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1. Additional file 3 of Rare deleterious mutations of HNRNP genes result in shared neurodevelopmental disorders

Author

Gillentine, Madelyn A., Tianyun Wang, Hoekzema, Kendra, Rosenfeld, Jill, Pengfei Liu, Guo, Hui, Kim, Chang N., De Vries, Bert B. A., Lisenka E. L. M. Vissers, Nordenskjold, Magnus, Kvarnung, Malin, Lindstrand, Anna, Nordgren, Ann, Gecz, Jozef, Iascone, Maria, Cereda, Anna, Scatigno, Agnese, Maitz, Silvia, Zanni, Ginevra, Bertini, Enrico, Zweier, Christiane, Schuhmann, Sarah, Wiesener, Antje, Pepper, Micah, Panjwani, Heena, Torti, Erin, Abid, Farida, Anselm, Irina, Siddharth Srivastava, Paldeep Atwal, Bacino, Carlos A., Gifty Bhat, Cobian, Katherine, Bird, Lynne M., Friedman, Jennifer, Wright, Meredith S., Callewaert, Bert, Petit, Florence, Mathieu, Sophie, Afenjar, Alexandra, Celenie K. Christensen, White, Kerry M., Elpeleg, Orly, Berger, Itai, Espineli, Edward J., Fagerberg, Christina, Brasch-Andersen, Charlotte, Hansen, Lars Kjærsgaard, Feyma, Timothy, Hughes, Susan, Thiffault, Isabelle, Sullivan, Bonnie, Yan, Shuang, Keller, Kory, Keren, Boris, Mignot, Cyril, Kooy, Frank, Meuwissen, Marije, Basinger, Alice, Kukolich, Mary, Philips, Meredith, Ortega, Lucia, Drummond-Borg, Margaret, Lauridsen, Mathilde, Sorensen, Kristina, Lehman, Anna, Lopez-Rangel, Elena, Levy, Paul, Lessel, Davor, Lotze, Timothy, Suneeta Madan-Khetarpal, Sebastian, Jessica, Vento, Jodie, Vats, Divya, L. Manace Benman, Mckee, Shane, Ghayda M. Mirzaa, Muss, Candace, Pappas, John, Peeters, Hilde, Romano, Corrado, Elia, Maurizio, Galesi, Ornella, Simon, Marleen E. H., Van Gassen, Koen L. I., Simpson, Kara, Stratton, Robert, Sabeen Syed, Thevenon, Julien, Palafoll, Irene Valenzuela, Vitobello, Antonio, Bournez, Marie, Faivre, Laurence, Xia, Kun, Earl, Rachel K., Nowakowski, Tomasz, Bernier, Raphael A., and Eichler, Evan E.

Subjects
Data_FILES
Abstract

Additional file 3: Table S13. GenBank accession numbers.

Published
2021
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2. Additional file 2 of Rare deleterious mutations of HNRNP genes result in shared neurodevelopmental disorders

Author

Gillentine, Madelyn A., Tianyun Wang, Hoekzema, Kendra, Rosenfeld, Jill, Pengfei Liu, Guo, Hui, Kim, Chang N., De Vries, Bert B. A., Lisenka E. L. M. Vissers, Nordenskjold, Magnus, Kvarnung, Malin, Lindstrand, Anna, Nordgren, Ann, Gecz, Jozef, Iascone, Maria, Cereda, Anna, Scatigno, Agnese, Maitz, Silvia, Zanni, Ginevra, Bertini, Enrico, Zweier, Christiane, Schuhmann, Sarah, Wiesener, Antje, Pepper, Micah, Panjwani, Heena, Torti, Erin, Abid, Farida, Anselm, Irina, Siddharth Srivastava, Paldeep Atwal, Bacino, Carlos A., Gifty Bhat, Cobian, Katherine, Bird, Lynne M., Friedman, Jennifer, Wright, Meredith S., Callewaert, Bert, Petit, Florence, Mathieu, Sophie, Afenjar, Alexandra, Celenie K. Christensen, White, Kerry M., Elpeleg, Orly, Berger, Itai, Espineli, Edward J., Fagerberg, Christina, Brasch-Andersen, Charlotte, Hansen, Lars Kjærsgaard, Feyma, Timothy, Hughes, Susan, Thiffault, Isabelle, Sullivan, Bonnie, Yan, Shuang, Keller, Kory, Keren, Boris, Mignot, Cyril, Kooy, Frank, Meuwissen, Marije, Basinger, Alice, Kukolich, Mary, Philips, Meredith, Ortega, Lucia, Drummond-Borg, Margaret, Lauridsen, Mathilde, Sorensen, Kristina, Lehman, Anna, Lopez-Rangel, Elena, Levy, Paul, Lessel, Davor, Lotze, Timothy, Suneeta Madan-Khetarpal, Sebastian, Jessica, Vento, Jodie, Vats, Divya, L. Manace Benman, Mckee, Shane, Ghayda M. Mirzaa, Muss, Candace, Pappas, John, Peeters, Hilde, Romano, Corrado, Elia, Maurizio, Galesi, Ornella, Simon, Marleen E. H., Van Gassen, Koen L. I., Simpson, Kara, Stratton, Robert, Sabeen Syed, Thevenon, Julien, Palafoll, Irene Valenzuela, Vitobello, Antonio, Bournez, Marie, Faivre, Laurence, Xia, Kun, Earl, Rachel K., Nowakowski, Tomasz, Bernier, Raphael A., and Eichler, Evan E.

