Article
Psychiatry
Danilo Jokovic, Filip Milosavljevic, Zvezdana Stojanovic, Gordana Supic, Danilo Vojvodic, Bojana Uzelac, Marin M. Jukic, Aleksandra Petkovic Curcin
Summary: The inter-individual variability in CYP2C19-mediated metabolism can impact the effectiveness and tolerability of antidepressant treatment. This study found that individuals with slow metabolism showed lower antidepressant efficacy and tolerability compared to normal metabolizers, possibly due to their reduced capacity to metabolize antidepressant drugs.
PSYCHIATRY RESEARCH
(2022)
Article
Health Care Sciences & Services
Pablo Zubiaur, Maria Dolores Benedicto, Gonzalo Villapalos-Garcia, Marcos Navares-Gomez, Gina Mejia-Abril, Manuel Roman, Samuel Martin-Vilchez, Dolores Ochoa, Francisco Abad-Santos
Summary: The study demonstrated the impact of SLCO1B1 phenotype and other genetic variants on atorvastatin pharmacokinetics, suggesting dose adjustments based on SLCO1B1 and revealing interesting findings related to CYP3A5 genotype.
JOURNAL OF PERSONALIZED MEDICINE
(2021)
Article
Medicine, Research & Experimental
Gonzalo Villapalos-Garcia, Pablo Zubiaur, Dolores Ochoa, Paula Soria-Chacartegui, Marcos Navares-Gomez, Miriam Matas, Gina Mejia-Abril, Ana Casajus-Rey, Diana Campodonico, Manuel Roman, Samuel Martin-Vilchez, Carmen Candau-Ramos, Marina Aldama-Martin, Francisco Abad-Santos
Summary: This study aimed to investigate the impact of genetic polymorphisms on the pharmacokinetics of rivaroxaban in DOACs users. The results showed a correlation between NAT2 slow acetylators and the pharmacokinetics of rivaroxaban, suggesting their potential influence on the efficacy and stability of the drug. However, further research is needed to confirm the clinical significance of NAT2 involvement in rivaroxaban pharmacokinetics.
BIOMEDICINE & PHARMACOTHERAPY
(2023)
Article
Psychiatry
Miao Li, Ning Yuan, John Nurnberger, Ney Alliey-Rodriguez, Jiaqi Zhou, Fangyuan Duan, Jiacheng Dai, Yu Chen, Jiaqi Lu, Li Xie, Fang Liu, Xuli Yang, Philippe Tapon, Vijay Gorrepati, Xuejun Liu, Chao Chen, Chunyu Liu, Elliot S. Gershon
Summary: Common genetic variants in calcium channel genes are important markers of genetic susceptibility for bipolar disorder (BD). Previous clinical trials have shown that Calcium Channel Blocker (CCB) medication can improve mood stability in some BD patients. In this pilot study, 50 BD patients (39 from China and 11 from the US) hospitalized for manic episodes were given add-on CCB treatment. The study found that certain intronic variants of the Calcium Voltage-Gated Channel Subunit Alpha1 B (CACNA1B) were associated with treatment outcomes for manic patients, suggesting that these variants could be predictors for response to add-on CCB treatment for bipolar mania patients.
PSYCHIATRY RESEARCH
(2023)
Article
Health Care Sciences & Services
Kiera Stein, Abdullah Al Maruf, Daniel J. Mueller, Jeffrey R. Bishop, Chad A. Bousman
Summary: Carriers of the 5-HTTLPR LL or LS genotypes were more likely to respond to antidepressant therapy, and relative to SS carriers, long (L) allele carriers taking SSRIs reported fewer ADRs.
JOURNAL OF PERSONALIZED MEDICINE
(2021)
Article
Biotechnology & Applied Microbiology
Kaja Wasik, Tomaz Berisa, Joseph K. Pickrell, Jeremiah H. Li, Dana J. Fraser, Karen King, Charles Cox
Summary: The study found that low-pass sequencing to a depth above 0.4x coverage achieves higher power for association studies in pharmacogenetics compared to genotyping arrays.
