Article
Health Care Sciences & Services
Zulfan Zazuli, Corine de Jong, Wei Xu, Susanne J. H. Vijverberg, Rosalinde Masereeuw, Devalben Patel, Maryam Mirshams, Khaleeq Khan, Dangxiao Cheng, Bayardo Ordonez-Perez, Shao Hui Huang, Anna Spreafico, Aaron R. Hansen, David P. Goldstein, John R. de Almeida, Scott V. Bratman, Andrew Hope, Jennifer J. Knox, Rebecca K. S. Wong, Gail E. Darling, Abhijat Kitchlu, Simone W. A. van Haarlem, Femke van der Meer, Anne S. R. van Lindert, Alexandra ten Heuvel, Jan Brouwer, Colin J. D. Ross, Bruce C. Carleton, Toine C. G. Egberts, Gerarda J. M. Herder, Vera H. M. Deneer, Anke H. Maitland-van der Zee, Geoffrey Liu
Summary: This study identified a specific variant of the BACH2 gene that may play an important role in cisplatin-induced nephrotoxicity, suggesting opportunities for mechanistic research, tailored therapy, and preventive strategies related to this pathology.
JOURNAL OF PERSONALIZED MEDICINE
(2021)
Review
Agriculture, Dairy & Animal Science
G. Sahana, Z. Cai, M. P. Sanchez, A. C. Bouwman, D. Boichard
Summary: Genotype data from dairy cattle selection programs greatly facilitate GWAS to identify variants related to economic traits. Results can enhance the accuracy of genomic prediction, analyze more complex models, elucidate the genetic architecture of a trait, and decipher the underlying biology of traits.
JOURNAL OF DAIRY SCIENCE
(2023)
Article
Pharmacology & Pharmacy
Junbo Tian, Jing Zhang, Zengguang Yang, Shuaisheng Feng, Shujuan Li, Shiqi Ren, Jianxiang Shi, Xinyue Hou, Xia Xue, Bei Yang, Hongen Xu, Jiancheng Guo
Summary: This study comprehensively analyzed the pharmacogenomic profiles of the central Han Chinese population in the context of medication safety and efficacy and compared them with other global populations, aiming to improve medical treatment guidelines.
FRONTIERS IN PHARMACOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Andrea Gelemanovic, Tatjana Catipovic Ardalic, Ajka Pribisalic, Caroline Hayward, Ivana Kolcic, Ozren Polasek
Summary: Infectious diseases remain a threat to global human health, and host genetic factors play a role in determining susceptibility, severity, and outcome. A genome-wide meta-analysis of 4624 subjects was conducted, identifying 29 infection-related genetic associations, primarily rare variants. Notably, genes with known roles in the immune response were detected, suggesting that understanding rare variants could aid in predicting an individual's susceptibility to infectious diseases.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Gaurav Thareja, Anne M. Evans, Spencer D. Wood, Nisha Stephan, Shaza Zaghlool, Anna Halama, Gabi Kastenmueller, Aziz Belkadi, Omar M. E. Albagha, Karsten Suhre
Summary: The study proposes the use of metabolite ratios as GWAS phenotypes to increase the power of detecting genetic associations. A GWAS with 520 individuals identified genetic variations related to acetaminophen metabolism, and confirmed the chemical structure of one of its products experimentally.
Article
Genetics & Heredity
Junke Wang, Alyssa I. Clay-Gilmour, Ezgi Karaesmen, Abbas Rizvi, Qianqian Zhu, Li Yan, Leah Preus, Song Liu, Yiwen Wang, Elizabeth Griffiths, Daniel O. Stram, Loreall Pooler, Xin Sheng, Christopher Haiman, David van den Berg, Amy Webb, Guy Brock, Stephen Spellman, Marcelo Pasquini, Philip McCarthy, James Allan, Friedrich Stoelzel, Kenan Onel, Theresa Hahn, Lara E. Sucheston-Campbell
Summary: This study identified an increased risk for de novo AML and MDS in patients carrying the T allele at the s12203592 locus in the IRF4 gene, which regulates myeloid and lymphoid hematopoietic differentiation. Additionally, increased IRF4 gene expression was found to be associated with an increased risk of de novo AML and MDS.
