311 results on '"Choi, Jung Kyoon"'
Search Results
2. Single-cell mapping of combinatorial target antigens for CAR switches using logic gates
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Kwon, Joonha, Kang, Junho, Jo, Areum, Seo, Kayoung, An, Dohyeon, Baykan, Mert Yakup, Lee, Jun Hyeong, Kim, Nayoung, Eum, Hye Hyeon, Hwang, Sohyun, Lee, Ji Min, Park, Woong-Yang, An, Hee Jung, Lee, Hae-Ock, Park, Jong-Eun, and Choi, Jung Kyoon
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- 2023
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3. Genomic hypomethylation in cell-free DNA predicts responses to checkpoint blockade in lung and breast cancer
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Kim, Kyeonghui, Kim, Hyemin, Shin, Inkyung, Noh, Seung-Jae, Kim, Jeong Yeon, Suh, Koung Jin, Kim, Yoo-Na, Lee, Jung-Yun, Cho, Dae-Yeon, Kim, Se Hyun, Kim, Jee Hyun, Lee, Se-Hoon, and Choi, Jung Kyoon
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- 2023
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4. Integrative modeling of tumor genomes and epigenomes for enhanced cancer diagnosis by cell-free DNA
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Bae, Mingyun, Kim, Gyuhee, Lee, Tae-Rim, Ahn, Jin Mo, Park, Hyunwook, Park, Sook Ryun, Song, Ki Byung, Jun, Eunsung, Oh, Dongryul, Lee, Jeong-Won, Park, Young Sik, Song, Ki-Won, Byeon, Jeong-Sik, Kim, Bo Hyun, Sohn, Joo Hyuk, Kim, Min Hwan, Kim, Gun Min, Chie, Eui Kyu, Kang, Hyun-Cheol, Kong, Sun-Young, Woo, Sang Myung, Lee, Jeong Eon, Ryu, Jai Min, Lee, Junnam, Kim, Dasom, Ki, Chang-Seok, Cho, Eun-Hae, and Choi, Jung Kyoon
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- 2023
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5. Integrative analysis of risk factors for immune-related adverse events of checkpoint blockade therapy in cancer
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Sung, Changhwan, An, Jinhyeon, Lee, Soohyeon, Park, Jaesoon, Lee, Kang Seon, Kim, Il-Hwan, Han, Ji-Youn, Park, Yeon Hee, Kim, Jee Hyun, Kang, Eun Joo, Hong, Min Hee, Kim, Tae-Yong, Lee, Jae Cheol, Lee, Jae Lyun, Yoon, Shinkyo, Choi, Chang-Min, Lee, Dae Ho, Yoo, Changhoon, Kim, Sang-We, Jeong, Jae Ho, Seo, Seyoung, Kim, Sun Young, Kong, Sun-Young, Choi, Jung Kyoon, and Park, Sook Ryun
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- 2023
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6. MHC II immunogenicity shapes the neoepitope landscape in human tumors
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Kim, Jeong Yeon, Cha, Hongui, Kim, Kyeonghui, Sung, Changhwan, An, Jinhyeon, Bang, Hyoeun, Kim, Hyungjoo, Yang, Jin Ok, Chang, Suhwan, Shin, Incheol, Noh, Seung-Jae, Shin, Inkyung, Cho, Dae-Yeon, Lee, Se-Hoon, and Choi, Jung Kyoon
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- 2023
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7. Non-coding de novo mutations in chromatin interactions are implicated in autism spectrum disorder
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Kim, Il Bin, Lee, Taeyeop, Lee, Junehawk, Kim, Jonghun, Lee, Suho, Koh, In Gyeong, Kim, Jae Hyun, An, Joon-Yong, Lee, Hyunseong, Kim, Woo Kyeong, Ju, Young Seok, Cho, Yongseong, Yu, Seok Jong, Kim, Soon Ae, Oh, Miae, Han, Dong Wook, Kim, Eunjoon, Choi, Jung Kyoon, Yoo, Hee Jeong, and Lee, Jeong Ho
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- 2022
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8. Unveiling the influence of tumor and immune signatures on immune checkpoint therapy in advanced lung cancer
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Kim, Nayoung, primary, Park, Sehhoon, additional, Jo, Areum, additional, Eum, Hye Hyeon, additional, Kim, Hong Kwan, additional, Lee, Kyungjong, additional, Cho, Jong Ho, additional, Ku, Bo Mi, additional, Jung, Hyun Ae, additional, Sun, Jong-Mu, additional, Lee, Se-Hoon, additional, Ahn, Jin Seok, additional, Lee, Jung-Il, additional, Choi, Jung Won, additional, Jeong, Dasom, additional, Na, Minsu, additional, Kang, Huiram, additional, Kim, Jeong Yeon, additional, Choi, Jung Kyoon, additional, Lee, Hae-Ock, additional, and Ahn, Myung-Ju, additional
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- 2024
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9. Author response: Unveiling the influence of tumor and immune signatures on immune checkpoint therapy in advanced lung cancer
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Kim, Nayoung, primary, Park, Sehhoon, additional, Jo, Areum, additional, Eum, Hye Hyeon, additional, Kim, Hong Kwan, additional, Lee, Kyungjong, additional, Cho, Jong Ho, additional, Ku, Bo Mi, additional, Jung, Hyun Ae, additional, Sun, Jong-Mu, additional, Lee, Se-Hoon, additional, Ahn, Jin Seok, additional, Lee, Jung-Il, additional, Choi, Jung Won, additional, Jeong, Dasom, additional, Na, Minsu, additional, Kang, Huiram, additional, Kim, Jeong Yeon, additional, Choi, Jung Kyoon, additional, Lee, Hae-Ock, additional, and Ahn, Myung-Ju, additional
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- 2024
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10. LncRNA HSPA7 in human atherosclerotic plaques sponges miR-223 and promotes the proinflammatory vascular smooth muscle cell transition
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Ann, Soo-jin, Bang, Hyoeun, Lee, Chan Joo, Oh, Jaewon, Park, Sungha, Kang, Seok-Min, Choi, Jung Kyoon, and Lee, Sang-Hak
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- 2021
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11. Short tandem repeat expansions in cortical layer‐specific genes implicate in phenotypic severity and adaptability of autism spectrum disorder.
