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21 results on '"Lin, Han-Jen"'

3. A rare missense variant of CASP7 is associated with familial late-onset Alzheimer's disease

Author

Bellair, Michelle, Dinh, Huyen, Doddapeneni, Harsha, Dugan-Perez, Shannon, English, Adam, Gibbs, Richard A., Han, Yi, Hu, Jianhong, Jayaseelan, Joy, Kalra, Divya, Khan, Ziad, Korchina, Viktoriya, Lee, Sandra, Liu, Yue, Liu, Xiuping, Muzny, Donna, Nasser, Waleed, Salerno, William, Santibanez, Jireh, Skinner, Evette, White, Simon, Worley, Kim, Zhu, Yiming, Beiser, Alexa, Chen, Yuning, Chung, Jaeyoon, Cupples, L. Adrienne, DeStefano, Anita, Dupuis, Josee, Farrell, John, Farrer, Lindsay, Lancour, Daniel, Lin, Honghuang, Liu, Ching Ti, Lunetta, Kathy, Ma, Yiyi, Patel, Devanshi, Sarnowski, Chloe, Satizabal, Claudia, Seshadri, Sudha, Sun, Fangui Jenny, Zhang, Xiaoling, Choi, Seung Hoan, Banks, Eric, Gabriel, Stacey, Gupta, Namrata, Bush, William, Butkiewicz, Mariusz, Haines, Jonathan, Smieszek, Sandra, Song, Yeunjoo, Barral, Sandra, De Jager, Phillip L., Mayeux, Richard, Reitz, Christiane, Reyes, Dolly, Tosto, Giuseppe, Vardarajan, Badri, Amad, Shahzad, Amin, Najaf, Ikram, M. Afran, van der Lee, Sven, van Duijn, Cornelia, Vanderspek, Ashley, Schmidt, Helena, Schmidt, Reinhold, Goate, Alison, Kapoor, Manav, Marcora, Edoardo, Renton, Alan, Faber, Kelley, Foroud, Tatiana, Feolo, Michael, Stine, Adam, Launer, Lenore J., Bennett, David A., Xia, Li Charlie, Beecham, Gary, Hamilton-Nelson, Kara, Jaworski, James, Kunkle, Brian, Martin, Eden, Pericak-Vance, Margaret, Rajabli, Farid, Schmidt, Michael, Mosley, Thomas H., Cantwell, Laura, Childress, Micah, Chou, Yi-Fan, Cweibel, Rebecca, Gangadharan, Prabhakaran, Kuzma, Amanda, Leung, Yuk Yee, Lin, Han-Jen, Malamon, John, Mlynarski, Elisabeth, Naj, Adam, Qu, Liming, Schellenberg, Gerard, Valladares, Otto, Wang, Li-San, Wang, Weixin, Zhang, Nancy, Below, Jennifer E., Boerwinkle, Eric, Bressler, Jan, Fornage, Myriam, Jian, Xueqiu, Liu, Xiaoming, Bis, Joshua C., Blue, Elizabeth, Brown, Lisa, Day, Tyler, Dorschner, Michael, Horimoto, Andrea R., Nafikov, Rafael, Nato, Alejandro Q., Jr., Navas, Pat, Nguyen, Hiep, Psaty, Bruce, Rice, Kenneth, Saad, Mohamad, Sohi, Harkirat, Thornton, Timothy, Tsuang, Debby, Wang, Bowen, Wijsman, Ellen, Witten, Daniela, Antonacci-Fulton, Lucinda, Appelbaum, Elizabeth, Cruchaga, Carlos, Fulton, Robert S., Koboldt, Daniel C., Larson, David E., Waligorski, Jason, Wilson, Richard K., Zhu, Congcong, Vardarajan, Badri N., Farrell, John J., Haines, Jonathan L., Schellenberg, Gerard D., Pericak-Vance, Margaret A., Lunetta, Kathryn L., and Farrer, Lindsay A.

