Article
Multidisciplinary Sciences
Jonas Schmidt, Sandro Berghaus, Frithjof Blessing, Holger Herbeck, Josef Blessing, Peter Schierack, Stefan Rodiger, Dirk Roggenbuck, Folker Wenzel
Summary: Nanopore sequencing has great potential for clinical diagnostics, but further validation and certification are required.
Article
Medicine, General & Internal
Maha Daghestani, Nashwa Othman, Mohammed A. Omair, Fahidah Alenzi, Maha A. Omair, Eman Alqurtas, Shireen Amin, Arjumand Warsy
Summary: This study conducted an investigation on the Saudi population and found that 6 single nucleotide polymorphisms (SNPs) were significantly associated with rheumatoid arthritis (RA), with 4 of them having a protective effect. Two SNPs showed significantly higher heterozygote frequencies in the control group compared to the patients. This indicates considerable heterogeneity in the genetics of RA in different populations.
JOURNAL OF CLINICAL MEDICINE
(2023)
Article
Health Care Sciences & Services
Yu-Ting Hsiao, Feng-Chih Shen, Shao-Wen Weng, Pei-Wen Wang, Yung-Jen Chen, Jong-Jer Lee
Summary: This study identified genetic determinants of increased risk of diabetic retinopathy (DR) in individuals with type 2 diabetes mellitus (T2DM), focusing on FTO (rs8050136) and PSMD6 (rs831571) genetic variations. By combining genetic and nongenetic risk factors, the predictive model showed improved accuracy in predicting DR risk, especially in patients with poor glycemic control or severe microalbuminuria.
JOURNAL OF PERSONALIZED MEDICINE
(2021)
Article
Ecology
Jose Luis Mijangos, Bernd Gruber, Oliver Berry, Carlo Pacioni, Arthur Georges
Summary: Numerous approaches to analyse genetic data are available, but easier-to-use tools are needed. dartR is a user-friendly tool for analysing genetic data, providing data quality control and marker selection functions. Version 2 of dartR has increased the number of functions and improved functionality, aiming to enhance the user experience.
METHODS IN ECOLOGY AND EVOLUTION
(2022)
Article
Biotechnology & Applied Microbiology
Guang-Bin Zhao, Lei Miao, Mengge Wang, Jia-Hui Yuan, Lan-Hai Wei, Yao-Sen Feng, Jie Zhao, Ke-Lai Kang, Chi Zhang, An-Quan Ji, Guanglin He, Le Wang
Summary: This article introduces a 639-plex panel including 633 Y-SNPs and 6 Y-Insertion/deletions for paternal studies and forensic applications in Chinese populations. The panel shows high concordance, accuracy, and reproducibility, and can represent the genetic diversity and complex population structures of the Chinese Y-chromosome.
Review
Biotechnology & Applied Microbiology
Luiz Alexandre Chisini, Rodrigo Varella de Carvalho, Francine dos Santos Costa, Luana Carla Salvi, Flavio Fernando Demarco, Marcos Britto Correa
Summary: The aim of this systematic review and meta-analysis was to investigate the influence of single nucleotide polymorphisms (SNPs), related to genes in salivary composition and flow, on dental caries experience. Sixteen studies were included in the systematic review and ten in the meta-analysis. Forty-four SNPS, covering four genes (CA6, AQP2, AQP5, and MUC5B) were identified. Most of the SNPs were not associated with caries in meta-analysis. Homozygous TT genotype of the SNP CA6 rs17032907(C/T) was associated with caries [OR = 3.23(1.39-7.49)]. The pool effect of the SNPs assessed in AQP5 was associated with a reduction in the likelihood of caries [OR = 0.75(0.59-0.95)]. Considering all SNPs of salivary composition and flow, the effect allele was associated with a 75% increase in the likelihood of caries [OR = 1.75(1.06-2.89)] in the homozygous genotype. The present findings showed that the genes in salivary composition and flow can play an important role in dental caries experience.
