Article
Biotechnology & Applied Microbiology
Seema Yadav, Elizabeth M. Ross, Karen S. Aitken, Lee T. Hickey, Owen Powell, Xianming Wei, Kai P. Voss-Fels, Ben J. Hayes
Summary: A LD-based algorithm is proposed to allocate unassigned SNPs to chromosome regions from sparse genetic maps, with an average proportion of over 94% SNP accuracy in placing them to chromosomes in sugarcane, wheat, and barley. This approach can improve genome-wide association studies and genomic prediction in crop species with fragmented and incomplete genome assemblies, benefiting genomic-assisted breeding for orphan crops.
Article
Biotechnology & Applied Microbiology
Dennis N. Lozada, Madhav Bhatta, Danise Coon, Paul W. Bosland
Summary: Genetic diversity among New Mexican chile peppers was assessed using GBS-derived SNP markers, revealing genetic relatedness among different populations. Introducing novel alleles from other breeding programs or wild species could help increase diversity in the current germplasm. Valuable information for future association mapping and genomic selection for genetic improvement through marker-assisted breeding in New Mexican chile peppers was presented.
Article
Biotechnology & Applied Microbiology
Ehsan Rabieyan, Reza Darvishzadeh, Reza Mohammadi, Alvina Gul, Awais Rasheed, Fatemeh Keykha Akhar, Hossein Abdi, Hadi Alipour
Summary: This study used SNP markers to analyze the genetic diversity of tetraploid wheat landraces collected from nine European and Asian countries. A total of 23,334 polymorphic SNPs were detected, revealing two main subpopulations. Landraces from Iran were grouped together, despite no clear pattern based on geographical origin. Different levels of diversity were observed in Durum wheat landraces from various countries.
Article
Biotechnology & Applied Microbiology
Johannes Geibel, Nora Paulina Praefke, Steffen Weigend, Henner Simianer, Christian Reimer
Summary: This study aimed to generate a precise SV callset from whole-genome short-read sequencing (WGS) data for three commercial chicken populations and to evaluate the linkage disequilibrium (LD) patterns between the called SVs and surrounding SNPs. The results indicated that LD between deletions (DELs) and SNPs was similar to LD between SNPs, while LD between other SVs and SNPs was significantly reduced. The main reason for the reduced LD was the presence of local minor allele frequency differences. Genotyping accuracy was lower for duplications (DUP), inversions (INV), and translocation breakpoints (BND) compared to SNPs and deletions (DELs). The presence of tag SNPs was slightly lower for DELs compared to WGS SNPs, but this difference disappeared when considering SNPs located on different chicken genotyping arrays.
Article
Medicine, General & Internal
Ikhlas A. Sindi, Ahmed O. Babalghith, Mohammed T. Tayeb, Ahmad H. Mufti, Hind Naffadi, Samar N. Ekram, Ezzeldin N. Elhawary, Munaifah Alenezi, Nasser A. Elhawary
Summary: The study identified associations between GSTM1 and TP53 rs1042522 genetic variants and increased risk of colorectal cancer in Saudi nonsmokers, while even having one variant allele in the CYP1A1 gene may predispose to colorectal cancer.
INTERNATIONAL JOURNAL OF GENERAL MEDICINE
(2021)
Article
Biochemistry & Molecular Biology
Antonela Blazekovic, Kristina Gotovacjercic, Fran Borovecki
Summary: The study aimed to assess differences in 3'UTR variants of the SNCA gene in a cohort of PD patients and control subjects from Croatia, identifying a significantly higher occurrence of a particular variant in the PD population which has not been reported previously. Further research is needed to explore the role of these variants in PD development and their impact on disease pathology.
Article
Agriculture, Dairy & Animal Science
Hadi Atashi, Helene Wilmot, Nicolas Gengler
Summary: Quantifying the level of linkage disequilibrium (LD) is important for genomic selection, and this study evaluated LD in Dual-Purpose Belgian Blue (DPBB) and compared it with Holstein. The results showed that LD in DPBB was generally lower than in Holstein, and the effective population size decreased over generations in both breeds. At least 68,000 SNPs are needed for implementing genomic selection in DPBB cattle.