Published
2019
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4. Rare genetic variation implicated in non-Hispanic white families with Alzheimer disease

Author

Beecham, Gary W., Vardarajan, Badri, Blue, Elizabeth, Bush, William, Jaworski, James, Barral, Sandra, DeStefano, Anita, Hamilton-Nelson, Kara, Kunkle, Brian, Martin, Eden R., Naj, Adam, Rajabli, Farid, Reitz, Christiane, Thornton, Timothy, van Duijn, Cornelia, Goate, Allison, Seshadri, Sudha, Farrer, Lindsay A., Boerwinkle, Eric, Schellenberg, Gerard, Haines, Jonathan L., Wijsman, Ellen, Mayeux, Richard, Pericak-Vance, Margaret A., English, Adam, Kalra, Divya, Muzny, Donna, Skinner, Evette, Doddapeneni, Harsha, Dinh, Huyen, Hu, Jianhong, Santibanez, Jireh, Jayaseelan, Joy, Worley, Kim, Bellair, Michelle, Gibbs, Richard A., Lee, Sandra, Dugan-Perez, Shannon, White, Simon, Korchina, Viktoriya, Nasser, Waleed, Salerno, William, Liu, Xiuping, Han, Yi, Zhu, Yiming, Liu, Yue, Khan, Ziad, Cupples, Adrienne, Beiser, Alexa, DeStefanos, Anita, Liu, Ching Ti, Sarnowski, Chloe, Satizabal, Claudia, Lancour, Dan, Patel, Devanshi, Sun, Fangui Jenny, Lin, Honghuang, Chung, Jaeyoon, Farrell, John, Dupuis, Josee, Lunetta, Kathy, Farrer, Lindsay, Seshadri, Sudha, Zhang, Xiaoling, Ma, Yiyi, Chen, Yuning, Banks, Eric, Gupta, Namrata, Choi, Seung Hoan, Gabriel, Stacey, Haines, Jonathan, Butkiewicz, Mariusz, Smieszek, Sandra, Bush, Will, Song, Yeunjoo, Vardarajan, Badri, Reitz, Christiane, Reyes, Dolly, Tosto, Giuseppe, De Jager, Phillip L, Mayeux, Richard, Barral, Sandra, Vanderspek, Ashley, van Duijn, Cornelia, Ikram, M Afran, Amin, Najaf, Amad, Shahzad, van der Lee, Sven, Faber, Kelley, Foroud, Tatiana, Schmidt, Helena, Schmidt, Reinhold, Renton, Alan, Goate, Alison, Marcora, Edoardo, Kapoor, Manav, Stine, Adam, Feolo, Michael, Launer, Lenore J., Bennett, David A, Xia, Li Charlie, Kunkle, Brian, Martin, Eden, Rajabli, Farid, Beecham, Gary, Jaworski, James, Hamilton-Nelson, Kara, Pericak-Vance, Margaret, Schmidt, Michael, Mosley, Thomas H., Kuzma, Amanda, Lin, Han-Jen, Qu, Liming, Wang, Micah Childress, Li-San, Valladares, Otto, Gangadharan, Prabhakaran, Cweibel, Rebecca, Zhao, Yi, Chou, Yi-Fan, Naj, Adam, Mlynarski, Elisabeth, Schellenberg, Gerard, Malamon, John, Cantwell, Laura, Zhang, Nancy, Wang, Weixin, Leung, Yuk Yee, Boerwinkle, Eric, Bressler, Jan, Below, Jennifer E., Fornage, Myriam, Liu, Xiaoming, Jian, Xueqiu, Nato, Alejandro Q, Jr., Horimoto, Andrea R, Wang, Bowen, Psaty, Bruce, Witten, Daniela, Tsuang, Debby, Blue, Elizabeth, Wijsman, Ellen, Sohi, Harkirat, Nguyen, Hiep, Bis, Joshua C., Rice, Kenneth, Brown, Lisa, Dorschner, Michael, Saad, Mohamad, Navas, Pat, Nafikov, Rafael, Thornton, Timothy, Day, Tyler, Cruchaga, Carlos, Koboldt, Daniel C., Larson, David E., Appelbaum, Elizabeth, Waligorski, Jason, Antonacci-Fulton, Lucinda, Wilson, Richard K., and Fulton, Robert S.

Published
2018
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7. SparkINFERNO: a scalable high-throughput pipeline for inferring molecular mechanisms of non-coding genetic variants.