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Kim, Jae Hyun, Koh, In Gyeong, Lee, Hyeji, Lee, Gang‐Hee, Song, Da‐Yea, Kim, Soo‐Whee, Kim, Yujin, Han, Jae Hyun, Bong, Guiyoung, Lee, Jeewon, Byun, Heejung, Son, Ji Hyun, Kim, Ye Rim, Lee, Yoojeong, Kim, Justine Jaewon, Park, Jung Woo, Kim, Il Bin, Choi, Jung Kyoon, Jang, Ja‐Hyun, and Trost, Brett
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MICROSATELLITE repeats ,AUTISM spectrum disorders ,PHENOTYPIC plasticity ,WHOLE genome sequencing ,PHENOTYPES ,GENE frequency ,Y chromosome - Abstract
Aim: Short tandem repeats (STRs) are repetitive DNA sequences and highly mutable in various human disorders. While the involvement of STRs in various genetic disorders has been extensively studied, their role in autism spectrum disorder (ASD) remains largely unexplored. In this study, we aimed to investigate genetic association of STR expansions with ASD using whole genome sequencing (WGS) and identify risk loci associated with ASD phenotypes. Methods: We analyzed WGS data of 634 ASD families and performed genome‐wide evaluation for 12,929 STR loci. We found rare STR expansions that exceeded normal repeat lengths in autism cases compared to unaffected controls. By integrating single cell RNA and ATAC sequencing datasets of human postmortem brains, we prioritized STR loci in genes specifically expressed in cortical development stages. A deep learning method was used to predict functionality of ASD‐associated STR loci. Results: In ASD cases, rare STR expansions predominantly occurred in early cortical layer‐specific genes involved in neurodevelopment, highlighting the cellular specificity of STR‐associated genes in ASD risk. Leveraging deep learning prediction models, we demonstrated that these STR expansions disrupted the regulatory activity of enhancers and promoters, suggesting a potential mechanism through which they contribute to ASD pathogenesis. We found that individuals with ASD‐associated STR expansions exhibited more severe ASD phenotypes and diminished adaptability compared to non‐carriers. Conclusion: Short tandem repeat expansions in cortical layer‐specific genes are associated with ASD and could potentially be a risk genetic factor for ASD. Our study is the first to show evidence of STR expansion associated with ASD in an under‐investigated population. [ABSTRACT FROM AUTHOR]
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- 2024
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12. Altered tumor signature and T‐cell profile after chemotherapy reveal new therapeutic opportunities in high‐grade serous ovarian carcinoma
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Kang, Huiram, primary, Hwang, Sohyun, additional, Kang, Haeyoun, additional, Jo, Areum, additional, Lee, Ji Min, additional, Choi, Jung Kyoon, additional, An, Hee Jung, additional, and Lee, Hae‐Ock, additional
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- 2024
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13. Comprehensive characterisation of intronic mis-splicing mutations in human cancers
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Jung, Hyunchul, Lee, Kang Seon, and Choi, Jung Kyoon
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- 2021
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14. Matrix stiffness epigenetically regulates the oncogenic activation of the Yes-associated protein in gastric cancer
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Jang, Minjeong, An, Jinhyeon, Oh, Seung Won, Lim, Joo Yeon, Kim, Joon, Choi, Jung Kyoon, Cheong, Jae-Ho, and Kim, Pilnam
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- 2021
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15. L1 retrotransposons exploit RNA m6A modification as an evolutionary driving force
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Hwang, Sung-Yeon, Jung, Hyunchul, Mun, Seyoung, Lee, Sungwon, Park, Kiwon, Baek, S. Chan, Moon, Hyungseok C., Kim, Hyewon, Kim, Baekgyu, Choi, Yongkuk, Go, Young-Hyun, Tang, Wanxiangfu, Choi, Jongsu, Choi, Jung Kyoon, Cha, Hyuk-Jin, Park, Hye Yoon, Liang, Ping, Kim, V. Narry, Han, Kyudong, and Ahn, Kwangseog
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- 2021
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16. Lineage-dependent gene expression programs influence the immune landscape of colorectal cancer
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Lee, Hae-Ock, Hong, Yourae, Etlioglu, Hakki Emre, Cho, Yong Beom, Pomella, Valentina, Van den Bosch, Ben, Vanhecke, Jasper, Verbandt, Sara, Hong, Hyekyung, Min, Jae-Woong, Kim, Nayoung, Eum, Hye Hyeon, Qian, Junbin, Boeckx, Bram, Lambrechts, Diether, Tsantoulis, Petros, De Hertogh, Gert, Chung, Woosung, Lee, Taeseob, An, Minae, Shin, Hyun-Tae, Joung, Je-Gun, Jung, Min-Hyeok, Ko, Gunhwan, Wirapati, Pratyaksha, Kim, Seok Hyung, Kim, Hee Cheol, Yun, Seong Hyeon, Tan, Iain Bee Huat, Ranjan, Bobby, Lee, Woo Yong, Kim, Tae-You, Choi, Jung Kyoon, Kim, Young-Joon, Prabhakar, Shyam, Tejpar, Sabine, and Park, Woong-Yang
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- 2020
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17. Pan-cancer analysis reveals multifaceted roles of retrotransposon-fusion RNAs
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Lee, Boram, primary, Park, Junseok, additional, Voshall, Adam, additional, Maury, Eduardo, additional, Kang, Yeeok, additional, Kim, Yoen Jeong, additional, Lee, Jin-Young, additional, Shim, Hye-Ran, additional, Kim, Hyo-Ju, additional, Lee, Jung-Woo, additional, Jung, Min-Hyeok, additional, Kim, Si-Cho, additional, Khanh Chu, Hoang Bao, additional, Kim, Da-Won, additional, Kim, Minjeong, additional, Choi, Eun-Ji, additional, Hwang, Ok Kyung, additional, Lee, Ho Won, additional, Ha, Kyungsoo, additional, Choi, Jung Kyoon, additional, Kim, Yongjoon, additional, Choi, Yoonjoo, additional, Park, Woong-Yang, additional, and Lee, Eunjung Alice, additional
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- 2023
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18. Serine metabolism in the brain regulates starvation-induced sleep suppression in Drosophila melanogaster
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Sonn, Jun Young, Lee, Jongbin, Sung, Min Kyung, Ri, Hwajung, Choi, Jung Kyoon, Lim, Chunghun, and Choe, Joonho
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- 2018
19. Genetic variants beyond amyloid and tau associated with cognitive decline: A cohort study
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Kim, Hang-Rai, Lee, Taeyeop, Choi, Jung Kyoon, and Jeong, Yong
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- 2020
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20. Genome-wide methylation patterns predict clinical benefit of immunotherapy in lung cancer
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Kim, Jeong Yeon, Choi, Jung Kyoon, and Jung, Hyunchul
