Single nucleotide polymorphisms within Adducin 3 and Adducin 3 antisense RNA1 genes are associated with biliary atresia in Thai infants

Laochareonsuk, Wison; Chiengkriwate, Piyawan; Sangkhathat, Surasak

doi:10.1007/s00383-018-4243-3

Cited by 13 publications

(14 citation statements)

References 19 publications

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“…We incorporated the published data before 2015, the newly published data and our current data to perform a further meta-analysis. In Asian population, rs17095355 showed consistent significant association with BA [11,18,19,21]. Rs17095355 also showed significant association in European descent, but rs7099604 showed more significant association [20].…”

Section: Discussionmentioning

confidence: 74%

“…These foundings indicated that ADD3 was the BA susceptibility gene at 10q24.2. The association between rs17095355 of ADD3 and BA was investigated repeatedly in multiple studies from different population [11,[18][19][20][21], and a meta-analysis comprising six case-control studies before 2015 has been conducted [26]. We incorporated the published data before 2015, the newly published data and our current data to perform a further meta-analysis.…”

Section: Discussionmentioning

confidence: 99%

“…Literature searches and selection yielded 7 involved studies, which comprised 8 case-control studies [9,11,[16][17][18][19]21]. The study of Garcia-Barcelo MM, et al included a GWAS stage and a replication stage in two independent samples [9], which were considered as two case-control studies in our meta-analysis (Table 7).…”

Section: Meta-analysismentioning

confidence: 99%

“…A previous GWAS in Chinese population firstly identified a susceptibility locus for BA on 10q24.2 with rs17095355 as the lead single nucleotide polymorphism (SNP), which is located in the intergenic region between the X-prolyl aminopeptidase 1 (XPNPEP1) and ADD3 genes [9]. The association was then validated in Thai, Chinese and European population [11,[17][18][19][20][21]. Further study in model organism revealed that both xpnpep1 and add3a were expressed in the liver of developing zebrafish, only knockdown of add3a produced intrahepatic defects and decreased biliary function by activating Hedgehog signaling [22].…”

Section: Introductionmentioning

confidence: 99%

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Association of common variation in ADD3 and GPC1 with biliary atresia susceptibility

Bai

Niu

Zhou

et al. 2020

Aging

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Biliary atresia (BA) is an idiopathic neonatal cholestatic disease. Recent genome-wide association study (GWAS) revealed that common variation of ADD3, GPC1, ARF6, and EFEMP1 gene was associated with BA susceptibility. We aimed to evaluate the association of these genes with BA in Chinese population. Twenty single nucleotide polymorphisms (SNPs) in these four genes were genotyped in 340 BA patients and 1,665 controls. Three SNPs in ADD3 were significantly associated with BA, and rs17095355 was the top SNP (PAllele = 3.23×10 -6 ). Meta-analysis of published data and current data indicated that rs17095355 was associated with BA susceptibility in Asians and Caucasians. Three associated SNPs were expression quantitative trait loci (eQTL) for ADD3. Two GPC1 SNPs in high linkage disequilibrium (LD) showed nominal association with BA susceptibility (PAllele = 0.03 for rs6707262 and PAllele = 0.04 for rs6750380), and were eQTL of GPC1. Haplotype harboring these two SNPs almost reached the study-wide significance (P = 0.0035). No association for ARF6 and EFEMP1 was found with BA risk in the current population. Our study validated associations of ADD3 and GPC1 SNPs with BA risk in Chinese population and provided evidence of epistatic contributions of genetic factors to BA susceptibility. Variables BA patients Male/Female 192 / 125 Age (month) 2.20 ± 0.09 bile acid (μmol/L) 128.62 ± 2.98 ALT (IU/L) 168.72 ± 6.29 AST (IU/L) 257.66 ± 8.31 ALP (IU/L) 567.75 ± 12.82 GGT (IU/L) 581.64 ± 27.79 TB (μmol/L) 166.01 ± 3.32 DB (μmol/L) 115.70 ± 2.40

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Section: Discussionmentioning

confidence: 74%

Section: Discussionmentioning

confidence: 99%

Section: Meta-analysismentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Association of common variation in ADD3 and GPC1 with biliary atresia susceptibility

Bai

Niu

Zhou

et al. 2020

Aging

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“…DNA extraction was performed according to the manufacturer's instructions as per the previous study. 7,8 Next-Generation Sequencing and Data Processing Following basic quality control assessment, the DNA libraries were sequenced on an Illumina NovaSeq 6000 platform with 150 pair-end read format with an average depth of 40x (median ¼ 30x). The raw sequencing reads were achieved using FastQC; therefore, trimming and mapping to the human genome (GRCH38, UCSC hg38) using the Burrows-Wheeler Aligner (BWA) software program.…”

Section: Frozen Tissue Specimensmentioning

confidence: 99%

Molecular Landscape for Malignant Transformation in Diffuse Astrocytoma

Tunthanathip

Sangkhathat

Kanjanapradit

2021

Global Medical Genetics

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Background Malignant transformation (MT) of low-grade gliomas changes dramatically the natural history to poor prognosis. Currently, factors associated with MT of gliomas have been inconclusive, in particular, diffuse astrocytoma (DA). Objective The present study aims to explore the molecular abnormalities related to MT in the same patients with different MT stages. Methods Twelve specimens from five DA patients with MT were genotyped using next-generation sequencing (NGS) to identify somatic variants in different stages of MT. We used cross-tabulated categorical biological variables and compared the mean of continuous variables to assess for association with MT. Results Ten samples succussed to perform NGS from one male and four females, with ages ranging from 28 to 58 years. The extent of resection was commonly a partial resection following postoperative temozolomide with radiotherapy in 25% of cases. For molecular findings, poly-T-nucleotide insertion in isocitrate dehydrogenase 1 (IDH1) was significantly related to MT as a dose–response relationship (Mann–Whitney's U test, p = 0.02). Also, mutations of KMT2C and GGT1 were frequently found in the present cohort, but those did not significantly differ between the two groups using Fisher's exact test. Conclusion In summary, we have identified a novel relationship between poly-T insertion polymorphisms that established the pathogenesis of MT in DA. A further study should be performed to confirm the molecular alteration with more patients.

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The correlation between rs2501577 gene polymorphism and biliary atresia: a systematic review and meta-analysis

Zhang

et al. 2023

Pediatr Surg Int

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Single nucleotide polymorphisms within Adducin 3 and Adducin 3 antisense RNA1 genes are associated with biliary atresia in Thai infants

Cited by 13 publications

References 19 publications

Association of common variation in ADD3 and GPC1 with biliary atresia susceptibility

Association of common variation in ADD3 and GPC1 with biliary atresia susceptibility

Molecular Landscape for Malignant Transformation in Diffuse Astrocytoma

The correlation between rs2501577 gene polymorphism and biliary atresia: a systematic review and meta-analysis

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