Author

Kuksa, Pavel P, Lee, Chien-Yueh, Amlie-Wolf, Alexandre, Gangadharan, Prabhakaran, Mlynarski, Elizabeth E, Chou, Yi-Fan, Lin, Han-Jen, Issen, Heather, Greenfest-Allen, Emily, Valladares, Otto, Leung, Yuk Yee, and Wang, Li-San

Subjects
MELANOGENESIS, FUNCTIONAL genomics, PIPELINES, TRANSCRIPTION factors, CIS-regulatory elements (Genetics), SCALABILITY, BIOINFORMATICS
Abstract

Summary We report Spark-based INFERence of the molecular mechanisms of NOn-coding genetic variants (SparkINFERNO), a scalable bioinformatics pipeline characterizing non-coding genome-wide association study (GWAS) association findings. SparkINFERNO prioritizes causal variants underlying GWAS association signals and reports relevant regulatory elements, tissue contexts and plausible target genes they affect. To achieve this, the SparkINFERNO algorithm integrates GWAS summary statistics with large-scale collection of functional genomics datasets spanning enhancer activity, transcription factor binding, expression quantitative trait loci and other functional datasets across more than 400 tissues and cell types. Scalability is achieved by an underlying API implemented using Apache Spark and Giggle-based genomic indexing. We evaluated SparkINFERNO on large GWASs and show that SparkINFERNO is more than 60 times efficient and scales with data size and amount of computational resources. Availability and implementation SparkINFERNO runs on clusters or a single server with Apache Spark environment, and is available at https://bitbucket.org/wanglab-upenn/SparkINFERNO or https://hub.docker.com/r/wanglab/spark-inferno. Contact lswang@pennmedicine.upenn.edu Supplementary information Supplementary data  are available at  Bioinformatics  online [ABSTRACT FROM AUTHOR]

Published
2020
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10. The role of pericardial adipose tissue in the heart of obese minipigs.

Author

Wang, Chia‐Yu, Li, Sin‐Jin, Wu, Twin‐Way, Lin, Han‐Jen, Chen, Jyun‐Wei, Mersmann, Harry J., Ding, Shih‐Torng, and Chen, Ching‐Yi

Subjects
ADIPOSE tissues, ADIPONECTIN, INSULIN resistance, OVERWEIGHT persons, FAT cells
Abstract

Abstract: Background: Pericardial adipose tissue (PAT) volume is highly associated with the presence and severity of cardiometabolic diseases, but the underlying mechanism is unknown. We previously demonstrated that a high‐fat diet (HFD) induced metabolic dysregulation, cardiac fibrosis and accumulation of more PAT in minipigs. This study used our obese minipig model to investigate the characteristics of PAT and omental visceral fat (VAT) induced by a HFD, and the potential link between PAT and HFD‐related myocardial fibrosis. Materials and methods: Five‐month‐old Lee‐Sung minipigs were made obese by feeding a HFD for 6 months. Results: The HFD induced dyslipidemia, cardiac fibrosis and more fat accumulation in the visceral and pericardial depots. The HFD changes the fatty acid composition in the adipose tissue by decreasing the portion of linoleic acid in the VAT and PAT. No arachidonic acid was detected in the VAT and PAT of control pigs, whereas it existed in the same tissues of obese pigs fed the HFD. Compared with the control pigs, elevated levels of malondialdehyde and TNFα were exhibited in the plasma and PAT of obese pigs. HFD induced greater size of adipocytes in VAT and PAT. Higher levels of GH, leptin, OPG, PDGF, resistin, SAA and TGFβ were observed in obese pig PAT compared to VAT. Conclusion: This study demonstrated the similarities and dissimilarities between PAT and VAT under HFD stimulus. In addition, this study suggested that alteration in PAT contributed to the myocardial damage. [ABSTRACT FROM AUTHOR]

Published
2018
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12. THE ALZHEIMER’S DISEASE SEQUENCING PROJECT (ADSP) DATA UPDATE 2017