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- 2020
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21. Functional fine-mapping of noncoding risk variants in amyotrophic lateral sclerosis utilizing convolutional neural network
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Yousefian-Jazi, Ali, Sung, Min Kyung, Lee, Taeyeop, Hong, Yoon-Ho, Choi, Jung Kyoon, and Choi, Jinwook
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- 2020
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22. Computational inference of cancer-specific vulnerabilities in clinical samples
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Jang, Kiwon, Park, Min Ji, Park, Jae Soon, Hwangbo, Haeun, Sung, Min Kyung, Kim, Sinae, Jung, Jaeyun, Lee, Jong Won, Ahn, Sei-Hyun, Chang, Suhwan, and Choi, Jung Kyoon
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- 2020
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23. Predicting clinical benefit of immunotherapy by antigenic or functional mutations affecting tumour immunogenicity
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Kim, Kwoneel, Kim, Hong Sook, Kim, Jeong Yeon, Jung, Hyunchul, Sun, Jong-Mu, Ahn, Jin Seok, Ahn, Myung-Ju, Park, Keunchil, Lee, Se-Hoon, and Choi, Jung Kyoon
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- 2020
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24. DeepNeo: a webserver for predicting immunogenic neoantigens
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Kim, Jeong Yeon, primary, Bang, Hyoeun, additional, Noh, Seung-Jae, additional, and Choi, Jung Kyoon, additional
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- 2023
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25. Abstract LB168: Efficacy analysis of the DeepNeo neoantigen prediction tool for antitumor vaccine development
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Lee, Eun Ji, primary, Park, Min Ji, additional, Kim, Soo Jin, additional, Noh, Seung-Jae, additional, Shin, Inkyung, additional, Kim, Jeong Yeon, additional, Shin, Incheol, additional, Choi, Jung Kyoon, additional, Cho, Dae-Yeon, additional, and Chang, Suhwan, additional
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- 2023
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26. Abstract 5475: Improved prediction of immunotherapy responses by constitutive neoantigen load and LINE-1 methylation
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Bang, Hyoeun, primary, Kim, Jeong Yeon, additional, Joe, Cheolyong, additional, Kim, Kyeonghui, additional, Bang, Younghak, additional, Kim, Hyemin, additional, Cha, Honghi, additional, Oh, Eunjoo, additional, Lee, Naeun, additional, Shin, Inkyung, additional, Noh, Seung-Jae, additional, Cho, Dae-Yeon, additional, Lee, Se-Hoon, additional, and Choi, Jung Kyoon, additional
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- 2023
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27. Abstract 1122: Pan-cancer analysis reveals roles of retrotransposon-fusion RNAs
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Lee, E. Alice, primary, Lee, Boram, additional, Choi, Yoonjoo, additional, Park, Junseok, additional, Voshall, Adam, additional, Maury, Eduardo, additional, Kang, Yeeok, additional, Kim, Yeon Jeong, additional, Lee, Jin-Young, additional, Shim, Hye-Ran, additional, Kim, Si-Cho, additional, Chu, Hoang Bao Khanh, additional, Kim, Da-Won, additional, Kim, Minjeong, additional, Choi, Eun-Ji, additional, Ha, Kyungsoo, additional, Choi, Jung Kyoon, additional, Kim, Yongjoon, additional, and Park, Woong-Yang, additional
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- 2023
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28. Supplementary Data from Aberrant Transcript Usage Is Associated with Homologous Recombination Deficiency and Predicts Therapeutic Response
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Kang, Hyeon Gu, primary, Hwangbo, Haeun, primary, Kim, Myung Ji, primary, Kim, Sinae, primary, Lee, Eun Ji, primary, Park, Min Ji, primary, Kim, Jae-Weon, primary, Kim, Byoung-Gie, primary, Cho, Eun-Hae, primary, Chang, Suhwan, primary, Lee, Jung-Yun, primary, and Choi, Jung Kyoon, primary
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- 2023
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29. Supplementary Figure from Aberrant Transcript Usage Is Associated with Homologous Recombination Deficiency and Predicts Therapeutic Response
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Kang, Hyeon Gu, primary, Hwangbo, Haeun, primary, Kim, Myung Ji, primary, Kim, Sinae, primary, Lee, Eun Ji, primary, Park, Min Ji, primary, Kim, Jae-Weon, primary, Kim, Byoung-Gie, primary, Cho, Eun-Hae, primary, Chang, Suhwan, primary, Lee, Jung-Yun, primary, and Choi, Jung Kyoon, primary
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- 2023
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30. Data from Aberrant Transcript Usage Is Associated with Homologous Recombination Deficiency and Predicts Therapeutic Response
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Kang, Hyeon Gu, primary, Hwangbo, Haeun, primary, Kim, Myung Ji, primary, Kim, Sinae, primary, Lee, Eun Ji, primary, Park, Min Ji, primary, Kim, Jae-Weon, primary, Kim, Byoung-Gie, primary, Cho, Eun-Hae, primary, Chang, Suhwan, primary, Lee, Jung-Yun, primary, and Choi, Jung Kyoon, primary
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- 2023
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31. DNA methylation loss promotes immune evasion of tumours with high mutation and copy number load
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Jung, Hyunchul, Kim, Hong Sook, Kim, Jeong Yeon, Sun, Jong-Mu, Ahn, Jin Seok, Ahn, Myung-Ju, Park, Keunchil, Esteller, Manel, Lee, Se-Hoon, and Choi, Jung Kyoon
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- 2019
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32. A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns
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Jiao, Wei, Atwal, Gurnit, Polak, Paz, Karlic, Rosa, Cuppen, Edwin, Al-Shahrour, Fatima, Bailey, Peter J, Biankin, Andrew V, Boutros, Paul C, Campbell, Peter J, Chang, David K, Cooke, Susanna L, Deshpande, Vikram, Faltas, Bishoy M, Faquin, William C, Garraway, Levi, Getz, Gad, Grimmond, Sean M, Haider, Syed, Hoadley, Katherine A, Kaiser, Vera B, Kato, Mamoru, Kübler, Kirsten, Lazar, Alexander J, Li, Constance H, Louis, David N, Margolin, Adam, Martin, Sancha, Nahal-Bose, Hardeep K, Nielsen, G Petur, Nik-Zainal, Serena, Omberg, Larsson, P’ng, Christine, Perry, Marc D, Rheinbay, Esther, Rubin, Mark A, Semple, Colin A, Sgroi, Dennis C, Shibata, Tatsuhiro, Siebert, Reiner, Smith, Jaclyn, Stein, Lincoln D, Stobbe, Miranda D, Sun, Ren X, Thai, Kevin, Wright, Derek W, Wu, Chin-Lee, Yuan, Ke, Zhang, Junjun, Danyi, Alexandra, de Ridder, Jeroen, van Herpen, Carla, Lolkema, Martijn P, Steeghs, Neeltje, Morris, Quaid D, Aaltonen, Lauri A, Abascal, Federico, Abeshouse, Adam, Aburatani, Hiroyuki, Adams, David J, Agrawal, Nishant, Ahn, Keun Soo, Ahn, Sung-Min, Aikata, Hiroshi, Akbani, Rehan, Akdemir, Kadir C, Al-Ahmadie, Hikmat, Al-Sedairy, Sultan T, Alawi, Malik, Albert, Monique, Aldape, Kenneth, Alexandrov, Ludmil B, Ally, Adrian, Alsop, Kathryn, Alvarez, Eva G, Amary, Fernanda, Amin, Samirkumar B, Aminou, Brice, Ammerpohl, Ole, Anderson, Matthew J, Ang, Yeng, Antonello, Davide, Anur, Pavana, Aparicio, Samuel, Appelbaum, Elizabeth L, Arai, Yasuhito, Aretz, Axel, Arihiro, Koji, Ariizumi, Shun-ichi, Armenia, Joshua, Arnould, Laurent, Asa, Sylvia, Assenov, Yassen, Aukema, Sietse, Auman, J Todd, Aure, Miriam RR, Awadalla, Philip, Aymerich, Marta, Bader, Gary D, Baez-Ortega, Adrian, Bailey, Matthew H, Balasundaram, Miruna, Balu, Saianand, Bandopadhayay, Pratiti, Banks, Rosamonde E, Barbi, Stefano, Barbour, Andrew P, Barenboim, Jonathan, Barnholtz-Sloan, Jill, Barr, Hugh, Barrera, Elisabet, Bartlett, John, Bartolome, Javier, Bassi, Claudio, Bathe, Oliver F, Baumhoer, Daniel, Bavi, Prashant, Baylin, Stephen B, Bazant, Wojciech, Beardsmore, Duncan, Beck, Timothy A, Behjati, Sam, Behren, Andreas, Niu, Beifang, Bell, Cindy, Beltran, Sergi, Benz, Christopher, Berchuck, Andrew, Bergmann, Anke K, Bergstrom, Erik N, Berman, Benjamin P, Berney, Daniel M, Bernhart, Stephan H, Beroukhim, Rameen, Berrios, Mario, Bersani, Samantha, Bertl, Johanna, Betancourt, Miguel, Bhandari, Vinayak, Bhosle, Shriram G, Bieg, Matthias, Bigner, Darell, Binder, Hans, Birney, Ewan, Birrer, Michael, Biswas, Nidhan K, Bjerkehagen, Bodil, Bodenheimer, Tom, Boice, Lori, Bonizzato, Giada, De Bono, Johann S, Boot, Arnoud, Bootwalla, Moiz S, Borg, Ake, Borkhardt, Arndt, Boroevich, Keith A, Borozan, Ivan, Borst, Christoph, Bosenberg, Marcus, Bosio, Mattia, Boultwood, Jacqueline, Bourque, Guillaume, Bova, G Steven, Bowen, David T, Bowlby, Reanne, Bowtell, David DL, Boyault, Sandrine, Boyce, Rich, Boyd, Jeffrey, Brazma, Alvis, Brennan, Paul, Brewer, Daniel S, Brinkman, Arie B, Bristow, Robert G, Broaddus, Russell R, Brock, Jane E, Brock, Malcolm, Broeks, Annegien, Brooks, Angela N, Brooks, Denise, Brors, Benedikt, Brunak, Søren, Bruxner, Timothy JC, Bruzos, Alicia L, Buchanan, Alex, Buchhalter, Ivo, Buchholz, Christiane, Bullman, Susan, Burke, Hazel, Burkhardt, Birgit, Burns, Kathleen H, Busanovich, John, Bustamante, Carlos D, Butler, Adam P, Butte, Atul J, Byrne, Niall J, Børresen-Dale, Anne-Lise, Caesar-Johnson, Samantha J, Cafferkey, Andy, Cahill, Declan, Calabrese, Claudia, Caldas, Carlos, Calvo, Fabien, Camacho, Niedzica, Campo, Elias, Cantù, Cinzia, Cao, Shaolong, Carey, Thomas E, Carlevaro-Fita, Joana, Carlsen, Rebecca, Cataldo, Ivana, Cazzola, Mario, Cebon, Jonathan, Cerfolio, Robert, Chadwick, Dianne E, Chakravarty, Dimple, Chalmers, Don, Chan, Calvin Wing Yiu, Chan, Kin, Chan-Seng-Yue, Michelle, Chandan, Vishal S, Chanock, Stephen J, Chantrill, Lorraine A, Chateigner, Aurélien, Chatterjee, Nilanjan, Chayama, Kazuaki, Chen, Hsiao-Wei, Chen, Jieming, Chen, Ken, Chen, Yiwen, Chen, Zhaohong, Cherniack, Andrew D, Chien, Jeremy, Chiew, Yoke-Eng, Chin, Suet-Feung, Cho, Juok, Cho, Sunghoon, Choi, Jung Kyoon, Choi, Wan, Chomienne, Christine, Chong, Zechen, Choo, Su Pin, Chou, Angela, Christ, Angelika N, Christie, Elizabeth L, Chuah, Eric, Cibulskis, Carrie, Cibulskis, Kristian, Cingarlini, Sara, Clapham, Peter, Claviez, Alexander, Cleary, Sean, Cloonan, Nicole, Cmero, Marek, Collins, Colin C, Connor, Ashton A, Cooper, Colin S, Cope, Leslie, Corbo, Vincenzo, Cordes, Matthew G, Cordner, Stephen M, Cortés-Ciriano, Isidro, Covington, Kyle, Cowin, Prue A, Craft, Brian, Craft, David, Creighton, Chad J, Cun, Yupeng, Curley, Erin, Cutcutache, Ioana, Czajka, Karolina, Czerniak, Bogdan, Dagg, Rebecca A, Danilova, Ludmila, Davi, Maria Vittoria, Davidson, Natalie R, Davies, Helen, Davis, Ian J, Davis-Dusenbery, Brandi N, Dawson, Kevin J, De La Vega, Francisco M, De Paoli-Iseppi, Ricardo, Defreitas, Timothy, Dei Tos, Angelo P, Delaneau, Olivier, Demchok, John A, Demeulemeester, Jonas, Demidov, German M, Demircioğlu, Deniz, Dennis, Nening M, Denroche, Robert E, Dentro, Stefan C, Desai, Nikita, Deshwar, Amit G, Desmedt, Christine, Deu-Pons, Jordi, Dhalla, Noreen, Dhani, Neesha C, Dhingra, Priyanka, Dhir, Rajiv, DiBiase, Anthony, Diamanti, Klev, Ding, Li, Ding, Shuai, Dinh, Huy Q, Dirix, Luc, Doddapaneni, HarshaVardhan, Donmez, Nilgun, Dow, Michelle T, Drapkin, Ronny, Drechsel, Oliver, Drews, Ruben M, Serge, Serge, Dudderidge, Tim, Dueso-Barroso, Ana, Dunford, Andrew J, Dunn, Michael, Dursi, Lewis Jonathan, Duthie, Fraser R, Dutton-Regester, Ken, Eagles, Jenna, Easton, Douglas F, Edmonds, Stuart, Edwards, Paul A, Edwards, Sandra E, Eeles, Rosalind A, Ehinger, Anna, Eils, Juergen, Eils, Roland, El-Naggar, Adel, Eldridge, Matthew, Ellrott, Kyle, Erkek, Serap, Escaramis, Georgia, Espiritu, Shadrielle MG, Estivill, Xavier, Etemadmoghadam, Dariush, Eyfjord, Jorunn E, Fan, Daiming, Fan, Yu, Farcas, Claudiu, Fassan, Matteo, Fatima, Aquila, Favero, Francesco, Fayzullaev, Nodirjon, Felau, Ina, Fereday, Sian, Ferguson, Martin L, Ferretti, Vincent, Feuerbach, Lars, Field, Matthew A, Fink, J Lynn, Finocchiaro, Gaetano, Fisher, Cyril, Fittall, Matthew W, Fitzgerald, Anna, Fitzgerald, Rebecca C, Flanagan, Adrienne M, Fleshner, Neil E, Flicek, Paul, Foekens, John A, Fong, Kwun M, Fonseca, Nuno A, Foster, Christopher S, Fox, Natalie S, Fraser, Michael, Frazer, Scott, Frenkel-Morgenstern, Milana, Friedman, William, Frigola, Joan, Fronick, Catrina C, Fujimoto, Akihiro, Fujita, Masashi, Fukayama, Masashi, Fulton, Lucinda A, Fulton, Robert S, Furuta, Mayuko, Futreal, P Andrew, Füllgrabe, Anja, Gabriel, Stacey B, Gallinger, Steven, Gambacorti-Passerini, Carlo, Gao, Jianjiong, Gao, Shengjie, Garred, Øystein, Garrison, Erik, Garsed, Dale W, Gehlenborg, Nils, Gelpi, Josep LL, George, Joshy, Gerhard, Daniela S, Gerhauser, Clarissa, Gershenwald, Jeffrey E, Gerstein, Mark, Gerstung, Moritz, Ghori, Mohammed, Ghossein, Ronald, Giama, Nasra H, Gibbs, Richard A, Gibson, Bob, Gill, Anthony J, Gill, Pelvender, Giri, Dilip D, Glodzik, Dominik, Gnanapragasam, Vincent J, Goebler, Maria Elisabeth, Goldman, Mary J, Gomez, Carmen, Gonzalez, Santiago, Gonzalez-Perez, Abel, Gordenin, Dmitry A, Gossage, James, Gotoh, Kunihito, Govindan, Ramaswamy, Grabau, Dorthe, Graham, Janet S, Grant, Robert C, Green, Anthony R, Green, Eric, Greger, Liliana, Grehan, Nicola, Grimaldi, Sonia, Grossman, Robert L, Grundhoff, Adam, Gundem, Gunes, Guo, Qianyun, Gupta, Manaswi, Gupta, Shailja, Gut, Ivo G, Gut, Marta, Göke, Jonathan, Ha, Gavin, Haake, Andrea, Haan, David, Haas, Siegfried, Haase, Kerstin, Haber, James E, Habermann, Nina, Hach, Faraz, Hama, Natsuko, Hamdy, Freddie C, Hamilton, Anne, Hamilton, Mark P, Han, Leng, Hanna, George B, Hansmann, Martin, Haradhvala, Nicholas J, Harismendy, Olivier, Harliwong, Ivon, Harmanci, Arif O, Harrington, Eoghan, Hasegawa, Takanori, Haussler, David, Hawkins, Steve, Hayami, Shinya, Hayashi, Shuto, Hayes, D Neil, Hayes, 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Deurzen, Carolien HM, van de Vijver, Marc J, Veer, L van’t, and von Mering, Christian
