scholarly journals KRGDB: the large-scale variant database of 1722 Koreans based on whole genome sequencing

Database ◽  
2020 ◽  
Vol 2020 ◽  
Author(s):  
Kwang Su Jung ◽  
Kyung-Won Hong ◽  
Hyun Youn Jo ◽  
Jongpill Choi ◽  
Hyo-Jeong Ban ◽  
...  
Keyword(s):  
Large Scale ◽  
Genome Wide Association Study ◽  
Regulatory Elements ◽  
Genome Database ◽  
Genome Wide ◽  
Variant Frequency ◽  
Different Origins ◽  
Java Server Page ◽  
First Time ◽  
Reference Genome Database

Abstract Since 2012, the Center for Genome Science of the Korea National Institute of Health (KNIH) has been sequencing complete genomes of 1722 Korean individuals. As a result, more than 32 million variant sites have been identified, and a large proportion of the variant sites have been detected for the first time. In this article, we describe the Korean Reference Genome Database (KRGDB) and its genome browser. The current version of our database contains both single nucleotide and short insertion/deletion variants. The DNA samples were obtained from four different origins and sequenced in different sequencing depths (10× coverage of 63 individuals, 20× coverage of 194 individuals, combined 10× and 20× coverage of 135 individuals, 30× coverage of 230 individuals and 30× coverage of 1100 individuals). The major features of the KRGDB are that it contains information on the Korean genomic variant frequency, frequency difference between the Korean and other populations and the variant functional annotation (such as regulatory elements in ENCODE regions and coding variant functions) of the variant sites. Additionally, we performed the genome-wide association study (GWAS) between Korean genome variant sites for the 30×230 individuals and three major common diseases (diabetes, hypertension and metabolic syndrome). The association results are displayed on our browser. The KRGDB uses the MySQL database and Apache-Tomcat web server adopted with Java Server Page (JSP) and is freely available at http://coda.nih.go.kr/coda/KRGDB/index.jsp. Availability: http://coda.nih.go.kr/coda/KRGDB/index.jsp

scholarly journals Comparison of HapMap and 1000 Genomes Reference Panels in a Large-Scale Genome-Wide Association Study

PLoS ONE ◽  
2017 ◽  
Vol 12 (1) ◽  
pp. e0167742 ◽  
Author(s):  
Paul S. de Vries ◽  
Maria Sabater-Lleal ◽  
Daniel I. Chasman ◽  
Stella Trompet ◽  
Tarunveer S. Ahluwalia ◽  
...  
Keyword(s):  
Association Study ◽  
Large Scale ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
1000 Genomes ◽  
Genome Wide

scholarly journals Genome-wide analysis of BURP genes and identification of a BURP-V gene RcBURP4 in Rosachienesis

2021 ◽  
Author(s):  
Lufeng Fu ◽  
Zhujun Zhang ◽  
Hai Wang ◽  
Xiaojuan Zhao ◽  
Lin Su ◽  
...  
Keyword(s):  
Stress Responses ◽  
Light Response ◽  
Regulatory Elements ◽  
Vital Role ◽  
Severe Drought ◽  
Comprehensive Overview ◽  
Genome Database ◽  
Genome Wide ◽  
Bioinformatic Approaches ◽  
The Rose

Abstract BURP proteins are unique to plants and may contribute greatly to growth, development, and stress responses of plants. Despite the vital role of BURP proteins, little is known about these proteins in rose (Rosa spp.). In the present study, nine genes belonging to the BURP family in R. chienesis were identified by using multiple bioinformatic approaches against the rose genome database. The nine RcBURPs, with diverse structures, were located on all chromosomes of the rose genome, except for Chr2 and Chr3. Phylogenic analysis revealed that these RcBURPs can be classified into eight subfamilies, including BNM2-like, PG1β-like, USP-like, RD22-like, BURP-V, BURP-VI, BURP-VII, and BURP-VIII. Conserved motif and exon-intron analyses indicated a conserved pattern within the same subfamily. The presumed cis-regulatory elements (CREs) within the promoter region of each RcBURP were analyzed and the results showed that all RcBURPs contained different types of CREs, including abiotic stress-, light response-, phytohormones response-, and plant growth and development-related CREs. Transcriptomic analysis revealed that a BURP-V member, RcBURP4, was induced in rose leaves and roots under mild and severe drought treatments. We then overexpressed RcBURP4 in Arabidopsis and examined its role under abscisic acid (ABA), NaCl, polyethylene glycol (PEG), and drought treatments. Furthermore, RcBURP4-silenced rose plants exhibited decreased tolerance to dehydration. The results obtained from this study provide the first comprehensive overview of RcBURPs and highlight the importance of RcBURP4 in rose plant.

