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Updated: Jun 28, 2025

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Long-read sequencing and optical mapping generates near T2T assemblies that resolves a centromeric translocation.

Esmee Ten Berk de Boer1,2,3, Adam Ameur4, Ignas Bunikis4

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Long-read genome sequencing (lrGS) accurately identifies complex chromosomal translocations, including centromeric breakpoints. This advanced method shows high concordance with short-read sequencing for small variants, offering a comprehensive diagnostic solution.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Genetic Diagnostics

Background:

  • Long-read genome sequencing (lrGS) is emerging as a powerful tool for genetic diagnostics.
  • Detecting complex structural variants (SVs), such as chromosomal translocations, remains challenging with traditional methods.

Purpose of the Study:

  • To evaluate the capability of lrGS in detecting a specific disease-associated chromosomal translocation.
  • To assess the accuracy of variant calling, including small variants, using lrGS compared to short-read genome sequencing (srGS).

Main Methods:

  • Construction of phased and non-phased de novo assemblies using lrGS alone and hybrid assemblies combining lrGS with optical mapping.
  • Analysis of structural variants (SVs) and small variants using variant calling algorithms.
  • Comparison of small variant calling accuracy between lrGS and srGS.

Main Results:

  • High-quality and contiguous de novo and hybrid assemblies were achieved (N50 of 62.85 Mb), enabling near telomere-to-telomere assembly.
  • Successfully identified the centromeric breakpoint of a disease-associated translocation.
  • Achieved 92% concordance for small variant calling between lrGS and srGS.

Conclusions:

  • lrGS demonstrates significant potential as a comprehensive and accurate method for analyzing both SVs and small variants.
  • lrGS can facilitate digital karyotyping and potentially replace multiple genetic tests for diagnosing translocation carriers.