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2. Analysis of blood methylation quantitative trait loci in East Asians reveals ancestry-specific impacts on complex traits

Author

Peng, Qianqian, Liu, Xinxuan, Li, Wenran, Jing, Han, Li, Jiarui, Gao, Xingjian, Luo, Qi, Breeze, Charles E., Pan, Siyu, Zheng, Qiwen, Li, Guochao, Qian, Jiaqiang, Yuan, Liyun, Yuan, Na, You, Chenglong, Du, Siyuan, Zheng, Yuanting, Yuan, Ziyu, Tan, Jingze, Jia, Peilin, Wang, Jiucun, Zhang, Guoqing, Lu, Xianping, Shi, Leming, Guo, Shicheng, Liu, Yun, Ni, Ting, Wen, Bo, Zeng, Changqing, Jin, Li, Teschendorff, Andrew E., Liu, Fan, and Wang, Sijia

Published
2024
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8. Rewired m6A epitranscriptomic networks link mutant p53 to neoplastic transformation

Author

Xu, An, Liu, Mo, Huang, Mo-Fan, Zhang, Yang, Hu, Ruifeng, Gingold, Julian A., Liu, Ying, Zhu, Dandan, Chien, Chian-Shiu, Wang, Wei-Chen, Liao, Zian, Yuan, Fei, Hsu, Chih-Wei, Tu, Jian, Yu, Yao, Rosen, Taylor, Xiong, Feng, Jia, Peilin, Yang, Yi-Ping, Bazer, Danielle A., Chen, Ya-Wen, Li, Wenbo, Huff, Chad D., Zhu, Jay-Jiguang, Aguilo, Francesca, Chiou, Shih-Hwa, Boles, Nathan C., Lai, Chien-Chen, Hung, Mien-Chie, Zhao, Zhongming, Van Nostrand, Eric L., Zhao, Ruiying, and Lee, Dung-Fang

Published
2023
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9. Retraction Note: Identification of de novo mutations in prenatal neurodevelopment-associated genes in schizophrenia in two Han Chinese patient-sibling family-based cohorts.

Author

Jiang, Shan, Zhou, Daizhan, Wang, Yin-Ying, Jia, Peilin, Wan, Chunling, Li, Xingwang, He, Guang, Cao, Dongmei, Jiang, Xiaoqian, Kendler, Kenneth S, Tsuang, Ming, Mize, Travis, Wu, Jain-Shing, Lu, Yimei, He, Lin, Chen, Jingchun, Zhao, Zhongming, and Chen, Xiangning

Subjects
Clinical Sciences, Public Health and Health Services, Psychology
Abstract

This article has been retracted. Please see the Retraction Notice for more detail: https://doi.org/10.1038/s41398-020-00987-z.

Published
2020

10. Identification of de novo mutations in prenatal neurodevelopment-associated genes in schizophrenia in two Han Chinese patient-sibling family-based cohorts.

Author

Jiang, Shan, Zhou, Daizhan, Wang, Yin-Ying, Jia, Peilin, Wan, Chunling, Li, Xingwang, He, Guang, Cao, Dongmei, Jiang, Xiaoqian, Kendler, Kenneth S, Tsuang, Ming, Mize, Travis, Wu, Jain-Shing, Lu, Yimei, He, Lin, Chen, Jingchun, Zhao, Zhongming, and Chen, Xiangning

Subjects
Clinical Sciences, Public Health and Health Services, Psychology
Abstract

Schizophrenia (SCZ) is a severe psychiatric disorder with a strong genetic component. High heritability of SCZ suggests a major role for transmitted genetic variants. Furthermore, SCZ is also associated with a marked reduction in fecundity, leading to the hypothesis that alleles with large effects on risk might often occur de novo. In this study, we conducted whole-genome sequencing for 23 families from two cohorts with unaffected siblings and parents. Two nonsense de novo mutations (DNMs) in GJC1 and HIST1H2AD were identified in SCZ patients. Ten genes (DPYSL2, NBPF1, SDK1, ZNF595, ZNF718, GCNT2, SNX9, AACS, KCNQ1, and MSI2) were found to carry more DNMs in SCZ patients than their unaffected siblings by burden test. Expression analyses indicated that these DNM implicated genes showed significantly higher expression in prefrontal cortex in prenatal stage. The DNM in the GJC1 gene is highly likely a loss function mutation (pLI = 0.94), leading to the dysregulation of ion channel in the glutamatergic excitatory neurons. Analysis of rare variants in independent exome sequencing dataset indicates that GJC1 has significantly more rare variants in SCZ patients than in unaffected controls. Data from genome-wide association studies suggested that common variants in the GJC1 gene may be associated with SCZ and SCZ-related traits. Genes co-expressed with GJC1 are involved in SCZ, SCZ-associated pathways, and drug targets. These evidences suggest that GJC1 may be a risk gene for SCZ and its function may be involved in prenatal and early neurodevelopment, a vulnerable period for developmental disorders such as SCZ.

Published
2020

11. Retracted: Identification of de novo mutations in prenatal neurodevelopment-associated genes in schizophrenia in two Han Chinese patient-sibling family-based cohorts

Author

Jiang, Shan, Zhou, Daizhan, Wang, Yin-Ying, Jia, Peilin, Wan, Chunling, Li, Xingwang, He, Guang, Cao, Dongmei, Jiang, Xiaoqian, Kendler, Kenneth S, Tsuang, Ming, Mize, Travis, Wu, Jain-Shing, Lu, Yimei, He, Lin, Chen, Jingchun, Zhao, Zhongming, and Chen, Xiangning

Subjects
Biological Psychology, Pharmacology and Pharmaceutical Sciences, Biomedical and Clinical Sciences, Psychology, Serious Mental Illness, Brain Disorders, Neurosciences, Clinical Research, Schizophrenia, Pediatric, Human Genome, Biotechnology, Mental Health, Prevention, Genetics, Genetic Testing, 2.1 Biological and endogenous factors, Aetiology, Mental health, China, Connexins, Genetic Predisposition to Disease, Genome-Wide Association Study, Humans, Mutation, Siblings, Clinical Sciences, Public Health and Health Services, Clinical sciences, Biological psychology
Abstract

Schizophrenia (SCZ) is a severe psychiatric disorder with a strong genetic component. High heritability of SCZ suggests a major role for transmitted genetic variants. Furthermore, SCZ is also associated with a marked reduction in fecundity, leading to the hypothesis that alleles with large effects on risk might often occur de novo. In this study, we conducted whole-genome sequencing for 23 families from two cohorts with unaffected siblings and parents. Two nonsense de novo mutations (DNMs) in GJC1 and HIST1H2AD were identified in SCZ patients. Ten genes (DPYSL2, NBPF1, SDK1, ZNF595, ZNF718, GCNT2, SNX9, AACS, KCNQ1, and MSI2) were found to carry more DNMs in SCZ patients than their unaffected siblings by burden test. Expression analyses indicated that these DNM implicated genes showed significantly higher expression in prefrontal cortex in prenatal stage. The DNM in the GJC1 gene is highly likely a loss function mutation (pLI = 0.94), leading to the dysregulation of ion channel in the glutamatergic excitatory neurons. Analysis of rare variants in independent exome sequencing dataset indicates that GJC1 has significantly more rare variants in SCZ patients than in unaffected controls. Data from genome-wide association studies suggested that common variants in the GJC1 gene may be associated with SCZ and SCZ-related traits. Genes co-expressed with GJC1 are involved in SCZ, SCZ-associated pathways, and drug targets. These evidences suggest that GJC1 may be a risk gene for SCZ and its function may be involved in prenatal and early neurodevelopment, a vulnerable period for developmental disorders such as SCZ.