Abstract

Additional file 2: Supplementary Figures S1-S5. Fig. S1. Dendrogram of hnRNPs based on multiple sequence alignment of canonical amino acid sequences. Colors match those seen in Fig. 2. NDD hnRNPs are shown in black boxes. Fig. S2. Pathogenicity assessment of variation in hnRNPs. A) Gene Variation Intolerance Ranking (GeVIR), loss-of-function observed/expected upper bound fraction (LOEUF), and Variation Intolerant Region Loss-of-Function (VIRLoF) percentiles. Average LOEUF percentile is significantly higher for NDD HNRNPs (n = 13) compared to other HNRNPs (n = 15). B) Average fold change for GeVIR, LEOUF, and VIRLoF for autosomal dominant (AD) and autosomal recessive (AR) variants. Average LEOUF fold change for AD mutations is significantly higher for NDD HNRNPs compared to other HNRNPs, with the AD VIRLoF fold change trending in the same direction. The AR LEOUF fold change is trending towards being significantly higher among other HNRNPs compared to NDD HNRNPs. One-way t-test. * p

Published
2021
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3. Additional file 10: of Inherited and multiple de novo mutations in autism/developmental delay risk genes suggest a multifactorial model

Author

Guo, Hui, Tianyun Wang, Huidan Wu, Long, Min, Coe, Bradley, Honghui Li, Guanglei Xun, Jianjun Ou, Biyuan Chen, Guiqin Duan, Bai, Ting, Ningxia Zhao, Yidong Shen, Li, Yun, Yazhe Wang, Zhang, Yu, Baker, Carl, Yanling Liu, Pang, Nan, Huang, Lian, Han, Lin, Xiangbin Jia, Cenying Liu, Hailun Ni, Xinyi Yang, Xia, Lu, Jingjing Chen, Shen, Lu, Li, Ying, Rongjuan Zhao, Wenjing Zhao, Peng, Jing, Pan, Qian, Zhigao Long, Su, Wei, Jieqiong Tan, Xiaogang Du, Xiaoyan Ke, Meiling Yao, Zhengmao Hu, Xiaobing Zou, Jingping Zhao, Bernier, Raphael, Eichler, Evan, and Xia, Kun

Abstract

Figure S6. Distribution of mutations in some of the top mutated genes (DYRK1A, ASXL3, WDFY3 and MECP2) in the ACGC cohort (above) compared to previously published LGD and missense DNMs identified in the SSC and ASC cohorts. (PDF 896 kb)

Published
2018
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4. Additional file 14: of Inherited and multiple de novo mutations in autism/developmental delay risk genes suggest a multifactorial model

Author

Guo, Hui, Tianyun Wang, Huidan Wu, Long, Min, Coe, Bradley, Honghui Li, Guanglei Xun, Jianjun Ou, Biyuan Chen, Guiqin Duan, Bai, Ting, Ningxia Zhao, Yidong Shen, Li, Yun, Yazhe Wang, Zhang, Yu, Baker, Carl, Yanling Liu, Pang, Nan, Huang, Lian, Han, Lin, Xiangbin Jia, Cenying Liu, Hailun Ni, Xinyi Yang, Xia, Lu, Jingjing Chen, Shen, Lu, Li, Ying, Rongjuan Zhao, Wenjing Zhao, Peng, Jing, Pan, Qian, Zhigao Long, Su, Wei, Jieqiong Tan, Xiaogang Du, Xiaoyan Ke, Meiling Yao, Zhengmao Hu, Xiaobing Zou, Jingping Zhao, Bernier, Raphael, Eichler, Evan, and Xia, Kun

