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Browsing by Author "Chen, Yan"
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Item Endocrine and Metabolic Disorders in Survivors of Childhood Cancers and Health-Related Quality of Life and Physical Activity(Oxford, 2019-11) Pradhan, Kamnesh R.; Chen, Yan; Moustoufi-Moab, Sogol; Krull, Kevin; Oeffinger, Kevin C.; Sklar, Charles; Armstrong, Gregory T.; Ness, Kirsten K.; Robison, Leslie; Yasui, Yutaka; Nathan, Paul C.; Pediatrics, School of MedicineContext Childhood cancer survivors experience chronic health conditions that impact health-related quality of life (HRQOL) and participation in optimal physical activity. Objective The study aimed to determine independent effects of endocrine and metabolic disorders on HRQOL and physical activity. Design, Setting, and Patients Retrospective cohort with longitudinal follow-up of survivors of childhood cancer enrolled in the North American Childhood Cancer Survivor Study. Main Outcome Measures Medical Outcomes Short Form-36 estimated HRQOL, and participation in physical activity was dichotomized as meeting or not meeting recommendations from the Centers for Disease Control and Prevention. Log binomial regression evaluated the association of each endocrine/metabolic disorder with HRQOL scales and physical activity. Results Of 7287 survivors, with a median age of 32 years (range, 18 to 54 years) at their last follow-up survey, 4884 (67%) reported one or more endocrine/metabolic disorders. Survivors with either disorder were significantly more likely to be male, older, have received radiation treatment, and have experienced other chronic health conditions. After controlling for covariates, survivors with any endocrine/metabolic disorder were more likely to report poor physical function risk ratio (RR, 1.25; 95% CI, 1.05 to 1.48), increased bodily pain (RR, 1.27; 95% CI, 1.12 to 1.44), poor general health (RR, 1.49; 95% CI, 1.32 to 1.68), and lower vitality (RR, 1.21; 95% CI, 1.09 to 1.34) compared with survivors without. The likelihood of meeting recommended physical activity was lower among survivors with growth disorders (RR, 0.90; 95% CI, 0.83 to 0.97), osteoporosis (RR, 0.87; 95% CI, 0.76 to 0.99), and overweight/obesity (RR, 0.92; 95% CI, 0.88 to 0.96). Conclusion Endocrine and metabolic disorders are independently associated with poor HRQOL and suboptimal physical activity among childhood cancer survivors.Item Genome-wide association studies identify multiple genetic loci influencing eyebrow color variation in Europeans(Elsevier, 2019) Peng, Fuduan; Zhu, Gu; Hysi, Pirro G.; Eller, Ryan J.; Chen, Yan; Li, Yi; Hamer, Merel A.; Zeng, Changqing; Hopkins, Racquel L.; Jacobus, Case L.; Wallace, Paige L.; Uitterlinden, André G.; Ikram, M. Arfan; Duffy, David L.; Nijsten, Tamar; Medland, Sarah E.; Spector, Timothy D.; Walsh, Susan; Martin, Nicholas G.; Liu, Fan; Kayser, Manfred; Biology, School of ScienceItem Genome-wide association study in 176,678 Europeans reveals genetic loci for tanning response to sun exposure(Nature Publishing Group, 2018-05-08) Visconti, Alessia; Duffy, David L.; Liu, Fan; Zhu, Gu; Wu, Wenting; Chen, Yan; Hysi, Pirro G.; Zeng, Changqing; Sanna, Marianna; Iles, Mark M.; Kanetsky, Peter A.; Demenais, Florence; Hamer, Merel A.; Uitterlinden, Andre G.; Ikram, M. Arfan; Nijsten, Tamar; Martin, Nicholas G.; Kayser, Manfred; Spector, Tim D.; Han, Jiali; Bataille, Veronique; Falchi, Mario; Epidemiology, School of Public HealthThe skin's tendency to sunburn rather than tan is a major risk factor for skin cancer. Here we report a large genome-wide association study of ease of skin tanning in 176,678 subjects of European ancestry. We identify significant association with tanning ability at 20 loci. We confirm previously identified associations at six of these loci, and report 14 novel loci, of which ten have never been associated with pigmentation-related phenotypes. Our results also suggest that variants at the AHR/AGR3 locus, previously associated with cutaneous malignant melanoma the underlying mechanism of which is poorly understood, might act on disease risk through modulation of tanning