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Wang M, Huang S. The collective effects of genetic variants and complex traits. J Hum Genet 2022; 68:255-262. [PMID: 36513763 DOI: 10.1038/s10038-022-01105-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 12/01/2022] [Accepted: 12/02/2022] [Indexed: 12/15/2022]
Abstract
Traditional approaches in studying the genetics of complex traits have focused on identifying specific genetic variants. However, the collective effects of variants have remained largely unexplored. Here, we evaluated whether traits could be influenced by the collective effects of variants across the entire protein coding-region of the genome or the entire genome. We studied the UK Biobank exome sequencing data of 167,246 individuals as well as the genome-wide SNP array data of 408,868 individuals. We calculated for each individual four different measures of genetic variation such as heterozygosity and number of variants and two different measures of the overall deleteriousness of all variants, and performed correlations with 17 representative traits that have been studied previously. Linear regression analysis was performed with adjustment for age, sex, and genetic principal components. The results showed a high correlation among the six different measures and an inverse association of two well-correlated traits (educational attainment and height) with the total number of all variants as well as the overall deleteriousness of all variants. We have also categorized the genes based on whether they are expressed in the brain and found that the association with educational attainment only held for the brain-expressed genes. No other traits examined showed a significant correlation with the brain-expressed genes. The study demonstrates that common traits could be studied by analyzing the overall genetic variation and suggests that educational attainment is inversely related to genetic variation.
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Affiliation(s)
- Mingrui Wang
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, 110 Xiangya Road, Changsha, Hunan, 410078, PR China
| | - Shi Huang
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, 110 Xiangya Road, Changsha, Hunan, 410078, PR China.
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He J, Yu L, Qiao Z, Yu B, Liu Y, Ren H. Genetic polymorphisms of FCGR2A, ORAI1 and CD40 are associated with risk of lung cancer. Eur J Cancer Prev 2022; 31:7-13. [PMID: 34871197 DOI: 10.1097/cej.0000000000000671] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
FCGR2A, ORAI1 and CD40 are all involved in the immune and inflammatory responses in the human body, whereas its association with lung cancer is still unclear. This study aimed to investigate the effects of polymorphisms in these genes on the susceptibility to lung cancer. Six candidate single nucleotide polymorphisms (SNPs) were genotyped using a MassARRAY platform in a discovery cohort, including 400 lung cancer patients and 400 healthy controls, and validated in a replication cohort, including 529 lung cancer cases and 532 controls. Comparing the allele frequency distributions, we found that the rs1801274-G, rs511278-T and rs1883832-T were risk alleles for lung cancer (P < 0.05), whereas the minor allele of rs12320939-T was a protective allele for the disease (P = 0.037). Comparing the genotype frequency distributions, we found that rs1801274-GG, rs511278-CT and of rs1883832-TT were risk genotype for lung cancer (P < 0.05). Genetic model analysis showed that the rs1801274 A>G was correlated with an elevated risk of lung cancer in recessive and log-additive models (P < 0.05); rs511278 C>T exhibited an increased risk of disease in dominant and log-additive models (P < 0.05); rs1883832 C>T had a strong relationship with risk of disease in all three models (P < 0.001), whereas rs12320939 G>T was correlated to a reduced risk of disease in recessive and log-additive models (P < 0.05). Finally, the association between the above SNPs and lung cancer risk was validated in a replication cohort (P < 0.05). These results shed new light on the association between immune-related genes and risk of lung cancer, and might be useful for the identification of high-risk individuals.
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Affiliation(s)
- Jinxi He
- Department of Thoracic Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi
- Department of Thoracic Surgery, General Hospital of Ningxia Medical University, Yinchuan, Ningxia, China
| | - Liang Yu
- Department of Thoracic Surgery, General Hospital of Ningxia Medical University, Yinchuan, Ningxia, China
| | - Zhixiong Qiao
- Department of Thoracic Surgery, General Hospital of Ningxia Medical University, Yinchuan, Ningxia, China
| | - Bo Yu
- Department of Thoracic Surgery, General Hospital of Ningxia Medical University, Yinchuan, Ningxia, China
| | - Yang Liu
- Department of Thoracic Surgery, General Hospital of Ningxia Medical University, Yinchuan, Ningxia, China
| | - Hong Ren
- Department of Thoracic Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi
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Zhou Z, Li Y, Ma Y, Zhang H, Deng Y, Zhu Z. Multi-biomarker is an early-stage predictor for progression of Coronavirus disease 2019 (COVID-19) infection. Int J Med Sci 2021; 18:2789-2798. [PMID: 34220307 PMCID: PMC8241766 DOI: 10.7150/ijms.58742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 04/27/2021] [Indexed: 12/12/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) has spread widely in the communities in many countries. Although most of the mild patients could be cured by their body's ability to self-heal, many patients quickly progressed to severe disease and had to undergo treatment in the intensive care unit (ICU). Thus, it is very important to effectively predict which patients with mild disease are more likely to progress to severe disease. A total of 72 patients hospitalized with COVID-19 in Shandong Provincial Public Health Clinical Center and 1141 patients included in the published papers were enrolled in this study. We determined that the combination of interleukin-6 (IL-6), Neutrophil (NEUT), and Natural Killer (NK) cells had the highest prediction accuracy (with 75% sensitivity and 95% specificity) for progression of COVID-19 infection. A binomial regression equation that accounted for a multiple risk score for the combination of IL-6, NEUT, and NK was also established. The multiple risk score is a good indicator for early stratification of mild patients into risk categories, which is very important for adjusting the treatment plan and preventing death.
