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Analysis of Genetic Ancestry from NGS Data Using EthSEQ.

Davide Dalfovo1, Alessandro Romanel1

  • 1Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy.

Current Protocols
|February 13, 2023
PubMed
Summary

EthSEQ is a computational workflow that determines individual ancestry using single nucleotide polymorphism genotypes from next-generation sequencing data. This tool aids in interpreting genetic profiles for precision medicine and cancer genomics research.

Keywords:
NGSSNPsancestry analysis

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Next-generation sequencing (NGS) is crucial for translational cancer genomics and precision medicine.
  • Accurate individual ancestry identification is essential for interpreting genetic and genomic profiling.
  • Existing methods may lack efficiency or ease of integration into NGS pipelines.

Purpose of the Study:

  • To develop and present EthSEQ, an accessible computational workflow for determining individual ancestry.
  • To enable accurate interpretation of genetic data in diverse research and clinical settings.
  • To provide a robust tool for integration into existing next-generation sequencing analysis pipelines.

Main Methods:

  • EthSEQ processes single nucleotide polymorphism genotypes derived from NGS data (whole-exome, targeted sequencing).
  • Input formats include BAM, Variant Call Format (VCF), or CoreArray Genomic Data Structure (GDS) files.
  • Ancestry determination utilizes a reference model and Principal Component Analysis (PCA) with standard or multi-step refinement approaches.

Main Results:

  • EthSEQ effectively determines and assigns ancestry for individuals.
  • The workflow generates comprehensive textual and graphical output files.
  • The tool is designed for ease of use and integration, supporting multi-core processing.

Conclusions:

  • EthSEQ offers an efficient and effective solution for ancestry determination from NGS data.
  • The workflow supports precision medicine and cancer genomics by providing accurate genetic stratification.
  • EthSEQ is a valuable addition to NGS analysis pipelines, enhancing data interpretation capabilities.