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Articles by Jie Ping
Multi-ancestry genome- and transcriptome-wide association studies expand the susceptibility landscape for breast cancer overall and across subtypes
Abstract Breast cancer genomic studies have been conducted primarily in European-ancestry populations, limiting diversity and statistical power. To address this, this study increases representation of African- and Asian-ancestry women and expands the European-ancestry sample size to better define inherited susceptibility to breast cancer overall and by subtypes.
Multi-ancestry transcriptome-wide association studies uncover insights into breast cancer genetics and biology
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Abstract Genome-wide association studies (GWAS) have identified over 200 genetic risk loci for breast cancer, yet their target genes remain largely unknown. We conduct multi-ancestry transcriptome-wide association studies (TWAS) to discover potential breast cancer susceptibility genes.
By Jie Ping, Guochong Jia, Qiuyin Cai, Xingyi Guo, Jifeng Wang, Ran Tao, Bingshan Li, Joshua A. Bauer, Yuhan Xie, Stefan Ambs, Mollie E Barnard, Yu Chen, Ji-Yeob Choi, Yu-Tang Gao, Montserrat Garcia-Closas, Jian Gu, Jennifer Hu, Motoki Iwasaki, Esther M John, Sun-Seog Kweon, Christopher I Li, Koichi Matsuda, Keitaro Matsuo, Katherine L. Nathanson, Barbara Nemesure, Olufunmilayo I. Olopade, Tuya Pal, Sue K Park, Boyoung Park, Michael Press, Maureen Sanderson, Dale P. Sandler, Song T. Yao, Ying Zheng, Thomas Ahearn, Abenaa M. Brewster, Anselm Hennis, Hidemi Ito, Michiaki Kubo, Eun-Sook Lee, Katie O’Brien, Oladosu Ojengbede, Andrew F. Olshan, Min-Ho Park, Sonya Reid, Taiki Yamaji, Gary R. Zirpoli, Ebonee N. Butler, Maosheng Huang, Siew-Kee Low, John Oladapo Obafunwa, Clarice R. Weinberg, Haoyu Zhang, Hongyu Zhao, Christine B. Ambrosone, Michelle Cote, Dezheng Huo, Christopher A. Haiman, Daehee Kang, Julie Palmer, Melissa A. Troester, Xiao-Ou Shu, Jirong Long, Wei Zheng, Adeyinka Falusi, Timothy Makumbi, Berthe S. E. Mapoko, Dong-Young Noh
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Nature
Verified
Improved polygenic risk prediction models for breast cancer subtypes in women of African ancestry - Nature Genetics
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Abstract Polygenic risk score (PRS) models effectively predict breast cancer (BC) risk in European-ancestry women but have limited accuracy for African-ancestry women, particularly for aggressive subtypes. We developed PRS models for overall BC, estrogen receptor (ER)-positive, ER-negative and triple-negative BC (TNBC) in African-ancestry women using data from the African Ancestry Breast Cancer Genetics consortium (17,391 cases and 18,800 controls).
By James Li, Haoyu Zhang, Guochong Jia, Wenji Guo, Peter N. Fiorica, Stefan Ambs, Mollie E Barnard, Montserrat Garcia-Closas, Jian Gu, Jennifer Hu, Katherine L. Nathanson, Michael Press, Dale P. Sandler, Melissa A. Troester, Song T. Yao, Jirong Long, Thomas Ahearn, Peter Kraft, Katie O’Brien, Gary R. Zirpoli, Qiuyin Cai, Ebonee N. Butler, Christine B. Ambrosone, Jie Ping, Ran Tao, Bingshan Li, Xingyi Guo, David Conti, Nilanjan Chatterjee, Olufunmilayo I. Olopade, Wei Zheng, Christopher A. Haiman
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Nature
Verified
Mixed-model and transcriptome-wide association analyses identify transcription factors and genes associated with colorectal cancer susceptibility - Nature Communications
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Abstract Susceptibility transcription factors (TF) whose DNA bindings are altered by genetic variants regulating colorectal cancer (CRC) risk genes remain poorly defined. Using generalized linear mixed models, we analyze 218 TF ChIP-Seq datasets alongside GWAS data from 100,204 CRC cases and 154,587 controls of East Asian and European ancestries. We identify 51 TFs and TF-cofactor interactions, including VDR-cofactors, as key regulators of CRC risk.
