Article
Pharmacology & Pharmacy
Stavroula Siamoglou, Maria Koromina, Eiji Hishinuma, Shuki Yamazaki, Evangelia-Eirini Tsermpini, Zoe Kordou, Koya Fukunaga, Wasun Chantratita, Yitian Zhou, Volker M. Lauschke, Taisei Mushiroda, Masahiro Hiratsuka, George P. Patrinos
Summary: Inter-individual variability in pharmacokinetics and drug response is influenced by SNVs and CNVs in drug disposition genes. Next generation sequencing is used to discover PGx variants that affect drug response. We present a comprehensive workflow for integrating next-generation sequencing into PGx testing, from re-sequencing to in vitro validation assays.
PHARMACOLOGICAL RESEARCH
(2022)
Review
Biochemical Research Methods
Tingting Gong, Vanessa M. Hayes, Eva K. F. Chan
Summary: This review highlights important factors affecting somatic SV detection and compares the performance of seven commonly used SV callers. By focusing on changes in sensitivity and precision for detecting different SV types and size ranges from samples with varying variant allele frequencies and sequencing depths, the evaluation findings extend beyond the seven SV callers examined in this paper.
BRIEFINGS IN BIOINFORMATICS
(2021)
Review
Pharmacology & Pharmacy
Alireza Tafazoli, Henk-Jan Guchelaar, Wojciech Miltyk, Adam J. Kretowski, Jesse J. Swen
Summary: Pharmacogenomics (PGx) utilizes genetic data to optimize drug therapy, with next-generation sequencing (NGS) emerging as a more comprehensive and cost-effective approach. The advantages and challenges of implementing NGS-based tests in PGx are discussed, along with solutions for managing these technologies in clinical practice.
FRONTIERS IN 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
Genetics & Heredity
Alesa Kristan, Tadej Pajic, Ales Maver, Tadeja Rezen, Tanja Kunej, Rok Kolic, Andrej Vuga, Martina Fink, Spela Zula, Helena Podgornik, Sasa Anzej Doma, Irena Preloznik Zupan, Damjana Rozman, Natasa Debeljak
Summary: An erythrocytosis is characterized by an increase in red blood cell mass, often associated with genetic variants in genes related to oxygen sensing, hematopoietic cell maturation, and oxygen transfer. Classical sequencing approaches may only provide a correct diagnosis for a fraction of patients with congenital erythrocytosis, as the genetic background of the disorder is more complex and involves additional genes. A targeted next-generation sequencing approach was used in this study to identify genetic variants in patients with unexplained erythrocytosis, leading to the discovery of pathogenic and novel variants in relevant genes, as well as the identification of potential associations with iron metabolism genes. This study contributes to improving the diagnosis and management of Slovenian patients with erythrocytosis and provides insights for future research into the etiology of this rare hematological disorder.
FRONTIERS IN GENETICS
(2021)
Article
Biochemical Research Methods
Brendan O'Fallon, Jacob Durtschi, Ana Kellogg, Tracey Lewis, Devin Close, Hunter Best
Summary: This study proposes two algorithmic adaptations to improve the accuracy of CNV detection in a Hidden Markov Model (HMM) context. First, it improves the accuracy by computing target- and copy number-specific emission distributions. Second, it enhances the sensitivity for small CNV calls using the Pointwise Maximum a posteriori (PMAP) HMM decoding procedure. The prototype implementation, called Cobalt, shows similar sensitivity to other CNV detection tools but significantly reduces false positive detections.
BMC BIOINFORMATICS
(2022)
Article
Oncology
Angeliki Andrikopoulou, Eleni Zografos, Kleoniki Apostolidou, Anastasios Kyriazoglou, Alksistis-Maria Papatheodoridi, Maria Kaparelou, Konstantinos Koutsoukos, Michalis Liontos, Meletios-Athanasios Dimopoulos, Flora Zagouri
Summary: This study aimed to identify the molecular landscape of germline and somatic mutations in ovarian cancer patients through NGS analysis. The results revealed that TP53 and BRCA1 were the most common somatic mutations in high grade serous carcinoma patients, while BRCA1 and BRCA2 were the most common genes with pathogenic alterations in germline mutations.