Published
2020

14. A Frameshift Variant in the CHST9 Gene Identified by Family-Based Whole Genome Sequencing Is Associated with Schizophrenia in Chinese Population.

Author

Chen, Jingchun, Wu, Jain-Shing, Mize, Travis, Moreno, Marvi, Hamid, Mahtab, Servin, Francisco, Bashy, Bita, Zhao, Zhongming, Jia, Peilin, Tsuang, Ming T, Kendler, Kenneth S, Xiong, Momiao, and Chen, Xiangning

Abstract

Recent studies imply that rare variants contribute to the risk of schizophrenia, however, the exact variants or genes responsible for this condition are largely unknown. In this study, we conducted whole genome sequencing (WGS) of 20 Chinese families. Each family consisted of at least two affected siblings diagnosed with schizophrenia and at least one unaffected sibling. We examined functional variants that were found in affected sibling(s) but not in unaffected sibling(s) within a family. Matching this criterion, a frameshift heterozygous deletion of CA (-/CA) at chromosome 18:24722722, also referred to as rs752084147, in the Carbohydrate Sulfotransferase 9 (CHST9) gene, was detected in two families. This deletion was confirmed by PCR-based Sanger sequencing. With the observed frequency of 0.00076 in Han Chinese population, we performed both case-control and family-based analyses to evaluate its association with schizophrenia. In the case-control analyses, Chi-square test P-value was 6.80e-12 and the P-value was 0.0008 after one million simulations. In family-based segregation analyses, segregation P-value was 7.72e-7 and simulated P-value was 5.70e-6. For both the case-control and family-based analyses, the CA deletion was significantly associated with schizophrenia in the Chinese population. Further investigation of this gene  is warranted in the development of schizophrenia by utilizing larger and more ethnically diverse samples.

Published
2019

18. Comprehensive assessment of long-read sequencing platforms and calling algorithms for detection of copy number variation.

Author

Yuan, Na and Jia, Peilin

Subjects
*DISEASE susceptibility, *RESEARCH personnel, *HUMAN experimentation, *ALGORITHMS
Abstract

Copy number variations (CNVs) play pivotal roles in disease susceptibility and have been intensively investigated in human disease studies. Long-read sequencing technologies offer opportunities for comprehensive structural variation (SV) detection, and numerous methodologies have been developed recently. Consequently, there is a pressing need to assess these methods and aid researchers in selecting appropriate techniques for CNV detection using long-read sequencing. Hence, we conducted an evaluation of eight CNV calling methods across 22 datasets from nine publicly available samples and 15 simulated datasets, covering multiple sequencing platforms. The overall performance of CNV callers varied substantially and was influenced by the input dataset type, sequencing depth, and CNV type, among others. Specifically, the PacBio CCS sequencing platform outperformed PacBio CLR and Nanopore platforms regarding CNV detection recall rates. A sequencing depth of 10x demonstrated the capability to identify 85% of the CNVs detected in a 50x dataset. Moreover, deletions were more generally detectable than duplications. Among the eight benchmarked methods, cuteSV, Delly, pbsv, and Sniffles2 demonstrated superior accuracy, while SVIM exhibited high recall rates. [ABSTRACT FROM AUTHOR]

Published
2024
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19. Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas

Author

Knijnenburg, Theo A, Wang, Linghua, Zimmermann, Michael T, Chambwe, Nyasha, Gao, Galen F, Cherniack, Andrew D, Fan, Huihui, Shen, Hui, Way, Gregory P, Greene, Casey S, Liu, Yuexin, Akbani, Rehan, Feng, Bin, Donehower, Lawrence A, Miller, Chase, Shen, Yang, Karimi, Mostafa, Chen, Haoran, Kim, Pora, Jia, Peilin, Shinbrot, Eve, Zhang, Shaojun, Liu, Jianfang, Hu, Hai, Bailey, Matthew H, Yau, Christina, Wolf, Denise, Zhao, Zhongming, Weinstein, John N, Li, Lei, Ding, Li, Mills, Gordon B, Laird, Peter W, Wheeler, David A, Shmulevich, Ilya, Network, The Cancer Genome Atlas Research, Caesar-Johnson, Samantha J, Demchok, John A, Felau, Ina, Kasapi, Melpomeni, Ferguson, Martin L, Hutter, Carolyn M, Sofia, Heidi J, Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Zenklusen, Jean C, Zhang, Jiashan, Chudamani, Sudha, Liu, Jia, Lolla, Laxmi, Naresh, Rashi, Pihl, Todd, Sun, Qiang, Wan, Yunhu, Wu, Ye, Cho, Juok, DeFreitas, Timothy, Frazer, Scott, Gehlenborg, Nils, Getz, Gad, Heiman, David I, Kim, Jaegil, Lawrence, Michael S, Lin, Pei, Meier, Sam, Noble, Michael S, Saksena, Gordon, Voet, Doug, Zhang, Hailei, Bernard, Brady, Dhankani, Varsha, Knijnenburg, Theo, Kramer, Roger, Leinonen, Kalle, Miller, Michael, Reynolds, Sheila, Thorsson, Vesteinn, Zhang, Wei, Broom, Bradley M, Hegde, Apurva M, Ju, Zhenlin, Kanchi, Rupa S, Korkut, Anil, Li, Jun, Liang, Han, Ling, Shiyun, Liu, Wenbin, Lu, Yiling, Ng, Kwok-Shing, Rao, Arvind, Ryan, Michael, Wang, Jing, and Zhang, Jiexin

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Women's Health, Orphan Drug, Rare Diseases, Human Genome, Ovarian Cancer, Cancer Genomics, Cancer, 2.1 Biological and endogenous factors, Cell Line, Tumor, DNA Damage, Gene Silencing, Genome, Human, Humans, Loss of Heterozygosity, Machine Learning, Mutation, Neoplasms, Recombinational DNA Repair, Tumor Suppressor Proteins, Cancer Genome Atlas Research Network, DNA damage footprints, DNA damage repair, The Cancer Genome Atlas PanCanAtlas project, epigenetic silencing, integrative statistical analysis, mutational signatures, protein structure analysis, somatic copy-number alterations, somatic mutations, Biochemistry and Cell Biology, Medical Physiology, Biological sciences
Abstract

DNA damage repair (DDR) pathways modulate cancer risk, progression, and therapeutic response. We systematically analyzed somatic alterations to provide a comprehensive view of DDR deficiency across 33 cancer types. Mutations with accompanying loss of heterozygosity were observed in over 1/3 of DDR genes, including TP53 and BRCA1/2. Other prevalent alterations included epigenetic silencing of the direct repair genes EXO5, MGMT, and ALKBH3 in ∼20% of samples. Homologous recombination deficiency (HRD) was present at varying frequency in many cancer types, most notably ovarian cancer. However, in contrast to ovarian cancer, HRD was associated with worse outcomes in several other cancers. Protein structure-based analyses allowed us to predict functional consequences of rare, recurrent DDR mutations. A new machine-learning-based classifier developed from gene expression data allowed us to identify alterations that phenocopy deleterious TP53 mutations. These frequent DDR gene alterations in many human cancers have functional consequences that may determine cancer progression and guide therapy.