- Subjects
Human Biology & Physiology ,Ecology,Evolution & Ethology ,Tumour Biology ,Genetics & Genomics ,Structural Biology & Biophysics ,Computational & Systems Biology - Abstract
In cancer, the primary tumour’s organ of origin and histopathology are the strongest determinants of its clinical behaviour, but in 3% of cases a patient presents with a metastatic tumour and no obvious primary. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, we train a deep learning classifier to predict cancer type based on patterns of somatic passenger mutations detected in whole genome sequencing (WGS) of 2606 tumours representing 24 common cancer types produced by the PCAWG Consortium. Our classifier achieves an accuracy of 91% on held-out tumor samples and 88% and 83% respectively on independent primary and metastatic samples, roughly double the accuracy of trained pathologists when presented with a metastatic tumour without knowledge of the primary. Surprisingly, adding information on driver mutations reduced accuracy. Our results have clinical applicability, underscore how patterns of somatic passenger mutations encode the state of the cell of origin, and can inform future strategies to detect the source of circulating tumour DNA.
- Published
- 2023
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33. Combined burden and functional impact tests for cancer driver discovery using DriverPower
- Author
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Shuai, Shimin, Abascal, Federico, Amin, Samirkumar B, Bader, Gary D, Bandopadhayay, Pratiti, Barenboim, Jonathan, Beroukhim, Rameen, Bertl, Johanna, Boroevich, Keith A, Brunak, Søren, Campbell, Peter J, Carlevaro-Fita, Joana, Chakravarty, Dimple, Chan, Calvin Wing Yiu, Chen, Ken, Choi, Jung Kyoon, Deu-Pons, Jordi, Dhingra, Priyanka, Diamanti, Klev, Feuerbach, Lars, Fink, J Lynn, Fonseca, Nuno A, Frigola, Joan, Gambacorti-Passerini, Carlo, Garsed, Dale W, Gerstein, Mark, Getz, Gad, Guo, Qianyun, Gut, Ivo G, Haan, David, Hamilton, Mark P, Haradhvala, Nicholas J, Harmanci, Arif O, Helmy, Mohamed, Herrmann, Carl, Hess, Julian M, Hobolth, Asger, Hodzic, Ermin, Hong, Chen, Hornshøj, Henrik, Isaev, Keren, Izarzugaza, Jose MG, Johnson, Rory, Johnson, Todd A, Juul, Malene, Juul, Randi Istrup, Kahles, Andre, Kahraman, Abdullah, Kellis, Manolis, Khurana, Ekta, Kim, Jaegil, Kim, Jong K, Kim, Youngwook, Komorowski, Jan, Korbel, Jan O, Kumar, Sushant, Lanzós, Andrés, Larsson, Erik, Lawrence, Michael 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Human Biology & Physiology ,Ecology,Evolution & Ethology ,Tumour Biology ,Genetics & Genomics ,Structural Biology & Biophysics ,Computational & Systems Biology - Abstract
The discovery of driver mutations is one of the key motivations for cancer genome sequencing. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumour types, we describe DriverPower, a software package that uses mutational burden and functional impact evidence to identify driver mutations in coding and non-coding sites within cancer whole genomes. Using a total of 1373 genomic features derived from public sources, DriverPower’s background mutation model explains up to 93% of the regional variance in the mutation rate across multiple tumour types. By incorporating functional impact scores, we are able to further increase the accuracy of driver discovery. Testing across a collection of 2583 cancer genomes from the PCAWG project, DriverPower identifies 217 coding and 95 non-coding driver candidates. Comparing to six published methods used by the PCAWG Drivers and Functional Interpretation Working Group, DriverPower has the highest F1 score for both coding and non-coding driver discovery. This demonstrates that DriverPower is an effective framework for computational driver discovery.
- Published
- 2023
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34. Integrative pathway enrichment analysis of multivariate omics data
- Author
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Paczkowska, Marta, Barenboim, Jonathan, Sintupisut, Nardnisa, Fox, Natalie S, Zhu, Helen, Abd-Rabbo, Diala, Mee, Miles W, Boutros, Paul C, Abascal, Federico, Amin, Samirkumar B, Bader, Gary D, Beroukhim, Rameen, Bertl, Johanna, Boroevich, Keith A, Brunak, Søren, Campbell, Peter J, Carlevaro-Fita, Joana, Chakravarty, Dimple, Chan, Calvin Wing Yiu, Chen, Ken, Choi, Jung Kyoon, Deu-Pons, Jordi, Dhingra, Priyanka, Diamanti, Klev, Feuerbach, Lars, Fink, J Lynn, Fonseca, Nuno A, Frigola, Joan, Gambacorti-Passerini, Carlo, Garsed, Dale W, Gerstein, Mark, Getz, Gad, Gonzalez-Perez, Abel, Guo, Qianyun, Gut, Ivo G, Haan, David, Hamilton, Mark P, Haradhvala, Nicholas J, Harmanci, Arif O, Helmy, Mohamed, Herrmann, Carl, Hess, Julian M, Hobolth, Asger, Hodzic, Ermin, Hong, Chen, Hornshøj, Henrik, Isaev, Keren, Izarzugaza, Jose MG, Johnson, Rory, Johnson, Todd A, Juul, Malene, Juul, Randi Istrup, Kahles, Andre, Kahraman, Abdullah, Kellis, Manolis, Khurana, Ekta, Kim, Jaegil, Kim, Jong K, Kim, 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Vijver, Marc J, and Veer, L van’t
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Human Biology & Physiology ,Ecology,Evolution & Ethology ,Tumour Biology ,Genetics & Genomics ,Structural Biology & Biophysics ,Computational & Systems Biology - Abstract
Multi-omics datasets represent distinct aspects of the central dogma of molecular biology. Such high-dimensional molecular profiles pose challenges to data interpretation and hypothesis generation. ActivePathways is an integrative method that discovers significantly enriched pathways across multiple datasets using statistical data fusion, rationalizes contributing evidence and highlights associated genes. As part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumor types, we integrated genes with coding and non-coding mutations and revealed frequently mutated pathways and additional cancer genes with infrequent mutations. We also analyzed prognostic molecular pathways by integrating genomic and transcriptomic features of 1780 breast cancers and highlighted associations with immune response and anti-apoptotic signaling. Integration of ChIP-seq and RNA-seq data for master regulators of the Hippo pathway across normal human tissues identified processes of tissue regeneration and stem cell regulation. ActivePathways is a versatile method that improves systems-level understanding of cellular organization in health and disease through integration of multiple molecular datasets and pathway annotations.