FRONTIERS IN ONCOLOGY
(2022)
Article
Genetics & Heredity
Karim Hasanpur, Sevda Hosseinzadeh, Atiye Mirzaaghayi, Sadegh Alijani
Summary: Accurate normalization of gene expression assays using housekeeping genes is crucial, but there is no consensus on the suitable set of housekeeping genes for quantitative real-time PCR analyses of chicken tissues. This study utilized high-throughput gene expression data to identify the most suitable and stable reference genes for 16 chicken tissues. The results revealed tissue-specific sets of reference genes and disproved the suitability of previously widely used housekeeping genes. The newly identified reference genes can contribute to more accurate normalization for future expression analysis of chicken genes.
FRONTIERS IN GENETICS
(2022)
Review
Biochemical Research Methods
Sergey Knyazev, Lauren Hughes, Pavel Skums, Alexander Zelikovsky
Summary: Advancements in next-generation sequencing have enabled detailed assessment of viral population complexity within hosts, extracting crucial epidemiological and biomedical information. However, the complex analysis of NGS data is required to handle the rapidly mutating viral populations.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Genetics & Heredity
Jaymi Tan, Yock Ping Chow, Norziha Zainul Abidin, Kian Meng Chang, Veena Selvaratnam, Nor Rafeah Tumian, Yang Ming Poh, Abhi Veerakumarasivam, Michael Arthur Laffan, Chieh Lee Wong
Summary: This study validated the technical performance of a custom 22-gene NGS panel and used it to screen 10 clinical MPN samples. The NGS analysis showed high accuracy and identified known and novel variants, supporting its potential clinical utility in the management of MPNs.
BMC MEDICAL GENOMICS
(2022)
Article
Biochemistry & Molecular Biology
Claudia Maria Hattinger, Chiara Casotti, Maria Pia Patrizio, Silvia Luppi, Leonardo Fantoni, Katia Scotlandi, Toni Ibrahim, Massimo Serra
Summary: This study investigated the relationship between SNPs and CDDP resistance in high-grade osteosarcoma cells, providing a basis for further research on the topic.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Christos Tzaferis, Evangelos Karatzas, Fotis A. Baltoumas, Georgios A. Pavlopoulos, George Kollias, Dimitris Konstantopoulos
Summary: Analysis and interpretation of high-throughput transcriptional and chromatin accessibility data at single-cell resolution remain challenges in the biomedical field. SCALA is a bioinformatics tool for analyzing and visualizing single-cell RNA sequencing and Assay for Transposase-Accessible Chromatin using sequencing data-sets. It offers independent or integrative analysis options and various analysis modules to aid biomedical researchers in exploring, analyzing, and visualizing their data without coding experience.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Genetics & Heredity
Manal Alaamery, Jahad Alghamdi, Salam Massadeh, Mona Alsawaji, Nora Aljawini, Nour Albesher, Bader Alghamdi, Mansour Almutairi, Fayez Hejaili, Majid Alfadhel, Batoul Baz, Bader Almuzzaini, Adel F. Almutairi, Mubarak Abdullah, Francisco J. Quintana, Abdullah Sayyari
Summary: This study aimed to investigate the genetic causes of end-stage renal disease (ESRD) in Saudi kidney disease patients, using a targeted next-generation sequencing gene panel. The results identified several genetic variants associated with ESRD and CKD in this population, including novel variants not previously reported in other populations. Further studies are needed to validate these findings in larger sample sizes and different ethnic groups.
