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1. Genome-wide association study identifies high-impact susceptibility loci for HCC in North America.

Author

Hassan, Manal, Li, Donghui, Han, Younghun, Byun, Jinyoung, Hatia, Rikita, Long, Erping, Choi, Jiyeon, Kelley, Robin, Cleary, Sean, Lok, Anna, Bracci, Paige, Permuth, Jennifer, Bucur, Roxana, Yuan, Jian-Min, Singal, Amit, Jalal, Prasun, Ghobrial, R, Santella, Regina, Kono, Yuko, Shah, Dimpy, Nguyen, Mindie, Liu, Geoffrey, Parikh, Neehar, Kim, Richard, Wu, Hui-Chen, El-Serag, Hashem, Chang, Ping, Li, Yanan, Chun, Yun, Lee, Sunyoung, Gu, Jian, Hawk, Ernest, Sun, Ryan, Huff, Chad, Rashid, Asif, Amin, Hesham, Beretta, Laura, Wolff, Robert, Antwi, Samuel, Patt, Yehuda, Hwang, Lu-Yu, Klein, Alison, Zhang, Karen, Schmidt, Mikayla, White, Donna, Goss, John, Khaderi, Saira, Marrero, Jorge, Cigarroa, Francisco, Shah, Pankil, Kaseb, Ahmed, Roberts, Lewis, and Amos, Christopher

Subjects
Humans, Genome-Wide Association Study, Liver Neoplasms, Genetic Predisposition to Disease, Carcinoma, Hepatocellular, Male, Female, Middle Aged, North America, Case-Control Studies, Polymorphism, Single Nucleotide, Aged, Genetic Loci, White People
Abstract

BACKGROUND AND AIMS: Despite the substantial impact of environmental factors, individuals with a family history of liver cancer have an increased risk for HCC. However, genetic factors have not been studied systematically by genome-wide approaches in large numbers of individuals from European descent populations (EDP). APPROACH AND RESULTS: We conducted a 2-stage genome-wide association study (GWAS) on HCC not affected by HBV infections. A total of 1872 HCC cases and 2907 controls were included in the discovery stage, and 1200 HCC cases and 1832 controls in the validation. We analyzed the discovery and validation samples separately and then conducted a meta-analysis. All analyses were conducted in the presence and absence of HCV. The liability-scale heritability was 24.4% for overall HCC. Five regions with significant ORs (95% CI) were identified for nonviral HCC: 3p22.1, MOBP , rs9842969, (0.51, [0.40-0.65]); 5p15.33, TERT , rs2242652, (0.70, (0.62-0.79]); 19q13.11, TM6SF2 , rs58542926, (1.49, [1.29-1.72]); 19p13.11 MAU2 , rs58489806, (1.53, (1.33-1.75]); and 22q13.31, PNPLA3 , rs738409, (1.66, [1.51-1.83]). One region was identified for HCV-induced HCC: 6p21.31, human leukocyte antigen DQ beta 1, rs9275224, (0.79, [0.74-0.84]). A combination of homozygous variants of PNPLA3 and TERT showing a 6.5-fold higher risk for nonviral-related HCC compared to individuals lacking these genotypes. This observation suggests that gene-gene interactions may identify individuals at elevated risk for developing HCC. CONCLUSIONS: Our GWAS highlights novel genetic susceptibility of nonviral HCC among European descent populations from North America with substantial heritability. Selected genetic influences were observed for HCV-positive HCC. Our findings indicate the importance of genetic susceptibility to HCC development.

Published
2024

2. Aligning Large Language Models for Enhancing Psychiatric Interviews through Symptom Delineation and Summarization

Author

So, Jae-hee, Chang, Joonhwan, Kim, Eunji, Na, Junho, Choi, JiYeon, Sohn, Jy-yong, Kim, Byung-Hoon, and Chu, Sang Hui

Subjects
Computer Science - Artificial Intelligence, Computer Science - Computation and Language
Abstract

Recent advancements in Large Language Models (LLMs) have accelerated their usage in various domains. Given the fact that psychiatric interviews are goal-oriented and structured dialogues between the professional interviewer and the interviewee, it is one of the most underexplored areas where LLMs can contribute substantial value. Here, we explore the use of LLMs for enhancing psychiatric interviews, by analyzing counseling data from North Korean defectors with traumatic events and mental health issues. Specifically, we investigate whether LLMs can (1) delineate the part of the conversation that suggests psychiatric symptoms and name the symptoms, and (2) summarize stressors and symptoms, based on the interview dialogue transcript. Here, the transcript data was labeled by mental health experts for training and evaluation of LLMs. Our experimental results show that appropriately prompted LLMs can achieve high performance on both the symptom delineation task and the summarization task. This research contributes to the nascent field of applying LLMs to psychiatric interview and demonstrates their potential effectiveness in aiding mental health practitioners.