Published
2018

20. Asprosin is a centrally acting orexigenic hormone

Author

Duerrschmid, Clemens, He, Yanlin, Wang, Chunmei, Li, Chia, Bournat, Juan C, Romere, Chase, Saha, Pradip K, Lee, Mark E, Phillips, Kevin J, Jain, Mahim, Jia, Peilin, Zhao, Zhongming, Farias, Monica, Wu, Qi, Milewicz, Dianna M, Sutton, V Reid, Moore, David D, Butte, Nancy F, Krashes, Michael J, Xu, Yong, and Chopra, Atul R

Subjects
Biomedical and Clinical Sciences, Nutrition and Dietetics, Adolescent, Adult, Animals, Appetite Depressants, Appetite Regulation, Female, Fibrillin-1, Humans, Hypothalamus, Male, Mice, Mice, Inbred C57BL, Mice, Transgenic, Microfilament Proteins, Neurons, Peptide Fragments, Peptide Hormones, Rats, Signal Transduction, Young Adult, Medical and Health Sciences, Immunology, Biomedical and clinical sciences, Health sciences
Abstract

Asprosin is a recently discovered fasting-induced hormone that promotes hepatic glucose production. Here we demonstrate that asprosin in the circulation crosses the blood-brain barrier and directly activates orexigenic AgRP+ neurons via a cAMP-dependent pathway. This signaling results in inhibition of downstream anorexigenic proopiomelanocortin (POMC)-positive neurons in a GABA-dependent manner, which then leads to appetite stimulation and a drive to accumulate adiposity and body weight. In humans, a genetic deficiency in asprosin causes a syndrome characterized by low appetite and extreme leanness; this is phenocopied by mice carrying similar mutations and can be fully rescued by asprosin. Furthermore, we found that obese humans and mice had pathologically elevated concentrations of circulating asprosin, and neutralization of asprosin in the blood with a monoclonal antibody reduced appetite and body weight in obese mice, in addition to improving their glycemic profile. Thus, in addition to performing a glucogenic function, asprosin is a centrally acting orexigenic hormone that is a potential therapeutic target in the treatment of both obesity and diabetes.

Published
2017

21. Cerebrospinal fluid (CSF) biomarkers of iron status are associated with CSF viral load, antiretroviral therapy, and demographic factors in HIV-infected adults

Author

Patton, Stephanie M, Wang, Quan, Hulgan, Todd, Connor, James R, Jia, Peilin, Zhao, Zhongming, Letendre, Scott L, Ellis, Ronald J, Bush, William S, Samuels, David C, Franklin, Donald R, Kaur, Harpreet, Iudicello, Jennifer, Grant, Igor, and Kallianpur, Asha R

Subjects
Medical Microbiology, Biomedical and Clinical Sciences, Immunology, Clinical Research, Mental Health, Pediatric AIDS, Acquired Cognitive Impairment, HIV/AIDS, Pediatric, Infectious Diseases, Brain Disorders, Evaluation of treatments and therapeutic interventions, 6.1 Pharmaceuticals, Infection, Good Health and Well Being, Adult, Anti-Retroviral Agents, Apoferritins, Blood-Brain Barrier, Cohort Studies, Demography, Female, HIV Infections, Humans, Iron, Male, Middle Aged, Transferrin, Viral Load, Iron transport, Cerebrospinal fluid, HIV, H-ferritin, HIV-associated neurocognitive disorders, Biological Sciences, Medical and Health Sciences, Neurosciences
Abstract

BackgroundHIV-associated neurocognitive disorder (HAND) remains common, despite antiretroviral therapy (ART). HIV dysregulates iron metabolism, but cerebrospinal fluid (CSF) levels of iron and iron-transport proteins in HIV-infected (HIV+) persons are largely unknown. The objectives of this study were to characterize CSF iron-related biomarkers in HIV+ adults and explore their relationships to known predictors of HAND.MethodsWe quantified total iron, transferrin and heavy-chain (H)-ferritin by immunoassay in CSF sampled by lumbar puncture in 403 HIV+ participants in a multi-center, observational study and evaluated biomarker associations with demographic and HIV-related correlates of HAND [e.g., age, sex, self-reported race/ethnicity, ART, and detectable plasma virus and CSF viral load (VL)] by multivariable regression. In a subset (N = 110) with existing CSF: serum albumin (QAlb) measurements, QAlb and comorbidity severity were also included as covariates to account for variability in the blood-CSF-barrier.ResultsAmong 403 individuals (median age 43 years, 19% women, 56% non-Whites, median nadir CD4+ T cell count 180 cells/µL, 46% with undetectable plasma virus), men had 25% higher CSF transferrin (median 18.1 vs. 14.5 µg/mL), and 71% higher H-ferritin (median 2.9 vs. 1.7 ng/mL) than women (both p-values ≤0.01). CSF iron was 41% higher in self-reported Hispanics and 27% higher in (non-Hispanic) Whites than in (non-Hispanic) Blacks (median 5.2 and 4.7 µg/dL in Hispanics and Whites, respectively, vs. 3.7 µg/dL in Blacks, both p ≤ 0.01); these findings persisted after adjustment for age, sex, and HIV-specific factors. Median H-ferritin was 25% higher (p  50 years) than in younger persons (age ≤ 35 years; both p

Published
2017

22. DNA methylation clocks for estimating biological age in Chinese cohorts

Author

Zheng, Zikai, primary, Li, Jiaming, additional, Liu, Tianzi, additional, Fan, Yanling, additional, Zhai, Qiao-Cheng, additional, Xiong, Muzhao, additional, Wang, Qiao-Ran, additional, Sun, Xiaoyan, additional, Zheng, Qi-Wen, additional, Che, Shanshan, additional, Jiang, Beier, additional, Zheng, Quan, additional, Wang, Cui, additional, Liu, Lixiao, additional, Ping, Jiale, additional, Wang, Si, additional, Gao, Dan-Dan, additional, Ye, Jinlin, additional, Yang, Kuan, additional, Zuo, Yuesheng, additional, Ma, Shuai, additional, Yang, Yun-Gui, additional, Qu, Jing, additional, Zhang, Feng, additional, Jia, Peilin, additional, Liu, Guang-Hui, additional, and Zhang, Weiqi, additional