Author

Kuzma, Amanda B., Faber, Kelley, Salerno, William, Leung, Yuk Yee, Cantwell, Laura B., Feolo, Mike, Stine, Adam, Gupta, Namrata, Fulton, Robert, Valladares, Otto, Cweibel, Rebecca, Appelbaum, Elizabeth, Choi, Seung Hoan, Hamilton-Nelson, Kara L., Lin, Han-Jen, Muzny, Donna, Qu, Liming, Reyes-Dumeyer, Dolly, Waligorski, Jason, Farrell, John, Naj, Adam C., Bis, Joshua C., Destefano, Anita L., Seshadri, Sudha, Boerwinkle, Eric, Schellenberg, Gerard D., Foroud, Tatiana M., and Wang, Li-San

Published
2017
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13. Embryonic cholesterol esterification is regulated by a cyclic AMP-dependent pathway in yolk sac membrane-derived endodermal epithelial cells.

Author

Wang, Siou-Huei, Lin, Han-Jen, Lin, Yuan-Yu, Chen, Yu-Jen, Pan, Yu-Hui, Tung, Cheng-Ting, Mersmann, Harry John, and Ding, Shih-Torng

Subjects
*EMBRYOLOGY, *CHOLESTEROL metabolism, *ESTERIFICATION, *CYCLIC adenylic acid, *YOLK sac, *EPITHELIAL cells
Abstract

During avian embryonic development, endodermal epithelial cells (EECs) absorb yolk through the yolk sac membrane. Sterol O-acyltransferase (SOAT) is important for esterification and yolk lipid utilization during development. Because the major enzyme for yolk sac membrane cholesteryl ester synthesis is SOAT1, we cloned the avian SOAT1 promoter and elucidated the cellular functions of SOAT1. Treatments with either glucagon, isobutylmethylxanthine (IBMX), an adenylate cyclase activator (forskolin), a cAMP analog (dibutyryl-cAMP), or a low glucose concentration all increased SOAT1 mRNA accumulation in EECs from Japanese quail, suggesting that SOAT1 is regulated by nutrients and hormones through a cAMP-dependent pathway. Activity of protein kinase A (PKA) was increased by IBMX, whereas co-treatment with the PKA inhibitor, H89 negated the increase in PKA activity. Cyclic AMP-induced EECs had greater cholesterol esterification than untreated EECs. By promoter deletion and point-mutation, the cAMP-response element (-349 to -341 bp) was identified as critical in mediating transcription of SOAT1. In conclusion, expression of SOAT1 was regulated by a cAMP-dependent pathway and factors that increase PKA will increase SOAT1 to improve the utilization of lipids in the EECs and potentially modify embryonic growth. [ABSTRACT FROM AUTHOR]

Published
2017
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14. VCPA: genomic variant calling pipeline and data management tool for Alzheimer's Disease Sequencing Project.

Author

Leung, Yuk Yee, Valladares, Otto, Chou, Yi-Fan, Lin, Han-Jen, Kuzma, Amanda B, Cantwell, Laura, Qu, Liming, Gangadharan, Prabhakaran, Salerno, William J, Schellenberg, Gerard D, and Wang, Li-San

Subjects
ALZHEIMER'S disease, DATA analysis, GENOMICS, RNA sequencing, MEDICAL care
Abstract

Summary We report VCPA, our SNP/Indel Variant Calling Pipeline and data management tool used for the analysis of whole genome and exome sequencing (WGS/WES) for the Alzheimer's Disease Sequencing Project. VCPA consists of two independent but linkable components: pipeline and tracking database. The pipeline, implemented using the Workflow Description Language and fully optimized for the Amazon elastic compute cloud environment, includes steps from aligning raw sequence reads to variant calling using GATK. The tracking database allows users to view job running status in real time and visualize >100 quality metrics per genome. VCPA is functionally equivalent to the CCDG/TOPMed pipeline. Users can use the pipeline and the dockerized database to process large WGS/WES datasets on Amazon cloud with minimal configuration. Availability and implementation VCPA is released under the MIT license and is available for academic and nonprofit use for free. The pipeline source code and step-by-step instructions are available from the National Institute on Aging Genetics of Alzheimer's Disease Data Storage Site (http://www.niagads.org/VCPA). Supplementary information Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]

Published
2019
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16. NIA genetics of Alzheimer's disease data storage site (NIAGADS): Update 2020: Genetics/genetic factors of Alzheimer's disease.