ability.Item Genome-wide association study in almost 195,000 individuals identifies 50 previously unidentified genetic loci for eye color(American Association for the Advancement of Science, 2021-03-10) Simcoe, Mark; Valdes, Ana; Liu, Fan; Furlotte, Nicholas A.; Evans, David M.; Hemani, Gibran; Ring, Susan M.; Smith, George Davey; Duffy, David L.; Zhu, Gu; Gordon, Scott D.; Medland, Sarah E.; Vuckovic, Dragana; Girotto, Giorgia; Sala, Cinzia; Catamo, Eulalia; Concas, Maria Pina; Brumat, Marco; Gasparini, Paolo; Toniolo, Daniela; Cocca, Massimiliano; Robino, Antonietta; Yazar, Seyhan; Hewitt, Alex; Wu, Wenting; Kraft, Peter; Hammond, Christopher J.; Shi, Yuan; Chen, Yan; Zeng, Changqing; Klaver, Caroline C. W.; Uitterlinden, Andre G.; Ikram, M. Arfan; Hamer, Merel A.; van Duijn, Cornelia M.; Nijsten, Tamar; Han, Jiali; Mackey, David A.; Martin, Nicholas G.; Cheng, Ching-Yu; 23andMe Research Team; International Visible Trait Genetics Consortium; Hinds, David A.; Spector, Timothy D.; Kayser, Manfred; Hysi, Pirro G.; Epidemiology, School of Public HealthHuman eye color is highly heritable, but its genetic architecture is not yet fully understood. We report the results of the largest genome-wide association study for eye color to date, involving up to 192,986 European participants from 10 populations. We identify 124 independent associations arising from 61 discrete genomic regions, including 50 previously unidentified. We find evidence for genes involved in melanin pigmentation, but we also find associations with genes involved in iris morphology and structure. Further analyses in 1636 Asian participants from two populations suggest that iris pigmentation variation in Asians is genetically similar to Europeans, albeit with smaller effect sizes. Our findings collectively explain 53.2% (95% confidence interval, 45.4 to 61.0%) of eye color variation using common single-nucleotide polymorphisms. Overall, our study outcomes demonstrate that the genetic complexity of human eye color considerably exceeds previous knowledge and expectations, highlighting eye color as a genetically highly complex human trait.Item The impact of correlations between pigmentation phenotypes and underlying genotypes on genetic prediction of pigmentation traits(Elsevier, 2021-01) Chen, Yan; Branicki, Wojciech; Walsh, Susan; Nothnagel, Michael; Kayser, Manfred; Liu, Fan; Biology, School of SciencePredicting appearance phenotypes from genotypes is relevant for various areas of human genetic research and applications such as genetic epidemiology, human history, anthropology, and particularly in forensics. Many appearance phenotypes, and thus their underlying genotypes, are highly correlated, with pigmentation traits serving as primary examples. However, all available genetic prediction models, including those for pigmentation traits currently used in forensic DNA phenotyping, ignore phenotype correlations. Here, we investigated the impact of appearance phenotype correlations on genetic appearance prediction in the exemplary case of three pigmentation traits. We used data for categorical eye, hair and skin colour as well as 41 DNA markers utilized in the recently established HIrisPlex-S system from 762 individuals with complete phenotype and genotype information. Based on these data, we performed genetic prediction modelling of eye, hair and skin colour via three different strategies, namely the established approach of predicting phenotypes solely based on genotypes while not considering phenotype correlations, and two novel approaches that considered phenotype correlations, either incorporating truly observed correlated phenotypes or DNA-predicted correlated phenotypes in addition to the DNA predictors. We found that using truly observed correlated pigmentation phenotypes as additional predictors increased the DNA-based prediction accuracies for almost all eye, hair and skin colour categories, with the largest increase for intermediate eye colour, brown hair colour, dark to black skin colour, and particularly for dark skin colour. Outcomes of dedicated computer simulations suggest that this prediction accuracy increase is due to