JOURNAL OF ANIMAL BREEDING AND GENETICS
(2022)
Article
Plant Sciences
Wenchong Chen, Weiwu Yu, Ang Dong, Yanru Zeng, Huwei Yuan, Bingsong Zheng, Rongling Wu
Summary: This study utilizes advanced genotyping technologies to investigate the genetic structure of Torreya grandis, a species with high economic and ornamental values. A high-density linkage map is constructed, and the results suggest that the identified QTLs are relatively young and can be better utilized through clonal propagation.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Genetics & Heredity
Sitwat Zehra, Maham Ghouri, Halima Jafari, Saima Saleem, Sehrish Fatima, Abid Azhar
Summary: This study found that SNPs rs3736228 and rs4988321 are significantly associated with increased susceptibility to RA. The study provides baseline data on targeted SNPs and their association with disease progression. The findings may be utilized for the development of potential diagnostic biomarkers and precision medicine approaches.
Article
Multidisciplinary Sciences
Qaisar Mansoor, Muhammad Ismail, Shah Ali Ul Qader
Summary: This study aims to identify the prognostic genetic elements of FTO gene linkage disequilibrium block SNPs rs9940128 and rs9939609 in breast cancer and type II diabetes in the Pakistani population. These genetic markers are closely associated with disease onset and can help understand the underlying disease genetics and identify treatment targets. The study found that these genetic markers are significantly associated with the incidence of breast cancer and type II diabetes.
Article
Biochemistry & Molecular Biology
Justyna Basak, Danuta Piotrzkowska, Ireneusz Majsterek, Ewa Kucharska
Summary: Multiple sclerosis (MS) is an autoimmune disorder of the central nervous system with no cure and unclear etiology. This study aimed to identify SNPs associated with an increased risk of developing MS. The findings suggest that the GG AGO1 rs636832 and AA GEMIN4 rs7813 genotypes are associated with an increased risk of MS.
Article
Agriculture, Dairy & Animal Science
N. Dementieva, O. Mitrofanova, A. P. Dysin, A. A. Kudinov, O. Stanishevskaya, T. A. Larkina, K. Plemyashov, D. K. Griffin, M. N. Romanov, M. G. Smaragdov
Summary: Phenotypic diversity in poultry is mainly influenced by artificial selection and genetic drift. This study assessed genetic diversity within and between Russian chicken breeds and populations, revealing genetic differences among populations. LD pruning is crucial for studying genetic diversity, with the Russian White RG population showing a significant impact due to its large sample size.
Article
Biochemical Research Methods
Jingfen Lan, Wenxiang Chen, Ganggang Yin, A. K. Alvi Haque, Kun Xie, Qiang Yu, Xiguo Yuan
Summary: Single nucleotide variants (SNVs) are common in human genome and have significant effects on tumor development and genetic diseases. LDSSNV is a new method that can detect and distinguish between somatic and germline SNVs. It shows great potential in tumor genome analysis.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2023)
Article
Plant Sciences
Gabrielle Sousa Mafra, Janeo Eustaquio de Almeida Filho, Antonio Teixeira do Amaral Junior, Carlos Maldonado, Samuel Henrique Kamphorst, Valter Jario de Lima, Divino Rosa dos Santos Junior, Jhean Torres Leite, Pedro Henrique Araujo Diniz Santos, Talles de Oliveira Santos, Rosimeire Barboza Bispo, Ueliton Alves de Oliveira, Vitor Batista Pinto, Alexandre Pio Viana, Caio Cezar Guedes Correa, Sunny Ahmar, Freddy Mora-Poblete
Summary: The study applied the method of regional heritability mapping (RHM) in a popcorn breeding population to identify QTLs and candidate genes for various traits, revealing associations with forty-six candidate genes within the significant genomic regions. The results obtained by the RHM method have the potential to contribute to knowledge on the genetic architecture of growth and yield traits in popcorn.
Article
Plant Sciences
Xihua Liu, Min Luo, Xiaofei Chen, Changjun Ding
Summary: This study analyzed partial sequences of six genes involved in nitrogen use efficiency in 32 different bamboo species, revealing relatively conserved nucleotide sequences with high haplotype diversity. The results of evolutionary neutrality tests indicated that the genes conform to neutral evolution, with some sequences potentially experiencing negative selection. Estimation and analysis of linkage disequilibrium and population genetic structure classified the 32 bamboo species into five categories, showing multivariate characteristics and heterogeneity within the overall population.
