-locus interacting SNPs in the presence of noise. Int J Med Inform 2018; 119:134-151. [DOI: 10.1016/j.ijmedinf.2018.09.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 04/13/2018] [Accepted: 09/03/2018] [Indexed: 01/17/2023]
|
9
|
Sun R, Weng H, Men R, Xia X, Chong KC, Wu WKK, Zee BCY, Wang MH. Gene-methylation epistatic analyses via the W-test identifies enriched signals of neuronal genes in patients undergoing lipid-control treatment. BMC Proc 2018; 12:53. [PMID: 30263051 PMCID: PMC6156903 DOI: 10.1186/s12919-018-0143-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
An increasing number of studies are focused on the epigenetic regulation of DNA to affect gene expression without modifications to the DNA sequence. Methylation plays an important role in shaping disease traits; however, previous studies were mainly experiment, based, resulting in few reports that measured gene-methylation interaction effects via statistical means. In this study, we applied the data set adaptive W-test to measure gene-methylation interactions. Performance was evaluated by the ability to detect a given set of causal markers in the data set obtained from the GAW20. Results from simulation data analyses showed that the W-test was able to detect most markers. The method was also applied to chromosome 11 of the experimental data set and identified clusters of genes with neuronal and retinal functions, including MPPED2I, GUCY2E, NAV2, and ZBTB16. Genes from the TRIM family were also identified; these genes are potentially related to the regulation of triglyceride levels. Our results suggest that the W-test could be an efficient and effective method to detect gene-methylation interactions. Furthermore, the identified genes suggest an interesting relationship between lipid levels and the etiology of neurological disorders.
Collapse
Affiliation(s)
- Rui Sun
- Division of Biostatistics, Centre for Clinical Research and Biostatistics, JC School of Public Health and Primary Care, the Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Hong Kong, Special Administrative Region of China.,2The Chinese University of Hong Kong Shenzhen Research Institute, Shenzhen, China
| | - Haoyi Weng
- Division of Biostatistics, Centre for Clinical Research and Biostatistics, JC School of Public Health and Primary Care, the Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Hong Kong, Special Administrative Region of China.,2The Chinese University of Hong Kong Shenzhen Research Institute, Shenzhen, China
| | - Ruoting Men
- Division of Biostatistics, Centre for Clinical Research and Biostatistics, JC School of Public Health and Primary Care, the Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Hong Kong, Special Administrative Region of China.,2The Chinese University of Hong Kong Shenzhen Research Institute, Shenzhen, China
| | - Xiaoxuan Xia
- Division of Biostatistics, Centre for Clinical Research and Biostatistics, JC School of Public Health and Primary Care, the Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Hong Kong, Special Administrative Region of China.,2The Chinese University of Hong Kong Shenzhen Research Institute, Shenzhen, China
| | - Ka Chun Chong
- Division of Biostatistics, Centre for Clinical Research and Biostatistics, JC School of Public Health and Primary Care, the Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Hong Kong, Special Administrative Region of China.,2The Chinese University of Hong Kong Shenzhen Research Institute, Shenzhen, China
| | - William K K Wu
- Department of Anaesthesia and Intensive Care, the Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Hong Kong, Special Administrative Region of China
| | - Benny Chung-Ying Zee
- Division of Biostatistics, Centre for Clinical Research and Biostatistics, JC School of Public Health and Primary Care, the Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Hong Kong, Special Administrative Region of China.,2The Chinese University of Hong Kong Shenzhen Research Institute, Shenzhen, China
| | - Maggie Haitian Wang
- Division of Biostatistics, Centre for Clinical Research and Biostatistics, JC School of Public Health and Primary Care, the Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Hong Kong, Special Administrative Region of China.,2The Chinese University of Hong Kong Shenzhen Research Institute, Shenzhen, China
| |
Collapse
|
10
|
Wang YM, Ma L, Lu SY, Chan TCY, Yam JCS, Tang SM, Kam KW, Tam POS, Tham CC, Young AL, Jhanji V, Pang CP, Chen LJ. Analysis of multiple genetic loci reveals MPDZ-NF1B rs1324183 as a putative genetic marker for keratoconus. Br J Ophthalmol 2018; 102:1736-1741. [PMID: 30002070 DOI: 10.1136/bjophthalmol-2018-312218] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 05/24/2018] [Accepted: 06/24/2018] [Indexed: 11/03/2022]