By Qing Li, Wanqing Wen, Jeroen R. Huyghe, Philip J Law, Ceres Fernández-Rozadilla, Minta Thomas, Stephanie Schmit, Vicente Martin, Matthew Devall, Ferran Moratalla-Navarro, Qiuyin Cai, Jifeng Wang, Jiajun Shi, Wei-Hua Jia, Xiang Shu, Jirong Long, Jeongseon Kim, Aesun Shin, Keitaro Matsuo, Sun Ha Jee, Keum Ji Jung, Jie Ping, Min-Ho Shin, Zefang Ren, Isao Oze, Yoichiro Kamatani, Luc Van Kaer, Bingshan Li, Koichi Matsuda, Li Chuan Hsu, Malcolm G. Dunlop, Stephen B. Gruber, Richard S. Houlston, Ian Tomlinson, Victor Moreno, Ulrike Peters
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Nature
Verified
Large-scale integration of omics and electronic health records to identify potential risk protein biomarkers and therapeutic drugs for cancer prevention
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Keywords human cancers risk variants GWAS pQTL proteomics EHR therapeutic drug caffeine acetazolamide drug trial emulation Get full text access Log in, subscribe or purchase for full access. References 1. Nelson, M.R. ∙ Tipney, H. ∙ Painter, J.L. ... The support of human genetic evidence for approved drug indications Nat. Genet. 2015; 47:856-860 2. Diogo, D. ∙ Tian, C. ∙ Franklin, C.S. ... Phenome-wide association studies across large population cohorts support drug target validation Nat. Commun.
By Qing Li, Qingyuan Song, Zhishan Chen, Jungyoon Choi, Victor Moreno, Jie Ping, Wanqing Wen, Xiang Shu, Jun Yan, Xiao-Ou Shu, Qiuyin Cai, Jirong Long, Jeroen R. Huyghe, Rish K Pai, Stephen B. Gruber, Yaohua Yang, Graham Casey, Xusheng Wang, Adetunji T. Toriola, Bhuminder Singh, Ken S. Lau, Li Zhou Verified, Zichen Zhang, Chong Wu, Ulrike Peters, Wei Zheng, Quan Long, Zhijun Yin, Xingyi Guo
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The American Journal of Human Genetics
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Integrating multi‐ancestry genomic and proteomic data to identify blood risk biomarkers and target proteins for breast cancer genetic risk loci
CONFLICT OF INTEREST STATEMENT Olufunmilayo I. Olopade is co-founder at CancerIQ, serves as Scientific Advisor at Tempus, and is on the Board of 54gene. Atara Ntekim received research support from Roche. Other authors declare no competing interests related to this study. Supporting Information Filename Description ijc70041-sup-0001-Supinfo.pdfPDF document, 128.4 KB APPENDIX S1: Supporting information.
"A Proteome-Wide Association Study Identifies Putative Causal Proteins " by Tianying Zhao, Shuai Xu et al.
Keywords Humans, Breast Neoplasms, Female, Genome-Wide Association Study, Proteome, Genetic Predisposition to Disease, Polymorphism, Single Nucleotide, Middle Aged, Case-Control Studies, Risk Factors, Cancer epidemiology, Breast cancer Abstract BACKGROUND: Genome-wide association studies (GWAS) have identified more than 200 breast cancer risk-associated genetic loci, yet the causal genes and biological mechanisms for most loci remain elusive.
A proteome-wide association study identifies putative causal proteins for breast cancer risk - British Journal of Cancer
Abstract Genome-wide association studies (GWAS) have identified more than 200 breast cancer risk-associated genetic loci, yet the causal genes and biological mechanisms for most loci remain elusive. Proteins, as final gene products, are pivotal in cellular function. In this study, we conducted a proteome-wide association study (PWAS) to identify proteins in breast tissue related to breast cancer risk.
Using Genome and Transcriptome Data From African-Ancestry Female Participants To Identify Putative Breast Cancer Susceptibility Genes
African-ancestry (AA) participants are underrepresented in genetics research. Here, we conducted a transcriptome-wide association study (TWAS) in AA female participants to identify putative breast cancer susceptibility genes.
