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Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
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Determining Complete Chromosomal Haplotypes by mLinker.

Sumit Sinha1,2, Cheng-Zhong Zhang3,4,5

  • 1Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA. ssinha@g.harvard.edu.

Methods in Molecular Biology (Clifton, N.J.)
|November 6, 2022
PubMed
Summary
This summary is machine-generated.

Determining complete chromosomal haplotype phase in human genomes is now possible. This guide details using mLinker software with Hi-C and linked-reads sequencing for accurate haplotype inference.

Keywords:
Haplotype phasingHi-C sequencingLong-read sequencing

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Haplotype phase defines the combination of genotypes along a chromosome.
  • Previous research established methods for determining complete chromosomal haplotypes in human genomes.
  • These methods utilized molecular linkage data from Hi-C and linked-reads sequencing.

Purpose of the Study:

  • To provide a comprehensive, step-by-step guide for haplotype inference.
  • To demonstrate the application of the mLinker software package.
  • To facilitate the determination of complete chromosomal haplotype phase in diploid human genomes.

Main Methods:

  • Utilizing Hi-C sequencing data for molecular linkage information.
  • Employing linked-reads sequencing for enhanced genomic data.
  • Applying the mLinker software package for haplotype inference analysis.

Main Results:

  • Successful determination of complete chromosomal haplotype phase.
  • Demonstration of mLinker's capability in haplotype inference.
  • Validation of the integrated sequencing approach for genomic analysis.

Conclusions:

  • The mLinker software package provides a practical tool for haplotype inference.
  • Combining Hi-C and linked-reads sequencing enables accurate determination of haplotype phase.
  • This methodology advances the field of human genomics and genetic variation analysis.