Article
Pharmacology & Pharmacy
Chiara Casotti, Claudia Maria Hattinger, Maria Pia Patrizio, Silvia Luppi, Leonardo Fantoni, Michela Pasello, Katia Scotlandi, Toni Ibrahim, Massimo Serra
Summary: In this study, an innovative mmNGS approach was used to investigate SNPs associated with MTX resistance in HGOS cell lines. The results showed that allele changes in TP53, SLC19A1, and MTHFR were functionally involved in the development of MTX resistance. In addition, a fusion transcript of DHFR and MSH3 was identified in the cells with the highest MTX resistance level.
FRONTIERS IN PHARMACOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Melanie K. Hess, Hannah E. Hodgkinson, Andrew S. Hess, Larissa Zetouni, Juliana C. C. Budel, Hannah Henry, Alistair Donaldson, Timothy P. Bilton, Tracey C. van Stijn, Michelle R. Kirk, Ken G. Dodds, Rudiger Brauning, Alan F. Mcculloch, Sharon M. Hickey, Patricia L. Johnson, Arjan Jonker, Nickolas Morton, Shaun Hendy, V. Hutton Oddy, Peter H. Janssen, John C. Mcewan, Suzanne J. Rowe
Summary: The study explored the factors influencing rumen metagenome profiles and identified diet as the major driver of differences between samples, followed by time off feed and age of the sheep. The reference-free approach showed better resolution in distinguishing between groups compared to the reference-based approach. Normalizing relative abundances within the sampling cohort eliminated structures related to age, diet, and time off feed, enabling a clear signal based on methane emissions to be elucidated. The abundances of some rumen microbial genera were consistently heritable and repeatable across different environments.
Article
Plant Sciences
Seoyeon Park, Ye-Ok Park, Younghoon Park
Summary: This study examined the genetic diversity and population structure of a persimmon collection in South Korea through the analysis of genome-wide single-nucleotide polymorphisms (SNPs) in 93 cultivars. The results showed clear separation between cultivar groups based on astringency types, with the highest genetic diversity observed in the pollination-variant nonastringent group. Analysis of molecular variance indicated that variation within individuals was higher than among groups, and there was a low level of cultivar type differentiation. These findings demonstrate the potential of biallelic SNPs in population genetics studies and provide important insights for persimmon breeding and cultivar identification.
Article
Infectious Diseases
Patrick Lypaczewski, Wen-Wei Zhang, Greg Matlashewski
Summary: The study investigated the impact of the RagC R231C mutation on the virulence of L. donovani in causing visceral disease, finding that the mutant retained the ability to interact with RagA and had reduced parasitemia in the liver of infected mice. The RagC gene was not essential under promastigote culture conditions, but was essential for survival in the liver of experimentally infected mice, demonstrating the role of the TOR associated sensing pathway in L. donovani visceral disease.
PLOS NEGLECTED TROPICAL DISEASES
(2021)
Review
Oncology
Huitong Chen, Qian Guan, Huiqin Guo, Lei Miao, Zhenjian Zhuo
Summary: Hepatoblastoma, the most common malignant liver cancer in childhood, is believed to have genetic predisposition, although specific exposures or genetic events related to its occurrence are still unclear. Recent advances in understanding the genetic changes underlying hepatoblastoma may lead to improved patient outcomes. Single nucleotide polymorphisms (SNPs) have been widely used in researching etiology, disease treatment, and prognosis assessment for hepatoblastoma.
FRONTIERS IN ONCOLOGY
(2021)
Article
Genetics & Heredity
Guang-Bin Zhao, Guan-Ju Ma, Chi Zhang, Ke-Lai Kang, Shu-Jin Li, Le Wang
Summary: This study developed a panel of 448-plex SNP for SNP genotyping on the BGISEQ-500RS platform. The results demonstrated that this panel showed high sequencing depth and sensitivity, making it a powerful tool for forensic individual identification and kinship analysis.
