Article
Biochemistry & Molecular Biology
Md. Mostafa Kamal, Md. Numan Islam, Md. Golam Rabby, Md. Ashrafuzzaman Zahid, Md. Mahmudul Hasan
Summary: This study investigates the role of PAX4 gene polymorphisms in the pathogenesis of various human diseases. Bioinformatic analyzes were conducted to identify the SNPs of PAX4 gene that contribute to diseases. The results show that certain nsSNPs in PAX4 gene can lead to structural and functional changes in the protein, potentially progressing diseases.
BIOCHEMICAL GENETICS
(2023)
Article
Automation & Control Systems
Fang Ge, Arif Muhammad, Dong-Jun Yu
Summary: A novel deep learning model MSCNN was proposed in this study, which utilized multi-scale convolution with different kernel sizes for feature processing and incorporated three types of nominal structural features to enhance nsSNPs prediction performance. Experimental results showed that DeepnsSNPs outperformed individual classifiers and consensus classifiers on three datasets, demonstrating its effectiveness in predicting nsSNPs.
CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS
(2021)
Article
Multidisciplinary Sciences
Ishtiaque Ahammad, Tabassum Binte Jamal, Arittra Bhattacharjee, Zeshan Mahmud Chowdhury, Suparna Rahman, Md Rakibul Hassan, Mohammad Uzzal Hossain, Keshob Chandra Das, Chaman Ara Keya, Md Salimullah
Summary: GRIN2A is a gene encoding NMDA receptors in the central nervous system, playing a crucial role in synaptic transmission, plasticity, and excitotoxicity. Variants in this gene, particularly the I463S variant, are predicted to have deleterious effects on protein structure and function. Bioinformatics tools were used to assess the impact of these variants, providing valuable insights for future research on GRIN2A-related diseases.
Article
Biochemistry & Molecular Biology
Jie Yue, You-Fei Qi, Wen-Bo Zhang, Sa-Hua Liu, Hao Chen, Zhen-Zhen Li, Hong-Fei Wu
Summary: This study aimed to investigate the effect of single nucleotide polymorphisms (SNPs) in the tropoelastin gene on the expression of tropoelastin mRNA and elastin in human aortic smooth muscle cells (HASMCs). The results showed that SNP mutations affected the expression of tropoelastin mRNA and elastin, suggesting that these polymorphisms might be important factors in the development of aortic aneurysms.
DNA AND CELL BIOLOGY
(2023)
Article
Computer Science, Artificial Intelligence
Enas M. F. El Houby
Summary: The proposed framework aims to distinguish disease-causing missense variants from neutral mutations by predicting the pathogenicity of SNP-induced amino acid changes. It utilizes an attributes selection tool and a machine learning-based classifier to optimize the set of selected attributes for improved classification accuracy. Benchmark datasets were used to evaluate the framework, and it outperformed other methods in terms of accuracy. Artificial neural network was found to be the best machine learning technique for this task.
JOURNAL OF AMBIENT INTELLIGENCE AND HUMANIZED COMPUTING
(2022)
Article
Genetics & Heredity
Fatima Muccee, Osama Bijou, Steve Harakeh, Rabi'atul Adawiyah, R. Z. Sayyed, Leila Haghshenas, Dikhnah Alshehri, Mohammad Javed Ansari, Shakira Ghazanfar
Summary: PCOS is a reproductive disorder with multiple etiologies. The present study investigates the effect of single nucleotide polymorphisms in human CYP11A1 gene on different attributes of mutated proteins. These genetic variants can serve as potential biomarkers for determining the probability of being predisposed to PCOS.
Article
Multidisciplinary Sciences
Makda S. Gebre, Susanne Rauch, Nicole Roth, Jingyou Yu, Abishek Chandrashekar, Noe B. Mercado, Xuan He, Jinyan Liu, Katherine McMahan, Amanda Martinot, David R. Martinez, Victoria Giffin, David Hope, Shivani Patel, Daniel Sellers, Owen Sanborn, Julia Barrett, Xiaowen Liu, Andrew C. Cole, Laurent Pessaint, Daniel Valentin, Zack Flinchbaugh, Jake Yalley-Ogunro, Jeanne Muench, Renita Brown, Anthony Cook, Elyse Teow, Hanne Andersen, Mark G. Lewis, Adrianus C. M. Boon, Ralph S. Baric, Stefan O. Mueller, Benjamin Petsch, Dan H. Barouch
Summary: In non-human primates, the second-generation mRNA vaccine CV2CoV was found to induce higher levels of immune responses and provide stronger protection against SARS-CoV-2 variants compared to CVnCoV. The optimization of non-coding regions greatly improved the immunogenicity and protective efficacy of the non-modified mRNA vaccine in non-human primates.