FRONTIERS IN GENETICS
(2021)
Review
Oncology
Hedy Maagdenberg, Natanja Oosterom, Jolanda Zanen, Donato Gemmati, Rachael E. Windsor, Sandra G. Heil, Patricia Esperon, Shakila Jabeen, Guillermo J. Ruiz-Arguelles, Oliver Zolk, Susanne Hoerning, Charlotte Sleurs, Elixabet Lopez-Lopez, Monica Moreno-Galvan, Marry M. van den Heuvel-Eibrink, Anke H. van der Zee, Bruce C. Carleton
Summary: Methotrexate-induced mucositis varies greatly among individuals, and genetic variants such as MTHFR c.677C > T and MTRR c.66A > G have been found to have statistically significant associations with the occurrence of mucositis. Further research in this area may help in predicting and managing this common side effect of MTX treatment.
CRITICAL REVIEWS IN ONCOLOGY HEMATOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Surajit Bhattacharya, Hayk Barseghyan, Emmanuele C. Delot, Eric Vilain
Summary: nanotatoR, an R-based package, provides comprehensive annotation for SV classification, enabling analysts to rapidly identify potential pathogenic SVs.
Article
Medicine, Research & Experimental
Daniela Nachmanson, Meghana Pagadala, Joseph Steward, Callie Cheung, Lauryn Keeler Bruce, Nicole Q. Lee, Thomas J. O'Keefe, Grace Y. Lin, Farnaz Hasteh, Gerald P. Morris, Hannah Carter, Olivier Harismendy
Summary: This study demonstrates that germline DNA profiling from archival tissue using low-coverage whole-genome sequencing and genotype imputation can accurately determine genotypes at common SNPs and evaluate disease-related polygenic risk scores. Tissue-derived PRS in DCIS patients is significantly associated with BCSE. Breast cancer patients have a 5% to 28% chance of BCSE within 10 years.
JOURNAL OF TRANSLATIONAL MEDICINE
(2022)
Review
Biochemistry & Molecular Biology
Xinbao Ding, John C. Schimenti
Summary: Genetic factors contribute to about 50% of infertility cases, and modern genomics tools have enabled a more sophisticated exploration of genetic causes. Advanced techniques like genome modulation and editing offer potential for functional testing and clinical correction of infertility variants.
TRENDS IN MOLECULAR MEDICINE
(2021)
Article
Pharmacology & Pharmacy
Luciana Bertholim-Nasciben, Marilia O. Scliar, Guilherme Debortoli, Bhooma Thiruvahindrapuram, Stephen W. Scherer, Yeda A. O. Duarte, Mayana Zatz, Guilherme Suarez-Kurtz, Esteban J. Parra, Michel S. Naslavsky
Summary: This study evaluated the frequency of pharmacogenomics markers in the Brazilian population using whole-genome sequencing. The findings showed that some variants may lead to high-risk gene-drug interactions. The study concluded that next-generation sequencing for pharmacogenomics testing is feasible in the Brazilian population.
FRONTIERS IN PHARMACOLOGY
(2023)
Article
Genetics & Heredity
Bingxin Zhao, Tengfei Li, Stephen M. Smith, Di Xiong, Xifeng Wang, Yue Yang, Tianyou Luo, Ziliang Zhu, Yue Shan, Nana Matoba, Quan Sun, Yuchen Yang, Mads E. Hauberg, Jaroslav Bendl, John F. Fullard, Panagiotis Roussos, Weili Lin, Yun Li, Jason L. Stein, Hongtu Zhu
Summary: Association analyses using resting-state functional magnetic resonance images have identified common genetic variants influencing intrinsic brain activity. These variants are correlated with neuropsychiatric traits and disorders, providing insights into the genetic architecture of brain functional networks and their links to brain-related complex traits and disorders.