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- 2023
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35. Pathway and network analysis of more than 2500 whole cancer genomes
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Human Biology & Physiology ,Ecology,Evolution & Ethology ,Tumour Biology ,Genetics & Genomics ,Structural Biology & Biophysics ,Computational & Systems Biology - Abstract
The catalog of cancer driver mutations in protein-coding genes has greatly expanded in the past decade. However, non-coding cancer driver mutations are less well-characterized and only a handful of recurrent non-coding mutations, most notably TERT promoter mutations, have been reported. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancer across 38 tumor types, we perform multi-faceted pathway and network analyses of non-coding mutations across 2583 whole cancer genomes from 27 tumor types compiled by the ICGC/TCGA PCAWG project that was motivated by the success of pathway and network analyses in prioritizing rare mutations in protein-coding genes. While few non-coding genomic elements are recurrently mutated in this cohort, we identify 93 genes harboring non-coding mutations that cluster into several modules of interacting proteins. Among these are promoter mutations associated with reduced mRNA expression in TP53, TLE4, and TCF4. We find that biological processes had variable proportions of coding and non-coding mutations, with chromatin remodeling and proliferation pathways altered primarily by coding mutations, while developmental pathways, including Wnt and Notch, altered by both coding and non-coding mutations. RNA splicing is primarily altered by non-coding mutations in this cohort, and samples containing non-coding mutations in well-known RNA splicing factors exhibit similar gene expression signatures as samples with coding mutations in these genes. These analyses contribute a new repertoire of possible cancer genes and mechanisms that are altered by non-coding mutations and offer insights into additional cancer vulnerabilities that can be investigated for potential therapeutic treatments.
- Published
- 2023
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36. Divergent mutational processes distinguish hypoxic and normoxic tumours
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Bhandari, Vinayak, Li, Constance H, Bristow, Robert G, Boutros, Paul C, Aaltonen, Lauri A, Abascal, Federico, Abeshouse, Adam, Aburatani, Hiroyuki, Adams, David J, Agrawal, Nishant, Ahn, Keun Soo, Ahn, Sung-Min, Aikata, Hiroshi, Akbani, Rehan, Akdemir, Kadir C, Al-Ahmadie, Hikmat, Al-Sedairy, Sultan T, Al-Shahrour, Fatima, Alawi, Malik, Albert, Monique, Aldape, Kenneth, Alexandrov, Ludmil B, Ally, Adrian, Alsop, Kathryn, Alvarez, Eva G, Amary, Fernanda, Amin, Samirkumar B, Aminou, Brice, Ammerpohl, Ole, Anderson, Matthew J, Ang, Yeng, Antonello, Davide, Anur, Pavana, Aparicio, Samuel, Appelbaum, Elizabeth L, Arai, Yasuhito, Aretz, Axel, Arihiro, Koji, Ariizumi, Shun-ichi, Armenia, Joshua, Arnould, Laurent, Asa, Sylvia, Assenov, Yassen, Atwal, Gurnit, Aukema, Sietse, Auman, J Todd, Aure, Miriam RR, Awadalla, Philip, Aymerich, Marta, Bader, Gary D, Baez-Ortega, Adrian, Bailey, Matthew H, Bailey, Peter J, Balasundaram, Miruna, Balu, Saianand, Bandopadhayay, Pratiti, Banks, Rosamonde E, 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Human Biology & Physiology ,Ecology,Evolution & Ethology ,Tumour Biology ,Genetics & Genomics ,Structural Biology & Biophysics ,Computational & Systems Biology - Abstract
Many primary tumours have low levels of molecular oxygen (hypoxia), and hypoxic tumours respond poorly to therapy. Pan-cancer molecular hallmarks of tumour hypoxia remain poorly understood, with limited comprehension of its associations with specific mutational processes, non-coding driver genes and evolutionary features. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumour types, we quantify hypoxia in 1188 tumours spanning 27 cancer types. Elevated hypoxia associates with increased mutational load across cancer types, irrespective of underlying mutational class. The proportion of mutations attributed to several mutational signatures of unknown aetiology directly associates with the level of hypoxia, suggesting underlying mutational processes for these signatures. At the gene level, driver mutations in TP53, MYC and PTEN are enriched in hypoxic tumours, and mutations in PTEN interact with hypoxia to direct tumour evolutionary trajectories. Overall, hypoxia plays a critical role in shaping the genomic and evolutionary landscapes of cancer.