Article
Dermatology
Weilong Zhong, Linghan Hu, Xu Cao, Jiahui Zhao, Xianning Zhang, Mingyang Lee, Huijun Wang, Jie Zhang, Quan Chen, Cheng Feng, Lina Duo, Xiuli Wang, Li Tang, Zhimiao Lin, Yong Yang
Summary: The study identified new and recurrent variations in the TRPV3 gene in patients with Olmsted syndrome, finding that variations in specific regions of the gene significantly enhance channel function and lead to severe phenotypes, while other variations have milder effects.
JOURNAL OF INVESTIGATIVE DERMATOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Valeria Opazo-Toro, Virginia Fortuna, Wladimiro Jimenez, Marta Pazos Lopez, Maria Jesus Muniesa Royo, Nestor Ventura-Abreu, Merce Brunet, Elena Milla
Summary: This study analyzed the genotype of glaucoma and ocular hypertension patients and examined its correlation with their response to beta-blockers and prostaglandin analogues. The results showed that patients carrying a mutated allele had higher intraocular pressure and more severe visual field damage.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Medicine, Research & Experimental
Trine Frederiksen, Johan Areberg, Ellen Schmidt, Tore Bjerregaard Stage, Kim Brosen
Summary: The polymorphism of the CYP2D6 gene leads to interindividual variability in CYP2D6 enzyme activity, while ethnicity could contribute to this variability. This study investigated interethnic differences in CYP2D6 activity using clinical datasets of three CYP2D6 substrates. The findings showed that African Americans had lower CYP2D6 activity compared to Asians and Whites among CYP2D6 normal metabolizers, and Asian carriers of CYP2D6 decreased function alleles tended to have higher CYP2D6 activity compared to Whites and African Americans among CYP2D6 intermediate metabolizers. The observed interethnic differences were driven by differences in CYP2D6 allele frequencies across ethnicities.
CTS-CLINICAL AND TRANSLATIONAL SCIENCE
(2023)
Article
Pharmacology & Pharmacy
Espen Molden, Marin M. Jukic
Summary: This article discusses genetic differences in drug metabolism related to the CYP2D6 gene, particularly its impact on antidepressants and antipsychotics. The study highlights that the current guidelines for assigning activity scores to reduced function variant alleles are not precise enough, necessitating updates to accurately predict individual dose requirements for medications.
FRONTIERS IN PHARMACOLOGY
(2021)
Article
Pharmacology & Pharmacy
Laura Suominen, Noora Sjostedt, Kati-Sisko Vellonen, Mikko Gynther, Seppo Auriola, Heidi Kidron
Summary: Reducing the activity of ABCG2 transporter can lead to increased drug absorption and plasma levels. The Q141K variant of ABCG2 has a clinically significant effect of decreasing protein levels and transport activity. In addition, there are over 500 rare variants of ABCG2, but their functionality is still unknown. This study identified 14 rare variants that have a decreased function phenotype, potentially leading to increased drug exposure.
EUROPEAN JOURNAL OF PHARMACEUTICAL SCIENCES
(2023)
Article
Physics, Multidisciplinary
Pablo Catalan, Juan Antonio Garcia-Martin, Jacobo Aguirre, Jose A. Cuesta, Susanna Manrubia
Summary: Not all phenotypes are equally accessible to evolving populations. Larger phenotypes resulting from a variety of genotypes are more common and easily maintained. Genotypes that map to these phenotypes form connected networks, allowing access to numerous alternative phenotypes. The reproductive ability and topology of the genotype network impact the fitness of a phenotype, and a fraction of phenotypes is unattainable.