Article
Pharmacology & Pharmacy
Chenxue Mao, Juan Chen, Ting Zou, Yuankang Zhou, Junyan Liu, Xi Li, Xiangping Li, Min Li, Pinhua Pan, Wei Zhuo, Yang Gao, Shuo Hu, Desheng Xiao, Lin Wu, Zhan Wang, Heng Xu, Wen Yang, Yingjie Xu, Haihua Xiao, Kazuhiko Hanada, Wei Zhang, Honghao Zhou, Jiye Yin, Zhaoqian Liu
Summary: This study investigated the pharmacogenomic markers associated with platinum-based chemotherapy response in NSCLC patients through genome-wide association studies and validated the findings in independent cohorts. The results identified two genetic variations (rs2280496 and rs189178649) in the ADCY1 gene that were associated with the sensitivity of platinum-based chemotherapy in NSCLC patients.
ACTA PHARMACEUTICA SINICA B
(2022)
Article
Critical Care Medicine
Anna L. Peljto, Rachel Z. Blumhagen, Avram D. Walts, Jonathan Cardwell, Julia Powers, Tamera J. Corte, Joanne L. Dickinson, Ian Glaspole, Yuben P. Moodley, Martina Koziar Vasakova, Elisabeth Bendstrup, Jesper R. Davidsen, Raphael Borie, Bruno Crestani, Philippe Dieude, Francesco Bonella, Ulrich Costabel, Gunnar Gudmundsson, Seamas C. Donnelly, Jim Egan, Michael T. Henry, Michael P. Keane, Marcus P. Kennedy, Cormac McCarthy, Aoife N. McElroy, Joshua A. Olaniyi, Katherine M. A. O'Reilly, Luca Richeldi, Paolo M. Leone, Venerino Poletti, Francesco Puppo, Sara Tomassetti, Valentina Luzzi, Nurdan Kokturk, Nesrin Mogulkoc, Christine A. Fiddler, Nikhil Hirani, R. Gisli Jenkins, Toby M. Maher, Philip L. Molyneaux, Helen Parfrey, Rebecca Braybrooke, Timothy S. Blackwell, Peter D. Jackson, Steven D. Nathan, Mary K. Porteous, Kevin K. Brown, Jason D. Christie, Harold R. Collard, Oliver Eickelberg, Elena E. Foster, Kevin F. Gibson, Marilyn Glassberg, Daniel J. Kass, Jonathan A. Kropski, David Lederer, Angela L. Linderholm, Jim Loyd, Susan K. Mathai, Sydney B. Montesi, Imre Noth, Justin M. Oldham, Amy J. Palmisciano, Cristina A. Reichner, Mauricio Rojas, Jesse Roman, Neil Schluger, Barry S. Shea, Jeffrey J. Swigris, Paul J. Wolters, Yingze Zhang, Cecilia M. A. Prele, Juan I. Enghelmayer, Maria Otaola, Christopher J. Ryerson, Mauricio Salinas, Martina Sterclova, Tewodros H. Gebremariam, Marjukka Myllarniemi, Roberto G. Carbone, Haruhiko Furusawa, Masaki Hirose, Yoshikazu Inoue, Yasunari Miyazaki, Ken Ohta, Shin Ohta, Tsukasa Okamoto, Dong Soon Kim, Annie Pardo, Moises Selman, Alvaro U. Aranda, Moo Suk Park, Jong Sun Park, Jin Woo Song, Maria Molina-Molina, Lurdes Planas-Cerezales, Gunilla Westergren-Thorsson, Albert V. Smith, Ani W. Manichaikul, John S. Kim, Stephen S. Rich, Elizabeth C. Oelsner, R. Graham Barr, Jerome I. Rotter, Josee Dupuis, George O'Connor, Ramachandran S. Vasan, Michael H. Cho, Edwin K. Silverman, Marvin I. Schwarz, Mark P. Steele, Joyce S. Lee, Ivana V. Yang, Tasha E. Fingerlin, David A. Schwartz
Summary: This study investigated the role of rare variants, genome-wide, on the risk of idiopathic pulmonary fibrosis (IPF) using whole-genome sequencing. The results showed that rare variants within the TERT and RTEL1 genes were significantly associated with IPF, along with well-established common variants. Therefore, including TERT, RTEL1, common variants, and environmental risk factors in risk profiling and IPF therapy development is likely to have the largest impact on this complex disease.
AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE
(2023)
Article
Multidisciplinary Sciences
Hannah McConnell, T. Daniel Andrews, Matt A. Field
Summary: This study evaluated the effectiveness of eleven missense mutation functional inference tools on all known pharmacogenetic missense variants in the Pharmacogenomics Knowledgebase (PharmGKB) repository. The results showed variable performance of functional inference tools on PharmGKB variants, particularly on variants causing off-target, type B adverse drug reactions. New predictive algorithms are needed to accurately predict the effects of these variants in order to improve the adoption of pharmacogenetics in clinical practice.
Article
Oncology
Masaaki Komatsu, Heather E. Wheeler, Suyoun Chung, Siew-Kee Low, Claudia Wing, Shannon M. Delaney, Lidija K. Gorsic, Atsushi Takahashi, Michiaki Kubo, Deanna L. Kroetz, Wei Zhang, Yusuke Nakamura, M. Eileen Dolan
CLINICAL CANCER RESEARCH
(2015)
Article
Biotechnology & Applied Microbiology
Yun Kyoung Kim, Ji Hee Oh, Young Jin Kim, Mi Yeong Hwang, Sanghoon Moon, Siew-Kee Low, Atsushi Takahashi, Koichi Matsuda, Michiaki Kubo, Juyoung Lee, Bong-Jo Kim
BIOMED RESEARCH INTERNATIONAL
(2015)
Article
Obstetrics & Gynecology
Yadav Sapkota, Siew-Kee Low, John Attia, Scott D. Gordon, Anjali K. Henders, Elizabeth G. Holliday, Stuart MacGregor, Nicholas G. Martin, Mark McEvoy, Andrew P. Morris, Atsushi Takahashi, Rodney J. Scott, Michiaki Kubo, Krina T. Zondervan, Grant W. Montgomery, Dale R. Nyholt
HUMAN REPRODUCTION
(2015)
Article
Genetics & Heredity
Qiuyin Cai, Ben Zhang, Hyuna Sung, Siew-Kee Low, Sun-Seog Kweon, Wei Lu, Jiajun Shi, Jirong Long, Wanqing Wen, Ji-Yeob Choi, Dong-Young Noh, Chen-Yang Shen, Keitaro Matsuo, Soo-Hwang Teo, Mi Kyung Kim, Ui Soon Khoo, Motoki Iwasaki, Mikael Hartman, Atsushi Takahashi, Kyota Ashikawa, Koichi Matsuda, Min-Ho Shin, Min Ho Park, Ying Zheng, Yong-Bing Xiang, Bu-Tian Ji, Sue K. Park, Pei-Ei Wu, Chia-Ni Hsiung, Hidemi Ito, Yoshio Kasuga, Peter Kang, Shivaani Mariapun, Sei Hyun Ahn, Han Sung Kang, Kelvin Y. K. Chan, Ellen P. S. Man, Hiroji Iwata, Shoichiro Tsugane, Hui Miao, Jiemin Liao, Yusuke Nakamura, Michiaki Kubo, Ryan J. Delahanty, Yanfeng Zhang, Bingshan Li, Chun Li, Yu-Tang Gao, Xiao-Ou Shu, Daehee Kang, Wei Zheng
Article
Multidisciplinary Sciences
Siew-Kee Low, Koya Fukunaga, Atsushi Takahashi, Koichi Matsuda, Fumiya Hongo, Hiroyuki Nakanishi, Hiroshi Kitamura, Takamitsu Inoue, Yoichiro Kato, Yoshihiko Tomita, Satoshi Fukasawa, Tomoaki Tanaka, Kazuo Nishimura, Hirotsugu Uemura, Isao Hara, Masato Fujisawa, Hideyasu Matsuyama, Katsuyoshi Hashine, Katsunori Tatsugami, Hideki Enokida, Michiaki Kubo, Tsuneharu Miki, Taisei Mushiroda
Article
Oncology
Eisaku Miyauchi, Tatsuo Matsuda, Kazuma Kiyotani, Siew-Kee Low, Yu-Wen Hsu, Yoko Tsukita, Masakazu Ichinose, Akira Sakurada, Yoshinori Okada, Ryoko Saito, Yusuke Nakamura
Article
Biochemistry & Molecular Biology
Tatsuo Masuda, Siew-Kee Low, Masato Akiyama, Makoto Hirata, Yutaka Ueda, Koichi Matsuda, Tadashi Kimura, Yoshinori Murakami, Michiaki Kubo, Yoichiro Kamatani, Yukinori Okada
EUROPEAN JOURNAL OF HUMAN GENETICS
(2020)
Article
Multidisciplinary Sciences