- Published
- 2023
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37. Genomic footprints of activated telomere maintenance mechanisms in cancer
- Author
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Staaf, Johan, Stadler, Peter F, Staib, Peter, Stark, Stefan G, Stebbings, Lucy, Stefánsson, Ólafur Andri, Stegle, Oliver, Stein, Lincoln D, Stenhouse, Alasdair, Stilgenbauer, Stephan, Stobbe, Miranda D, Stratton, Michael R, Stretch, Jonathan R, Struck, Adam J, Stuart, Joshua M, Stunnenberg, Henk G, Su, Hong, Su, Xiaoping, Sun, Ren X, Sungalee, Stephanie, Susak, Hana, Suzuki, Akihiro, Sweep, Fred, Szczepanowski, Monika, Sültmann, Holger, Yugawa, Takashi, Tam, Angela, Tamborero, David, Tan, Benita Kiat Tee, Tan, Donghui, Tan, Patrick, Tanaka, Hiroko, Taniguchi, Hirokazu, Tanskanen, Tomas J, Tarabichi, Maxime, Tarnuzzer, Roy, Tarpey, Patrick, Taschuk, Morgan L, Tatsuno, Kenji, Tavaré, Simon, Taylor, Darrin F, Taylor-Weiner, Amaro, Teague, Jon W, Teh, Bin Tean, Tembe, Varsha, Temes, Javier, Thai, Kevin, Thayer, Sarah P, Thiessen, Nina, Thomas, Gilles, Thomas, Sarah, Thompson, Alan, Thompson, Alastair M, Thompson, John FF, Thompson, R Houston, Thorne, Heather, Thorne, Leigh B, Thorogood, Adrian, Tiao, Grace, Tijanic, Nebojsa, Timms, Lee E, Tirabosco, Roberto, Tojo, Marta, Tommasi, Stefania, Toon, Christopher W, Toprak, Umut H, Tortora, Giampaolo, Tost, Jörg, Totoki, Yasushi, Townend, David, Traficante, Nadia, Treilleux, Isabelle, Trotta, Jean-Rémi, Trümper, Lorenz HP, Tsao, Ming, Tsunoda, Tatsuhiko, Tucker, Olga, Turkington, Richard, Turner, Daniel J, Tutt, Andrew, Ueno, Masaki, Ueno, Naoto T, Umbricht, Christopher, Umer, Husen M, Underwood, Timothy J, Urban, Lara, Urushidate, Tomoko, Ushiku, Tetsuo, Uusküla-Reimand, Liis, Valencia, Alfonso, Van Den Berg, David J, Van Laere, Steven, Van Loo, Peter, Van Meir, Erwin G, Van den Eynden, Gert G, Van der Kwast, Theodorus, Vasudev, Naveen, Vazquez, Miguel, Vedururu, Ravikiran, Veluvolu, Umadevi, Vembu, Shankar, Verbeke, Lieven PC, Vermeulen, Peter, Verrill, Clare, Viari, Alain, Vicente, David, Vicentini, Caterina, VijayRaghavan, K, Viksna, Juris, Vilain, Ricardo E, Vincent-Salomon, Anne, Visakorpi, Tapio, Voet, Douglas, Vyas, Paresh, Vázquez-García, Ignacio, Waddell, Nick M, Wadelius, Claes, Wadi, Lina, Wagener, Rabea, Wang, Jian, Wang, Jiayin, Wang, Linghua, Wang, Qi, Wang, Wenyi, Wang, Yumeng, Wang, Zhining, Waring, Paul M, Warnatz, Hans-Jörg, Warrell, Jonathan, Warren, Anne Y, Waszak, Sebastian M, Wedge, David C, Weichenhan, Dieter, Weinberger, Paul, Weinstein, John N, Weisenberger, Daniel J, Welch, Ian, Wendl, Michael C, Werner, Johannes, Whalley, Justin P, Wheeler, David A, Whitaker, Hayley C, Wigle, Dennis, Wilkerson, Matthew D, Williams, Ashley, Wilmott, James S, Wilson, Gavin W, Wilson, Julie M, Wilson, Richard K, Winterhoff, Boris, Wintersinger, Jeffrey A, Wiznerowicz, Maciej, Wolf, Stephan, Wong, Bernice H, Wong, Tina, Wong, Winghing, Woo, Youngchoon, Wood, Scott, Wouters, Bradly G, Wright, Adam J, Wright, Derek W, Wright, Mark H, Wu, Chin-Lee, Wu, Dai-Ying, Wu, Guanming, Wu, Jianmin, Wu, Kui, Wu, Yang, Wu, Zhenggang, Xi, Liu, Xia, Tian, Xiang, Qian, Xiao, Xiao, Xing, Rui, Xiong, Heng, Xu, Qinying, Xu, Yanxun, Xue, Hong, Yachida, Shinichi, Yakneen, Sergei, Yamaguchi, Rui, Yamaguchi, Takafumi N, Yamamoto, Masakazu, Yamamoto, Shogo, Yamaue, Hiroki, Yang, Fan, Yang, Huanming, Yang, Jean Y, Yang, Liming, Yang, Shanlin, Yang, Tsun-Po, Yang, Yang, Yaspo, Marie-Laure, Yates, Lucy, Yau, Christina, Ye, Chen, Ye, Kai, Yellapantula, Venkata D, Yoon, Christopher J, Yousif, Fouad, Yu, Jun, Yu, Kaixian, Yu, Willie, Yu, Yingyan, Yuan, Ke, Yuan, Yuan, Yuen, Denis, Yung, Christina K, Zaikova, Olga, Zapatka, Marc, Zenklusen, Jean C, Zenz, Thorsten, Zeps, Nikolajs, Zhang, Fan, Zhang, Hailei, Zhang, Hongwei, Zhang, Hongxin, Zhang, Jiashan, Zhang, Jing, Zhang, Junjun, Zhang, Xiuqing, Zhang, Xuanping, Zhang, Yan, Zhang, Zemin, Zhao, Zhongming, Zheng, Liangtao, Zheng, Xiuqing, Zhou, Wanding, Zhou, Yong, Zhu, Bin, Zhu, Hongtu, Zhu, Jingchun, Zhu, Shida, Zou, Lihua, Zou, Xueqing, deFazio, Anna, van As, Nicholas, van Deurzen, Carolien HM, van de Vijver, Marc J, Veer, L van’t, and von Mering, Christian
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Human Biology & Physiology ,Ecology,Evolution & Ethology ,Tumour Biology ,Genetics & Genomics ,Structural Biology & Biophysics ,Computational & Systems Biology - Abstract
Cancers require telomere maintenance mechanisms for unlimited replicative potential. They achieve this through TERT activation or alternative telomere lengthening associated with ATRX or DAXX loss. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, we dissect whole-genome sequencing data of over 2500 matched tumor-control samples from 36 different tumor types aggregated within the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium to characterize the genomic footprints of these mechanisms. While the telomere content of tumors with ATRX or DAXX mutations (ATRX/DAXXtrunc) is increased, tumors with TERT modifications show a moderate decrease of telomere content. One quarter of all tumor samples contain somatic integrations of telomeric sequences into non-telomeric DNA. This fraction is increased to 80% prevalence in ATRX/DAXXtrunc tumors, which carry an aberrant telomere variant repeat (TVR) distribution as another genomic marker. The latter feature includes enrichment or depletion of the previously undescribed singleton TVRs TTCGGG and TTTGGG, respectively. Our systematic analysis provides new insight into the recurrent genomic alterations associated with telomere maintenance mechanisms in cancer.
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- 2023
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38. Integrative single-cell mapping of combinatorial target antigens for logical CAR switches
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Joonha Kwon, Junho Kang, Areum Jo, Kayoung Seo, Dohyeon An, Baykan, Mert Yakup, Lee, Jun Hyeong, Nayoung Kim, Eum, Hye Hyeon, Sohyun Hwang, Lee, Ji Min, An, Hee Jung, Hae-Ock Lee, Jong-Eun Park, and Choi, Jung Kyoon
- Abstract
This is the collection of datasets described in the paper "Integrative single-cell mapping of combinatorial target antigens for logical CAR switches" This repository contains thescRNA-seq matrix in h5ad format The description for each item are as follows: tumor-normal_meta-atlas_car-switch_geosketch_bbknn.h5ad.xz: Subsampled and batch-corrected matrix normal_meta-atlas_raw.h5ad.xz: Raw normal meta-atlas scRNA-seq dataset of401,717 cells tumor_meta-atlas_raw.h5ad.xz: Raw tumor meta-atlas scRNA-seq dataset of1,007,414 cells Ovarian cancer single-cell transcriptome data generated in this work is available on the Gene Expression Omnibus (GEO) with the accession number GSE192898. Source codes for CAR antigen identification, named PCASA (Prioritization of combinatorial Cancer-Associated Surface Antigens), are available on GitHub at https://github.com/kaistomics/PCASA.