Subjects
education
Abstract

Figure S9. Parent carriers of CHD8 LGD mutations show autistic traits. The density plots are based on the BAPQ scores of all SSC parents. Left: father; Right: mother. Red arrows point to the corresponding BAPQ scores of the three parents with CHD8 LGD mutations. (PDF 249 kb)

Published
2018
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5. Additional file 9: of Inherited and multiple de novo mutations in autism/developmental delay risk genes suggest a multifactorial model

Author

Guo, Hui, Tianyun Wang, Huidan Wu, Long, Min, Coe, Bradley, Honghui Li, Guanglei Xun, Jianjun Ou, Biyuan Chen, Guiqin Duan, Bai, Ting, Ningxia Zhao, Yidong Shen, Li, Yun, Yazhe Wang, Zhang, Yu, Baker, Carl, Yanling Liu, Pang, Nan, Huang, Lian, Han, Lin, Xiangbin Jia, Cenying Liu, Hailun Ni, Xinyi Yang, Xia, Lu, Jingjing Chen, Shen, Lu, Li, Ying, Rongjuan Zhao, Wenjing Zhao, Peng, Jing, Pan, Qian, Zhigao Long, Su, Wei, Jieqiong Tan, Xiaogang Du, Xiaoyan Ke, Meiling Yao, Zhengmao Hu, Xiaobing Zou, Jingping Zhao, Bernier, Raphael, Eichler, Evan, and Xia, Kun

Abstract

Figure S5. Distribution of missense mutations in SCN2A and CHD8. a. Missense DNMs in SCN2A are mainly located in the ion transport domain. Three recurrent missense DNM sites were identified at R937 (4), R379 (2), and G1744 (2). b. Distribution of missense DNMs in CHD8. One recurrent missense DNM site was identified at M904. c. The overall CADD score distributions of the missense DNMs within SCN2A and CHD8 are significantly higher than the distribution of rare missense mutations of SCN2A and CHD8 from ExAC. P values were corrected for the two tests. (PDF 1001 kb)

Published
2018
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6. Additional file 1: of Inherited and multiple de novo mutations in autism/developmental delay risk genes suggest a multifactorial model

Author

Guo, Hui, Tianyun Wang, Huidan Wu, Long, Min, Coe, Bradley, Honghui Li, Guanglei Xun, Jianjun Ou, Biyuan Chen, Guiqin Duan, Bai, Ting, Ningxia Zhao, Yidong Shen, Li, Yun, Yazhe Wang, Zhang, Yu, Baker, Carl, Yanling Liu, Pang, Nan, Huang, Lian, Han, Lin, Xiangbin Jia, Cenying Liu, Hailun Ni, Xinyi Yang, Xia, Lu, Jingjing Chen, Shen, Lu, Li, Ying, Rongjuan Zhao, Wenjing Zhao, Peng, Jing, Pan, Qian, Zhigao Long, Su, Wei, Jieqiong Tan, Xiaogang Du, Xiaoyan Ke, Meiling Yao, Zhengmao Hu, Xiaobing Zou, Jingping Zhao, Bernier, Raphael, Eichler, Evan, and Xia, Kun

Subjects
body regions, nervous system, mental disorders, fungi
Abstract

Figure S1. Location distribution of clinical centers in the Autism Clinical and Genetic Resources in China (ACGC). (PDF 1173 kb)

Published
2018
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7. Additional file 12: of Inherited and multiple de novo mutations in autism/developmental delay risk genes suggest a multifactorial model