PHYTON-INTERNATIONAL JOURNAL OF EXPERIMENTAL BOTANY
(2021)
Article
Rheumatology
Cindy Germaine Boer, Michelle S. Yau, Sarah J. Rice, Rodrigo Coutinho de Almeida, Kathleen Cheung, Unnur Styrkarsdottir, Lorraine Southam, Linda Broer, Jeremy Mark Wilkinson, Andre G. Uitterlinden, Eleftheria Zeggini, David Felson, John Loughlin, Mariel Young, Terence Dante Capellini, Ingrid Meulenbelt, Joyce B. J. van Meurs
Summary: This study identified two novel genome-wide significant loci for OA in the thumb joints, with WNT9A identified as a possible novel causal gene for OA pathogenesis. Furthermore, several previously identified genetic loci for OA appear to confer risk for OA across multiple joints.
ANNALS OF THE RHEUMATIC DISEASES
(2021)
Review
Orthopedics
G. Aubourg, S. J. Rice, P. Bruce-Wootton, J. Loughlin
Summary: Osteoarthritis genetics has made significant progress through large-scale genome-wide association scans. Over 100 genetic risk variants associated with osteoarthritis have been identified, accounting for more than 20% of its heritability. These variants are mainly located in non-protein coding regions of the genome and regulate the expression of target genes. Epigenetic factors, particularly cartilage DNA methylation changes, are also correlated with some of these variants, suggesting a potential mediation of genetic effects on gene expression.
OSTEOARTHRITIS AND CARTILAGE
(2022)
Article
Rheumatology
Yulia S. Kehayova, Emily Watson, J. Mark Wilkinson, John Loughlin, Sarah J. Rice
Summary: The study showed that the genotype at rs11583641 affects DNA methylation in cartilage, which in turn modulates the expression of COLGALT2, an enzyme involved in posttranslational glycosylation of collagens and plays a key role in OA susceptibility.
ARTHRITIS & RHEUMATOLOGY
(2021)
Article
Rheumatology
Sarah J. Rice, Jack B. Roberts, Maria Tselepi, Abby Brumwell, Julia Falk, Charlotte Steven, John Loughlin
Summary: This study found that the OA risk SNP rs75621460 impacts TGFB1 expression by modulating the function of a gene enhancer. The research proposed a mechanism by which the SNP affects enhancer function, providing novel biological insights into one mechanism of OA genetic risk. This may help facilitate the development of future pharmacologic therapies for OA.
ARTHRITIS & RHEUMATOLOGY
(2021)
Review
Cell Biology
Saad Aldalaqan, Caroline Dalgliesh, Sara Luzzi, Chileleko Siachisumo, Louise N. Reynard, Ingrid Ehrmann, David J. Elliott
Summary: Recent findings highlight the essential role of RNA binding protein RBMXL2 in male meiosis, acting as a guardian of the transcriptome to prevent aberrant splice sites and maintain gene expression. This protective mechanism in meiosis may have evolved to ensure sperm production and male fertility, with implications for understanding neurodegenerative diseases like ALS and Alzheimer's.
Review
Biochemistry & Molecular Biology
John Loughlin
Summary: The ultimate goal of molecular genetic studies of human diseases is to benefit patients through translation of discoveries. The lack of licensed disease-modifying therapies for diseases like osteoarthritis (OA) creates an urgent need. OA is a polygenic disease that primarily affects older individuals, and recent genome-wide studies have identified 52 novel association signals. Many of these signals involve effector genes that encode proteins targeted by drugs for other indications, indicating potential repurposing opportunities. This article discusses the potential for translating OA genetic data and whether the developmental origin of OA may limit its use for disease modification.
TRENDS IN MOLECULAR MEDICINE
(2022)
Article
Rheumatology
Eefje Martine van Helvoort, Paco M. J. Welsing, Mylene P. Jansen, Willem Paul Gielis, Marieke Loef, Margreet Kloppenburg, Francisco Blanco, Ida K. Haugen, Francis Berenbaum, Anne-C Bay-Jensen, Christoph Ladel, Agnes Lalande, Jonathan Larkin, John Loughlin, Ali Mobasheri, Harrie Weinans, Floris Lafeber, Niels Eijkelkamp, Simon Mastbergen
Summary: Patients with osteoarthritis and a likely neuropathic pain component may represent a specific phenotype where joint damage is not the main cause of pain and disability. Those with a higher painDETECT score had less radiographic joint damage but impaired physical function compared to those with a lower painDETECT score. Severe pain was also found in joints other than the index knee, indicating the need for targeted treatment approaches.