Published
2024
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24. Genome‐wide association study of HIV‐associated neurocognitive disorder (HAND): A CHARTER group study

Author

Jia, Peilin, Zhao, Zhongming, Hulgan, Todd, Bush, William S, Samuels, David C, Bloss, Cinnamon S, Heaton, Robert K, Ellis, Ronald J, Schork, Nicholas, Marra, Christina M, Collier, Ann C, Clifford, David B, Gelman, Benjamin B, Sacktor, Ned, Morgello, Susan, Simpson, David M, McCutchan, J Allen, Barnholtz‐Sloan, Jill S, Franklin, Donald R, Rosario, Debralee, Letendre, Scott L, Grant, Igor, Kallianpur, Asha R, and Group, for the CHARTER Study

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Genetics, Mental Health, HIV/AIDS, Human Genome, Infectious Diseases, Neurosciences, Prevention, Brain Disorders, 2.1 Biological and endogenous factors, Aetiology, Good Health and Well Being, AIDS Dementia Complex, Adult, Biomarkers, Female, Follow-Up Studies, Genome-Wide Association Study, Genotype, Humans, Male, Middle Aged, Neurocognitive Disorders, Neuropsychological Tests, Polymorphism, Single Nucleotide, Prognosis, Prospective Studies, HIV-associated neurocognitive disorder, neuro-cognitive impairment, GWAS, genotype, CHARTER study, global deficit score, CHARTER Study Group, neurocognitive impairment, Clinical Sciences, Clinical sciences
Abstract

HIV-associated neurocognitive disorder (HAND) often complicates HIV infection despite combination antiretroviral therapy (ART) and may be influenced by host genomics. We performed a genome-wide association study (GWAS) of HAND in 1,050 CNS HIV Anti-Retroviral Therapy Effects Research (CHARTER) Study participants. All participants underwent standardized, comprehensive neurocognitive, and neuromedical assessments to determine if they had cognitive impairment as assessed by the Global Deficit Score (GDS), and individuals with comorbidities that could confound diagnosis of HAND were excluded. Neurocognitive outcomes included GDS-defined neurocognitive impairment (NCI; binary GDS, 366 cases with GDS ≥ 0.5 and 684 controls with GDS

Published
2017

26. Pd-Doped WO3 Nanoplates for Hydrogen Sensing: Experimental Studies and Density Functional Theory Investigations.

Author

Ma, Shiteng, Chen, Fengjiao, Liu, Yukun, Zhang, Hao, Jia, Peilin, and Zhang, Dongzhi

Abstract

In this article, a hydrogen sensor with excellent performance was synthesized using the hydrothermal method, with Pd-modified WO3 nanoplates as the sensing layer. At an optimum operating temperature of 200 °C, the hydrogen gas sensing capabilities of WO3 and Pd-WO3 composite sensors were investigated. The findings indicate that in contrast to the WO3 sensor, the Pd-WO3 composite sensor exhibits superior hydrogen sensing performance, showcasing remarkable selectivity, reliable repeatability, sustained long-term stability, and quick response and recovery (8 s/10 s@100 ppm). The first-principles density functional theory was used to explain the sensing mechanism of the Pd-WO3 composite. The improved sensing performance of Pd-WO3 composite sensors was explained from the perspectives of the Schottky junction formed between Pd nanoparticles and WO3, the catalytic effect of metal Pd nanoparticles, and gas adsorption–desorption. This article confirms that Pd-modified WO3 nanoplates are good candidates for efficient hydrogen gas sensing. [ABSTRACT FROM AUTHOR]

Published
2024
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27. Anemia and Red Blood Cell Indices Predict HIV-Associated Neurocognitive Impairment in the Highly Active Antiretroviral Therapy Era

Author

Kallianpur, Asha R, Wang, Quan, Jia, Peilin, Hulgan, Todd, Zhao, Zhongming, Letendre, Scott L, Ellis, Ronald J, Heaton, Robert K, Franklin, Donald R, Barnholtz-Sloan, Jill, Collier, Ann C, Marra, Christina M, Clifford, David B, Gelman, Benjamin B, McArthur, Justin C, Morgello, Susan, Simpson, David M, McCutchan, JA, and Grant, Igor

Subjects
Medical Microbiology, Biomedical and Clinical Sciences, Acquired Cognitive Impairment, Infectious Diseases, Brain Disorders, Neurosciences, HIV/AIDS, Hematology, Clinical Research, Dementia, Neurodegenerative, Evaluation of treatments and therapeutic interventions, 6.1 Pharmaceuticals, Infection, Good Health and Well Being, AIDS Dementia Complex, Adult, Anemia, Anti-HIV Agents, Antiretroviral Therapy, Highly Active, Cohort Studies, Cross-Sectional Studies, Erythrocyte Count, Erythrocyte Indices, Female, HIV Infections, Humans, Male, Middle Aged, Multivariate Analysis, Odds Ratio, Predictive Value of Tests, Risk Factors, human immunodeficiency virus, anemia, red blood cell indices, mitochondrial dysfunction, HIV-associated neurocognitive disorder, neurocognitive impairment, iron metabolism, CHARTER Study Group, Biological Sciences, Medical and Health Sciences, Microbiology, Biological sciences, Biomedical and clinical sciences, Health sciences
Abstract

BackgroundAnemia has been linked to adverse human immunodeficiency virus (HIV) outcomes, including dementia, in the era before highly active antiretroviral therapy (HAART). Milder forms of HIV-associated neurocognitive disorder (HAND) remain common in HIV-infected persons, despite HAART, but whether anemia predicts HAND in the HAART era is unknown.MethodsWe evaluated time-dependent associations of anemia and cross-sectional associations of red blood cell indices with neurocognitive impairment in a multicenter, HAART-era HIV cohort study (N = 1261), adjusting for potential confounders, including age, nadir CD4(+) T-cell count, zidovudine use, and comorbid conditions. Subjects underwent comprehensive neuropsychiatric and neuromedical assessments.ResultsHAND, defined according to standardized criteria, occurred in 595 subjects (47%) at entry. Mean corpuscular volume and mean corpuscular hemoglobin were positively associated with the global deficit score, a continuous measure of neurocognitive impairment (both P < .01), as well as with all HAND, milder forms of HAND, and HIV-associated dementia in multivariable analyses (all P < .05). Anemia independently predicted development of HAND during a median follow-up of 72 months (adjusted hazard ratio, 1.55; P < .01).ConclusionsAnemia and red blood cell indices predict HAND in the HAART era and may contribute to risk assessment. Future studies should address whether treating anemia may help to prevent HAND or improve cognitive function in HIV-infected persons.