Author

Guo, Hui, Tianyun Wang, Huidan Wu, Long, Min, Coe, Bradley, Honghui Li, Guanglei Xun, Jianjun Ou, Biyuan Chen, Guiqin Duan, Bai, Ting, Ningxia Zhao, Yidong Shen, Li, Yun, Yazhe Wang, Zhang, Yu, Baker, Carl, Yanling Liu, Pang, Nan, Huang, Lian, Han, Lin, Xiangbin Jia, Cenying Liu, Hailun Ni, Xinyi Yang, Xia, Lu, Jingjing Chen, Shen, Lu, Li, Ying, Rongjuan Zhao, Wenjing Zhao, Peng, Jing, Pan, Qian, Zhigao Long, Su, Wei, Jieqiong Tan, Xiaogang Du, Xiaoyan Ke, Meiling Yao, Zhengmao Hu, Xiaobing Zou, Jingping Zhao, Bernier, Raphael, Eichler, Evan, and Xia, Kun

Subjects
body regions, nervous system
Abstract

Figure S7. Logistic regression model performed to test the relationship between affected probability and DNM numbers correcting for fatherâ s age at birth and gender. The logistic regression histogram plot shows that individuals with more DNM numbers are more likely to be affected. (PDF 879 kb)

Published
2018
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8. Additional file 4: of Inherited and multiple de novo mutations in autism/developmental delay risk genes suggest a multifactorial model

Author

Guo, Hui, Tianyun Wang, Huidan Wu, Long, Min, Coe, Bradley, Honghui Li, Guanglei Xun, Jianjun Ou, Biyuan Chen, Guiqin Duan, Bai, Ting, Ningxia Zhao, Yidong Shen, Li, Yun, Yazhe Wang, Zhang, Yu, Baker, Carl, Yanling Liu, Pang, Nan, Huang, Lian, Han, Lin, Xiangbin Jia, Cenying Liu, Hailun Ni, Xinyi Yang, Xia, Lu, Jingjing Chen, Shen, Lu, Li, Ying, Rongjuan Zhao, Wenjing Zhao, Peng, Jing, Pan, Qian, Zhigao Long, Su, Wei, Jieqiong Tan, Xiaogang Du, Xiaoyan Ke, Meiling Yao, Zhengmao Hu, Xiaobing Zou, Jingping Zhao, Bernier, Raphael, Eichler, Evan, and Xia, Kun

Abstract

Figure S3. Fraction of target based on >â 8-fold sequence coverage by gene. Box and whisker plots show the fraction of a sampleâ s target bases at 8X or greater coverage split by gene. All capture samples are included (along with QC failures). (PDF 109 kb)

Published
2018
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9. Additional file 3: of Inherited and multiple de novo mutations in autism/developmental delay risk genes suggest a multifactorial model

Author

Guo, Hui, Tianyun Wang, Huidan Wu, Long, Min, Coe, Bradley, Honghui Li, Guanglei Xun, Jianjun Ou, Biyuan Chen, Guiqin Duan, Bai, Ting, Ningxia Zhao, Yidong Shen, Li, Yun, Yazhe Wang, Zhang, Yu, Baker, Carl, Yanling Liu, Pang, Nan, Huang, Lian, Han, Lin, Xiangbin Jia, Cenying Liu, Hailun Ni, Xinyi Yang, Xia, Lu, Jingjing Chen, Shen, Lu, Li, Ying, Rongjuan Zhao, Wenjing Zhao, Peng, Jing, Pan, Qian, Zhigao Long, Su, Wei, Jieqiong Tan, Xiaogang Du, Xiaoyan Ke, Meiling Yao, Zhengmao Hu, Xiaobing Zou, Jingping Zhao, Bernier, Raphael, Eichler, Evan, and Xia, Kun

Abstract

Figure S2. QC of MIPs cohort. QC analysis of the percentage of MIPs with at least eight reads per sample. (PDF 84 kb)

Published
2018
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10. Additional file 8: of Inherited and multiple de novo mutations in autism/developmental delay risk genes suggest a multifactorial model

Author

Guo, Hui, Tianyun Wang, Huidan Wu, Long, Min, Coe, Bradley, Honghui Li, Guanglei Xun, Jianjun Ou, Biyuan Chen, Guiqin Duan, Bai, Ting, Ningxia Zhao, Yidong Shen, Li, Yun, Yazhe Wang, Zhang, Yu, Baker, Carl, Yanling Liu, Pang, Nan, Huang, Lian, Han, Lin, Xiangbin Jia, Cenying Liu, Hailun Ni, Xinyi Yang, Xia, Lu, Jingjing Chen, Shen, Lu, Li, Ying, Rongjuan Zhao, Wenjing Zhao, Peng, Jing, Pan, Qian, Zhigao Long, Su, Wei, Jieqiong Tan, Xiaogang Du, Xiaoyan Ke, Meiling Yao, Zhengmao Hu, Xiaobing Zou, Jingping Zhao, Bernier, Raphael, Eichler, Evan, and Xia, Kun