JOURNAL OF PHYSICS A-MATHEMATICAL AND THEORETICAL
(2023)
Article
Biochemistry & Molecular Biology
Bin Li, Zheng Wang, Qian Chen, Kuokuo Li, Xiaomeng Wang, Yijing Wang, Qian Zeng, Ying Han, Bin Lu, Yuwen Zhao, Rui Zhang, Li Jiang, Hongxu Pan, Tengfei Luo, Yi Zhang, Zhenghuan Fang, Xuewen Xiao, Xun Zhou, Rui Wang, Lu Zhou, Yige Wang, Zhenhua Yuan, Lu Xia, Jifeng Guo, Beisha Tang, Kun Xia, Guihu Zhao, Jinchen Li
Summary: To address the challenge of accessing detailed clinical phenotypic features of patients with genetic variants, researchers developed an online database called GPCards, which integrates genetic and clinical data to provide interpretation of genotype-phenotype correlations and prioritization of candidate functional variants. This tool accelerates the interpretation of genotype-phenotype correlations in human genetic diseases and aids researchers in making faster diagnostic and treatment decisions.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Pharmacology & Pharmacy
Alyson L. Dickson, Laura L. Daniel, Jacy Zanussi, W. Dale Plummer, Wei-Qi Wei, Ge Liu, Tyler Reese, Prathima Anandi, Kelly A. Birdwell, Vivian Kawai, Nancy J. Cox, William D. Dupont, Adriana M. Hung, QiPing Feng, C. Michael Stein, Cecilia P. Chung
Summary: The study suggests that TPMT and NUDT15 metabolizer status can predict the risk of discontinuing azathioprine due to myelotoxicity in patients with inflammatory diseases.
CLINICAL PHARMACOLOGY & THERAPEUTICS
(2022)
Article
Endocrinology & Metabolism
Peng Tang, Jun Zhang, Song Peng, Yapeng Wang, Haoyang Li, Ze Wang, Yao Zhang, Yiqiang Huang, Jing Xu, Dianzheng Zhang, Qiuli Liu, Luofu Wang, Weihua Lan, Jun Jiang
Summary: 21-hydroxylase deficiency is the most common cause of congenital adrenal hyperplasia. This study analyzed 15 patients from three families and found that different phenotypes were caused by different CYP21A2 mutations. Gender and mutation type influence the phenotypes, and genetic analysis can aid in the diagnosis of atypical 21-hydroxylase deficiency patients.
FRONTIERS IN ENDOCRINOLOGY
(2023)
Article
Toxicology
Si Chen, Qiangen Wu, Xilin Li, Dongying Li, Michelle Fan, Zhen Ren, Matthew Bryant, Nan Mei, Baitang Ning, Lei Guo
ARCHIVES OF TOXICOLOGY
(2020)
Article
Toxicology
Dongying Li, Leihong Wu, Bridgett Knox, Si Chen, William H. Tolleson, Fang Liu, Dianke Yu, Lei Guo, Weida Tong, Baitang Ning
ARCHIVES OF TOXICOLOGY
(2020)
Article
Pharmacology & Pharmacy
Xubing Wang, Yanjie Zhao, Jiao Luo, Lin Xu, Xinmei Li, Yuan Jin, Chuanhai Li, Meiyao Feng, Ying Wang, Jing Chen, Yufei Hou, Qianwen Zhao, Jinquan Zhao, Baitang Ning, Yuxin Zheng, Dianke Yu
MOLECULAR PHARMACOLOGY
(2020)
Article
Biochemistry & Molecular Biology
Xiangjun Ji, Peng Li, James C. Fuscoe, Geng Chen, Wenzhong Xiao, Leming Shi, Baitang Ning, Zhichao Liu, Huixiao Hong, Jun Wu, Jinghua Liu, Lei Guo, David P. Kreil, Pawel P. Labaj, Liping Zhong, Wenjun Bao, Yong Huang, Jian He, Yongxiang Zhao, Weida Tong, Tieliu Shi
NUCLEIC ACIDS RESEARCH
(2020)
Article
Toxicology
Dongying Li, Bridgett Knox, Binsheng Gong, Si Chen, Lei Guo, Zhichao Liu, Weida Tong, Baitang Ning
Summary: The study focused on investigating miRNA biomarkers for KCZ-induced liver injury by integrating in vivo, in vitro, and bioinformatics analyses. Significant dysregulation of miR-34a-5p, miR-331-3p, and miR-15b-3p was associated with cytoplasmic vacuolization in rat livers with KCZ-induced injury. These miRNAs, along with miR-676, showed evolutionary conservation and could potentially serve as translational biomarkers for early detection of liver injury.
