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Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

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Bioinformatic processing to identify single nucleotide polymorphism that potentially affect Ape1 function.

Eizadora T Yu¹, Masood Z Hadi

¹Biosystems Research Department, Sandia National Laboratories, Livermore, CA 94551-0969, USA.

Mutation Research

|July 17, 2010

Summary

This summary is machine-generated.

Researchers identified 80 amino acid variants in the Ape1 gene, crucial for DNA repair. Twenty-six variants may impair base excision repair (BER) function, offering insights into DNA repair and disease susceptibility.

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Rare Event Detection Using Error-corrected DNA and RNA Sequencing

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Area of Science:

Genetics
Molecular Biology
Biochemistry

Background:

DNA damage response mechanisms are vital for preventing diseases like cancer and neurodegeneration.
Base excision repair (BER) is a key pathway for correcting DNA damage from alkylation and oxidation.
Ape1 is an essential enzyme within the BER pathway, making its variants critical for study.

Purpose of the Study:

To identify and characterize amino acid variations in the human Ape1 gene.
To predict the functional impact of identified Ape1 variants using computational tools.
To explore the potential role of Ape1 variants in disease susceptibility.

Main Methods:

Utilized the expressed sequence tag (EST) database to identify amino acid variations in the Ape1 gene.
Validated nucleotide substitutions by requiring at least two independent EST reports.
Employed SIFT and PolyPhen software to predict the deleterious effects of amino acid substitutions on Ape1 function.

Main Results:

Identified a total of eighty amino acid variants for the Ape1 gene.
Predicted twenty-six variants as deleterious to Ape1 protein function using both SIFT and PolyPhen.
Observed that many deleterious variants are located in the protein core or near the active site, potentially affecting stability, folding, or function.

Conclusions:

The identified Ape1 variants provide valuable reagents for further functional and molecular epidemiology studies.
Understanding Ape1 variants can contribute to insights into cancer susceptibility and other disease syndromes.
This study highlights the importance of genetic variation in DNA repair pathways for human health.