Siew-Kee Low, Yoon Ming Chin, Hidemi Ito, Keitaro Matsuo, Chizu Tanikawa, Koichi Matsuda, Hiroko Saito, Mika Sakurai-Yageta, Naoki Nakaya, Atsushi Shimizu, Satoshi S. Nishizuka, Taiki Yamaji, Norie Sawada, Motoki Iwasaki, Shoichiro Tsugane, Toshiro Takezaki, Sadao Suzuki, Mariko Naito, Kenji Wakai, Yoichiro Kamatani, Yukihide Momozawa, Yoshinori Murakami, Johji Inazawa, Yusuke Nakamura, Michiaki Kubo, Toyomasa Katagiri, Yoshio Miki
SCIENTIFIC REPORTS
(2019)
Article
Oncology
Yoon Ming Chin, Yoko Takahashi, Hiu Ting Chan, Masumi Otaki, Makoto Fujishima, Tomoko Shibayama, Yoshio Miki, Takayuki Ueno, Yusuke Nakamura, Siew-Kee Low
Summary: This study evaluated the feasibility and clinical utility of amplicon-based Oncomine Pan-Cancer cell-free assay for detecting ctDNA in patients with early or advanced breast cancer. Results showed different ctDNA detection rates in patients with different disease stages and metastatic status. Unique molecular tagging and ultradeep NGS were used to assess ctDNA mutation profiles, with the exclusion of false positive results contributed by clonal-hematopoietic origin.
Review
Genetics & Heredity
Seiichi Mori, Osamu Gotoh, Kazuma Kiyotani, Siew Kee Low
Summary: Gynecological malignancies have various histological subtypes, each reflecting the cell of origin and closely linked to clinical behavior and biological phenotype of the tumor. Advances in massive parallel sequencing have provided a comprehensive view of genomic alterations in individual tumors, highlighting driver-gene mutations and molecular subtypes associated with specific histotypes. Large genomic datasets, such as the Cancer Genome Atlas, have been crucial in identifying clinically relevant targets and biomarkers, and in characterizing genomes, driver mutations, and histotypes of even rare cancer types.
JOURNAL OF HUMAN GENETICS
(2021)
Review
Genetics & Heredity
Kazunori Watanabe, Yusuke Nakamura, Siew-Kee Low
Summary: Liquid biopsies have become a focus in cancer diagnosis for their easy, rapid, and non-invasive nature. They can be used for disease monitoring and to overcome the limitations of tissue biopsies, particularly in cases where obtaining tumor biopsies is clinically difficult. The detection of tumor-derived circulating tumor DNA from blood samples using next generation sequencing technologies shows promise as a complementary tool to traditional tissue biopsies or tumor biomarkers.
JOURNAL OF HUMAN GENETICS
(2021)
Article
Oncology
Takuya Sakashita, Noriko Yanagitani, Sumie Koike, Siew-Kee Low, Satoshi Takagi, Satoko Baba, Kengo Takeuchi, Makoto Nishio, Naoya Fujita, Ryohei Katayama
Summary: This study explores the mechanisms of ceritinib resistance in ALK-rearranged NSCLC cells. The researchers identified bypass signals mediated by overexpression and activation of FGFR3 as a mechanism of ceritinib resistance. They also found that amplification of cMET can counteractivate EGFR and/or Her3, leading to ceritinib resistance. Inhibition of FGFR3 and cMET resensitizes the resistant cells to ceritinib. These findings provide insights into potential strategies to overcome ceritinib resistance.
Review
Oncology
Siew-Kee Low, Hitoshi Zembutsu, Yusuke Nakamura
Article
Oncology
Suyoun Chung, Siew-Kee Low, Hitoshi Zembutsu, Atsushi Takahashi, Michiaki Kubo, Mitsunori Sasa, Yusuke Nakamura
BREAST CANCER RESEARCH
(2013)