TOXICOLOGICAL SCIENCES
(2021)
Review
Pharmacology & Pharmacy
Li Zeng, Dongying Li, Weida Tong, Tieliu Shi, Baitang Ning
Summary: The study proposes a method to monitor and predict the impact of viral mutations on drug safety and efficacy, emphasizing the importance of the three main viral proteins and suggesting the establishment of an interactive database.
BIOCHEMICAL PHARMACOLOGY
(2021)
Article
Chemistry, Medicinal
Dongying Li, Binsheng Gong, Joshua Xu, Baitang Ning, Weida Tong
Summary: This study investigated the impact of sequencing depth and library preparation on toxicological interpretation in RNA-seq using three samples. Results showed that a minimum of 20 million reads was sufficient to reveal key toxicity pathways, and identification of differentially expressed genes was positively associated with sequencing depth. Overall, RNA-seq had higher statistical power and overlap ratio in toxicological insights compared to TempO-seq and microarray.
CHEMICAL RESEARCH IN TOXICOLOGY
(2021)
Review
Pharmacology & Pharmacy
Kiara Fairman, Miao Li, Baitang Ning, Annie Lumen
Summary: PBPK modeling is a powerful tool with potential applications in the development of RNAi therapeutics, a class of drugs with unique pharmacokinetic properties. While there is active research in this area, there are still challenges to fully evaluating the utility of PBPK models for RNAi therapeutics. The current computational modeling approaches can support efficient development and approval of RNAi therapeutics, but further exploration and standardization are needed to optimize their use.
BIOCHEMICAL PHARMACOLOGY
(2021)
Editorial Material
Pharmacology & Pharmacy
Baitang Ning, Ai-Ming Yu
BIOCHEMICAL PHARMACOLOGY
(2021)
Review
Pharmacology & Pharmacy
Xiangjun Ji, Baitang Ning, Jinghua Liu, Ruth Roberts, Larry Lesko, Weida Tong, Zhichao Liu, Tieliu Shi
Summary: Pharmacogenomics plays essential roles in optimizing drug responses and avoiding adverse events. Population-specific therapeutic interventions and genotyping can improve clinical outcomes, highlighting the importance of precision medicine strategies. Challenges and regulatory efforts still exist in advancing this field further.
DRUG DISCOVERY TODAY
(2021)
Article
Biotechnology & Applied Microbiology
Wenming Xiao, Luyao Ren, Zhong Chen, Li Tai Fang, Yongmei Zhao, Justin Lack, Meijian Guan, Bin Zhu, Erich Jaeger, Liz Kerrigan, Thomas M. Blomquist, Tiffany Hung, Marc Sultan, Kenneth Idler, Charles Lu, Andreas Scherer, Rebecca Kusko, Malcolm Moos, Chunlin Xiao, Stephen T. Sherry, Ogan D. Abaan, Wanqiu Chen, Xin Chen, Jessica Nordlund, Ulrika Liljedahl, Roberta Maestro, Maurizio Polano, Jiri Drabek, Petr Vojta, Sulev Koks, Ene Reimann, Bindu Swapna Madala, Timothy Mercer, Chris Miller, Howard Jacob, Tiffany Truong, Ali Moshrefi, Aparna Natarajan, Ana Granat, Gary P. Schroth, Rasika Kalamegham, Eric Peters, Virginie Petitjean, Ashley Walton, Tsai-Wei Shen, Keyur Talsania, Cristobal Juan Vera, Kurt Langenbach, Maryellen de Mars, Jennifer A. Hipp, James C. Willey, Jing Wang, Jyoti Shetty, Yuliya Kriga, Arati Raziuddin, Bao Tran, Yuanting Zheng, Ying Yu, Margaret Cam, Parthav Jailwala, Cu Nguyen, Daoud Meerzaman, Qingrong Chen, Chunhua Yan, Ben Ernest, Urvashi Mehra, Roderick Jensen, Wendell Jones, Jian-Liang Li, Brian N. Papas, Mehdi Pirooznia, Yun-Ching Chen, Fayaz Seifuddin, Zhipan Li, Xuelu Liu, Wolfgang Resch, Jingya Wang, Leihong Wu, Gokhan Yavas, Corey Miles, Baitang Ning, Weida Tong, Christopher E. Mason, Eric Donaldson, Samir Lababidi, Louis M. Staudt, Zivana Tezak, Huixiao Hong, Charles Wang, Leming Shi
Summary: This study systematically investigates factors affecting detection reproducibility and accuracy of somatic mutations in paired tumor-normal cell lines at six different centers. It evaluates the reproducibility of whole-genome sequencing (WGS) and whole-exome sequencing (WES) for different sample types, input amounts, tumor purity, and library construction protocols with nine bioinformatics pipelines. The study found that read coverage and callers affected both WGS and WES reproducibility, with WES performance also affected by insert fragment size, genomic copy content, and the global imbalance score.