FORENSIC SCIENCE INTERNATIONAL-GENETICS
(2021)
Article
Ecology
Brandon T. Sinn, Sandra J. Simon, Mathilda Santee, Stephen P. DiFazio, Nicole M. Fama, Craig F. Barrett
Summary: Generating densely sampled single nucleotide polymorphism (SNP) data is essential in various fields of biology, but wet-laboratory expertise and bioinformatics training can be limiting factors. ISSRseq, a PCR-based method, offers a straightforward approach to reduced representation of genomic variation, requiring only simple wet-laboratory skills and commonplace instrumentation. This method is highly repeatable, flexible, and capable of genomic-scale variant discovery on par with existing methods that are more complex.
METHODS IN ECOLOGY AND EVOLUTION
(2022)
Article
Genetics & Heredity
Adam Staadig, Johannes Hedman, Andreas Tillmar
Summary: One major challenge in forensic genetics is detecting very small amounts of DNA. Applying UMIs can improve the accuracy and sensitivity of forensic genotyping.
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
Genetics & Heredity
Fen Wu, Hao Sun, Shaoxiong Lu, Xiao Gou, Dawei Yan, Zhong Xu, Zhenyang Zhang, Qamar Raza Qadri, Zhe Zhang, Zhen Wang, Qiang Chen, Mingli Li, Xiaoyi Wang, Xinxing Dong, Qishan Wang, Yuchun Pan
FRONTIERS IN GENETICS
(2020)
Article
Agriculture, Dairy & Animal Science
Z. Zhang, Z. Zhang, F. O. Oyelami, H. Sun, Z. Xu, P. Ma, Q. Wang, Y. Pan
Summary: The study conducted a single-step GWAS on 950 Duroc pigs and identified genomic loci that may affect intramuscular fat (IMF) without changing backfat thickness (BF). Specific genetic variants were found to potentially improve IMF without altering BF, indicating valuable targets for molecular breeding of IMF in Duroc pigs.
Article
Genetics & Heredity
Favour Oluwapelumi Oyelami, Qingbo Zhao, Zhong Xu, Zhe Zhang, Hao Sun, Zhenyang Zhang, Peipei Ma, Qishan Wang, Yuchun Pan
FRONTIERS IN GENETICS
(2020)
Article
Genetics & Heredity
Wei Zhao, Xueshuang Lai, Dengying Liu, Zhenyang Zhang, Peipei Ma, Qishan Wang, Zhe Zhang, Yuchun Pan
FRONTIERS IN GENETICS
(2020)
Article
Biotechnology & Applied Microbiology
Qing-bo Zhao, Favour Oluwapelumi Oyelami, Qamar Raza Qadri, Hao Sun, Zhong Xu, Qi-shan Wang, Yu-chun Pan
Summary: This study identified significant specific SNPs of 19 local Chinese pig breeds and 5 Western pig breeds using the partial least squares method. The results showed that Chinese local pig breeds like Hongdenglong, Huaibei, and others have significant specific SNPs, while Western pig breeds are more related to growth rate. The study provides insights into genetic differences among local Chinese and Western pig breeds for better conservation strategies in the future.
Article
Genetics & Heredity
Qing-bo Zhao, Eugenio Lopez-Cortegano, Favour Oluwapelumi Oyelami, Zhe Zhang, Pei-pei Ma, Qi-shan Wang, Yu-chun Pan
Summary: The study found that different indigenous pig breeds contribute differently to the gene and allelic diversity within and between subpopulations. Different conservation priorities can be set for these breeds based on different priority criteria.
FRONTIERS IN GENETICS
(2021)
Article
Biotechnology & Applied Microbiology
Zhe Zhang, Peipei Ma, Zhenyang Zhang, Zhen Wang, Qishan Wang, Yuchun Pan
Summary: The study utilized extremely low coverage whole genome sequencing (lcWGS) to construct a haplotype reference panel (lcHRP) for pigs, which significantly improved the accuracy of genomic prediction and identified more signals in genome-wide association study (GWAS) compared to traditional methods like SNP arrays.