Abstract
OBJECTIVE To investigate the associations between 16 single-nucleotide polymorphisms (SNPs) in 14 genetic loci and keratoconus in an independent Chinese cohort. METHODS This cross-sectional, case-control association study included a Chinese cohort of 133 patients with keratoconus and 371 control subjects. In a recent meta-analysis study, we identified association of 16 SNPs in 14 gene loci with keratoconus. In this study, we genotyped these 16 SNPs in all the patients and controls and analysed their association with keratoconus, its clinical severities and progression profiles. We also analysed the genotype-phenotype correlation between individual SNPs and steep keratometry, flat keratometry (Kf), average keratometry (Avg K) and best-fit sphere diameter (BFS) of the anterior and posterior corneal surface. RESULTS Among the 16 selected SNPs, rs1324183 in the MPDZ-NF1B locus showed a significant association with keratoconus (OR=2.22; 95% CI 1.42 to 3.45, p=4.30×10-4), especially severe keratoconus (OR=5.10, 95% CI 1.63 to 15.93, p=0.005). The rs1324183 A allele was positively associated with anterior Kf (p=0.008), anterior Avg K (p=0.017), posterior Kf (p=0.01) and negatively associated with apex pachymetry (p=0.007) and anterior BFS (p=0.023) in keratoconus. The other 15 SNPs had no significant association with keratoconus or genotype-phenotype correlations. CONCLUSIONS This study confirmed the association of SNP rs1324183 in MPDZ-NF1B with keratoconus and revealed the association of this SNP with keratoconus severity and corneal parameters. It is thus a putative genetic marker for monitoring the progression of keratoconus to a severe form and facilitating early intervention.
Collapse
Affiliation(s)
- Yu Meng Wang
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Li Ma
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Shi Yao Lu
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Tommy Chung Yan Chan
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Jason C S Yam
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Shu Min Tang
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Ka Wai Kam
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Department of Ophthalmology and Visual Sciences, Prince of Wales Hospital, Hong Kong, China
| | - Pancy O S Tam
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Clement C Tham
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Alvin L Young
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Department of Ophthalmology and Visual Sciences, Prince of Wales Hospital, Hong Kong, China
| | - Vishal Jhanji
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China.,UPMC Eye Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Chi Pui Pang
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Li Jia Chen
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China .,Department of Ophthalmology and Visual Sciences, Prince of Wales Hospital, Hong Kong, China
| |
Collapse
|
11
|
Wu WK, Sun R, Zuo T, Tian Y, Zeng Z, Ho J, Wu JC, Chan FK, Chan MT, Yu J, Sung JJ, Wong SH, Wang MH, Ng SC. A novel susceptibility locus in MST1 and gene-gene interaction network for Crohn's disease in the Chinese population. J Cell Mol Med 2018; 22:2368-2377. [PMID: 29441677 PMCID: PMC5867068 DOI: 10.1111/jcmm.13530] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Accepted: 12/11/2017] [Indexed: 12/13/2022] Open
Abstract
The incidence of Crohn's disease is increasing in many Asian countries, but considerable differences in genetic susceptibility have been reported between Western and Asian populations. This study aimed to fine-map 23 previously reported Crohn's disease genes and identify their interactions in the Chinese population by Illumina-based targeted capture sequencing. Our results showed that the genetic polymorphism A>G at rs144982232 in MST1 showed the most significant association (P = 1.78 × 10-5 ; odds ratio = 4.87). JAK2 rs1159782 (T>C) was also strongly associated with Crohn's disease (P = 2.34 × 10-4 ; odds ratio = 3.72). Gene-gene interaction analysis revealed significant interactions between MST1 and other susceptibility genes, including NOD2, MUC19 and ATG16L1 in contributing to Crohn's disease risk. Main genetic associations and gene-gene interactions were verified using ImmunoChip data set. In conclusion, a novel susceptibility locus in MST1 was identified. Our analysis suggests that MST1 might interact with key susceptibility genes involved in autophagy and bacterial recognition. These findings provide insight into the genetic architecture of Crohn's disease in Chinese and may partially explain the disparity of genetic signals in Crohn's disease susceptibility across different ethnic populations by highlighting the contribution of gene-gene interactions.