scholarly journals Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort

2020 ◽  
Author(s):  
Youwen Qin ◽  
Aki S Havulinna ◽  
Yang Liu ◽  
Pekka Jousilahti ◽  
Scott C Ritchie ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Microbial Communities ◽  
Large Scale ◽  
Genome Wide Association Study ◽  
Dietary Habits ◽  
Population Based ◽  
Genome Wide ◽  
Scale Population ◽  
Important Health ◽  
Disease Analysis

Co-evolution between humans and the microbial communities colonizing them has resulted in an intimate assembly of thousands of microbial species mutualistically living on and in their body and impacting multiple aspects of host physiology and health. Several studies examining whether human genetic variation can affect gut microbiota suggest a complex combination of environmental and host factors. Here, we leverage a single large-scale population-based cohort of 5,959 genotyped individuals with matched gut microbial shotgun metagenomes, dietary information and health records up to 16 years post-sampling, to characterize human genetic variations associated with microbial abundances, and predict possible causal links with various diseases using Mendelian randomization (MR). Genome-wide association study (GWAS) identified 583 independent SNP-taxon associations at genome-wide significance (p<5.0×10-8), which included notable strong associations with LCT (p=5.02×10-35), ABO (p=1.1×10-12), and MED13L (p=1.84×10-12). A combination of genetics and dietary habits was shown to strongly shape the abundances of certain key bacterial members of the gut microbiota, and explain their genetic association. Genetic effects from the LCT locus on Bifidobacterium and three other associated taxa significantly differed according to dairy intake. Variation in mucin-degrading Faecalicatena lactaris abundances were associated with ABO, highlighting a preferential utilization of secreted A/B/AB-antigens as energy source in the gut, irrespectively of fibre intake. Enterococcus faecalis levels showed a robust association with a variant in MED13L, with putative links to colorectal cancer. Finally, we identified putative causal relationships between gut microbes and complex diseases using MR, with a predicted effect of Morganella on major depressive disorder that was consistent with observational incident disease analysis. Overall, we present striking examples of the intricate relationship between humans and their gut microbial communities, and highlight important health implications.

scholarly journals Large-scale genome-wide association study in a Japanese population identifies novel susceptibility loci across different diseases

2020 ◽  
Vol 52 (7) ◽  
pp. 669-679 ◽  
Author(s):  
Kazuyoshi Ishigaki ◽  
Masato Akiyama ◽  
Masahiro Kanai ◽  
Atsushi Takahashi ◽  
Eiryo Kawakami ◽  
...  
Keyword(s):  
Association Study ◽  
Japanese Population ◽  
Large Scale ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Susceptibility Loci ◽  
Genome Wide

scholarly journals Large-scale GWAS reveals insights into the genetic architecture of same-sex sexual behavior

Science ◽  
2019 ◽  
Vol 365 (6456) ◽  
pp. eaat7693 ◽  
Author(s):  
Andrea Ganna ◽  
Karin J. H. Verweij ◽  
Michel G. Nivard ◽  
Robert Maier ◽  
Robbee Wedow ◽  
...  
Keyword(s):  
Sexual Behavior ◽  
Genetic Architecture ◽  
Large Scale ◽  
Genome Wide Association Study ◽  
Same Sex ◽  
Genome Wide ◽  
A Genome ◽  
Number Of Sexual Partners ◽  
Opposite Sex ◽  
Males And Females

Twin and family studies have shown that same-sex sexual behavior is partly genetically influenced, but previous searches for specific genes involved have been underpowered. We performed a genome-wide association study (GWAS) on 477,522 individuals, revealing five loci significantly associated with same-sex sexual behavior. In aggregate, all tested genetic variants accounted for 8 to 25% of variation in same-sex sexual behavior, only partially overlapped between males and females, and do not allow meaningful prediction of an individual’s sexual behavior. Comparing these GWAS results with those for the proportion of same-sex to total number of sexual partners among nonheterosexuals suggests that there is no single continuum from opposite-sex to same-sex sexual behavior. Overall, our findings provide insights into the genetics underlying same-sex sexual behavior and underscore the complexity of sexuality.

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