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Affiliation(s)
- Zheng Zhou
- Katharine Hsu International Research Institute of Infectious Disease, Shandong Provincial Public Health Clinical Center, Shandong University, Jinan 250013, China
| | - Ying Li
- Medical Technology School of Xuzhou Medical University, Xuzhou 221004, China
| | - Yuanhui Ma
- Department of Pathology, Shandong Provincial Public Health Clinical Center, Shandong University, Jinan 250013, China
| | - Heng Zhang
- Department of Labor, Jining Psychiatric Hospital, Jining 272051, China
| | - Yunfeng Deng
- Katharine Hsu International Research Institute of Infectious Disease, Shandong Provincial Public Health Clinical Center, Shandong University, Jinan 250013, China
| | - Zuobin Zhu
- Department of Genetics, Xuzhou Medical University, Xuzhou 221004, China
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Genome-wide genetic diversity yields insights into genomic responses of candidate climate-selected loci in an Andean wetland plant. Sci Rep 2020; 10:16851. [PMID: 33033367 PMCID: PMC7546723 DOI: 10.1038/s41598-020-73976-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 08/13/2020] [Indexed: 11/28/2022] Open
Abstract
Assessing population evolutionary potential has become a central tenet of conservation biology. Since adaptive responses require allelic variation at functional genes, consensus has grown that genetic variation at genes under selection is a better surrogate for adaptive evolutionary potential than neutral genetic diversity. Although consistent with prevailing theory, this argument lacks empirical support and ignores recent theoretical advances questioning the very concept of neutral genetic diversity. In this study, we quantified genome-wide responses of single nucleotide polymorphism loci linked to climatic factors over a strong latitudinal gradient in natural populations of the high Andean wetland plant, Carex gayana, and then assessed whether genetic variation of candidate climate-selected loci better predicted their genome-wide responses than genetic variation of non-candidate loci. Contrary to this expectation, genomic responses of climate-linked loci only related significantly to environmental variables and genetic diversity of non-candidate loci. The effects of genome-wide genetic diversity detected in this study may be a result of either the combined influence of small effect variants or neutral and demographic factors altering the adaptive evolutionary potential of C. gayana populations. Regardless of the processes involved, our results redeem genome-wide genetic diversity as a potentially useful indicator of population adaptive evolutionary potential.
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Wang M, Wang D, Yu J, Huang S. Enrichment in conservative amino acid changes among fixed and standing missense variations in slowly evolving proteins. PeerJ 2020; 8:e9983. [PMID: 32995099 PMCID: PMC7501800 DOI: 10.7717/peerj.9983] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 08/27/2020] [Indexed: 11/20/2022] Open
Abstract
The process of molecular evolution has many elements that are not yet fully understood. Evolutionary rates are known to vary among protein coding and noncoding DNAs, and most of the observed changes in amino acid or nucleotide sequences are assumed to be non-adaptive by the neutral theory of molecular evolution. However, it remains unclear whether fixed and standing missense changes in slowly evolving proteins are more or less neutral compared to those in fast evolving genes. Here, based on the evolutionary rates as inferred from identity scores between orthologs in human and Rhesus Macaques (Macaca mulatta), we found that the fraction of conservative substitutions between species was significantly higher in their slowly evolving proteins. Similar results were obtained by using four different methods of scoring conservative substitutions, including three that remove the impact of substitution probability, where conservative changes require fewer mutations. We also examined the single nucleotide polymorphisms (SNPs) by using the 1000 Genomes Project data and found that missense SNPs in slowly evolving proteins also had a higher fraction of conservative changes, especially for common SNPs, consistent with more non-conservative substitutions and hence stronger natural selection for SNPs, particularly rare ones, in fast evolving proteins. These results suggest that fixed and standing missense variants in slowly evolving proteins are more likely to be neutral.