Collapse
Affiliation(s)
- William K.K. Wu
- State Key Laboratory of Digestive DiseasesInstitute of Digestive Diseases and Department of Medicine & TherapeuticsLKS Institute of Health SciencesCUHK Shenzhen Research InstituteThe Chinese University of Hong KongHong Kong
- Department of Anaesthesia and Intensive CareThe Chinese University of Hong KongHong Kong
| | - Rui Sun
- The Jockey Club School of Public Health and Primary CareThe Chinese University of Hong KongHong Kong
| | - Tao Zuo
- State Key Laboratory of Digestive DiseasesInstitute of Digestive Diseases and Department of Medicine & TherapeuticsLKS Institute of Health SciencesCUHK Shenzhen Research InstituteThe Chinese University of Hong KongHong Kong
| | - Yuanyuan Tian
- Department of Anaesthesia and Intensive CareThe Chinese University of Hong KongHong Kong
| | - Zhirong Zeng
- Department of GastroenterologyThe First Affiliated Hospital of Sun Yat‐Sen UniversityGuangzhouChina
| | - Jeffery Ho
- Department of Anaesthesia and Intensive CareThe Chinese University of Hong KongHong Kong
| | - Justin C.Y. Wu
- State Key Laboratory of Digestive DiseasesInstitute of Digestive Diseases and Department of Medicine & TherapeuticsLKS Institute of Health SciencesCUHK Shenzhen Research InstituteThe Chinese University of Hong KongHong Kong
| | - Francis K.L. Chan
- State Key Laboratory of Digestive DiseasesInstitute of Digestive Diseases and Department of Medicine & TherapeuticsLKS Institute of Health SciencesCUHK Shenzhen Research InstituteThe Chinese University of Hong KongHong Kong
| | - Matthew T.V. Chan
- Department of Anaesthesia and Intensive CareThe Chinese University of Hong KongHong Kong
| | - Jun Yu
- State Key Laboratory of Digestive DiseasesInstitute of Digestive Diseases and Department of Medicine & TherapeuticsLKS Institute of Health SciencesCUHK Shenzhen Research InstituteThe Chinese University of Hong KongHong Kong
| | - Joseph J.Y. Sung
- State Key Laboratory of Digestive DiseasesInstitute of Digestive Diseases and Department of Medicine & TherapeuticsLKS Institute of Health SciencesCUHK Shenzhen Research InstituteThe Chinese University of Hong KongHong Kong
| | - Sunny H. Wong
- State Key Laboratory of Digestive DiseasesInstitute of Digestive Diseases and Department of Medicine & TherapeuticsLKS Institute of Health SciencesCUHK Shenzhen Research InstituteThe Chinese University of Hong KongHong Kong
| | - Maggie H. Wang
- The Jockey Club School of Public Health and Primary CareThe Chinese University of Hong KongHong Kong
| | - Siew C. Ng
- State Key Laboratory of Digestive DiseasesInstitute of Digestive Diseases and Department of Medicine & TherapeuticsLKS Institute of Health SciencesCUHK Shenzhen Research InstituteThe Chinese University of Hong KongHong Kong
| |
Collapse
|
12
|
Wang MH, Weng H, Sun R, Lee J, Wu WKK, Chong KC, Zee BCY. A Zoom-Focus algorithm (ZFA) to locate the optimal testing region for rare variant association tests. Bioinformatics 2018; 33:2330-2336. [PMID: 28334355 DOI: 10.1093/bioinformatics/btx130] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 03/09/2017] [Indexed: 01/24/2023] Open
Abstract
Motivation Increasing amounts of whole exome or genome sequencing data present the challenge of analysing rare variants with extremely small minor allele frequencies. Various statistical tests have been proposed, which are specifically configured to increase power for rare variants by conducting the test within a certain bin, such as a gene or a pathway. However, a gene may contain from several to thousands of markers, and not all of them are related to the phenotype. Combining functional and non-functional variants in an arbitrary genomic region could impair the testing power. Results We propose a Zoom-Focus algorithm (ZFA) to locate the optimal testing region within a given genomic region. It can be applied as a wrapper function in existing rare variant