Article
Multidisciplinary Sciences
Zhen Wang, Zhenyang Zhang, Zitao Chen, Jiabao Sun, Caiyun Cao, Fen Wu, Zhong Xu, Wei Zhao, Hao Sun, Longyu Guo, Zhe Zhang, Qishan Wang, Yuchun Pan
Summary: Pigs are not only a major meat source but also an important animal model for studying human traits. However, the lack of high-quality pig reference panels limits the application of genotype imputation. In response, the pig Haplotype Reference Panel (PHARP) database has been constructed, providing a large number of pig haplotypes and web-based tools.
SCIENTIFIC REPORTS
(2022)
Article
Genetics & Heredity
Qamar Raza Qadri, Qingbo Zhao, Xueshuang Lai, Zhenyang Zhang, Wei Zhao, Yuchun Pan, Qishan Wang
Summary: This study examines the application of holo-omics framework in breeding programs and demonstrates the effectiveness of holo-omics interaction models through comparisons with real data, providing important insights into the structure of complex traits.
Article
Genetics & Heredity
Rui Cao, Jian Feng, Yuejin Xu, Yifei Fang, Wei Zhao, Zhenyang Zhang, Zhe Zhang, Meng Li, Qishan Wang, Yuchun Pan
Summary: This study investigated the genetic differences and introgression between Lulai pigs, Laiwu pigs, and Yorkshires, identifying significantly different genes and genomic regions. The findings reveal the genetic exchanges among these breeds and shed light on the molecular background of synthesized Lulai pig breeds.
Article
Biochemical Research Methods
Wei Zhao, Qamar Raza Qadri, Zhenyang Zhang, Zhen Wang, Yuchun Pan, Qishan Wang, Zhe Zhang
Summary: This study developed a fast and user-friendly Python package, PyAGH, for calculating kinship matrices using pedigree, genotype, microbiome, and transcriptome data. It also provides functions for processing, analyzing, and visualizing the data and results. PyAGH integrates multiple methods for calculating kinship matrices and has advantages in terms of speed and data size compared to other software.
BMC BIOINFORMATICS
(2023)
Article
Genetics & Heredity
Jiamin Gu, Jianwei Guo, Zhenyang Zhang, Yuejin Xu, Qamar Raza Qadri, Zhe Zhang, Zhen Wang, Qishan Wang, Yuchun Pan
Summary: Genomic selection techniques have improved animal breeding by enhancing the prediction accuracy of breeding values, especially for traits that are difficult to measure and have low heritability, as well as reducing generation intervals. However, the requirement to establish genetic reference populations can limit the application of GS in pig breeds with small populations. We proposed the kinship index based selection (KIS) method which overcomes this limitation and showed that it is feasible, particularly for small population sizes.
Article
Agriculture, Dairy & Animal Science
Ziqi Zhong, Ziyi Wang, Xinfeng Xie, Shuaishuai Tian, Feifan Wang, Qishan Wang, Shiheng Ni, Yuchun Pan, Qian Xiao
Summary: Protection of genetic diversity is crucial for the sustainable development of the animal industry. The genetic diversity and population structure of three Chinese indigenous pig populations in Hainan Province were assessed in this study using whole-genome sequencing data. The analysis revealed that native Chinese pig populations have higher genetic diversity compared to commercial pigs, and identified candidate genes associated with certain traits such as stress resistance.
Article
Agriculture, Dairy & Animal Science
Jian Miao, Zitao Chen, Zhenyang Zhang, Zhen Wang, Qishan Wang, Zhe Zhang, Yuchun Pan
Summary: In this study, researchers demonstrated that accurate identification of different pig breeds is possible using the web tool iDIGs.
GENETICS SELECTION EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Zitao Chen, Zhenyang Zhang, Zhen Wang, Zhe Zhang, Qishan Wang, Yuchun Pan
Summary: This study investigated the effects of ROHet and ROH on reproductive traits in pigs and identified candidate genes associated with reproductive performance. Through multi-omics analysis, the roles of these genes in mammalian reproductive performance were revealed. The findings are of significant importance for genetic improvement and understanding the function of ROHet and ROH in mammals.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