Integrating muti-omics data to identify tissue-specific DNA methylation biomarkers for cancer risk - Nature Communications
Abstract The relationship between tissue-specific DNA methylation and cancer risk remains inadequately elucidated. Leveraging resources from the Genotype-Tissue Expression consortium, here we develop genetic models to predict DNA methylation at CpG sites across the genome for seven tissues and apply these models to genome-wide association study data of corresponding cancers, namely breast, colorectal, renal cell, lung, ovarian, prostate, and testicular germ cell cancers.
Genome-wide association analyses of breast cancer in women of African ancestry identify new susceptibility loci and improve risk prediction - Nature Genetics
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Abstract We performed genome-wide association studies of breast cancer including 18,034 cases and 22,104 controls of African ancestry. Genetic variants at 12 loci were associated with breast cancer risk (P < 5 × 10−8), including associations of a low-frequency missense variant rs61751053 in ARHGEF38 with overall breast cancer (odds ratio (OR) = 1.48) and a common variant rs76664032 at chromosome 2q14.2 with triple-negative breast cancer (TNBC) (OR = 1.30).
By Guochong Jia, Jie Ping, Xingyi Guo, Yaohua Yang, Bingshan Li, Stefan Ambs, Montserrat Garcia-Closas, Jian Gu, Jennifer Hu, Dezheng Huo, James Li, Katherine L. Nathanson, Michael Press, Dale P. Sandler, Melissa A. Troester, Song T. Yao, Thomas Ahearn, Katie O’Brien, Atara Ntekim, Huijun Qian, Haoyu Zhang, Christine B. Ambrosone, Qiuyin Cai, Christopher A. Haiman
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Nature
Verified
Using genome and transcriptome data from African-ancestry female participants to identify putative breast cancer susceptibility genes - Nature Communications
Abstract African-ancestry (AA) participants are underrepresented in genetics research. Here, we conducted a transcriptome-wide association study (TWAS) in AA female participants to identify putative breast cancer susceptibility genes.
"Deep Neural Network Based Tissue Deconvolution of Circulating Tumor Ce" by Fengyao Yan, Limin Jiang et al.
Authors Fengyao Yan, Department of Public Health and Sciences, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, 33136, USA. Department of Computer Science, University of South Carolina, Columbia, SC, 29208, USA. Limin Jiang, Department of Computer Science, University of South Carolina, Columbia, SC, 29208, USA. Fei Ye, Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, 37232, USA.
Genome- and transcriptome-wide association studies of 386,000 Asian and European-ancestry women provide new insights into breast cancer genetics
Sung H. Ferlay J. Siegel R.L. Laversanne M. Soerjomataram I. Jemal A. Bray F. Global cancer statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA A Cancer J. Clin. 2021; 71: 209-249https://doi.org/10.3322/caac.21660 Hu C. Hart S.N. Gnanaolivu R. Huang H. Lee K.Y. Na J. Gao C. Lilyquist J. Yadav S. Boddicker N.J. et al. A population-based study of genes previously implicated in breast cancer. N. Engl. J. Med.
VAP-A and its binding partner CERT drive biogenesis of RNA-containing extracellular vesicles at ER membrane contact sites
Abels E.R. Maas S.L.N. Nieland L. Wei Z. Cheah P.S. Tai E. Kolsteeg C.J. Dusoswa S.A. Ting D.T. Hickman S. et al. Glioblastoma-associated microglia reprogramming is mediated by functional transfer of extracellular miR-21. Cell Rep. 2019; 28: 3105-3119.e7https://doi.org/10.1016/j.celrep.2019.08.036 Albacete-Albacete L. Navarro-Lérida I. López J.A. Martín-Padura I. Astudillo A.M. Ferrarini A. Van-Der-Heyden M. Balsinde J. Orend G. Vázquez J. et al.
Characterization of structural variation in Tibetans reveals new evidence of high-altitude adaptation and introgression
Genome Biology volume 22, Article number: 159 (2021) Cite this article Abstract Background Structural variation (SV) acts as an essential mutational force shaping the evolution and function of the human genome. However, few studies have examined the role of SVs in high-altitude adaptation and little is known of adaptive introgressed SVs in Tibetans so far.
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