FRONTIERS IN GENETICS
(2022)
Article
Biochemical Research Methods
Timo Lassmann
Summary: SAMStat is an efficient program for extracting quality control metrics from fastq and SAM/BAM files. It displays sequence composition, base quality composition, and mapping error profiles based on mapping quality, allowing users to quickly identify reasons for poor mapping. A major update to SAMStat now supports paired-end and long-read data, with quality control plots drawn using the ploty javascript library.
Article
Multidisciplinary Sciences
Ewa Goljan, Mohammed Abouelhoda, Mohamed M. ElKalioby, Amjad Jabaan, Nada Alghithi, Brian F. Meyer, Dorota Monies
Summary: This study provides a comprehensive overview of pharmacogenetic variation in the Saudi population. It identifies functional variants in pharmacogenes, particularly in CYP genes, and highlights the high polymorphism of VKORC1 gene in this population. Unique rare variants are also found in the Saudi population.
Article
Environmental Sciences
Gyujin Heo, Catherine Apio, Kyulhee Han, Taewan Goo, Hye Won Chung, Taehyun Kim, Hakyong Kim, Yeonghyeon Ko, Doeun Lee, Jisun Lim, Taesung Park
Summary: The study found that the health and government indices in Korea were most effective in mitigating the spread of the COVID-19 virus, while restriction and stringency indices were mainly effective with lagging effects. It requires some time before the impact of certain policies can be observed.
INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH
(2021)
Article
Environmental Sciences
Chanhee Lee, Catherine Apio, Taesung Park
Summary: The study reveals the importance of estimating the proportion of undetected asymptomatic COVID-19 cases for controlling the pandemic. The probabilistic model suggests that South Korea may have 5200-139,900 undetected asymptomatic cases as of February 2, 2021.
INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH
(2021)
Article
Oncology
Suhyun Hwangbo, Se Ik Kim, Ju-Hyun Kim, Kyung Jin Eoh, Chanhee Lee, Young Tae Kim, Dae-Shik Suh, Taesung Park, Yong Sang Song
Summary: The study aimed to develop machine learning models predicting platinum sensitivity in patients with high-grade serous ovarian carcinoma (HGSOC). Six variables associated with platinum sensitivity were selected using clinical data from multiple hospitals, and the LR-based model was found to perform the best. A web-based nomogram was developed for clinical use based on the LR model results.
Article
Biology
Jae Ri Kim, Kyulhee Han, Youngmin Han, Nayeon Kang, Tae-Seop Shin, Hyeon Ju Park, Hongbeom Kim, Wooil Kwon, Seungyeoun Lee, Yoon-Keun Kim, Taesung Park, Jin-Young Jang
Summary: Novel microbiome markers were identified by analyzing compositional differences between pancreatic cancer patients and healthy controls, leading to the construction of a high-accuracy prediction model for early diagnosis of pancreatic cancer.
Article
Biochemical Research Methods
Seungyoon Nam, Sungyoung Lee, Sungjin Park, Jinhyuk Lee, Aron Park, Yon Hui Kim, Taesung Park
Summary: A subpathway-based polypharmacology drug repositioning method, PATHOME-Drug, was developed to address the limitations of existing methods in detecting potential drugs for diseases with no available treatments. The method showed better performance in identifying signaling context and specific drugs/compounds, demonstrating its potential in addressing the current shortage of targeted therapy agents.
Article
Statistics & Probability
Md Kamruzzaman, Oran Kwon, Taesung Park
Summary: In this study, a penalized generalized estimating equation was developed for high-dimensional longitudinal data with multinomial response to identify important variables and estimate their regression coefficients simultaneously. An iterative algorithm combining Fisher-scoring and minorization-maximization algorithms was used to solve the penalized estimating equation. The performance of the proposed method was investigated through a simulation study and demonstrated using real dataset.
JOURNAL OF THE KOREAN STATISTICAL SOCIETY
(2021)
Article
Nutrition & Dietetics
Ho-Sun Lee, Sanghwan In, Taesung Park
Summary: This study utilized Mendelian Randomization to investigate the causal influence of Homocysteine (Hcy) on Metabolic Syndrome (MetS) and found that increased Hcy levels were significantly associated with increased risk of MetS in the Korean population.
