Article
Biochemistry & Molecular Biology
Chen Cao, Jingni He, Lauren Mak, Deshan Perera, Devin Kwok, Jia Wang, Minghao Li, Tobias Mourier, Stefan Gavriliuc, Matthew Greenberg, A. Sorana Morrissy, Laura K. Sycuro, Guang Yang, Daniel C. Jeffares, Quan Long
Summary: DNA sequencing technologies offer unprecedented opportunities to study within-host evolution of microorganism populations, but current instruments struggle to directly distinguish long haplotypes. PoolHapX is a computational approach that integrates information from genetic sharing and genomic sequencing, outperforming other tools and capable of inferring whole-chromosome-scale haplotypes.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Genetics & Heredity
Haoqiang Ye, Zipeng Zhang, Duanyang Ren, Xiaodian Cai, Qianghui Zhu, Xiangdong Ding, Hao Zhang, Zhe Zhang, Jiaqi Li
Summary: The size of reference population is important for genomic prediction. This study used WGS data to construct LD-based haplotypes and explored the impact of different SNP densities, variant representation, and reference population size on prediction accuracy. The results showed that GBLUP using WGS data improved prediction accuracy in multi-population and haplotype method had better performance in multi-population genomic evaluation.
FRONTIERS IN GENETICS
(2022)
Article
Behavioral Sciences
Konstantinos Voskarides, Nefeli Giannopoulou, Rasha Eid, Konstantinos Parperis, Andreas Chatzittofis
Summary: Several studies have confirmed the association between autoimmune diseases and psychiatric disorders, with genetic evidence supporting this link. This study aimed to investigate the genetic linkage between genetic variants predisposing to autoimmune diseases and psychiatric disorders by constructing common haplotypes. The results showed multiple chromosomal regions containing genetic variants associated with both diseases, and specific genetic haplotypes were identified. Notably, six autoimmune diseases shared a common haplotype with psychiatric diseases at the HLA locus 6p21-22.
BRAIN AND BEHAVIOR
(2023)
Article
Multidisciplinary Sciences
Adriano De Marino, Abdallah Amr Mahmoud, Madhuchanda Bose, Karatug Ozan Bircan, Andrew Terpolovsky, Varuna Bamunusinghe, Sandra Bohn, Umar Khan, Biljana Novkovic, Puya G. Yazdi
Summary: This study compared the latest versions of popular HMM-based tools for phasing and imputation, evaluated them using multiple metrics, and determined the best combinations for different situations and analysis needs. An automated pipeline was also created to optimize imputation results.
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
Biochemistry & Molecular Biology
Garrett J. McKinney, Krista M. Nichols, Michael J. Ford
Summary: The study reveals sex-specific genetic architecture of age at maturity in Chinook salmon and provides evidence of translocation of the sex-determining gene between different chromosomes. This has significant implications for understanding shifting demography and sex determination mechanisms in this species.
Review
Biology
Javaid Akhter Bhat, Deyue Yu, Abhishek Bohra, Showkat Ahmad Ganie, Rajeev K. Varshney
Summary: The review discusses mining crop haplotypes for dissecting complex traits and enhancing genomics-assisted breeding, providing avenues for faster breeding of high-yielding cultivars to adapt to future climates. It highlights the vital role of genomics-assisted breeding in improving crop breeding efficiency and delivering better varieties.
COMMUNICATIONS BIOLOGY
(2021)
Article
Genetics & Heredity
Quan Sun, Yingxi Yang, Jonathan D. Rosen, Min-Zhi Jiang, Jiawen Chen, Weifang Liu, Jia Wen, Laura M. Raffield, Rhonda G. Pace, Yi-Hui Zhou, Fred A. Wright, Scott M. Blackman, Michael J. Bamshad, Ronald L. Gibson, Garry R. Cutting, Michael R. Knowles, Daniel R. Schrider, Christian Fuchsberger, Yun Li
Summary: The study proposes MagicalRsq, a machine-learning-based method that integrates variant-level imputation and population genetics statistics, to provide a better calibrated imputation quality metric. It outperforms the standard Rsq in partially sequenced studies for both European and African ancestry samples.