Article
Rheumatology
Eefje M. van Helvoort, Mylene P. Jansen, Anne C. A. Marijnissen, Margreet Kloppenburg, Francisco J. Blanco, Ida K. Haugen, Francis Berenbaum, Anne-Christine C. Bay-Jensen, Christoph Ladel, Agnes Lalande, Jonathan Larkin, John Loughlin, Ali Mobasheri, Harrie H. Weinans, Pawel Widera, Jaume Bacardit, Paco M. J. Welsing, Floris P. J. G. Lafeber
Summary: The IMI-APPROACH knee osteoarthritis study used machine learning to predict structural and pain progression. The study found that the predicted-progression scores were able to somewhat distinguish between actual progressors and non-progressors, with better prediction for pain progression than for structural progression.
Editorial Material
Rheumatology
Michelle S. Yau, John Loughlin
ARTHRITIS & RHEUMATOLOGY
(2022)
Article
Rheumatology
Faye A. H. Cooles, Jessica Tarn, Dennis W. Lendrem, Najib Naamane, Chung M. A. Lin, Ben Millar, Nicola J. Maney, Amy E. Anderson, Nishanthi Thalayasingam, Julie Diboll, Vincent Bondet, Darragh Duffy, Michael R. Barnes, Graham R. Smith, Sandra Ng, David Watson, Rafael Henkin, Andrew P. Cope, Louise N. Reynard, Arthur G. Pratt, John D. Isaacs
Summary: The interferon gene signature (IGS) in early, treatment naive rheumatoid arthritis (eRA) patients can negatively affect initial treatment response by causing sustained, epigenetically mediated increases in lymphocyte activation and proliferation. This highlights the importance of the IGS as a prognostic biomarker and suggests the rationale for targeting IFN-alpha in selected eRA patients.
ANNALS OF THE RHEUMATIC DISEASES
(2022)
Article
Rheumatology
Zoe Paskins, Clare E. Farmer, Fay Manning, David A. Andersson, Tim Barlow, Felicity L. Bishop, Christopher A. Brown, Amanda Clark, Emma M. Clark, Debra Dulake, Malvika Gulati, Christine L. Le Maitre, Richard K. Jones, John Loughlin, Deborah J. Mason, Maura McCarron, Neil L. Millar, Hemant Pandit, George Peat, Stephen M. Richardson, Emma J. Salt, E. Jane Taylor, Linda Troeberg, Ruth K. Wilcox, Elspeth Wise, Colin Wilkinson, Fiona E. Watt
Summary: Involving research users in setting research priorities is crucial for patient-centered outcomes and maximizing value and impact. This study used the Child Health and Nutrition Research Initiative (CHNRI) method to identify key research priorities for musculoskeletal disorders. The priorities included developing new treatments, improving treatment targeting, early diagnosis, prevention, and understanding and management of pain.
LANCET RHEUMATOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Sarah J. Rice, Abby Brumwell, Julia Falk, Yulia S. Kehayova, John Casement, Eleanor Parker, Ines M. J. Hofer, Colin Shepherd, John Loughlin
Summary: This study investigates the activity and impact of genetic risk factors for osteoarthritis (OA) during human skeletogenesis. It shows that OA genetic risk is present during fetal development and is associated with allelic expression imbalances of specific genes. These findings are significant for understanding the pathogenesis of OA and developing pharmacological interventions.
HUMAN MOLECULAR GENETICS
(2023)
Article
Rheumatology
Yulia S. Kehayova, J. Mark Wilkinson, Sarah J. Rice, John Loughlin
Summary: This study aims to determine the target gene(s) and mechanism of action of the osteoarthritis (OA) locus. It was found that COLGALT2 is the target gene of this OA locus, and its expression is regulated by DNA methylation.
ARTHRITIS & RHEUMATOLOGY
(2023)
Article
Rheumatology
Yulia S. Kehayova, J. Mark Wilkinson, Sarah J. Rice, John Loughlin
Summary: Investigation reveals that DNA variants rs11583641 and rs1046934 decrease methylation status and increase expression of COLGALT2 in cartilage, marking risk for osteoarthritis. This study investigates if these effects are present in non-cartilaginous joint tissues.
ARTHRITIS RESEARCH & THERAPY
(2023)
Article
Rheumatology
Abby Brumwell, Guillaume Aubourg, Juhel Hussain, Eleanor Parker, David J. Deehan, Sarah J. Rice, John Loughlin
Summary: This study investigated a genetic locus associated with osteoarthritis and identified TMEM129 as a target gene at the locus. The genotype at rs11732213 was found to impact the DNA methylation at an enhancer, which in turn modulated TMEM129 expression. This research provides new insights into the susceptibility of osteoarthritis.
ARTHRITIS RESEARCH & THERAPY
(2022)