Combined sequence and sequence-structure based methods for analyzing FGF23, CYP24A1 and VDR genes

Abstract

FGF23, CYP24A1 and VDR altogether play a significant role in genetic susceptibility to chronic kidney disease (CKD). Identification of possible causative mutations may serve as therapeutic targets and diagnostic markers for CKD. Thus, we adopted both sequence and sequence-structure based SNP analysis algorithm in order to overcome the limitations of both methods. We explore the functional significance towards the prediction of risky SNPs associated with CKD. We assessed the performance of four widely used pathogenicity prediction methods. We compared the performances of the programs using Mathews correlation Coefficient ranged from poor (MCC = 0.39) to reasonably good (MCC = 0.42). However, we got the best results for the combined sequence and structure based analysis method (MCC = 0.45). 4 SNPs from FGF23 gene, 8 SNPs from VDR gene and 13 SNPs from CYP24A1 gene were predicted to be the causative agents for human diseases. This study will be helpful in selecting potential SNPs for experimental study from the SNP pool and also will reduce the cost for identification of potential SNPs as a genetic marker.

Keywords: CYP24A1; Chronic kidney disease; Combined sequence and sequence-structure based methods; FGF23; SNP analysis; VDR.

Fig. 1

The schematic representation of the disease mechanism.

Fig. 2

The workflow followed in the study.

Fig. 3

Superimposed structure of wild type FGF23 and S71G mutant (A), wild type of VDR and R274L mutant (B), wild type CYP24A1 and L409S mutant. The SNPs in this figure are randomly selected from each gene for the easy interpretation of the result.

Fig. 4

The relative surface area (RSA) of wild type and selected mutant type of FGF23 gene (A), CYP24A1 gene (B) and VDR gene (C).

Fig. 5

The accessible surface area (ASA) of wild type and selected mutant type of FGF23 gene (A), CYP24A1 gene (B) and VDR gene (C).

Fig. 6

Multiple sequence alignment and secondary structure prediction of FGF23, CYP24A1 and VDR genes. Alignment of secondary structure identified the β–strand to alpha change in S71G mutant, β–strand to turn change in M96T mutant, addition of β–strand in S129F mutant, addition of coil in R160Q mutant (A), addition of β–strand in L230V mutant, addition of alpha helix in R274L and E329K mutants, turn to coil change in R385H mutant (B), Turn to coil change in R120H mutant, β–strand to coil change in L148P mutant, coil to β–strand mutant in T248K mutant and alpha helix to β–strand and turn change in L409S mutant.