association tests to increase testing power. The algorithm consists of two steps. In the first step, Zooming, a given genomic region is partitioned by an order of two, and the best partition is located. In the second step, Focusing, the boundaries of the zoomed region are refined. Simulation studies showed that ZFA substantially increased the statistical power of rare variants' tests, including the SKAT, SKAT-O, burden test and the W-test. The algorithm was applied on real exome sequencing data of hypertensive disorder, and identified biologically relevant genetic markers to metabolic disorders that were undetectable by a gene-based method. The proposed algorithm is an efficient and powerful tool to enhance the power of association study for whole exome or genome sequencing data. Availability and Implementation The ZFA software is available at: http://www2.ccrb.cuhk.edu.hk/statgene/software.html. Contact maggiew@cuhk.edu.hk or bzee@cuhk.edu.hk. Supplementary information Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Maggie Haitian Wang
- Division of Biostatistics and Centre for Clinical Research and Biostatistics, JC School of Public Health and Primary Care, The Chinese University of Hong Kong, Shatin, N.T, Hong Kong SAR.,CUHK Shenzhen Research Institute, Shenzhen, China
| | - Haoyi Weng
- Division of Biostatistics and Centre for Clinical Research and Biostatistics, JC School of Public Health and Primary Care, The Chinese University of Hong Kong, Shatin, N.T, Hong Kong SAR.,CUHK Shenzhen Research Institute, Shenzhen, China
| | - Rui Sun
- Division of Biostatistics and Centre for Clinical Research and Biostatistics, JC School of Public Health and Primary Care, The Chinese University of Hong Kong, Shatin, N.T, Hong Kong SAR.,CUHK Shenzhen Research Institute, Shenzhen, China
| | - Jack Lee
- Division of Biostatistics and Centre for Clinical Research and Biostatistics, JC School of Public Health and Primary Care, The Chinese University of Hong Kong, Shatin, N.T, Hong Kong SAR.,CUHK Shenzhen Research Institute, Shenzhen, China
| | - William Ka Kei Wu
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong SAR
| | - Ka Chun Chong
- Division of Biostatistics and Centre for Clinical Research and Biostatistics, JC School of Public Health and Primary Care, The Chinese University of Hong Kong, Shatin, N.T, Hong Kong SAR.,CUHK Shenzhen Research Institute, Shenzhen, China
| | - Benny Chung-Ying Zee
- Division of Biostatistics and Centre for Clinical Research and Biostatistics, JC School of Public Health and Primary Care, The Chinese University of Hong Kong, Shatin, N.T, Hong Kong SAR.,CUHK Shenzhen Research Institute, Shenzhen, China
| |
Collapse
|
13
|
Sanchez-Pulido L, Ponting CP. TMEM132: an ancient architecture of cohesin and immunoglobulin domains define a new family of neural adhesion molecules. Bioinformatics 2018; 34:721-724. [PMID: 29088312 PMCID: PMC6030884 DOI: 10.1093/bioinformatics/btx689] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 09/29/2017] [Accepted: 10/26/2017] [Indexed: 11/26/2022] Open
Abstract
Summary The molecular functions of TMEM132 genes remain poorly understood and under-investigated despite their mutations associated with non-syndromic hearing loss, panic disorder and cancer. Here we show the full domain architecture of human TMEM132 family proteins solved using in-depth sequence and structural analysis. We reveal them to be five previously unappreciated cell adhesion molecules whose domain architecture has an early holozoan origin prior to the emergence of choanoflagellates and metazoa. The extra-cellular portions of TMEM132 proteins contain five conserved domains including three tandem immunoglobulin domains, and a cohesin domain homologue, the first such domain found in animals. These findings strongly predict a cellular adhesion function for TMEM132 family, connecting the extracellular medium with the intracellular actin cytoskeleton. Contact luis.sanchez-pulido@igmm.ed.ac.uk. Supplementary information Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Luis Sanchez-Pulido