Published
2024

4. Measurement of Digital Literacy Among Older Adults: Systematic Review

Author

Oh, Sarah Soyeon, Kim, Kyoung-A, Kim, Minsu, Oh, Jaeuk, Chu, Sang Hui, and Choi, JiYeon

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Public aspects of medicine, RA1-1270
Abstract

BackgroundNumerous instruments are designed to measure digital literacy among the general population. However, few studies have assessed the use and appropriateness of these measurements for older populations. ObjectiveThis systematic review aims to identify and critically appraise studies assessing digital literacy among older adults and to evaluate how digital literacy instruments used in existing studies address the elements of age-appropriate digital literacy using the European Commission’s Digital Competence (DigComp) Framework. MethodsElectronic databases were searched for studies using validated instruments to assess digital literacy among older adults. The quality of all included studies was evaluated using the Crowe Critical Appraisal Tool (CCAT). Instruments were assessed according to their ability to incorporate the competence areas of digital literacy as defined by the DigComp Framework: (1) information and data literacy, (2) communication and collaboration, (3) digital content creation, (4) safety, and (5) problem-solving ability, or attitudes toward information and communication technology use. ResultsSearches yielded 1561 studies, of which 27 studies (17 cross-sectional, 2 before and after, 2 randomized controlled trials, 1 longitudinal, and 1 mixed methods) were included in the final analysis. Studies were conducted in the United States (18/27), Germany (3/27), China (1/27), Italy (1/27), Sweden (1/27), Canada (1/27), Iran (1/27), and Bangladesh (1/27). Studies mostly defined older adults as aged ≥50 years (10/27) or ≥60 years (8/27). Overall, the eHealth Literacy Scale (eHEALS) was the most frequently used instrument measuring digital literacy among older adults (16/27, 59%). Scores on the CCAT ranged from 34 (34/40, 85%) to 40 (40/40, 100%). Most instruments measured 1 or 2 of the DigComp Framework’s elements, but the Mobile Device Proficiency Questionnaire (MDPQ) measured all 5 elements, including “digital content creation” and “safety.” ConclusionsThe current digital literacy assessment instruments targeting older adults have both strengths and weaknesses, relative to their study design, administration method, and ease of use. Certain instrument modalities like the MDPQ are more generalizable and inclusive and thus, favorable for measuring the digital literacy of older adults. More studies focusing on the suitability of such instruments for older populations are warranted, especially for areas like “digital content creation” and “safety” that currently lack assessment. Evidence-based discussions regarding the implications of digitalization for the treatment of older adults and how health care professionals may benefit from this phenomenon are encouraged.

Published
2021
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8. Genome-wide association study of lung adenocarcinoma in East Asia and comparison with a European population

