Article
Clinical Neurology
Damiano Mistri, Nicolo Tedone, Diana Biondi, Carmen Vizzino, Elisabetta Pagani, Maria A. Rocca, Massimo Filippi
Summary: This study identified five cognitive phenotypes with varying degrees of impairment in multiple sclerosis (MS) patients and described their characteristics. The findings suggest potential variations in the neural substrates of dysfunction throughout disease stages in MS.
JOURNAL OF NEUROLOGY
(2023)
Article
Biochemistry & Molecular Biology
Yingbo Cui, Xiaolong Cheng, Qing Chen, Bicna Song, Anthony Chiu, Yuan Gao, Tyson Dawson, Lumen Chao, Wubing Zhang, Dian Li, Zexiang Zeng, Jijun Yu, Zexu Li, Teng Fei, Shaoliang Peng, Wei Li
Summary: CRISP-view is a comprehensive database containing high-throughput genetic screening datasets based on CRISPR/Cas9 and RNAi, covering various phenotypes. It has collected 10,321 human samples and 825 mouse samples from 167 papers, with curated and processed datasets available for visualization and exploration on a user-friendly webserver.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Genetics & Heredity
Kousik Kundu, Alice L. Mann, Manuel Tardaguila, Stephen Watt, Hannes Ponstingl, Louella Vasquez, Nicholas W. Morrell, Oliver Stegle, Tomi Pastinen, Stephen J. Sawcer, Carl A. Anderson, Klaudia Walter, Nicole Soranzo
Summary: The colocalization of regulatory quantitative trait loci from the BLUEPRINT project with genetic association data aids in the fine-mapping of putative causal variants for 12 immune-mediated diseases.
Article
Biotechnology & Applied Microbiology
Hongping Guo, Tong Li, Zixuan Wang
Summary: In this study, a new method called MRBSS is proposed for pleiotropic association analysis. It views high-dimensional genotypic data as response variables and multiple phenotypic data as predictor variables. The method reduces computational time and achieves higher statistical power in most scenarios, while controlling the type I error rate at a low level.
Article
Biochemistry & Molecular Biology
Scott C. Fears, Susan K. Service, Barbara Kremeyer, Carmen Araya, Xinia Araya, Julio Bejarano, Margarita Ramirez, Gabriel Castrillon, Juliana Gomez-Franco, Maria C. Lopez, Gabriel Montoya, Patricia Montoya, Ileana Aldana, Terri M. Teshiba, Noor B. Al-Sharif, Maria Jalbrzikowski, Todd A. Tishler, Javier Escobar, Andres Ruiz-Linares, Carlos Lopez-Jaramillo, Gabriel Macaya, Julio Molina, Victor Reus, Rita M. Cantor, Chiara Sabatti, Nelson B. Freimer, Carrie E. Bearden
Summary: Bipolar disorder is highly heritable and associated with brain structure alterations. Studies in genetically isolated populations in Latin America have shown that genes may play a significant role in differences in brain morphology related to bipolar disorder.
MOLECULAR PSYCHIATRY
(2021)
Article
Multidisciplinary Sciences
Mark Bustoros, Shankara Anand, Romanos Sklavenitis-Pistofidis, Robert Redd, Eileen M. Boyle, Benny Zhitomirsky, Andrew J. Dunford, Yu-Tzu Tai, Selina J. Chavda, Cody Boehner, Carl Jannes Neuse, Mahshid Rahmat, Ankit Dutta, Tineke Casneuf, Raluca Verona, Efstathis Kastritis, Lorenzo Trippa, Chip Stewart, Brian A. Walker, Faith E. Davies, Meletios-Athanasios Dimopoulos, P. Leif Bergsagel, Kwee Yong, Gareth J. Morgan, Francois Aguet, Gad Getz, Irene M. Ghobrial
Summary: This study identifies six distinct molecular and clinical subtypes of smoldering multiple myeloma (SMM) using genetic alterations analysis. Three of these subtypes are associated with an increased risk of progression to active multiple myeloma.
NATURE COMMUNICATIONS
(2022)
Article
Geography
Timothy Mulrooney, Chyi-Lyi Liang, Lyubov A. Kurkalova, Christopher McGinn, Chima Okoli
Summary: This paper explores the differences between rural areas and their urban/suburban counterparts in terms of social, economic, political, and health phenomena. However, due to the ambiguity of the definition of rural, there are varying meanings and applications of the term. The study investigates three popular uses of the term and finds that 1) statistical differences exist in the data depending on how rural is defined, and 2) the USDA's Rural-Urban Commuting Areas (RUCA) definition best aligns with other definitions of rural.
