Genome-Wide Analysis of the Temporal Genetic Changes in Streptococcus pneumoniae Isolates of Genotype ST320 and Serotype 19A from South Korea

Since the introduction of the pneumococcal conjugate vaccine, an increase in the incidence of Streptococcus pneumoniae serotype 19A and sequence type 320 (19A-ST320) isolates have been observed worldwide including in South Korea. We conducted a genome-wide analysis to investigate the temporal genetic changes in 26 penicillin-non-susceptible 19A-ST320 pneumococcal isolates from a hospital in South Korea over a period of 17 years (1999; 2004 to 2015). Although the strains were isolated from a single hospital and showed the same genotype and serotype, a whole-genome sequencing (WGS) analysis revealed that the S. pneumoniae isolates showed more extensive genetic variations compared with a reference isolate obtained in 1999. A phylogenetic analysis based on single nucleotide polymorphisms (SNPs) showed that the pneumococcal isolates from South Korea were not grouped together into limited clusters among the 19A-ST320 isolates from several continents. It was predicted that recombination events occurred in 11 isolates; larger numbers of SNPs were found within recombination blocks compared with point mutations identified in five isolates. WGS data indicated that S. pneumoniae 19A-ST320 isolates might have been introduced into South Korea from various other countries. In addition, it was revealed that recombination may play a great role in the evolution of pneumococci even in very limited places and periods.

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Genome-wide analysis of thyroid function in Australian adolescents highlights SERPINA7 and NCOA3

Acta Endocrinologica ◽

10.1530/eje-21-0614 ◽

2021 ◽

Author(s):

James Nolan ◽

Purdey J Campbell ◽

Suzanne J Brown ◽

Gu Zhu ◽

Scott Gordon ◽

...

Keyword(s):

Single Nucleotide Polymorphisms ◽

Thyroid Function ◽

Association Analysis ◽

Genetic Factors ◽

Meta Analysis ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Genome Wide Analysis ◽

Genome Wide ◽

A Genome

Objective Genetic factors underpin the narrow intraindividual variability of thyroid function, although precise contributions of environmental versus genetic factors remain uncertain. We sought to clarify the heritability of thyroid function traits and thyroid peroxidase antibody (TPOAb) positivity and identify single nucleotide polymorphisms (SNPs) contributing to the trait variance. Methods Heritability of thyroid stimulating hormone (TSH), free T4 (fT4), free T3 (fT3) and TPOAb in a cohort of 2854 euthyroid, dizygous and monozygous twins (age range 11.9-16.9 years) from the Brisbane Longitudinal Twin Study (BLTS) was assessed using structural equation modelling. A genome-wide analysis was conducted on 2832 of these individuals across 7,522,526 single nucleotide polymorphisms as well as gene-based association analyses. Replication analysis of the association results was performed in the Raine Study (n= 1115) followed by meta-analysis to maximise power for discovery. Results Heritability of thyroid function parameters in the BLTS was 70.8% (95% CI: 66.7-74.9%) for TSH, 67.5% (59.8-75.3%) for fT4, 59.7% (54.4-65.0%) for fT3 and 48.8% (40.6-56.9%) for TPOAb. The genome-wide association study (GWAS) in the discovery cohort identified a novel association between rs2026401 upstream of NCOA3 and TPOAb. GWAS meta-analysis found associations between TPOAb and rs445219, also near NCOA3, and fT3 and rs12687280 near SERPINA7. Gene-based association analysis highlighted SERPINA7 for fT3 and NPAS3 for fT4. Conclusion Our findings resolve former contention regarding heritability estimates of thyroid function traits and TPOAb positivity. GWAS and gene-based association analysis identified variants accounting for a component of this heritability.

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Bisphosphonate-related osteonecrosis of the jaw is associated with polymorphisms of the cytochrome P450 CYP2C8 in multiple myeloma: a genome-wide single nucleotide polymorphism analysis

Blood ◽

10.1182/blood-2008-04-147884 ◽

2008 ◽

Vol 112 (7) ◽

pp. 2709-2712 ◽

Cited By ~ 161

Author(s):

Maria E. Sarasquete ◽

Ramon García-Sanz ◽

Luis Marín ◽

Miguel Alcoceba ◽

Maria C. Chillón ◽

...

Keyword(s):

Multiple Myeloma ◽

Cytochrome P450 ◽

Genome Wide Association Study ◽

Osteonecrosis Of The Jaw ◽

Bisphosphonate Therapy ◽

Polymorphism Analysis ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Genome Wide ◽

A Genome

Abstract We have explored the potential role of genetics in the development of osteonecrosis of the jaw (ONJ) in multiple myeloma (MM) patients under bisphosphonate therapy. A genome-wide association study was performed using 500 568 single nucleotide polymorphisms (SNPs) in 2 series of homogeneously treated MM patients, one with ONJ (22 MM cases) and another without ONJ (65 matched MM controls). Four SNPs (rs1934951, rs1934980, rs1341162, and rs17110453) mapped within the cytochrome P450-2C gene (CYP2C8) showed a different distribution between cases and controls with statistically significant differences (P = 1.07 × 10−6, P = 4.231 × 10−6, P = 6.22 × 10−6, and P = 2.15 × 10−6, respectively). SNP rs1934951 was significantly associated with a higher risk of ONJ development even after Bonferroni correction (P corrected value = .02). Genotyping results displayed an overrepresentation of the T allele in cases compared with controls (48% vs 12%). Thus, individuals homozygous for the T allele had an increased likelihood of developing ONJ (odds ratio 12.75, 95% confidence interval 3.7-43.5).