Author

Shi, Jianxin, Shiraishi, Kouya, Choi, Jiyeon, Matsuo, Keitaro, Chen, Tzu-Yu, Dai, Juncheng, Hung, Rayjean J, Chen, Kexin, Shu, Xiao-Ou, Kim, Young Tae, Landi, Maria Teresa, Lin, Dongxin, Zheng, Wei, Yin, Zhihua, Zhou, Baosen, Song, Bao, Wang, Jiucun, Seow, Wei Jie, Song, Lei, Chang, I-Shou, Hu, Wei, Chien, Li-Hsin, Cai, Qiuyin, Hong, Yun-Chul, Kim, Hee Nam, Wu, Yi-Long, Wong, Maria Pik, Richardson, Brian Douglas, Funderburk, Karen M, Li, Shilan, Zhang, Tongwu, Breeze, Charles, Wang, Zhaoming, Blechter, Batel, Bassig, Bryan A, Kim, Jin Hee, Albanes, Demetrius, Wong, Jason YY, Shin, Min-Ho, Chung, Lap Ping, Yang, Yang, An, She-Juan, Zheng, Hong, Yatabe, Yasushi, Zhang, Xu-Chao, Kim, Young-Chul, Caporaso, Neil E, Chang, Jiang, Ho, James Chung Man, Kubo, Michiaki, Daigo, Yataro, Song, Minsun, Momozawa, Yukihide, Kamatani, Yoichiro, Kobayashi, Masashi, Okubo, Kenichi, Honda, Takayuki, Hosgood, Dean H, Kunitoh, Hideo, Patel, Harsh, Watanabe, Shun-ichi, Miyagi, Yohei, Nakayama, Haruhiko, Matsumoto, Shingo, Horinouchi, Hidehito, Tsuboi, Masahiro, Hamamoto, Ryuji, Goto, Koichi, Ohe, Yuichiro, Takahashi, Atsushi, Goto, Akiteru, Minamiya, Yoshihiro, Hara, Megumi, Nishida, Yuichiro, Takeuchi, Kenji, Wakai, Kenji, Matsuda, Koichi, Murakami, Yoshinori, Shimizu, Kimihiro, Suzuki, Hiroyuki, Saito, Motonobu, Ohtaki, Yoichi, Tanaka, Kazumi, Wu, Tangchun, Wei, Fusheng, Dai, Hongji, Machiela, Mitchell J, Su, Jian, Kim, Yeul Hong, Oh, In-Jae, Lee, Victor Ho Fun, Chang, Gee-Chen, Tsai, Ying-Huang, Chen, Kuan-Yu, Huang, Ming-Shyan, Su, Wu-Chou, Chen, Yuh-Min, Seow, Adeline, Park, Jae Yong, and Kweon, Sun-Seog

Subjects
Genetics, Cancer, Clinical Research, Human Genome, Prevention, Lung, Lung Cancer, Tobacco, Tobacco Smoke and Health, 2.1 Biological and endogenous factors, Aetiology, Respiratory, Humans, Genome-Wide Association Study, Genetic Predisposition to Disease, Adenocarcinoma of Lung, Asia, Eastern, Lung Neoplasms, Polymorphism, Single Nucleotide
Abstract

Lung adenocarcinoma is the most common type of lung cancer. Known risk variants explain only a small fraction of lung adenocarcinoma heritability. Here, we conducted a two-stage genome-wide association study of lung adenocarcinoma of East Asian ancestry (21,658 cases and 150,676 controls; 54.5% never-smokers) and identified 12 novel susceptibility variants, bringing the total number to 28 at 25 independent loci. Transcriptome-wide association analyses together with colocalization studies using a Taiwanese lung expression quantitative trait loci dataset (n = 115) identified novel candidate genes, including FADS1 at 11q12 and ELF5 at 11p13. In a multi-ancestry meta-analysis of East Asian and European studies, four loci were identified at 2p11, 4q32, 16q23, and 18q12. At the same time, most of our findings in East Asian populations showed no evidence of association in European populations. In our studies drawn from East Asian populations, a polygenic risk score based on the 25 loci had a stronger association in never-smokers vs. individuals with a history of smoking (Pinteraction = 0.0058). These findings provide new insights into the etiology of lung adenocarcinoma in individuals from East Asian populations, which could be important in developing translational applications.

Published
2023

9. Cross-ancestry genome-wide meta-analysis of 61,047 cases and 947,237 controls identifies new susceptibility loci contributing to lung cancer.

Author

Byun, Jinyoung, Han, Younghun, Li, Yafang, Xia, Jun, Long, Erping, Choi, Jiyeon, Xiao, Xiangjun, Zhu, Meng, Zhou, Wen, Sun, Ryan, Bossé, Yohan, Song, Zhuoyi, Schwartz, Ann, Lusk, Christine, Rafnar, Thorunn, Stefansson, Kari, Zhang, Tongwu, Zhao, Wei, Pettit, Rowland W, Liu, Yanhong, Li, Xihao, Zhou, Hufeng, Walsh, Kyle M, Gorlov, Ivan, Gorlova, Olga, Zhu, Dakai, Rosenberg, Susan M, Pinney, Susan, Bailey-Wilson, Joan E, Mandal, Diptasri, de Andrade, Mariza, Gaba, Colette, Willey, James C, You, Ming, Anderson, Marshall, Wiencke, John K, Albanes, Demetrius, Lam, Stephan, Tardon, Adonina, Chen, Chu, Goodman, Gary, Bojeson, Stig, Brenner, Hermann, Landi, Maria Teresa, Chanock, Stephen J, Johansson, Mattias, Muley, Thomas, Risch, Angela, Wichmann, H-Erich, Bickeböller, Heike, Christiani, David C, Rennert, Gad, Arnold, Susanne, Field, John K, Shete, Sanjay, Le Marchand, Loic, Melander, Olle, Brunnstrom, Hans, Liu, Geoffrey, Andrew, Angeline S, Kiemeney, Lambertus A, Shen, Hongbing, Zienolddiny, Shanbeh, Grankvist, Kjell, Johansson, Mikael, Caporaso, Neil, Cox, Angela, Hong, Yun-Chul, Yuan, Jian-Min, Lazarus, Philip, Schabath, Matthew B, Aldrich, Melinda C, Patel, Alpa, Lan, Qing, Rothman, Nathaniel, Taylor, Fiona, Kachuri, Linda, Witte, John S, Sakoda, Lori C, Spitz, Margaret, Brennan, Paul, Lin, Xihong, McKay, James, Hung, Rayjean J, and Amos, Christopher I