Published
2016

30. Genetic variation in iron metabolism is associated with neuropathic pain and pain severity in HIV-infected patients on antiretroviral therapy.

Author

Kallianpur, Asha R, Jia, Peilin, Ellis, Ronald J, Zhao, Zhongming, Bloss, Cinnamon, Wen, Wanqing, Marra, Christina M, Hulgan, Todd, Simpson, David M, Morgello, Susan, McArthur, Justin C, Clifford, David B, Collier, Ann C, Gelman, Benjamin B, McCutchan, J Allen, Franklin, Donald, Samuels, David C, Rosario, Debralee, Holzinger, Emily, Murdock, Deborah G, Letendre, Scott, Grant, Igor, and CHARTER Study Group

Subjects
CHARTER Study Group, Humans, HIV Infections, Neuralgia, Iron, Iron Regulatory Protein 1, Anti-Retroviral Agents, Multivariate Analysis, Genotype, Linkage Disequilibrium, Adult, Aged, Middle Aged, Female, Male, Genetic Variation, Young Adult, General Science & Technology
Abstract

HIV sensory neuropathy and distal neuropathic pain (DNP) are common, disabling complications associated with combination antiretroviral therapy (cART). We previously associated iron-regulatory genetic polymorphisms with a reduced risk of HIV sensory neuropathy during more neurotoxic types of cART. We here evaluated the impact of polymorphisms in 19 iron-regulatory genes on DNP in 560 HIV-infected subjects from a prospective, observational study, who underwent neurological examinations to ascertain peripheral neuropathy and structured interviews to ascertain DNP. Genotype-DNP associations were explored by logistic regression and permutation-based analytical methods. Among 559 evaluable subjects, 331 (59%) developed HIV-SN, and 168 (30%) reported DNP. Fifteen polymorphisms in 8 genes (p

Published
2014

34. Deciphering mechanisms of cardiomyocytes and non-cardiomyocyte transformation in myocardial remodeling of permanent atrial fibrillation

Author

Sheng, Yixuan, primary, Wang, Yin-Ying, additional, Chang, Yuan, additional, Ye, Dongting, additional, Wu, Liying, additional, Kang, Hongen, additional, Zhang, Xiong, additional, Chen, Xiao, additional, Li, Bin, additional, Zhu, Daliang, additional, Zhang, Ningning, additional, Zhao, Haisen, additional, Chen, Aijun, additional, Chen, Haisheng, additional, Jia, Peilin, additional, and Song, Jiangping, additional

Published
2023
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35. Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas

Author

Caesar-Johnson, Samantha J., Demchok, John A., Felau, Ina, Kasapi, Melpomeni, Ferguson, Martin L., Hutter, Carolyn M., Sofia, Heidi J., Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Zenklusen, Jean C., Zhang, Jiashan (Julia), Chudamani, Sudha, Liu, Jia, Lolla, Laxmi, Naresh, Rashi, Pihl, Todd, Sun, Qiang, Wan, Yunhu, Wu, Ye, Cho, Juok, DeFreitas, Timothy, Frazer, Scott, Gehlenborg, Nils, Getz, Gad, Heiman, David I., Kim, Jaegil, Lawrence, Michael S., Lin, Pei, Meier, Sam, Noble, Michael S., Saksena, Gordon, Voet, Doug, Zhang, Hailei, Bernard, Brady, Chambwe, Nyasha, Dhankani, Varsha, Knijnenburg, Theo, Kramer, Roger, Leinonen, Kalle, Liu, Yuexin, Miller, Michael, Reynolds, Sheila, Shmulevich, Ilya, Thorsson, Vesteinn, Zhang, Wei, Akbani, Rehan, Broom, Bradley M., Hegde, Apurva M., Ju, Zhenlin, Kanchi, Rupa S., Korkut, Anil, Li, Jun, Liang, Han, Ling, Shiyun, Liu, Wenbin, Lu, Yiling, Mills, Gordon B., Ng, Kwok-Shing, Rao, Arvind, Ryan, Michael, Wang, Jing, Weinstein, John N., Zhang, Jiexin, Abeshouse, Adam, Armenia, Joshua, Chakravarty, Debyani, Chatila, Walid K., de Bruijn, Ino, Gao, Jianjiong, Gross, Benjamin E., Heins, Zachary J., Kundra, Ritika, La, Konnor, Ladanyi, Marc, Luna, Augustin, Nissan, Moriah G., Ochoa, Angelica, Phillips, Sarah M., Reznik, Ed, Sanchez-Vega, Francisco, Sander, Chris, Schultz, Nikolaus, Sheridan, Robert, Sumer, S. Onur, Sun, Yichao, Taylor, Barry S., Wang, Jioajiao, Zhang, Hongxin, Anur, Pavana, Peto, Myron, Spellman, Paul, Benz, Christopher, Stuart, Joshua M., Wong, Christopher K., Yau, Christina, Hayes, D. Neil, Parker, Joel S., Wilkerson, Matthew D., Ally, Adrian, Balasundaram, Miruna, Bowlby, Reanne, Brooks, Denise, Carlsen, Rebecca, Chuah, Eric, Dhalla, Noreen, Holt, Robert, Jones, Steven J.M., Kasaian, Katayoon, Lee, Darlene, Ma, Yussanne, Marra, Marco A., Mayo, Michael, Moore, Richard A., Mungall, Andrew J., Mungall, Karen, Robertson, A. Gordon, Sadeghi, Sara, Schein, Jacqueline E., Sipahimalani, Payal, Tam, Angela, Thiessen, Nina, Tse, Kane, Wong, Tina, Berger, Ashton C., Beroukhim, Rameen, Cherniack, Andrew D., Cibulskis, Carrie, Gabriel, Stacey B., Gao, Galen F., Ha, Gavin, Meyerson, Matthew, Schumacher, Steven E., Shih, Juliann, Kucherlapati, Melanie H., Kucherlapati, Raju S., Baylin, Stephen, Cope, Leslie, Danilova, Ludmila, Bootwalla, Moiz S., Lai, Phillip H., Maglinte, Dennis T., Van Den Berg, David J., Weisenberger, Daniel J., Auman, J. Todd, Balu, Saianand, Bodenheimer, Tom, Fan, Cheng, Hoadley, Katherine A., Hoyle, Alan P., Jefferys, Stuart R., Jones, Corbin D., Meng, Shaowu, Mieczkowski, Piotr A., Mose, Lisle E., Perou, Amy H., Perou, Charles M., Roach, Jeffrey, Shi, Yan, Simons, Janae V., Skelly, Tara, Soloway, Matthew G., Tan, Donghui, Veluvolu, Umadevi, Fan, Huihui, Hinoue, Toshinori, Laird, Peter W., Shen, Hui, Zhou, Wanding, Bellair, Michelle, Chang, Kyle, Covington, Kyle, Creighton, Chad J., Dinh, Huyen, Doddapaneni, HarshaVardhan, Donehower, Lawrence A., Drummond, Jennifer, Gibbs, Richard A., Glenn, Robert, Hale, Walker, Han, Yi, Hu, Jianhong, Korchina, Viktoriya, Lee, Sandra, Lewis, Lora, Li, Wei, Liu, Xiuping, Morgan, Margaret, Morton, Donna, Muzny, Donna, Santibanez, Jireh, Sheth, Margi, Shinbrot, Eve, Wang, Linghua, Wang, Min, Wheeler, David A., Xi, Liu, Zhao, Fengmei, Hess, Julian, Appelbaum, Elizabeth L., Bailey, Matthew, Cordes, Matthew G., Ding, Li, Fronick, Catrina C., Fulton, Lucinda A., Fulton, Robert S., Kandoth, Cyriac, Mardis, Elaine R., McLellan, Michael D., Miller, Christopher A., Schmidt, Heather K., Wilson, Richard K., Crain, Daniel, Curley, Erin, Gardner, Johanna, Lau, Kevin, Mallery, David, Morris, Scott, Paulauskis, Joseph, Penny, Robert, Shelton, Candace, Shelton, Troy, Sherman, Mark, Thompson, Eric, Yena, Peggy, Bowen, Jay, Gastier-Foster, Julie M., Gerken, Mark, Leraas, Kristen M., Lichtenberg, Tara M., Ramirez, Nilsa C., Wise, Lisa, Zmuda, Erik, Corcoran, Niall, Costello, Tony, Hovens, Christopher, Carvalho, Andre L., de Carvalho, Ana C., Fregnani, José H., Longatto-Filho, Adhemar, Reis, Rui M., Scapulatempo-Neto, Cristovam, Silveira, Henrique C.S., Vidal, Daniel O., Burnette, Andrew, Eschbacher, Jennifer, Hermes, Beth, Noss, Ardene, Singh, Rosy, Anderson, Matthew L., Castro, Patricia D., Ittmann, Michael, Huntsman, David, Kohl, Bernard, Le, Xuan, Thorp, Richard, Andry, Chris, Duffy, Elizabeth R., Lyadov, Vladimir, Paklina, Oxana, Setdikova, Galiya, Shabunin, Alexey, Tavobilov, Mikhail, McPherson, Christopher, Warnick, Ronald, Berkowitz, Ross, Cramer, Daniel, Feltmate, Colleen, Horowitz, Neil, Kibel, Adam, Muto, Michael, Raut, Chandrajit P., Malykh, Andrei, Barnholtz-Sloan, Jill S., Barrett, Wendi, Devine, Karen, Fulop, Jordonna, Ostrom, Quinn T., Shimmel, Kristen, Wolinsky, Yingli, Sloan, Andrew E., De Rose, Agostino, Giuliante, Felice, Goodman, Marc, Karlan, Beth Y., Hagedorn, Curt H., Eckman, John, Harr, Jodi, Myers, Jerome, Tucker, Kelinda, Zach, Leigh Anne, Deyarmin, Brenda, Hu, Hai, Kvecher, Leonid, Larson, Caroline, Mural, Richard J., Somiari, Stella, Vicha, Ales, Zelinka, Tomas, Bennett, Joseph, Iacocca, Mary, Rabeno, Brenda, Swanson, Patricia, Latour, Mathieu, Lacombe, Louis, Têtu, Bernard, Bergeron, Alain, McGraw, Mary, Staugaitis, Susan M., Chabot, John, Hibshoosh, Hanina, Sepulveda, Antonia, Su, Tao, Wang, Timothy, Potapova, Olga, Voronina, Olga, Desjardins, Laurence, Mariani, Odette, Roman-Roman, Sergio, Sastre, Xavier, Stern, Marc-Henri, Cheng, Feixiong, Signoretti, Sabina, Berchuck, Andrew, Bigner, Darell, Lipp, Eric, Marks, Jeffrey, McCall, Shannon, McLendon, Roger, Secord, Angeles, Sharp, Alexis, Behera, Madhusmita, Brat, Daniel J., Chen, Amy, Delman, Keith, Force, Seth, Khuri, Fadlo, Magliocca, Kelly, Maithel, Shishir, Olson, Jeffrey J., Owonikoko, Taofeek, Pickens, Alan, Ramalingam, Suresh, Shin, Dong M., Sica, Gabriel, Van Meir, Erwin G., Zhang, Hongzheng, Eijckenboom, Wil, Gillis, Ad, Korpershoek, Esther, Looijenga, Leendert, Oosterhuis, Wolter, Stoop, Hans, van Kessel, Kim E., Zwarthoff, Ellen C., Calatozzolo, Chiara, Cuppini, Lucia, Cuzzubbo, Stefania, DiMeco, Francesco, Finocchiaro, Gaetano, Mattei, Luca, Perin, Alessandro, Pollo, Bianca, Chen, Chu, Houck, John, Lohavanichbutr, Pawadee, Hartmann, Arndt, Stoehr, Christine, Stoehr, Robert, Taubert, Helge, Wach, Sven, Wullich, Bernd, Kycler, Witold, Murawa, Dawid, Wiznerowicz, Maciej, Chung, Ki, Edenfield, W. Jeffrey, Martin, Julie, Baudin, Eric, Bubley, Glenn, Bueno, Raphael, De