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- 2022
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39. Systematic dissection of tumor ecosystems at single-cell resolution across a thousand tumors of 30 cancer types
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Kang, Junho, Lee, Jun Hyeong, Park, Jong-Eun, and Choi, Jung Kyoon
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pan-cancer analysis ,tumor ecosystem ,tertiary lymphoid structure ,immunotherapy ,single-cell RNA sequencing - Abstract
This is the collection of codes and datasets described in the paper "Systematic dissection of tumor ecosystems at single-cell resolution across a thousand tumors of 30 cancer types" This repository contains: The annotated NMF and scRNA-seq matrix in h5ad format Analysis codes used for analysis The weighted average of NMF cell states The description for each item are as follows: Log-normalized scRNA-seq matrix files for each cell type: filenameextensions with '*.xz' NMF module matrix files for each cell type:filenameextensions with '*.gzip' Analysis codes: filename extensions with'*.R', '*.ipynb', '*.py', '*.sh', and '*.tar' The weighted average of each NMF cell states: 'NMF_weighted_average.csv'
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- 2022
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40. Whole-Genome and Transcriptome Sequencing Identified NOTCH2 and HES1 as Potential Markers of Response to Imatinib in Desmoid Tumor (Aggressive Fibromatosis): A Phase II Trial Study
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Kwon, Joonha, primary, Lee, Jun Hyeong, additional, Lee, Young Han, additional, Lee, Jeeyun, additional, Ahn, Jin-Hee, additional, Kim, Se Hyun, additional, Kim, Seung Hyun, additional, Kim, Tae Il, additional, Yun, Kum-Hee, additional, Park, Young Suk, additional, Kim, Jeong Eun, additional, Lee, Kyu Sang, additional, Choi, Jung Kyoon, additional, and Kim, Hyo Song, additional
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- 2022
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41. F62. SHARED RARE GENETIC VARIANTS IN MULTIPLEX AUTISM FAMILIES SUGGEST A SOCIAL MEMORY GENE UNDER SELECTION
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Lee, Taeyeop, Lee, Kang Seon, Kim, Mujun, Ignatova, Elizaveta, Ban, Hyo-Jeong, Sung, Min Kyung, Kim, Younghoon, Kim, Youn-Jae, Han, Jin-Hee, and Choi, Jung Kyoon
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- 2024
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42. HBx induces hypomethylation of distal intragenic CpG islands required for active expression of developmental regulators
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Lee, Sun-Min, Lee, Young-gun, Bae, Jae-Bum, Choi, Jung Kyoon, Tayama, Chiharu, Hata, Kenichiro, Yun, Yungdae, Seong, Je-Kyung, and Kim, Young-Joon
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- 2014
43. Chromatin structure–based prediction of recurrent noncoding mutations in cancer
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Kim, Kwoneel, Jang, Kiwon, Yang, Woojin, Choi, Eun-Young, Park, Seong-Min, Bae, Mingyun, Kim, Youn-Jae, and Choi, Jung Kyoon
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- 2016
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44. Accelerated Evolution of the Regulatory Sequences of Brain Development in the Human Genome
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Lee, Kang Seon, Bang, Hyoeun, Choi, Jung Kyoon, and Kim, Kwoneel
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brain evolution ,Evolution, Molecular ,Rapid Report ,fetal brain ,Genome, Human ,ultra-conserved element ,Brain ,Humans ,chromatin interaction ,human accelerated region - Abstract
Genetic modifications in noncoding regulatory regions are likely critical to human evolution. Human-accelerated noncoding elements are highly conserved noncoding regions among vertebrates but have large differences across humans, which implies human-specific regulatory potential. In this study, we found that human-accelerated noncoding elements were frequently coupled with DNase I hypersensitive sites (DHSs), together with monomethylated and trimethylated histone H3 lysine 4, which are active regulatory markers. This coupling was particularly pronounced in fetal brains relative to adult brains, non-brain fetal tissues, and embryonic stem cells. However, fetal brain DHSs were also specifically enriched in deeply conserved sequences, implying coexistence of universal maintenance and human-specific fitness in human brain development. We assessed whether this coexisting pattern was a general one by quantitatively measuring evolutionary rates of DHSs. As a result, fetal brain DHSs showed a mixed but distinct signature of regional conservation and outlier point acceleration as compared to other DHSs. This finding suggests that brain developmental sequences are selectively constrained in general, whereas specific nucleotides are under positive selection or constraint relaxation simultaneously. Hence, we hypothesize that human- or primate-specific changes to universally conserved regulatory codes of brain development may drive the accelerated, and most likely adaptive, evolution of the regulatory network of the human brain.
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- 2020
45. Gene essentiality for tumour growth influences neoantigen‐directed immunoediting
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Bang, Hyoeun, primary, Park, Jae Soon, additional, Kim, Jeong Yeon, additional, Sung, Changhwan, additional, An, Jinhyeon, additional, Cho, Dae‐Yeon, additional, Lee, Se‐Hoon, additional, Shim, Seok Bo, additional, Choi, Jung Kyoon, additional, and Kim, Kwoneel, additional
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- 2022
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46. Genome-wide methylation profiling of ADPKD identified epigenetically regulated genes associated with renal cyst development
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Woo, Yu Mi, Bae, Jae-Bum, Oh, Yeon-Hee, Lee, Young-Gun, Lee, Min Joo, Park, Eun Young, Choi, Jung-Kyoon, Lee, Sunyoung, Shin, Yubin, Lyu, Jaemyun, Jung, Hye-Yoon, Lee, Yeon-Su, Hwang, Young-Hwan, Kim, Young-Joon, and Park, Jong Hoon
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- 2014
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47. Aberrant Transcript Usage Is Associated with Homologous Recombination Deficiency and Predicts Therapeutic Response
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Kang, Hyeon Gu, primary, Hwangbo, Haeun, additional, Kim, Myung Ji, additional, Kim, Sinae, additional, Lee, Eun Ji, additional, Park, Min Ji, additional, Kim, Jae-Weon, additional, Kim, Byoung-Gie, additional, Cho, Eun-Hae, additional, Chang, Suhwan, additional, Lee, Jung-Yun, additional, and Choi, Jung Kyoon, additional
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- 2021
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48. Whole-Genome and Transcriptome Sequencing Identified NOTCH2 and HES1 As Potential Markers of Response to Imatinib in Desmoid Tumor (Aggressive Fibromatosis): A Phase II Trial Study
- Author
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Kwon, Joonha, primary, Lee, Jun Hyeong, additional, Lee, Young Han, additional, Lee, Jeeyun, additional, Ahn, Jin-Hee, additional, Kim, Se Hyun, additional, Kim, Seung Hyun, additional, Kim, Tae Il, additional, Yun, Kum-Hee, additional, Park, Young Suk, additional, Kim, Jeong Eun, additional, Lee, Kyu Sang, additional, Choi, Jung Kyoon, additional, and Kim, Hyo Song, additional
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- 2021
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49. The emerging genetic diversity of hereditary spastic paraplegia in Korean patients
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Yang, Jin Ok, primary, Yoon, Ji-Yong, additional, Sung, Duk Hyun, additional, Yun, Sohyun, additional, Lee, Jeong-Ju, additional, Jun, Soo Young, additional, Halder, Debasish, additional, Jeon, Su-Jin, additional, Woo, Eui-Jeon, additional, Seok, Jin Myoung, additional, Cho, Jin Whan, additional, Jang, Ja-Hyun, additional, Choi, Jung Kyoon, additional, Kim, Byoung Joon, additional, and Kim, Nam-Soon, additional
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- 2021
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50. Aberrant transcript usage induces homologous recombination deficiency and predicts therapeutic responses
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Choi, Jung Kyoon, primary
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- 2021
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