Article
Biology
Muhammad Mazhar Fareed, Sana Ullah, Shan Aziz, Todd Axel Johnsen, Sergey Shityakov
Summary: This computational study on nsSNPs in the DEFB1 gene provides insights into how missense mutations can impair or change protein functions by altering the PIP2 binding site. The study identifies four most important nsSNPs in DEFB1, with two of them linked to decreased binding affinity with bacterial PIP2.
COMPUTATIONAL BIOLOGY AND CHEMISTRY
(2022)
Article
Multidisciplinary Sciences
Shu Wen Lim, Kennet JunKai Tan, Osman Mohd Azuraidi, Maran Sathiya, Ee Chen Lim, Kok Song Lai, Wai-Sum Yap, Nik Abd Rahman Nik Mohd Afizan
Summary: MYB proteins are highly conserved DNA-binding domains, and mutations in MYB oncoproteins can lead to aberrant cancer progression. A biomarker discovery pipeline was employed to investigate deleterious nsSNPs in the MYB family, which may alter protein stability and DNA-binding specificity. Results suggest potential implications for pharmacogenomic and cancer therapy.
SCIENTIFIC REPORTS
(2021)
Article
Biotechnology & Applied Microbiology
Jayanta Kumar Das, Swarup Roy
Summary: This study provides a comprehensive quantitative analysis of the protein-coding sequences of seven human coronaviruses, revealing the nucleotide sequence variability and codon usage patterns. Different categories of codons exhibit diverse adaptability, with notable variability in GC content at the third position among the seven coronaviruses. Phylogenetic analysis depicted the evolutionary relationships among these viruses and their positions in the tree.
Article
Immunology
Ding-Ping Chen, Tang-Her Jaing, Ai-Ling Hour, Wei-Tzu Lin, Fang-Ping Hsu
Summary: This study identified specific SNPs in non-HLA genes associated with the effectiveness of unrelated CBT, which can aid in selecting the best donor and predicting the risk of CBT adverse reactions, further suggesting the important role of SNPs in immune regulation.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Ho Jin Choi, Sarmistha Mitra, Yeasmin Akter Munni, Raju Dash, Sarmin Ummey Habiba, Md Sohel, Sultana Israt Jahan, Tae Jung Jang, Il Soo Moon
Summary: Disruptive neuronal migration during early brain development can cause severe brain malformation. This study identified high-risk nsSNPs in the LIS1 gene through bioinformatics and molecular modeling, and demonstrated their impact on the loss of LIS1 function through molecular dynamics simulation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Environmental Sciences
Gayatri Mohanty, Soumya Ranjan Jena, Sujata Kar, Luna Samanta
Summary: HSPA2 is a testis-specific molecular chaperone that plays a key role in spermatogenesis. Computational analysis revealed 18 deleterious nsSNPs in the HSPA2 gene, suggesting its potential impact on reproductive outcomes. Additionally, gene-gene interaction study identified a close association with antioxidant enzyme SOD1, providing insight into the oxidative scavenging regulatory mechanism in RPL patients.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2022)
Article
Zoology
Umer Farooq, Nimra Murtaza, Abubakar Siddique, Bilal Saleem, Obaid Ur Rehman, Nageen Zahra, Muhammad Uzair, Muhammad Naeem Riaz, Muhammad Ramzan Khan
Summary: By analyzing the genomic data of four different cattle breeds in Pakistan, deleterious SNPs and their associated genes that may disrupt protein structure and function and lead to genetic diseases were identified. These findings provide valuable insights into the molecular processes associated with these variations.
PAKISTAN JOURNAL OF ZOOLOGY
(2023)
Review
Cell Biology
Farbod Bahreini, Elham Rayzan, Nima Rezaei
Summary: Breast cancer, a multifactorial disease, may have an increased risk due to alterations in microRNA sequences. miR-SNPs are potential biomarkers for early detection of breast cancer.