the additional genetic information that is implicitly provided by the truly observed correlated pigmentation phenotypes used, yet not covered by the DNA predictors applied. In contrast, considering DNA-predicted correlated pigmentation phenotypes as additional predictors did not improve the performance of the genetic prediction of eye, hair and skin colour, which was in line with the results from our computer simulations. Hence, in practical applications of DNA-based appearance prediction where no phenotype knowledge is available, such as in forensic DNA phenotyping, it is not advised to use DNA-predicted correlated phenotypes as predictors in addition to the DNA predictors. In the very least, this is not recommended for the pigmentation traits and the established pigmentation DNA predictors tested here.Item Meta-analysis of genome-wide association studies identifies 8 novel loci involved in shape variation of human head hair(Oxford University Press, 2018-02-01) Liu, Fan; Chen, Yan; Zhu, Gu; Hysi, Pirro G.; Wu, Sijie; Adhikari, Kaustubh; Breslin, Krystal; Pośpiech, Ewelina; Hamer, Merel A.; Peng, Fuduan; Muralidharan, Charanya; Acuna-Alonzo, Victor; Canizales-Quinteros, Samuel; Bedoya, Gabriel; Gallo, Carla; Poletti, Giovanni; Rothhammer, Francisco; Bortolini, Maria Catira; Gonzalez-Jose, Rolando; Zeng, Changqing; Xu, Shuhua; Jin, Li; Uitterlinden, André G.; Ikram, M. Arfan; van Duijn, Cornelia M.; Nijsten, Tamar; Walsh, Susan; Branicki, Wojciech; Wang, Sijia; Ruiz-Linares, Andrés; Spector, Timothy D.; Martin, Nicholas G.; Medland, Sarah E.; Kayser, Manfred; Biology, School of ScienceShape variation of human head hair shows striking variation within and between human populations, while its genetic basis is far from being understood. We performed a series of genome-wide association studies (GWASs) and replication studies in a total of 28 964 subjects from 9 cohorts from multiple geographic origins. A meta-analysis of three European GWASs identified 8 novel loci (1p36.23 ERRFI1/SLC45A1, 1p36.22 PEX14, 1p36.13 PADI3, 2p13.3 TGFA, 11p14.1 LGR4, 12q13.13 HOXC13, 17q21.2 KRTAP, and 20q13.33 PTK6), and confirmed 4 previously known ones (1q21.3 TCHH/TCHHL1/LCE3E, 2q35 WNT10A, 4q21.21 FRAS1, and 10p14 LINC00708/GATA3), all showing genome-wide significant association with hair shape (P < 5e-8). All except one (1p36.22 PEX14) were replicated with nominal significance in at least one of the 6 additional cohorts of European, Native American and East Asian origins. Three additional previously known genes (EDAR, OFCC1, and PRSS53) were confirmed at the nominal significance level. A multivariable regression model revealed that 14 SNPs from different genes significantly and independently contribute to hair shape variation, reaching a cross-validated AUC value of 0.66 (95% CI: 0.62-0.70) and an AUC value of 0.64 in an independent validation cohort, providing an improved accuracy compared with a previous model. Prediction outcomes of 2504 individuals from a multiethnic sample were largely consistent with general knowledge on the global distribution of hair shape variation. Our study thus delivers target genes and DNA variants for future functional studies to further evaluate the molecular basis of hair shape in humans.Item Opioid receptors: molecular cloning and functional analysis(1994) Chen, YanItem Smad3 Mediates Activin-Induced Transcription of Follicle-Stimulating Hormone β-Subunit Gene(Oxford University Press, 2005-07-01) Suszko, Magdalena I.; Balkin, Daniel M.; Chen, Yan; Woodruff, Teresa K.; Medical and Molecular Genetics, School of MedicineSynthesis of FSH by the anterior pituitary is regulated by activin, a member of the TGFβ superfamily of ligands. Activin signals through a pathway that involves the activation of the transcriptional coregulators Smad2 and Smad3. Previous work from our laboratory demonstrated that Smad3, and not Smad2, is sufficient for stimulation of the rat FSHβ promoter in a pituitary-derived cell line LβT2. Here, we used RNA interference technology to independently decrease the expression of Smad proteins in LβT2 cells to further investigate Smad2 and Smad3 roles in activin-dependent