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Haplotypes within tandemly duplicated candidate genes at BnaA9.MRP5 modulate phytate concentration in canola (Brassica napus L.)

10.22541/au.161165160.08519096/v1 ◽

2021 ◽

Author(s):

Haijiang Liu ◽

xiaojuan Li ◽

Qianwen Zhang ◽

pan yuan ◽

Lei Liu ◽

...

Keyword(s):

Candidate Genes ◽

Oilseed Rape ◽

Genome Wide Association Study ◽

Mineral Elements ◽

Nucleotide Polymorphisms ◽

Brassica Napus L ◽

Single Nucleotide ◽

Genome Wide ◽

A Genome ◽

Phytate Content

Phytate is the storage form of phosphorus in angiosperm seeds and plays vitally important roles during seed development. However, in crop plants phytate decreases bioavailability of seed-sourced mineral elements for humans, livestock and poultry, and contributes to phosphate-related water pollution. However, there is little knowledge about this trait in oilseed rape B. napus (oilseed rape). Here, a panel of 505 diverse B. napus accessions was screened in a genome-wide association study (GWAS) using 3.28 x 106 single nucleotide polymorphisms (SNPs). This identified 119 SNPs significantly associated with phytate concentration (PA_Conc) and phytate content (PA_Cont) and six candidate genes were identified. Of these, BnaA9.MRP5 represented the candidate gene for the significant SNP chrA09_5198034 (27kb) for both PA_Cont and PA_Conc. Transcription of BnaA9.MRP5 in a low -phytate variety (LPA20) was significantly elevated compared with a high -phytate variety (HPA972). Association and haplotype analysis indicated that inbred lines carrying specific SNP haplotypes within BnaA9.MRP5 were associated with high- and low-phytate phenotypes. No significant differences in seed germination and seed yield were detected between low and high phytate cultivars examined. Candidate genes, favorable haplotypes and the low phytate varieties identified in this study will be useful for low-phytate breeding of B. napus.

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Three New Single Nucleotide Polymorphisms Identified by a Genome-Wide Association Study in Korean Patients with Vitiligo

Journal of Korean Medical Science ◽

10.3346/jkms.2013.28.5.775 ◽

2013 ◽

Vol 28 (5) ◽

pp. 775 ◽

Cited By ~ 11

Author(s):

Kyung Ah Cheong ◽

Nan-Hyung Kim ◽

Minsoo Noh ◽

Ai-Young Lee

Keyword(s):

Single Nucleotide Polymorphisms ◽

Association Study ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Korean Patients ◽

Genome Wide ◽

A Genome

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Lifestyle factors and genetic variants on two biological age measures: evidence from 94,443 Taiwan Biobank participants

The Journals of Gerontology Series A ◽

10.1093/gerona/glab251 ◽

2021 ◽

Author(s):

Wan-Yu Lin

Keyword(s):

Genetic Variants ◽

Genome Wide Association Study ◽

Lifestyle Factors ◽

Biological Age ◽

Biological Aging ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Genome Wide ◽

A Genome ◽

The Uk

Abstract Background Biological age (BA) can be estimated by phenotypes and is useful for predicting lifespan and healthspan. Levine et al. proposed a PhenoAge and a BioAge to measure BA. Although there have been studies investigating the genetic predisposition to BA acceleration in Europeans, little has been known regarding this topic in Asians. Methods I here estimated PhenoAgeAccel (age-adjusted PhenoAge) and BioAgeAccel (age-adjusted BioAge) of 94,443 Taiwan Biobank (TWB) participants, wherein 25,460 TWB1 subjects formed a discovery cohort and 68,983 TWB2 individuals constructed a replication cohort. Lifestyle factors and genetic variants associated with PhenoAgeAccel and BioAgeAccel were investigated through regression analysis and a genome-wide association study (GWAS). Results A unit (kg/m 2) increase of BMI was associated with a 0.177-year PhenoAgeAccel (95% C.I. = 0.163~0.191, p = 6.0×) and 0.171-year BioAgeAccel (95% C.I. = 0.165~0.177, p = 0). Smokers on average had a 1.134-year PhenoAgeAccel (95% C.I. = 0.966~1.303, p = 1.3×) compared with non-smokers. Drinkers on average had a 0.640-year PhenoAgeAccel (95% C.I. = 0.433~0.847, p = 1.3×) and 0.193-year BioAgeAccel (95% C.I. = 0.107~0.279, p = 1.1×) relative to non-drinkers. A total of 11 and 4 single-nucleotide polymorphisms (SNPs) were associated with PhenoAgeAccel and BioAgeAccel (p<5× in both TWB1 and TWB2), respectively. Conclusions A PhenoAgeAccel-associated SNP (rs1260326 in GCKR) and two BioAgeAccel-associated SNPs (rs7412 in APOE; rs16998073 near FGF5) were consistent with the finding from the UK Biobank. The lifestyle analysis shows that prevention from obesity, cigarette smoking, and alcohol consumption is associated with a slower rate of biological aging.

