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Related Experiment Video

Updated: May 14, 2026

Targeted DNA Methylation Analysis by Next-generation Sequencing
08:38

Targeted DNA Methylation Analysis by Next-generation Sequencing

Published on: February 24, 2015

Marker density and read depth for genotyping populations using genotyping-by-sequencing.

Timothy M Beissinger1, Candice N Hirsch, Rajandeep S Sekhon

  • 1Department of Agronomy, University of Wisconsin, Madison, WI 53706, USA.

Genetics
|February 16, 2013
PubMed
Summary

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Genotyping-by-sequencing (GBS) provides valuable genetic data but has missing data issues. This study characterizes GBS technical variation and optimizes read depth for better marker coverage in genetic mapping.

Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Genotyping-by-sequencing (GBS) is a cost-effective method for high-density genotype data acquisition.
  • GBS presents technical challenges, notably significant missing data and uneven sequence read distribution.
  • Optimizing GBS is crucial for maximizing its utility in genetic studies.

Purpose of the Study:

  • To characterize technical variation inherent in GBS methods.
  • To develop strategies for optimizing sequencing read depth.
  • To achieve desired marker coverage for genetic mapping.

Main Methods:

  • Generated approximately 8.69 Gb of GBS data from the Zea mays reference inbred B73.
  • Utilized ApeKI for genome reduction and single-end sequencing (75-81 bp).

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G2-seq: A High Throughput Sequencing-based Technique for Identifying Late Replicating Regions of the Genome
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G2-seq: A High Throughput Sequencing-based Technique for Identifying Late Replicating Regions of the Genome

Published on: March 22, 2018

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Last Updated: May 14, 2026

Targeted DNA Methylation Analysis by Next-generation Sequencing
08:38

Targeted DNA Methylation Analysis by Next-generation Sequencing

Published on: February 24, 2015

G2-seq: A High Throughput Sequencing-based Technique for Identifying Late Replicating Regions of the Genome
06:40

G2-seq: A High Throughput Sequencing-based Technique for Identifying Late Replicating Regions of the Genome

Published on: March 22, 2018

  • Empirically assessed the distribution of sequence fragments and read depth variation.

    • Main Results:

    • Observed substantial variation in sequence coverage across different sites.
    • Found that approximately 76% of potential fragments lacked sequencing reads.
    • Identified some fragments with extremely high read depths, exceeding the mean by up to 2369x.

    Conclusions:

    • GBS data exhibits significant technical variation in read depth and coverage.
    • Developed methods to determine optimal sequencing depth based on empirical data.
    • Enables enhanced marker density for robust genetic mapping studies.