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. 2018 May 14;27(R2):R234–R241. doi: 10.1093/hmg/ddy177

Table 1.

Advantages and applications of long-read sequencing

Limitations of short read data Applications and advantages of long-read sequencing
  • Access to high GC content regions

  • Resolution of complex regions of the genome (e.g. MHCa)

  • Repetitive regions where short reads will not map uniquely

  • Systematic context-specific error modes

  • Structural variation, and large segmental duplications

  • Paralogous regions of the genome

  • Resolution of phase (read-based phasing)

  • De novo assembly from long reads to span the low complexity and repetitive regions, to create accurate assemblies (3).

  • Targeted sequencing of complex genomic and paralogous regions and resolution of phase for clinical applications e.g. HLAb typing, ADPKDc (4).

  • Transcriptomics, allowing full length sequencing of isoforms and examination of splicing (5).

  • Detection of structural variants (e.g. segmental duplications, gene loss and fusion events)

  • Single molecule sequencing allows examination of clonal heterogeneity of pathogens, and immunogenic cells

  • Long-range characterization of methylation patterns

a

MHC: Major histocompatibility complex.

b

HLA: Histocompatibility leucocyte antigen.

c

ADPKD: Autosomal-dominant polycystic kidney disease.