Author

Vogel, Briana, Kuzma, Amanda B., Valladares, Otto, Greenfest‐Allen, Emily, Klamann, Conor, Issen, Heather, Gangadharan, Prabhakaran, Katanic, Zivadin, Zhao, Yi, Qu, Liming, Lin, Han‐Jen, Moon, Michelle K., Leung, Yuk Yee, Naj, Adam C., Stoeckert, Christian J., Schellenberg, Gerard D., and Wang, Li‐San

Abstract

Background: NIAGADS is a national genetics data repository that facilitates access of genotypic data to qualified investigators for the study of the genetics of late‐onset Alzheimer's disease (AD) and other neurological diseases. Collaborations with large consortia and centers such as the Alzheimer's Disease Genetics Consortium (ADGC), Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium, the Alzheimer's Disease Genome Sequencing Project (ADSP), and the Genome Center for Alzheimer's Disease (GCAD) allow NIAGADS to lead the effort in managing large AD datasets that can be easily accessed by the research community and utilized to their fullest extent. Method: NIAGADS is supported by National Institute on Aging (NIA) under a cooperative agreement (U24 AG041689). All data derived from NIA funded AD genetics studies are expected to be deposited in NIAGADS or another NIA approved site. NIAGADS manages a Data Sharing Service (DSS) that facilitates the deposition and sharing of genomic data and association results with approved users in the neurodegenerative research community. In addition, researchers are able to freely use the NIAGADS Genomics Database to search annotation resources that link published AD studies to AD‐relevant sequence features and genome‐wide annotations. Result: As of January 2020, NIAGADS houses 67 datasets (23 added in 2019) with >59,000 samples and nearly 34 billion genotypes. Qualified investigators can retrieve ADSP sequencing data with ease and flexibility through the NIAGADS DSS. The ADSP and other contributing studies have completed whole exome sequencing (WES) of 20,630 subjects and whole‐genome sequencing (WGS) of 4,750 subjects. Raw WES and WGS files, quality controlled VCF files, and phenotype data files are available via qualified access. The next planned dataset release will occur in late 2020 and will contain an additional 13,136 genomes jointly genotype called with the first release of 4,750 genomes, totaling about 17,886 genomes. Conclusion: NIAGADS is a rich resource for AD researchers, with the goal of facilitating advances in Alzheimer's genetics research. By housing datasets from multiple projects and institutions, NIAGADS enables AD researchers to be more efficient in meeting their research goals. Datasets, guidelines, and new features are available on our website at https://www.niagads.org. [ABSTRACT FROM AUTHOR]

Published
2020
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21. Primary Endodermal Epithelial Cell Culture from the Yolk Sac Membrane of Japanese Quail Embryos.

Author

Lin HJ, Wang SH, Pan YH, and Ding ST

Subjects
Animals, Cell Proliferation, Cells, Cultured, Coturnix, Epithelial Cells enzymology, Female, Gene Expression Regulation, Enzymologic physiology, Male, Real-Time Polymerase Chain Reaction, Sterol O-Acyltransferase genetics, Yolk Sac enzymology, Endoderm cytology, Epithelial Cells cytology, Yolk Sac cytology
Abstract

We established an endodermal epithelial cell culture model (EEC) for studying the function of certain enzymes and proteins in mediating nutrient utilization by avian embryos during development. Fertilized Japanese quail eggs were incubated at 37 °C for 5 days and then yolk sac membranes (YSM) were collected to establish the EEC culture system. We isolated the embryonic endoderm layer from YSM, and sliced the membrane into 2 - 3 mm pieces and partially digested with collagenase before seeding in 24-well culture plates. The EECs proliferate out of the tissue and are ready for cell culture studies. We found that the EECs had typical characteristics of YSM in vivo, for example, accumulation of lipid droplets, expression of sterol O-acyltransferase and lipoprotein lipase. The partial digestion treatment significantly increased the successful rate of EEC culture. Utilizing the EECs, we demonstrated that the expression of SOAT1 was regulated by the cAMP dependent protein kinase A related pathway. This primary Japanese quail EEC culture system is a useful tool to study embryonic lipid transportation and to clarify the role of genes involved in mediating nutrient utilization in YSM during avian embryonic development.

Published
2016
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