Subjects
Humans, Lung Neoplasms, Genetic Predisposition to Disease, RNA-Binding Proteins, DNA-Binding Proteins, Polymorphism, Single Nucleotide, Quantitative Trait Loci, Genome-Wide Association Study, Human Genome, Cancer, Genetics, Lung, 2.1 Biological and endogenous factors, Aetiology, Biological Sciences, Medical and Health Sciences, Developmental Biology
Abstract

To identify new susceptibility loci to lung cancer among diverse populations, we performed cross-ancestry genome-wide association studies in European, East Asian and African populations and discovered five loci that have not been previously reported. We replicated 26 signals and identified 10 new lead associations from previously reported loci. Rare-variant associations tended to be specific to populations, but even common-variant associations influencing smoking behavior, such as those with CHRNA5 and CYP2A6, showed population specificity. Fine-mapping and expression quantitative trait locus colocalization nominated several candidate variants and susceptibility genes such as IRF4 and FUBP1. DNA damage assays of prioritized genes in lung fibroblasts indicated that a subset of these genes, including the pleiotropic gene IRF4, potentially exert effects by promoting endogenous DNA damage.

Published
2022

36. Effect of High-Power Laser Cleaning for Surface Contaminants Removal on SS304L

Author

Choi, Soojin, primary, Yoo, Hyun Jong, additional, Choi, Jiyeon, additional, Noh, Jiwhan, additional, Kang, Heeshin, additional, Ahn, Sanghoon, additional, Park, Junsu, additional, Choi, Philgong, additional, Kim, Dohyun, additional, Kim, Yeonggyu, additional, Kim, Byeongju, additional, Jeon, Ikgeun, additional, Kim, Jeng O, additional, Sohn, Hyonkee, additional, Kim, Kyunghan, additional, and Park, Changkyoo, additional

Published
2024
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38. Genomic and evolutionary classification of lung cancer in never smokers

Author

Zhang, Tongwu, Joubert, Philippe, Ansari-Pour, Naser, Zhao, Wei, Hoang, Phuc H., Lokanga, Rachel, Moye, Aaron L., Rosenbaum, Jennifer, Gonzalez-Perez, Abel, Martínez-Jiménez, Francisco, Castro, Andrea, Muscarella, Lucia Anna, Hofman, Paul, Consonni, Dario, Pesatori, Angela C., Kebede, Michael, Li, Mengying, Gould Rothberg, Bonnie E., Peneva, Iliana, Schabath, Matthew B., Poeta, Maria Luana, Costantini, Manuela, Hirsch, Daniela, Heselmeyer-Haddad, Kerstin, Hutchinson, Amy, Olanich, Mary, Lawrence, Scott M., Lenz, Petra, Duggan, Maire, Bhawsar, Praphulla M. S., Sang, Jian, Kim, Jung, Mendoza, Laura, Saini, Natalie, Klimczak, Leszek J., Islam, S. M. Ashiqul, Otlu, Burcak, Khandekar, Azhar, Cole, Nathan, Stewart, Douglas R., Choi, Jiyeon, Brown, Kevin M., Caporaso, Neil E., Wilson, Samuel H., Pommier, Yves, Lan, Qing, Rothman, Nathaniel, Almeida, Jonas S., Carter, Hannah, Ried, Thomas, Kim, Carla F., Lopez-Bigas, Nuria, Garcia-Closas, Montserrat, Shi, Jianxin, Bossé, Yohan, Zhu, Bin, Gordenin, Dmitry A., Alexandrov, Ludmil B., Chanock, Stephen J., Wedge, David C., and Landi, Maria Teresa

Published
2021
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