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Progressive effects of single-nucleotide polymorphisms on 16 phenotypic traits based on longitudinal data

Genes & Genomics ◽

10.1007/s13258-019-00902-x ◽

2020 ◽

Vol 42 (4) ◽

pp. 393-403

Author(s):

Donghe Li ◽

Hahn Kang ◽

Sanghun Lee ◽

Sungho Won

Keyword(s):

Single Nucleotide Polymorphisms ◽

Longitudinal Data ◽

Density Lipoprotein ◽

Phenotypic Traits ◽

Chromosome 2 ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Longitudinal Changes ◽

Genome Wide ◽

A Genome

Abstract Background There are many research studies have estimated the heritability of phenotypic traits, but few have considered longitudinal changes in several phenotypic traits together. Objective To evaluate the progressive effect of single nucleotide polymorphisms (SNPs) on prominent health-related phenotypic traits by determining SNP-based heritability ($$h_{snp}^{2}$$hsnp2) using longitudinal data. Methods Sixteen phenotypic traits associated with major health indices were observed biennially for 6843 individuals with 10-year follow-up in a Korean community-based cohort. Average SNP heritability and longitudinal changes in the total period were estimated using a two-stage model. Average and periodic differences for each subject were considered responses to estimate SNP heritability. Furthermore, a genome-wide association study (GWAS) was performed for significant SNPs. Results Each SNP heritability for the phenotypic mean of all sixteen traits through 6 periods (baseline and five follow-ups) were significant. Gradually, the forced vital capacity in one second (FEV1) reflected the only significant SNP heritability among longitudinal changes at a false discovery rate (FDR)-adjusted 0.05 significance level ($$h_{snp}^{2} = 0.171$$hsnp2=0.171, FDR = 0.0012). On estimating chromosomal heritability, chromosome 2 displayed the highest heritability upon periodic changes in FEV1. SNPs including rs2272402 and rs7209788 displayed a genome-wide significant association with longitudinal changes in FEV1 (P = 1.22 × 10−8 for rs2272402 and P = 3.36 × 10−7 for rs7209788). De novo variants including rs4922117 (near LPL, P = 2.13 × 10−15) of log-transformed high-density lipoprotein (HDL) ratios and rs2335418 (near HMGCR, P = 3.2 $$\times$$× 10−9) of low-density lipoprotein were detected on GWAS. Conclusion Significant genetic effects on longitudinal changes in FEV1 among the middle-aged general population and chromosome 2 account for most of the genetic variance.

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Genome-wide identification, phylogenetic and expression pattern analysis of GATA family genes in Brassica napus

BMC Plant Biology ◽

10.1186/s12870-020-02752-2 ◽

2020 ◽

Vol 20 (1) ◽

Author(s):

Weizhuo Zhu ◽

Yiyi Guo ◽

Yeke Chen ◽

Dezhi Wu ◽

Lixi Jiang

Keyword(s):

Brassica Napus ◽

Stress Condition ◽

Expression Patterns ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Good Opportunity ◽

Domain Structures ◽

Genome Wide ◽

A Genome

Abstract Background Transcription factors GATAs are involved in plant developmental processes and respond to environmental stresses through binding DNA regulatory regions to regulate their downstream genes. However, little information on the GATA genes in Brassica napus is available. The release of the reference genome of B. napus provides a good opportunity to perform a genome-wide characterization of GATA family genes in rapeseed. Results In this study, 96 GATA genes randomly distributing on 19 chromosomes were identified in B. napus, which were classified into four subfamilies based on phylogenetic analysis and their domain structures. The amino acids of BnGATAs were obvious divergence among four subfamilies in terms of their GATA domains, structures and motif compositions. Gene duplication and synteny between the genomes of B. napus and A. thaliana were also analyzed to provide insights into evolutionary characteristics. Moreover, BnGATAs showed different expression patterns in various tissues and under diverse abiotic stresses. Single nucleotide polymorphisms (SNPs) distributions of BnGATAs in a core collection germplasm are probably associated with functional disparity under environmental stress condition in different genotypes of B. napus. Conclusion The present study was investigated genomic structures, evolution features, expression patterns and SNP distributions of 96 BnGATAs. The results enrich our understanding of the GATA genes in rapeseed.

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