JOURNAL OF CELLULAR PHYSIOLOGY
(2021)
Article
Psychiatry
Yichuan Liu, Hui-Qi Qu, Xiao Chang, Lifeng Tian, Joseph Glessner, Patrick A. M. Sleiman, Hakon Hakonarson
Summary: Given the complexity of schizophrenia gene networks, it is challenging to identify key genes and pathways associated with the disease. In this study, RNA sequencing data and machine learning methods were used to prioritize genes and reveal novel gene interactions related to schizophrenia. The findings provide important insights into the pathogenesis of schizophrenia.
FRONTIERS IN PSYCHIATRY
(2022)
Article
Allergy
Xiao Chang, Michael March, Frank Mentch, Huiqi Qu, Yichuan Liu, Joseph Glessner, Patrick Sleiman, Hakon Hakonarson
Summary: This study aimed to identify genetic loci associated with asthma in African American individuals. Through a meta-analysis of three cohorts, 12 genetic loci were found to be significantly associated with asthma. These loci may serve as candidate genetic loci for therapeutic target identification in African populations.
JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY
(2023)
Article
Genetics & Heredity
Hui-Qi Qu, Charlly Kao, James Garifallou, Fengxiang Wang, James Snyder, Diana J. Slater, Cuiping Hou, Michael March, John J. Connolly, Joseph T. Glessner, Hakon Hakonarson
Summary: This study investigated the impact of varying time periods from blood draw to PBMC isolation on the subsequent transcriptome profiling of different cell types in PBMCs using single cell RNA-seq. The results showed significant changes in the transcriptome expression of various cell types over time, highlighting the importance of considering this factor in interpreting experimental results.
Article
Immunology
Christopher J. Cardinale, Xiao Chang, Zhi Wei, Hui-Qi Qu, Jonathan P. Bradfield, Constantin Polychronakos, Hakon Hakonarson
Summary: This study conducted a genome-wide association study (GWAS) to identify genetic correlates of the age of onset in type 1 diabetes. The study found associations between the HLA-DQB1 gene and age of diagnosis, as well as the variant rs10833518 in the NELL1 gene on chromosome 11. The study also implicated the HTATIP2 gene in T cell regulation and its role in the development of type 1 diabetes.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Genetics & Heredity
Alanna Strong, Hui-Qi Qu, Sinead Cullina, Morgan L. McManus, Elaine H. Zackai, Joseph Glessner, Eimear E. Kenny, Hakon Hakonarson
Summary: Joubert syndrome (JBTS) is a genetic disorder characterized by primary cilium dysfunction, leading to hypotonia, developmental delay, and a specific cerebellar malformation. Although many causal genes have been identified, a significant proportion of individuals with clinical symptoms cannot be molecularly diagnosed.
AMERICAN JOURNAL OF MEDICAL GENETICS PART A
(2023)
Editorial Material
Cardiac & Cardiovascular Systems
Arthur M. Feldman, Edward K. Kasper, Hui-Qi Qu
JACC-HEART FAILURE
(2023)
Article
Genetics & Heredity
Wentao Zhou, Jun Jia, Hui-Qi Qu, Feier Ma, Junyi Li, Xiaohui Qi, Xinyi Meng, Zhiyong Ding, Gang Zheng, Hakon Hakonarson, Xiantie Zeng, Jin Li, Qianghua Xia
Summary: In this study, a genetic analysis was conducted on the structural variants underlying familial hallux valgus using whole exome sequencing approach. A total of 372 copy number variations were found, with 43 being present only in cases and not in controls or healthy individuals. These copy number variations were enriched in gene sets related to immune signaling pathway and cytochrome P450 metabolism. The study suggests that hallux valgus is a degenerative joint disease involving dysregulation of immune and metabolism signaling pathways.
FRONTIERS IN GENETICS
(2023)
Review
Cell Biology
Caitlyn M. Brenner, Muaaz Choudhary, Michael G. McCormick, David Cheung, Gavin P. Landesberg, Ju-Fang Wang, Jianliang Song, Thomas G. Martin, Joseph Y. Cheung, Hui-Qi Qu, Hakon Hakonarson, Arthur M. Feldman
Summary: BAG3 is a versatile protein found in animals and plants, with prominent expression in certain tissues and cancers. It plays multiple roles, including supporting autophagy, inhibiting apoptosis, maintaining mitochondrial homeostasis, and facilitating excitation-contraction coupling. High levels of BAG3 are associated with chemotherapy resistance in cancer cells, while loss or gain of function variants are linked to cardiomyopathy.