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Affiliation(s)
- Mingrui Wang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, P.R. China
| | - Dapeng Wang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, Beijing, P.R. China
- Current affiliation: LeedsOmics, University of Leeds, Leeds, UK
| | - Jun Yu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, Beijing, P.R. China
| | - Shi Huang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, P.R. China
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Chen H, Lei X, Yuan D, Huang S. The relationship between the minor allele content and Alzheimer's disease. Genomics 2020; 112:2426-2432. [PMID: 31982476 DOI: 10.1016/j.ygeno.2020.01.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 11/24/2019] [Accepted: 01/22/2020] [Indexed: 01/21/2023]
Abstract
Alzheimer's disease (AD) is a chronic neurodegenerative disease. The genetic risk factors of AD remain better understood. Using previously published dataset of common single nucleotide polymorphisms (SNPs), we studied the association between the minor allele content (MAC) in an individual and AD. We found that AD patients have higher average MAC values than matched controls. We identified a risk prediction model that could predict 2.19% of AD cases. We also identified 49 genes whose expression levels correlated with both MAC and AD. By pathway and process enrichment analyses, these genes were found in pathways or processes closely related to AD. Our study suggests that AD may be linked with too many genetic variations over a threshold. The method of correlations with both MAC and traits appears to be effective in high efficiency identification of target genes for complex traits.
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Affiliation(s)
- Hongyao Chen
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Central South University, 110 Xiangya Road, Changsha, Hunan 410078, China
| | - Xiaoyun Lei
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Central South University, 110 Xiangya Road, Changsha, Hunan 410078, China
| | - Dejian Yuan
- Department of Birth Health and Heredity, Liuzhou Municipal Maternity and Child Healthcare Hospital, Liuzhou 545000, China
| | - Shi Huang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Central South University, 110 Xiangya Road, Changsha, Hunan 410078, China.
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Bian H, Wang Y, Chen W, Zhang Y, Zhuang Z, Xia R, Dai H, Feng J, Pu W, Chen L, Cai W, Hu W, Liu Y. Multiple Organ Lesions in a Case of Contamination With Multiple Radionuclides After 38 Years. Dose Response 2018; 16:1559325818815019. [PMID: 30559637 PMCID: PMC6291884 DOI: 10.1177/1559325818815019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 09/05/2018] [Accepted: 10/25/2018] [Indexed: 11/15/2022] Open
Abstract
The patient was contaminated with multiple radionuclides 38 years ago due to an accident. To investigate the effects of radionuclide contamination on humans, he has been followed up by examinations for many years. Long-term effects gradually emerge in these years. Lung cancer was diagnosed by medical examinations. Besides, chronic gastritis with intestinal metaplasia was indicated by gastroscopic biopsies, while colorectal polyps found by colonoscopy. All 13 colorectal polyps were removed, and radical surgery for lung cancer was performed. Fortunately, pathological examinations indicated that it was early lung cancer. The ground glass nodule (GGN) in left lung identified during the follow-up will be resected when needed. It is speculated that multiple manifestations of the patient may be related to radiation, and different lesions in the organs may be related to systemic adaptive response. However, longer follow-up is needed due to a lack of effective and direct evidence. This work is expected to provide experiences for similar patients' treatment and follow-up.
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Affiliation(s)
- Huahui Bian
- Department of Nuclear Accident Medical Emergency, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Youyou Wang
- Department of Nuclear Accident Medical Emergency, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Weibo Chen
- Department of Nuclear Accident Medical Emergency, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Yusong Zhang
- Department of Nuclear Accident Medical Emergency, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Zhixiang Zhuang
- Department of Oncology, the Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Rui Xia
- Department of Oncology, the Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Hong Dai
- Department of Nuclear Accident Medical Emergency, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Junchao Feng
- Department of Nuclear Accident Medical Emergency, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Wangyang Pu
- Department of Oncology, the Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Lei Chen
- Department of Oncology, the Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Wu Cai
- Department of Medical Imaging, the Second Affiliated Hospital of Soochow University, Suzhou,China
| | - Wentao Hu
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Medical College of Soochow University, Suzhou, China
- Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Suzhou, China
| | - Yulong Liu
- Department of Nuclear Accident Medical Emergency, The Second Affiliated Hospital of Soochow University, Suzhou, China
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Medical College of Soochow University, Suzhou, China
- Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Suzhou, China
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