JOURNAL OF RURAL STUDIES
(2023)
Article
Biochemical Research Methods
Jinjuan Wang, Mingya Long, Qizhai Li
Summary: MaxKAT is a alternative method for genetic association analysis that allows for simultaneous analysis of multiple phenotypes with a set of genetic variants. It overcomes the power loss issue of the kernel-based association test (KAT) when there are moderate to strong correlations between phenotypes. The proposed method, implemented in the R package MaxKAT, demonstrates high accuracy and improved statistical power.
Article
Genetics & Heredity
Hongjing Xie, Xuewei Cao, Shuanglin Zhang, Qiuying Sha
Summary: This research presents a method to address the issue of inflated type I error rates in joint analysis of multiple unbalanced case-control phenotypes in genome-wide association studies. The method involves grouping the phenotypes into clusters, merging them into single phenotypes, and estimating p-values using the saddlepoint approximation. The proposed approach demonstrates good control of type I error rate and higher power compared to other available methods. Application of the method to the UK Biobank dataset identified more significant SNPs than other viable methods.
GENETIC EPIDEMIOLOGY
(2023)
Article
Biology
Hui Yu, Marcelo Rubinstein, Malcolm J. Low
Summary: This study used single-cell RNA sequencing and translating ribosome affinity purification with RNA sequencing to analyze the transcriptome and translatome of developing and mature POMC neurons in the hypothalamus. The results revealed diverse genetic programs specifying the identity and differentiation of arcuate POMC neurons, generating a heterogeneous repertoire of neuronal phenotypes early in development. These findings provide insights into the ontogenetic transcriptional programs of POMC neurons and their role in regulating food intake and energy balance.
Article
Mathematics
Mohammed Ibrahim, Umi Kalsom Yusof, Taiseer Abdalla Elfadil Eisa, Maged Nasser
Summary: This paper introduces an enhanced evolutionary-based multi-objective optimization method to simplify the problem of multiple sequence alignment and successfully mitigate computational complexities. Through experimental comparison and statistical analysis, the superior solution quality of this method is verified, providing promise for advancing multiple sequence alignment in the field of bioinformatics.
Article
Multidisciplinary Sciences
Seyhan Yazar, Jose Alquicira-Hernandez, Kristof Wing, Anne Senabouth, M. Grace Gordon, Stacey Andersen, Qinyi Lu, Antonia Rowson, Thomas R. P. Taylor, Linda Clarke, Katia Maccora, Christine Chen, Anthony L. Cook, Chun Jimmie Ye, Kirsten A. Fairfax, Alex W. Hewitt, Joseph E. Powell
Summary: This study utilizes single-cell RNA sequencing to uncover the genetic drivers of interindividual variation in the human immune system. The researchers identify specific loci that have cell type-specific effects on gene expression and demonstrate dynamic allelic effects in B cells. Additionally, they use Mendelian randomization to determine the causal route by which risk loci contribute to autoimmune disease at the cellular level.
Article
Substance Abuse
Kelly S. DeMartini, Ralitza Gueorguieva, Godfrey Pearlson, Suchitra Krishnan-Sarin, Alan Anticevic, Lisa J. Ji, John H. Krystal, Stephanie S. O'Malley
Summary: The study supported an intercorrelated 3-factor model of neurofunctional domains in alcohol use disorders, with executive function, incentive salience, and emotionality all being associated with current AUD. Additionally, childhood emotional abuse and physical neglect were significant predictors of these latent factors, indicating the negative impact of childhood neglect on later addiction development.
ALCOHOL-CLINICAL AND EXPERIMENTAL RESEARCH
(2021)
Article
Genetics & Heredity
Pooja Singh, Debleena Guin, Bijay Pattnaik, Ritushree Kukreti
Summary: Through systematic literature review and meta-analysis, it was found that idiopathic pulmonary fibrosis is significantly associated with 222 polymorphisms in 118 genes. Four polymorphisms - rs35705950/MUC5B, rs2736100/TERT, rs2076295/DSP, and rs111521887/TOLLIP, exhibited substantial epidemiological evidence supporting their association with IPF risk.
Article
Psychology, Clinical
Jessica S. Johnson, Alanna C. Cote, Amanda Dobbyn, Laura G. Sloofman, Jiayi Xu, Liam Cotter, Alexander W. Charney, Andreas Birgegard, Jennifer Jordan, Martin Kennedy, Mikael Landen, Sarah L. Maguire, Nicholas G. Martin, Preben Bo Mortensen, Laura M. Thornton, Cynthia M. Bulik, Laura M. Huckins
Summary: This study used transcriptomic imputation and phenome-wide association studies to explore the clinical consequences of genetically regulated gene expression in anorexia nervosa (AN). The results identified several genes associated with AN and revealed associations with autoimmune, metabolic, and gastrointestinal diagnoses, as well as other clinical measures. The analysis also showed that body mass index (BMI) and sex moderated some of the associations. These findings provide potential avenues for further investigation into the functional mechanisms of AN-associated genes.
PSYCHOLOGICAL MEDICINE
(2023)