Article
Oncology
Hui-Qi Qu, John J. Connolly, Peter Kraft, Jirong Long, Alexandre Pereira, Christopher Flatley, Constance Turman, Bram Prins, Frank Mentch, Paulo A. Lotufo, Per Magnus, Meir J. Stampfer, Rulla Tamimi, A. Heather Eliassen, Wei Zheng, Gun Peggy Stromstad Knudsen, Oyvind S. Helgeland, Adam Butterworth, Hakon M. Hakonarson, Patrick Sleiman
Summary: Through the collaboration model of IHCC, a globally applicable trans-ethnic PRS for BMI was developed, which can effectively estimate an individual's risk of developing complex traits such as obesity.
CLINICAL AND TRANSLATIONAL MEDICINE
(2023)
Article
Clinical Neurology
Patrick M. Sleiman, Hui-Qi Qu, John J. Connolly, Frank Mentch, Alexandre Pereira, Paulo A. Lotufo, Stephen Tollman, Ananyo Choudhury, Michele Ramsay, Norihiro Kato, Kouichi Ozaki, Risa Mitsumori, Jae-Pil Jeon, Chang Hyung Hong, Sang Joon Son, Hyun Woong Roh, Dong-gi Lee, Naaheed Mukadam, Isabelle F. Foote, Charles R. Marshall, Adam Butterworth, Bram P. Prins, Joseph T. Glessner, Hakon Hakonarson
Summary: The aim of this study was to develop a trans-ethnic genomic informed risk assessment (GIRA) algorithm for Alzheimer's disease (AD) through collaboration between IHCC and DAC. The GIRA model included polygenic risk score, apolipoprotein E haplotypes, and non-genetic covariates. The performance of the GIRA model was validated in different populations and proteins related to female infertility and autoimmune thyroiditis were identified. This study provides a potential tool for identifying high-risk individuals for future clinical applications.
ALZHEIMERS & DEMENTIA
(2023)
Article
Biochemistry & Molecular Biology
Yichuan Liu, Hui-Qi Qu, Xiao Chang, Frank D. Mentch, Haijun Qiu, Xiang Wang, Amir Hossein Saeidian, Deborah Watson, Joseph Glessner, Hakon Hakonarson
Summary: Children with birth defects often have distinct clinical features and are predisposed to developing cancer. We performed a whole genome sequencing study and identified recurrent genetic variants associated with cancer development in these children. These variants were found in protein-coding and non-coding regions of the genome, including exons, introns, and ncRNAs.
Letter
Oncology
Yichuan Liu, Hui-Qi Qu, Xiao Chang, Frank D. Mentch, Haijun Qiu, Kenny Nguyen, Xiang Wang, Amir Hossein Saeidian, Deborah Watson, Joseph Glessner, Hakon Hakonarson
CANCER COMMUNICATIONS
(2023)
Meeting Abstract
Peripheral Vascular Disease
Anna Felicja Dominiczak
JOURNAL OF HYPERTENSION
(2023)
Review
Cell & Tissue Engineering
Hui-Qi Qu, Charlly Kao, Hakon Hakonarson
Summary: Single-cell RNA sequencing (scRNA-seq) is a revolutionary technology that has greatly contributed to our understanding of cellular heterogeneity and gene expression dynamics, particularly in stem cell research. Different types of scRNA-seq technologies have been developed and they offer distinct advantages in capturing cellular heterogeneity and characterizing rare cell populations within complex tissues.
Review
Genetics & Heredity
Sara Abudahab, Nancy Hakooz, Laith Al-Etian, Kawkab Shishani, Adel Bashqawi, John Connolly, Joseph T. Glessner, Hui-Qi Qu, Jingchun Qu, Hakon Hakonarson, Rana Dajani
Summary: This review article discusses the genetic characteristics, disease predisposition, and medication response variations among the Circassian and Chechen populations in Jordan. The research findings provide valuable insights into the unique genetic traits, disease prevalence, and medication responses of these populations.
JOURNAL OF COMMUNITY GENETICS
(2023)