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Comprehensive DNA Methylation Analysis Using a Methyl-CpG-binding Domain Capture-based Method in Chronic Lymphocytic Leukemia Patients
Published on: June 16, 2017
Computational identification and structural analysis of deleterious functional SNPs in MLL gene causing acute
C George Priya Doss1, R Rajasekaran, Rao Sethumadhavan
1Bioinformatics Division, School of BioSciences and Technology, VIT University, Vellore, 632014, Tamil Nadu, India.
Interdisciplinary Sciences, Computational Life Sciences
|July 27, 2010
Summary
This study identifies specific Single Nucleotide Polymorphisms (SNPs) in the MLL gene that may cause acute leukemia. These genetic variations, particularly rs1784246 (Q1198P), are predicted to be deleterious, impacting MLL protein function.
Area of Science:
- Genomics
- Cancer Genetics
- Bioinformatics
Background:
- The Human Genome Project provides vast data for understanding complex diseases like cancer.
- Cancer genetics focuses on mutations driving tumorigenesis, offering therapeutic and diagnostic targets.
- Single Nucleotide Polymorphisms (SNPs) can influence gene expression and protein function, contributing to disease.
Purpose of the Study:
- To computationally evaluate Single Nucleotide Polymorphisms (SNPs) in the MLL gene for their potential impact on protein function and structure.
- To identify specific deleterious SNPs in the MLL gene associated with cancer predisposition, particularly acute leukemia.
Main Methods:
- Utilized computational tools including SIFT, PolyPhen, and PupaSuite to analyze SNPs in the MLL gene.
- Employed sequence homology and structure-based approaches to predict the functional and phenotypic effects of non-synonymous SNPs (nsSNPs).
- Performed structural analysis of MLL protein mutations, focusing on solvent accessibility changes.
Main Results:
- Identified 10 deleterious nsSNPs (50%) using SIFT and 5 nsSNPs (25%) predicted to disrupt protein function by PolyPhen.
- Structural analysis revealed significant changes in solvent accessibility for the Q1198P mutation.
- The nsSNP rs1784246 at amino acid position Q1198P was identified as a potentially deleterious mutation in MLL-related acute leukemia.
Conclusions:
- Computational analysis effectively predicts the deleterious effects of MLL gene SNPs on protein function.
- The nsSNP rs1784246 (Q1198P) is a strong candidate for a causal mutation in MLL-associated acute leukemia.
- These findings highlight the utility of bioinformatics in identifying genetic predispositions for complex diseases.