NATURE BIOTECHNOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Li Tai Fang, Bin Zhu, Yongmei Zhao, Wanqiu Chen, Zhaowei Yang, Liz Kerrigan, Kurt Langenbach, Maryellen de Mars, Charles Lu, Kenneth Idler, Howard Jacob, Yuanting Zheng, Luyao Ren, Ying Yu, Erich Jaeger, Gary P. Schroth, Ogan D. Abaan, Keyur Talsania, Justin Lack, Tsai-Wei Shen, Zhong Chen, Seta Stanbouly, Bao Tran, Jyoti Shetty, Yuliya Kriga, Daoud Meerzaman, Cu Nguyen, Virginie Petitjean, Marc Sultan, Margaret Cam, Monika Mehta, Tiffany Hung, Eric Peters, Rasika Kalamegham, Sayed Mohammad Ebrahim Sahraeian, Marghoob Mohiyuddin, Yunfei Guo, Lijing Yao, Lei Song, Hugo Y. K. Lam, Jiri Drabek, Petr Vojta, Roberta Maestro, Daniela Gasparotto, Sulev Koks, Ene Reimann, Andreas Scherer, Jessica Nordlund, Ulrika Liljedahl, Roderick Jensen, Mehdi Pirooznia, Zhipan Li, Chunlin Xiao, Stephen T. Sherry, Rebecca Kusko, Malcolm Moos, Eric Donaldson, Zivana Tezak, Baitang Ning, Weida Tong, Jing Li, Penelope Duerken-Hughes, Claudia Catalanotti, Shamoni Maheshwari, Joe Shuga, Winnie S. Liang, Jonathan Keats, Jonathan Adkins, Erica Tassone, Victoria Zismann, Timothy McDaniel, Jeffrey Trent, Jonathan Foox, Daniel Butler, Christopher E. Mason, Huixiao Hong, Leming Shi, Charles Wang, Wenming Xiao
Summary: This study presents reference call sets obtained from paired tumor-normal genomic DNA samples from a breast cancer cell line and a lymphoblastoid cell line. These samples were partially validated for somatic mutations and germline variants through whole-exome sequencing and targeted sequencing. The use of these samples can help calibrate clinical sequencing pipelines and provide a unique resource for benchmarking 'tumor-only' or 'matched tumor-normal' analyses.
NATURE BIOTECHNOLOGY
(2021)
Article
Genetics & Heredity
Li Zhang, Jingru Shi, Jian Ouyang, Riquan Zhang, Yiran Tao, Dongsheng Yuan, Chengkai Lv, Ruiyuan Wang, Baitang Ning, Ruth Roberts, Weida Tong, Zhichao Liu, Tieliu Shi
Summary: The research team developed the X-CNV computational framework, integrating multiple informative features to predict the pathogenicity of CNVs, outperforming other tools. They also proposed an MVP score to quantitatively measure the pathogenic effect of CNVs, demonstrating high discriminative power.