- Medical Research Council Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, UK
| | - Chris P Ponting
- Medical Research Council Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, UK
| |
Collapse
|
14
|
Cole BS, Hall MA, Urbanowicz RJ, Gilbert‐Diamond D, Moore JH. Analysis of Gene‐Gene Interactions. ACTA ACUST UNITED AC 2018; 95:1.14.1-1.14.10. [DOI: 10.1002/cphg.45] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Brian S. Cole
- Department of Biostatistics and Epidemiology, Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania Philadelphia Pennsylvania
| | - Molly A. Hall
- Department of Biostatistics and Epidemiology, Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania Philadelphia Pennsylvania
- The Center for Systems Genomics, The Pennsylvania State University, University Park Pennsylvania
| | - Ryan J. Urbanowicz
- Department of Biostatistics and Epidemiology, Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania Philadelphia Pennsylvania
| | - Diane Gilbert‐Diamond
- Institute for Quantitative Biomedical Sciences at Dartmouth Hanover New Hampshire
- Department of Epidemiology, Geisel School of Medicine at Dartmouth Hanover New Hampshire
| | - Jason H. Moore
- Department of Biostatistics and Epidemiology, Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania Philadelphia Pennsylvania
| |
Collapse
|
15
|
Howey R, Cordell HJ. Further investigations of the W-test for pairwise epistasis testing. Wellcome Open Res 2017; 2:54. [PMID: 28852712 PMCID: PMC5553086 DOI: 10.12688/wellcomeopenres.11926.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2017] [Indexed: 12/30/2022] Open
Abstract
Background: In a recent paper, a novel W-test for pairwise epistasis testing was proposed that appeared, in computer simulations, to have higher power than competing alternatives. Application to genome-wide bipolar data detected significant epistasis between SNPs in genes of relevant biological function. Network analysis indicated that the implicated genes formed two separate interaction networks, each containing genes highly related to autism and neurodegenerative disorders. Methods: Here we investigate further the properties and performance of the W-test via theoretical evaluation, computer simulations and application to real data. Results: We demonstrate that, for common variants, the W-test is closely related to several existing tests of association allowing for interaction, including logistic regression on 8 degrees of freedom, although logistic regression can show inflated type I error for low minor allele frequencies, whereas the W-test shows good/conservative type I error control. Although in some situations the W-test can show higher power, logistic regression is not limited to tests on 8 degrees of freedom but can instead be tailored to impose greater structure on the assumed alternative hypothesis, offering a power advantage when the imposed structure matches the true structure. Conclusions: The W-test is a potentially useful method for testing for association - without necessarily implying interaction - between genetic variants disease, particularly when one or more of the genetic variants are rare. For common variants, the advantages of the W-test are less clear, and, indeed, there are situations where existing methods perform better. In our investigations, we further uncover a number of problems with the practical implementation and application of the W-test (to bipolar disorder) previously described, apparently due to inadequate use of standard data quality-control procedures. This observation leads us to urge caution in interpretation of the previously-presented results, most of which we consider are highly likely to be artefacts.