regulation of the FSHβ promoter. Down-regulation of Smad2 protein by small interfering RNA duplexes affects only basal transcription of FSHβ, whereas decreased expression of Smad3 abrogates activin-mediated stimulation of FSHβ transcription. Although highly related, Smad2 and Smad3 differ in their Mad homolog (MH) 1 domains, where the Smad2 protein contains two additional stretches of amino acids that prevent this factor from binding to DNA. We investigated whether these structural features contribute to differential FSHβ transactivation by Smad2 and Smad3. A variety of Smad chimera constructs were generated and used in transient transfection studies to address this question. Only cotransfection of chimera constructs that contain the MH1 domain of Smad3 results in activin-mediated stimulation of the rat FSHβ promoter. Furthermore, the insertion of Smad2 loops into Smad3 protein renders it inactive, suggesting that DNA binding is necessary for Smad3-mediated stimulation of the rat FSHβ promoter. Taken together, these results indicate that the functional differences between Smad2 and Smad3 in their ability to transactivate the rat FSHβ promoter lie primarily within the MH1 domain and involve structural motifs that affect DNA binding.Item Towards broadening Forensic DNA Phenotyping beyond pigmentation: Improving the prediction of head hair shape from DNA(Elsevier, 2018-11) Pośpiech, Ewelina; Chen, Yan; Kukla-Bartoszek, Magdalena; Breslin, Krystal; Aliferi, Anastasia; Andersen, Jeppe D.; Ballard, David; Chaitanya, Lakshmi; Freire-Aradas, Ana; van der Gaag, Kristiaan J.; Girón-Santamaría, Lorena; Gross, Theresa E.; Gysi, Mario; Huber, Gabriela; Mosquera-Miguel, Ana; Muralidharan, Charanya; Skowron, Malgorzata; Carracedo, Ángel; Haas, Cordula; Morling, Niels; Parson, Walther; Phillips, Christopher; Schneider, Peter M.; Sijen, Titia; Syndercombe-Court, Denise; Vennemann, Marielle; Wu, Sijie; Xu, Shuhua; Jin, Li; Wang, Sijia; Zhu, Ghu; Martin, Nick G.; Medland, Sarah E.; Branicki, Wojciech; Walsh, Susan; Liu, Fan; Kayser, Manfred; Biology, School of ScienceHuman head hair shape, commonly classified as straight, wavy, curly or frizzy, is an attractive target for Forensic DNA Phenotyping and other applications of human appearance prediction from DNA such as in paleogenetics. The genetic knowledge underlying head hair shape variation was recently improved by the outcome of a series of genome-wide association and replication studies in a total of 26,964 subjects, highlighting 12 loci of which 8 were novel and introducing a prediction model for Europeans based on 14 SNPs. In the present study, we evaluated the capacity of DNA-based head hair shape prediction by investigating an extended set of candidate SNP predictors and by using an independent set of samples for model validation. Prediction model building was carried out in 9674 subjects (6068 from Europe, 2899 from Asia and 707 of admixed European and Asian ancestries), used previously, by considering a novel list of 90 candidate SNPs. For model validation, genotype and phenotype data were newly collected in 2415 independent subjects (2138 Europeans and 277 non-Europeans) by applying two targeted massively parallel sequencing platforms, Ion Torrent PGM and MiSeq, or the MassARRAY platform. A binomial model was developed to predict straight vs. non-straight hair based on 32 SNPs from 26 genetic loci we identified as significantly contributing to the model. This model achieved prediction accuracies, expressed as AUC, of 0.664 in Europeans and 0.789 in non-Europeans; the statistically significant difference was explained mostly by the effect of one EDAR SNP in non-Europeans. Considering sex and age, in addition to the SNPs, slightly and insignificantly increased the prediction accuracies (AUC of 0.680 and 0.800, respectively). Based on the sample size and candidate DNA markers investigated, this study provides the most robust, validated, and accurate statistical prediction models and SNP predictor marker sets currently available for predicting head hair shape from DNA, providing the next step towards broadening Forensic DNA Phenotyping beyond pigmentation traits.