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NGSCheckMate: software for validating sample identity in next-generation sequencing studies within and across data

Sejoon Lee1,2, Soohyun Lee3, Scott Ouellette3

  • 1Samsung Genome Institute, Samsung Medical Center, Seoul, 06351, South Korea.

Nucleic Acids Research
|April 4, 2017
PubMed
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NGSCheckMate is a new software tool that verifies sample identities in next-generation sequencing (NGS) studies. It ensures accurate data pairing across diverse data types and sequencing depths, improving data quality control.

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Next-generation sequencing (NGS) studies often involve multiple samples and data types per individual.
  • Ensuring correct sample pairing is a critical quality control (QC) step.
  • Heterogeneity in data types, file formats, and sequencing depths complicates sample identity verification.

Purpose of the Study:

  • To introduce NGSCheckMate, a user-friendly software package for verifying sample identities in NGS data.
  • To provide a standardized metric for genotype comparisons across diverse datasets.
  • To enhance the reliability of multi-dimensional NGS studies.

Main Methods:

  • NGSCheckMate employs a model-based method to compare allele read fractions at known single-nucleotide polymorphisms.

Related Experiment Videos

  • It accounts for depth-dependent behavior of similarity metrics for both identical and unrelated samples.
  • An alignment-free module allows for rapid initial checks directly on FASTQ files.

    • Main Results:

    • NGSCheckMate effectively verifies sample identities across various NGS data types, including exome, whole-genome, RNA-seq, ChIP-seq, targeted, and single-cell sequencing.
    • The software demonstrates efficacy with minimal sequencing depth requirements (as low as 0.5X).
    • It provides a robust solution for genotype comparisons, ensuring data integrity.

    Conclusions:

    • NGSCheckMate is a valuable and user-friendly QC tool for NGS studies.
    • Its ability to handle diverse data types and low sequencing depths makes it broadly applicable.
    • Implementing NGSCheckMate as a QC step is recommended to ensure accurate sample pairing and reliable study outcomes.