Rienzo, Assunta, Richards, William G., Kalkanis, Steven, Mikkelsen, Tom, Noushmehr, Houtan, Scarpace, Lisa, Girard, Nicolas, Aymerich, Marta, Campo, Elias, Giné, Eva, Guillermo, Armando López, Van Bang, Nguyen, Hanh, Phan Thi, Phu, Bui Duc, Tang, Yufang, Colman, Howard, Evason, Kimberley, Dottino, Peter R., Martignetti, John A., Gabra, Hani, Juhl, Hartmut, Akeredolu, Teniola, Stepa, Serghei, Hoon, Dave, Ahn, Keunsoo, Kang, Koo Jeong, Beuschlein, Felix, Breggia, Anne, Birrer, Michael, Bell, Debra, Borad, Mitesh, Bryce, Alan H., Castle, Erik, Chandan, Vishal, Cheville, John, Copland, John A., Farnell, Michael, Flotte, Thomas, Giama, Nasra, Ho, Thai, Kendrick, Michael, Kocher, Jean-Pierre, Kopp, Karla, Moser, Catherine, Nagorney, David, O’Brien, Daniel, O’Neill, Brian Patrick, Patel, Tushar, Petersen, Gloria, Que, Florencia, Rivera, Michael, Roberts, Lewis, Smallridge, Robert, Smyrk, Thomas, Stanton, Melissa, Thompson, R. Houston, Torbenson, Michael, Yang, Ju Dong, Zhang, Lizhi, Brimo, Fadi, Ajani, Jaffer A., Gonzalez, Ana Maria Angulo, Behrens, Carmen, Bondaruk, Jolanta, Broaddus, Russell, Czerniak, Bogdan, Esmaeli, Bita, Fujimoto, Junya, Gershenwald, Jeffrey, Guo, Charles, Lazar, Alexander J., Logothetis, Christopher, Meric-Bernstam, Funda, Moran, Cesar, Ramondetta, Lois, Rice, David, Sood, Anil, Tamboli, Pheroze, Thompson, Timothy, Troncoso, Patricia, Tsao, Anne, Wistuba, Ignacio, Carter, Candace, Haydu, Lauren, Hersey, Peter, Jakrot, Valerie, Kakavand, Hojabr, Kefford, Richard, Lee, Kenneth, Long, Georgina, Mann, Graham, Quinn, Michael, Saw, Robyn, Scolyer, Richard, Shannon, Kerwin, Spillane, Andrew, Stretch, Jonathan, Synott, Maria, Thompson, John, Wilmott, James, Al-Ahmadie, Hikmat, Chan, Timothy A., Ghossein, Ronald, Gopalan, Anuradha, Levine, Douglas A., Reuter, Victor, Singer, Samuel, Singh, Bhuvanesh, Tien, Nguyen Viet, Broudy, Thomas, Mirsaidi, Cyrus, Nair, Praveen, Drwiega, Paul, Miller, Judy, Smith, Jennifer, Zaren, Howard, Park, Joong-Won, Hung, Nguyen Phi, Kebebew, Electron, Linehan, W. Marston, Metwalli, Adam R., Pacak, Karel, Pinto, Peter A., Schiffman, Mark, Schmidt, Laura S., Vocke, Cathy D., Wentzensen, Nicolas, Worrell, Robert, Yang, Hannah, Moncrieff, Marc, Goparaju, Chandra, Melamed, Jonathan, Pass, Harvey, Botnariuc, Natalia, Caraman, Irina, Cernat, Mircea, Chemencedji, Inga, Clipca, Adrian, Doruc, Serghei, Gorincioi, Ghenadie, Mura, Sergiu, Pirtac, Maria, Stancul, Irina, Tcaciuc, Diana, Albert, Monique, Alexopoulou, Iakovina, Arnaout, Angel, Bartlett, John, Engel, Jay, Gilbert, Sebastien, Parfitt, Jeremy, Sekhon, Harman, Thomas, George, Rassl, Doris M., Rintoul, Robert C., Bifulco, Carlo, Tamakawa, Raina, Urba, Walter, Hayward, Nicholas, Timmers, Henri, Antenucci, Anna, Facciolo, Francesco, Grazi, Gianluca, Marino, Mirella, Merola, Roberta, de Krijger, Ronald, Gimenez-Roqueplo, Anne-Paule, Piché, Alain, Chevalier, Simone, McKercher, Ginette, Birsoy, Kivanc, Barnett, Gene, Brewer, Cathy, Farver, Carol, Naska, Theresa, Pennell, Nathan A., Raymond, Daniel, Schilero, Cathy, Smolenski, Kathy, Williams, Felicia, Morrison, Carl, Borgia, Jeffrey A., Liptay, Michael J., Pool, Mark, Seder, Christopher W., Junker, Kerstin, Omberg, Larsson, Dinkin, Mikhail, Manikhas, George, Alvaro, Domenico, Bragazzi, Maria Consiglia, Cardinale, Vincenzo, Carpino, Guido, Gaudio, Eugenio, Chesla, David, Cottingham, Sandra, Dubina, Michael, Moiseenko, Fedor, Dhanasekaran, Renumathy, Becker, Karl-Friedrich, Janssen, Klaus-Peter, Slotta-Huspenina, Julia, Abdel-Rahman, Mohamed H., Aziz, Dina, Bell, Sue, Cebulla, Colleen M., Davis, Amy, Duell, Rebecca, Elder, J. Bradley, Hilty, Joe, Kumar, Bahavna, Lang, James, Lehman, Norman L., Mandt, Randy, Nguyen, Phuong, Pilarski, Robert, Rai, Karan, Schoenfield, Lynn, Senecal, Kelly, Wakely, Paul, Hansen, Paul, Lechan, Ronald, Powers, James, Tischler, Arthur, Grizzle, William E., Sexton, Katherine C., Kastl, Alison, Henderson, Joel, Porten, Sima, Waldmann, Jens, Fassnacht, Martin, Asa, Sylvia L., Schadendorf, Dirk, Couce, Marta, Graefen, Markus, Huland, Hartwig, Sauter, Guido, Schlomm, Thorsten, Simon, Ronald, Tennstedt, Pierre, Olabode, Oluwole, Nelson, Mark, Bathe, Oliver, Carroll, Peter R., Chan, June M., Disaia, Philip, Glenn, Pat, Kelley, Robin K., Landen, Charles N., Phillips, Joanna, Prados, Michael, Simko, Jeffry, Smith-McCune, Karen, VandenBerg, Scott, Roggin, Kevin, Fehrenbach, Ashley, Kendler, Ady, Sifri, Suzanne, Steele, Ruth, Jimeno, Antonio, Carey, Francis, Forgie, Ian, Mannelli, Massimo, Carney, Michael, Hernandez, Brenda, Campos, Benito, Herold-Mende, Christel, Jungk, Christin, Unterberg, Andreas, von Deimling, Andreas, Bossler, Aaron, Galbraith, Joseph, Jacobus, Laura, Knudson, Michael, Knutson, Tina, Ma, Deqin, Milhem, Mohammed, Sigmund, Rita, Godwin, Andrew K., Madan, Rashna, Rosenthal, Howard G., Adebamowo, Clement, Adebamowo, Sally N., Boussioutas, Alex, Beer, David, Giordano, Thomas, Mes-Masson, Anne-Marie, Saad, Fred, Bocklage, Therese, Landrum, Lisa, Mannel, Robert, Moore, Kathleen, Moxley, Katherine, Postier, Russel, Walker, Joan, Zuna, Rosemary, Feldman, Michael, Valdivieso, Federico, Dhir, Rajiv, Luketich, James, Pinero, Edna M. Mora, Quintero-Aguilo, Mario, Carlotti, Carlos Gilberto, Jr., Dos Santos, Jose Sebastião, Kemp, Rafael, Sankarankuty, Ajith, Tirapelli, Daniela, Catto, James, Agnew, Kathy, Swisher, Elizabeth, Creaney, Jenette, Robinson, Bruce, Shelley, Carl Simon, Godwin, Eryn M., Kendall, Sara, Shipman, Cassaundra, Bradford, Carol, Carey, Thomas, Haddad, Andrea, Moyer, Jeffey, Peterson, Lisa, Prince, Mark, Rozek, Laura, Wolf, Gregory, Bowman, Rayleen, Fong, Kwun M., Yang, Ian, Korst, Robert, Rathmell, W. Kimryn, Fantacone-Campbell, J. Leigh, Hooke, Jeffrey A., Kovatich, Albert J., Shriver, Craig D., DiPersio, John, Drake, Bettina, Govindan, Ramaswamy, Heath, Sharon, Ley, Timothy, Van Tine, Brian, Westervelt, Peter, Rubin, Mark A., Lee, Jung Il, Aredes, Natália D., Mariamidze, Armaz, Knijnenburg, Theo A., Zimmermann, Michael T., Way, Gregory P., Greene, Casey S., Feng, Bin, Miller, Chase, Shen, Yang, Karimi, Mostafa, Chen, Haoran, Kim, Pora, Jia, Peilin, Zhang, Shaojun, Liu, Jianfang, Bailey, Matthew H., Wolf, Denise, Zhao, Zhongming, Li, Lei, Monnat, Raymond J., Jr., Xiao, Yonghong, and Wang, Chen