Collapse
Affiliation(s)
- Richard Howey
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, NE1 3BZ, UK
| | - Heather J Cordell
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, NE1 3BZ, UK
| |
Collapse
|
16
|
Processing closely spaced lesions during Nucleotide Excision Repair triggers mutagenesis in E. coli. PLoS Genet 2017; 13:e1006881. [PMID: 28686598 PMCID: PMC5521853 DOI: 10.1371/journal.pgen.1006881] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 07/21/2017] [Accepted: 06/21/2017] [Indexed: 11/19/2022] Open
Abstract
It is generally assumed that most point mutations are fixed when damage containing template DNA undergoes replication, either right at the fork or behind the fork during gap filling. Here we provide genetic evidence for a pathway, dependent on Nucleotide Excision Repair, that induces mutations when processing closely spaced lesions. This pathway, referred to as Nucleotide Excision Repair-induced Mutagenesis (NERiM), exhibits several characteristics distinct from mutations that occur within the course of replication: i) following UV irradiation, NER-induced mutations are fixed much more rapidly (t ½ ≈ 30 min) than replication dependent mutations (t ½ ≈ 80–100 min) ii) NERiM specifically requires DNA Pol IV in addition to Pol V iii) NERiM exhibits a two-hit dose-response curve that suggests processing of closely spaced lesions. A mathematical model let us define the geometry (infer the structure) of the toxic intermediate as being formed when NER incises a lesion that resides in close proximity of another lesion in the complementary strand. This critical NER intermediate requires Pol IV / Pol II for repair, it is either lethal if left unrepaired or mutation-prone when repaired. Finally, NERiM is found to operate in stationary phase cells providing an intriguing possibility for ongoing evolution in the absence of replication. In this paper, we report the surprising finding that in addition to the well-known properties of Nucleotide Excision Repair (NER) in efficiently repairing a large number of DNA lesions, NER entails a mutagenic sub-pathway. Our data suggest that closely spaced lesions are processed by NER into a toxic DNA intermediate, i.e. a gap containing a lesion, that leads either to mutagenesis during its repair or to cell death in the absence of repair. The paper describes a new pathway for the generation of mutations in stationary phase bacteria or quiescent cells; it also provides an additional role for Pol IV, the most widely distributed specialized DNA polymerase in all forms of life.
Collapse
|
17
|
Wang MH, Chang B, Sun R, Hu I, Xia X, Wu WKK, Chong KC, Zee BCY. Stratified polygenic risk prediction model with application to CAGI bipolar disorder sequencing data. Hum Mutat 2017; 38:1235-1239. [PMID: 28419606 DOI: 10.1002/humu.23229] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 03/13/2017] [Accepted: 04/04/2017] [Indexed: 01/31/2023]
Abstract
Genetic data consists of a wide range of marker types, including common, low-frequency, and rare variants. Multiple genetic markers and their interactions play central roles in the heritability of complex disease. In this study, we propose an algorithm that uses a stratified variable selection design by genetic architectures and interaction effects, achieved by a dataset-adaptive W-test. The polygenic sets in all strata were integrated to form a classification rule. The algorithm was applied to the Critical Assessment of Genome Interpretation 4 bipolar challenge sequencing data. The prediction accuracy was 60% using genetic markers on an independent test set. We found that epistasis among common genetic variants contributed most substantially to prediction precision. However, the sample size was not large enough to draw conclusions for the lack of predictability of low-frequency variants and their epistasis.