Abstract

Figure S4. Distribution of DNMs for SCN2A and CHD8. LGD (red) and missense (blue) DNMs with respect to the protein model in the ACGC cohort (above the protein model) are compared to previously published DNMs (below the model) primarily from European cohorts. â DNMs unique to Phase II samples; *DNMs from SSC and ASC cohorts. (PDF 931 kb)

Published
2018
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11. Additional file 13: of Inherited and multiple de novo mutations in autism/developmental delay risk genes suggest a multifactorial model

Author

Guo, Hui, Tianyun Wang, Huidan Wu, Long, Min, Coe, Bradley, Honghui Li, Guanglei Xun, Jianjun Ou, Biyuan Chen, Guiqin Duan, Bai, Ting, Ningxia Zhao, Yidong Shen, Li, Yun, Yazhe Wang, Zhang, Yu, Baker, Carl, Yanling Liu, Pang, Nan, Huang, Lian, Han, Lin, Xiangbin Jia, Cenying Liu, Hailun Ni, Xinyi Yang, Xia, Lu, Jingjing Chen, Shen, Lu, Li, Ying, Rongjuan Zhao, Wenjing Zhao, Peng, Jing, Pan, Qian, Zhigao Long, Su, Wei, Jieqiong Tan, Xiaogang Du, Xiaoyan Ke, Meiling Yao, Zhengmao Hu, Xiaobing Zou, Jingping Zhao, Bernier, Raphael, Eichler, Evan, and Xia, Kun

Subjects
10. No inequality
Abstract

Figure S8. Multiple-hit model for ASD excluding DNM cases. Shown are comparisons of autism probands and unaffected siblings with one or more DNM. Logistic histograms compare residual DNM counts (DNM number residuals, note: after correction, a residual of 0 does not represent a count of 0) adjusted for the father’s age at birth and gender, and the probability of being a proband or unaffected sibling. This analysis demonstrates an increased burden of multiple hits among affected individuals (OR = 1.15, p = 0.0278) (a). When samples are stratified by genetic sex, we observe a slight increase but no significant effect among males (OR = 1.09, p = 0.6) (b), while females demonstrate a stronger (OR = 1.3, p = 0.037) (c) effect than the grouped analysis. (PDF 957 kb)

12. Additional file 13: of Inherited and multiple de novo mutations in autism/developmental delay risk genes suggest a multifactorial model

Author

Guo, Hui, Tianyun Wang, Huidan Wu, Long, Min, Coe, Bradley, Honghui Li, Guanglei Xun, Jianjun Ou, Biyuan Chen, Guiqin Duan, Bai, Ting, Ningxia Zhao, Yidong Shen, Li, Yun, Yazhe Wang, Zhang, Yu, Baker, Carl, Yanling Liu, Pang, Nan, Huang, Lian, Han, Lin, Xiangbin Jia, Cenying Liu, Hailun Ni, Xinyi Yang, Xia, Lu, Jingjing Chen, Shen, Lu, Li, Ying, Rongjuan Zhao, Wenjing Zhao, Peng, Jing, Pan, Qian, Zhigao Long, Su, Wei, Jieqiong Tan, Xiaogang Du, Xiaoyan Ke, Meiling Yao, Zhengmao Hu, Xiaobing Zou, Jingping Zhao, Bernier, Raphael, Eichler, Evan, and Xia, Kun

Subjects
10. No inequality
Abstract

Figure S8. Multiple-hit model for ASD excluding DNM cases. Shown are comparisons of autism probands and unaffected siblings with one or more DNM. Logistic histograms compare residual DNM counts (DNM number residuals, note: after correction, a residual of 0 does not represent a count of 0) adjusted for the father’s age at birth and gender, and the probability of being a proband or unaffected sibling. This analysis demonstrates an increased burden of multiple hits among affected individuals (OR = 1.15, p = 0.0278) (a). When samples are stratified by genetic sex, we observe a slight increase but no significant effect among males (OR = 1.09, p = 0.6) (b), while females demonstrate a stronger (OR = 1.3, p = 0.037) (c) effect than the grouped analysis. (PDF 957 kb)

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