Article
Environmental Sciences
Hakyong Kim, Catherine Apio, Yeonghyeon Ko, Kyulhee Han, Taewan Goo, Gyujin Heo, Taehyun Kim, Hye Won Chung, Doeun Lee, Jisun Lim, Taesung Park
Summary: The study found that different national factors have significant variations in their impact on the spread of COVID-19. Factors such as total population size have a major influence on the parameter related to the maximum number of predicted cumulative confirmed cases, while aging index, cardiovascular death rate, extreme poverty, and other factors have a significant impact on the parameter related to the rate of spread of COVID-19.
INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH
(2021)
Article
Oncology
Kidong Kim, Suhyun Hwangbo, Hyojin Kim, Yong Beom Kim, Jae Hong No, Dong Hoon Suh, Taesung Park
Summary: The study identified clinicopathologic and protein markers that distinguish the POLE subtype of endometrial cancer from the CN-low subtype. BMI and expression of cyclin B1, caspase 8, and XBP1 were found to be candidate markers. Immunohistochemistry validation supported the findings.
JOURNAL OF GYNECOLOGIC ONCOLOGY
(2022)
Article
Biochemical Research Methods
Suhyun Hwangbo, Sungyoung Lee, Seungyeoun Lee, Heungsun Hwang, Inyoung Kim, Taesung Park
Summary: The study proposes a new approach that takes into account non-linear effects and correlations among pathways in omics data analysis. The method is validated in real and simulated datasets and demonstrates superior performance in identifying biologically meaningful pathways.
Article
Biochemical Research Methods
Chanwoo Park, Boram Kim, Taesung Park
Summary: This study proposes a deep-learning pathway analysis method that considers the nonlinear complex contribution of biological factors to pathways. The method uses a multilayered model to account for hierarchical biological structure. Simulation and application results demonstrate the effectiveness of the method in identifying disease-associated pathways.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Ho-Sun Lee, Boram Kim, Taesung Park
Summary: Novel rare variants of genes associated with MetS susceptibility were discovered in transethnic MetS association studies, which are shared with diverse populations in Europeans.
Article
Nutrition & Dietetics
Seoyoung Lee, Iksoo Huh, Seunghee Kang, Yea-eun Nam, Youngseo Cho, Md Kamruzzaman, Jina Hong, Oran Kwon, Taesung Park
Summary: This study conducted a meta-analysis of six randomized placebo-controlled trials to examine the relationship between plant-based multivitamin/mineral supplementation (PMS) and oxidative stress. The results showed a significant association between PMS and alleviation of oxidative stress by providing exogenous oxidant scavengers.
Article
Biochemical Research Methods
Sun Ah Kim, Nayeon Kang, Taesung Park
Summary: The recent development of high-throughput sequencing technology has allowed us to examine the connections between human microbiome and diseases. This paper introduces a hierarchical structural component model for microbiome data analysis that incorporates taxonomy information along with OTU table data. This model successfully reveals the relationships between each taxon and disease status and identifies key OTUs for the disease.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2022)
Article
Medicine, General & Internal
Shin-Woo Kim, Seung-Mee Kim, Yu Kyung Kim, Jong-yeon Kim, Yu-Mi Lee, Bong-Ok Kim, Suhyun Hwangbo, Taesung Park
Summary: The COVID-19 outbreak in Daegu, Korea was controlled by the end of March 2020. A retrospective, multicenter cohort study conducted on 7,057 laboratory-confirmed patients revealed that 77% were asymptomatic to mild. Key risk factors for 28-day mortality included age, need for O-2 supply, fever, and underlying health conditions like diabetes and cancer.
JOURNAL OF KOREAN MEDICAL SCIENCE
(2021)