Collapse
Affiliation(s)
- Maggie Haitian Wang
- Division of Biostatistics and Centre for Clinical Research and Biostatistics, JC School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong SAR, China.,CUHK Shenzhen Research Institute, Shenzhen, China
| | - Billy Chang
- Division of Biostatistics and Centre for Clinical Research and Biostatistics, JC School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Rui Sun
- Division of Biostatistics and Centre for Clinical Research and Biostatistics, JC School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong SAR, China.,CUHK Shenzhen Research Institute, Shenzhen, China
| | - Inchi Hu
- ISOM Department and Biomedical Engineering Division, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
| | - Xiaoxuan Xia
- Division of Biostatistics and Centre for Clinical Research and Biostatistics, JC School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - William Ka Kei Wu
- Department of Anaethesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Ka Chun Chong
- Division of Biostatistics and Centre for Clinical Research and Biostatistics, JC School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong SAR, China.,CUHK Shenzhen Research Institute, Shenzhen, China
| | - Benny Chung-Ying Zee
- Division of Biostatistics and Centre for Clinical Research and Biostatistics, JC School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong SAR, China.,CUHK Shenzhen Research Institute, Shenzhen, China
| |
Collapse
|
18
|
Wang MH, Weng H. Genetic Test, Risk Prediction, and Counseling. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1005:21-46. [DOI: 10.1007/978-981-10-5717-5_2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
|
19
|
Sun R, Weng H, Hu I, Guo J, Wu WKK, Zee BCY, Wang MH. A W-test collapsing method for rare-variant association testing in exome sequencing data. Genet Epidemiol 2016; 40:591-596. [PMID: 27531462 DOI: 10.1002/gepi.22000] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 06/06/2016] [Accepted: 07/17/2016] [Indexed: 12/20/2022]
Abstract
Advancement in sequencing technology enables the study of association between complex disorder phenotypes and single-nucleotide polymorphisms with rare mutations. However, the rare genetic variant has extremely small variance and impairs testing power of traditional statistical methods. We introduce a W-test collapsing method to evaluate rare-variant association by measuring the distributional differences between cases and controls through combined log of odds ratio within a genomic region. The method is model-free and inherits chi-squared distribution with degrees of freedom estimated from bootstrapped samples of the data, and allows for fast and accurate P-value calculation without the need of permutations. The proposed method is compared with the Weighted-Sum Statistic and Sequence Kernel Association Test on simulation datasets, and showed good performances and significantly faster computing speed. In the application of real next-generation sequencing dataset of hypertensive disorder, it identified genes of interesting biological functions associated to metabolism disorder and inflammation, including the MACROD1, NLRP7, AGK, PAK6, and APBB1. The proposed method offers an efficient and effective way for testing rare genetic variants in whole exome sequencing datasets.
Collapse
Affiliation(s)
- Rui Sun
- Division of Biostatistics, Centre for Clinical Research and Biostatistics, JC School of Public Health and Primary Care, Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR.,Centre for Clinical Trials and Biostatistics, CUHK Shenzhen Research Institute, Shenzhen, China
| | - Haoyi Weng
- Division of Biostatistics, Centre for Clinical Research and Biostatistics, JC School of Public Health and Primary Care, Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR.,Centre for Clinical Trials and Biostatistics, CUHK Shenzhen Research Institute, Shenzhen, China
| | - Inchi Hu
- ISOM Department, Biomedical Engineering Division, Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR
| | - Junfeng Guo
- Division of Biostatistics, Centre for Clinical Research and Biostatistics, JC School of Public Health and Primary Care, Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR.,Centre for Clinical Trials and Biostatistics, CUHK Shenzhen Research Institute, Shenzhen, China.,Australian National University, Canberra, Australia
| | - William K K Wu
- Department of Anesthesia and Intensive Care, Chinese University of Hong Kong, Hong Kong, Hong Kong SAR
| | - Benny Chung-Ying Zee
- Division of Biostatistics, Centre for Clinical Research and Biostatistics, JC School of Public Health and Primary Care, Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR.,Centre for Clinical Trials and Biostatistics, CUHK Shenzhen Research Institute, Shenzhen, China
| | - Maggie Haitian Wang
- Division of Biostatistics, Centre for Clinical Research and Biostatistics, JC School of Public Health and Primary Care, Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR. .,Centre for Clinical Trials and Biostatistics, CUHK Shenzhen Research Institute, Shenzhen, China.
| |
Collapse
|