Article
Biotechnology & Applied Microbiology
Binsheng Gong, Dan Li, Rebecca Kusko, Natalia Novoradovskaya, Yifan Zhang, Shangzi Wang, Carlos Pabon-Pena, Zhihong Zhang, Kevin Lai, Wanshi Cai, Jennifer S. LoCoco, Eric Lader, Todd A. Richmond, Vinay K. Mittal, Liang-Chun Liu, Donald J. Johann, James C. Willey, Pierre R. Bushel, Ying Yu, Chang Xu, Guangchun Chen, Daniel Burgess, Simon Cawley, Kristina Giorda, Nathan Haseley, Fujun Qiu, Katherine Wilkins, Hanane Arib, Claire Attwooll, Kevin Babson, Longlong Bao, Wenjun Bao, Anne Bergstrom Lucas, Hunter Best, Ambica Bhandari, Halil Bisgin, James Blackburn, Thomas M. Blomquist, Lisa Boardman, Blake Burgher, Daniel J. Butler, Chia-Jung Chang, Alka Chaubey, Tao Chen, Marco Chierici, Christopher R. Chin, Devin Close, Jeffrey Conroy, Jessica Cooley Coleman, Daniel J. Craig, Erin Crawford, Angela del Pozo, Ira W. Deveson, Daniel Duncan, Agda Karina Eterovic, Xiaohui Fan, Jonathan Foox, Cesare Furlanello, Abhisek Ghosal, Sean Glenn, Meijian Guan, Christine Haag, Xinyi Hang, Scott Happe, Brittany Hennigan, Jennifer Hipp, Huixiao Hong, Kyle Horvath, Jianhong Hu, Li-Yuan Hung, Mirna Jarosz, Jennifer Kerkhof, Benjamin Kipp, David Philip Kreil, Pablo Lapunzina, Peng Li, Quan-Zhen Li, Weihua Li, Zhiguang Li, Yu Liang, Shaoqing Liu, Zhichao Liu, Charles Ma, Narasimha Marella, Ruben Martin-Arenas, Dalila B. Megherbi, Qingchang Meng, Piotr A. Mieczkowski, Tom Morrison, Donna Muzny, Baitang Ning, Barbara L. Parsons, Cloud P. Paweletz, Mehdi Pirooznia, Wubin Qu, Amelia Raymond, Paul Rindler, Rebecca Ringler, Bekim Sadikovic, Andreas Scherer, Egbert Schulze, Robert Sebra, Rita Shaknovich, Qiang Shi, Tieliu Shi, Juan Carlos Silla-Castro, Melissa Smith, Mario Solis Lopez, Ping Song, Daniel Stetson, Maya Strahl, Alan Stuart, Julianna Supplee, Philippe Szankasi, Haowen Tan, Lin-ya Tang, Yonghui Tao, Shraddha Thakkar, Danielle Thierry-Mieg, Jean Thierry-Mieg, Venkat J. Thodima, David Thomas, Boris Tichy, Nikola Tom, Elena Vallespin Garcia, Suman Verma, Kimbley Walker, Charles Wang, Junwen Wang, Yexun Wang, Zhining Wen, Valtteri Wirta, Leihong Wu, Chunlin Xiao, Wenzhong Xiao, Shibei Xu, Mary Yang, Jianming Ying, Shun H. Yip, Guangliang Zhang, Sa Zhang, Meiru Zhao, Yuanting Zheng, Xiaoyan Zhou, Christopher E. Mason, Timothy Mercer, Weida Tong, Leming Shi, Wendell Jones, Joshua Xu
Summary: All panels exhibit high sensitivity for variants within the 5-20% VAF range in high-confidence coding regions, but sensitivity decreases when using VAF thresholds due to variability in VAF measurements. Enforcing a VAF threshold for reporting reduces false positive calls, and false positive rate is higher outside high-confidence coding regions, leading to lower reproducibility. Region restriction and VAF thresholds result in low technical variability in estimating promising biomarkers and tumor mutational burden.
Article
Oncology
Si Chen, Qiangen Wu, Xilin Li, Dongying Li, Nan Mei, Baitang Ning, Montserrat Puig, Zhen Ren, William H. Tolleson, Lei Guo
Summary: This study confirmed the stability of CYP-overexpressing HepG2 cell lines in long-term cultures and demonstrated consistency in response to stimuli, providing valuable information for the broader use of these cells in pharmacologic and toxicologic research.
JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH PART C-ENVIRONMENTAL CARCINOGENESIS & ECOTOXICOLOGY REVIEWS
(2021)