Published
2018
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36. Multi-species data integration and gene ranking enrich significant results in an alcoholism genome-wide association study

Author

Zhao, Zhongming, Guo, An-Yuan, van den Oord, Edwin JCG, Aliev, Fazil, Jia, Peilin, Edenberg, Howard J, Riley, Brien P, Dick, Danielle M, Bettinger, Jill C, Davies, Andrew G, Grotewiel, Michael S, Schuckit, Marc A, Agrawal, Arpana, Kramer, John, Nurnberger, John I, Kendler, Kenneth S, Webb, Bradley T, and Miles, Michael F

Abstract

Abstract Background A variety of species and experimental designs have been used to study genetic influences on alcohol dependence, ethanol response, and related traits. Integration of these heterogeneous data can be used to produce a ranked target gene list for additional investigation. Results In this study, we performed a unique multi-species evidence-based data integration using three microarray experiments in mice or humans that generated an initial alcohol dependence (AD) related genes list, human linkage and association results, and gene sets implicated in C. elegans and Drosophila. We then used permutation and false discovery rate (FDR) analyses on the genome-wide association studies (GWAS) dataset from the Collaborative Study on the Genetics of Alcoholism (COGA) to evaluate the ranking results and weighting matrices. We found one weighting score matrix could increase FDR based q-values for a list of 47 genes with a score greater than 2. Our follow up functional enrichment tests revealed these genes were primarily involved in brain responses to ethanol and neural adaptations occurring with alcoholism. Conclusions These results, along with our experimental validation of specific genes in mice, C. elegans and Drosophila, suggest that a cross-species evidence-based approach is useful to identify candidate genes contributing to alcoholism.

Published
2012

41. Combined genome-wide association study of 136 quantitative ear morphology traits in multiple populations reveal 8 novel loci

Author

Li, Yi, primary, Xiong, Ziyi, additional, Zhang, Manfei, additional, Hysi, Pirro G., additional, Qian, Yu, additional, Adhikari, Kaustubh, additional, Weng, Jun, additional, Wu, Sijie, additional, Du, Siyuan, additional, Gonzalez-Jose, Rolando, additional, Schuler-Faccini, Lavinia, additional, Bortolini, Maria-Catira, additional, Acuna-Alonzo, Victor, additional, Canizales-Quinteros, Samuel, additional, Gallo, Carla, additional, Poletti, Giovanni, additional, Bedoya, Gabriel, additional, Rothhammer, Francisco, additional, Wang, Jiucun, additional, Tan, Jingze, additional, Yuan, Ziyu, additional, Jin, Li, additional, Uitterlinden, André G., additional, Ghanbari, Mohsen, additional, Ikram, M. Arfan, additional, Nijsten, Tamar, additional, Zhu, Xiangyu, additional, Lei, Zhen, additional, Jia, Peilin, additional, Ruiz-Linares, Andres, additional, Spector, Timothy D., additional, Wang, Sijia, additional, Kayser, Manfred, additional, and Liu, Fan, additional

Published
2023
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46. Searching across-cohort relatives in 54,092 GWAS samples via encrypted genotype regression.

Author

Zhang, Qi-Xin, Liu, Tianzi, Guo, Xinxin, Zhen, Jianxin, Yang, Meng-yuan, Khederzadeh, Saber, Zhou, Fang, Han, Xiaotong, Zheng, Qiwen, Jia, Peilin, Ding, Xiaohu, He, Mingguang, Zou, Xin, Liao, Jia-Kai, Zhang, Hongxin, He, Ji, Zhu, Xiaofeng, Lu, Daru, Chen, Hongyan, and Zeng, Changqing

Subjects
GENOTYPES, GENOME-wide association studies, RANDOM matrices, STATISTICAL power analysis, RELATIVES, DATA encryption, IMAGE encryption
Abstract

Explicitly sharing individual level data in genomics studies has many merits comparing to sharing summary statistics, including more strict QCs, common statistical analyses, relative identification and improved statistical power in GWAS, but it is hampered by privacy or ethical constraints. In this study, we developed encG-reg, a regression approach that can detect relatives of various degrees based on encrypted genomic data, which is immune of ethical constraints. The encryption properties of encG-reg are based on the random matrix theory by masking the original genotypic matrix without sacrificing precision of individual-level genotype data. We established a connection between the dimension of a random matrix, which masked genotype matrices, and the required precision of a study for encrypted genotype data. encG-reg has false positive and false negative rates equivalent to sharing original individual level data, and is computationally efficient when searching relatives. We split the UK Biobank into their respective centers, and then encrypted the genotype data. We observed that the relatives estimated using encG-reg was equivalently accurate with the estimation by KING, which is a widely used software but requires original genotype data. In a more complex application, we launched a finely devised multi-center collaboration across 5 research institutes in China, covering 9 cohorts of 54,092 GWAS samples. encG-reg again identified true relatives existing across the cohorts with even different ethnic backgrounds and genotypic qualities. Our study clearly demonstrates that encrypted genomic data can be used for data sharing without loss of information or data sharing barrier. Author summary: Estimating pairwise genetic relatedness within a single cohort is straightforward. However, in practice, related samples are often distributed across different cohorts, making it challenging to estimate inter-cohort relatedness. In this study, we propose a method called encrypted genotype regression (encG-reg), which provides an unbiased estimation of inter-cohort relatedness using encrypted genotypes. The genotype matrix of each cohort is masked by a random matrix, which acts similarly to a private key in a cryptographic scheme. This masking process produces encrypted genotypes, which are a projection of the original genotype matrix. We derive the expectation and particularly the sampling variance for encG-reg, the latter involves eighth-order moments calculation. encG-reg allows us to accurately identify relatedness across cohorts, even for large-scale biobank data. To demonstrate the efficacy of encG-reg, we verified it in a multi-ethnicity UK Biobank dataset comprising 485,158 samples. For this case, we successfully tracked down to the 1st-degree relatedness (such as full sibs and parent-offspring). Furthermore, we used encG-reg in a collaboration involving 9 Chinese cohorts, encompassing a total of 54,092 samples from 5 genomic centers. It is worth noting that if the number of effective markers is sufficient encG-reg has the potential to detect even more distant degrees of relatedness beyond what we demonstrated. [ABSTRACT FROM AUTHOR]

Published
2024
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