AMERICAN JOURNAL OF HUMAN GENETICS
(2022)
Article
Plant Sciences
Bhupender Kumar, Sujay Rakshit, Sonu Kumar, Brijesh Kumar Singh, Chayanika Lahkar, Abhishek Kumar Jha, Krishan Kumar, Pardeep Kumar, Mukesh Choudhary, Shyam Bir Singh, John J. Amalraj, Bhukya Prakash, Rajesh Khulbe, Mehar Chand Kamboj, Neeraja N. Chirravuri, Firoz Hossain
Summary: In this study, high-density molecular markers were used to characterize maize inbred lines in India. The analysis revealed a high level of genetic diversity and heterogeneity among the inbred lines. The population structure analysis did not show clear clustering patterns, but the genotypes were partially grouped based on their source germplasm.
Article
Multidisciplinary Sciences
Friedrich Teuscher
Summary: This study improves parts of the theory underlying the use of contingency tables by introducing the linkage disequilibrium parameter as a measure of two-way interactions applied to three-way tables. It also presents a simple formula to quantify Simpson's paradox. Additionally, the study addresses the determination of fixed cells in a contingency table and the limitations of methods simulating contingency tables with given pairwise associations.
Article
Cell Biology
Tengteng Zhang, Yang Li, Xiaoni Yuan, Xiaojing Bao, Luyao Chen, Xue Jiang, Jun He
Summary: In this study, HLA typing data from 653 families in the Eastern Han Chinese population were collected. HLA-A, B, C, DRB1, DRB3, DRB4, DRB5, DQA1, DQB1, DPA1, and DPB1 (HLA-11 loci) typing was performed using a commercial next-generation sequencing (NGS) method. Haplotype analysis revealed different haplotypes, with the predominant haplotype being A*30:01-C*06:02-B*13:02-DRB1*07:01-DRB4*01:03-DQA1*02:01-DQB1*02:02-DPA1*02:01-DPB1*17:01. The study also found that HLA-DP affects the donor selection strategy and emphasized the importance of considering 9-locus HLA haplotype matching, particularly the effect of DP loci.
Article
Plant Sciences
Sajal R. Sthapit, Travis M. Ruff, Marcus A. Hooker, Deven R. See
Summary: The population structure and genetic diversity of wheat varieties in the United States were examined using a panel of historical and modern varieties. The results showed that population structure was related to growth habit and kernel characteristics, which also corresponded with geographic distribution. Market class classification accounted for the greatest amount of variation. There was no evidence of decreased genetic diversity after the release of the first semidwarf wheat variety in 1961, and some varieties even showed increases in genetic diversity. The findings suggest that overall genetic diversity in wheat varieties has not declined in the long term, despite occasional fluctuations.
Article
Genetics & Heredity
Robin J. Hofmeister, Diogo M. Ribeiro, Simone Rubinacci, Olivier Delaneau
Summary: SHAPEIT5, a new phasing method, accurately processes large sequencing datasets and improves imputation accuracy by generating reference panels of haplotypes. The method was applied to UK Biobank data, which resulted in the identification of 549 genes with compound heterozygous loss-of-function events. The use of UK Biobank as a reference panel, coupled with SHAPEIT5 phasing, further enhances genotype imputation accuracy.
Article
Immunology
Vassilios Birtsas, Anthimia Batrinou, Amalia Dinou, John Routsias, Vassiliki Gennimata, Aliki Iniotaki, Maria Spyropoulou, Athanassios Tsakris
Summary: This study aimed to identify the frequencies of MICA alleles and MICA-HLA-B haplotypes in the Greek population, revealing the five most common MICA alleles and their percentages. The study found differences in the frequencies of certain MICA alleles in the Greek population compared to other Caucasian groups, which may have implications for organ and stem cell transplantation as well as susceptibility to specific diseases.
Editorial Material
Microbiology
Daniel Falush
Summary: The genome of Helicobacter pylori undergoes extensive mixing through homologous recombination, resulting in significant free recombination within populations. A recent study reveals that the UvrC gene in H. pylori has evolved an additional function, allowing very short DNA tracts to be imported into the genome during natural transformation.