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Is it time to change the reference genome?

Sara Ballouz1, Alexander Dobin1, Jesse A Gillis2

  • 1Cold Spring Harbor Laboratory, The Stanley Institute for Cognitive Genomics, Cold Spring Harbor, NY, 11724, USA.

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|August 11, 2019
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Summary
This summary is machine-generated.

The human reference genome aids genomics but has limitations. Switching to a consensus reference could improve variant-calling and genomic analyses with minimal drawbacks.

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Area of Science:

  • Genomics
  • Bioinformatics

Background:

  • The human reference genome is foundational in modern genomics, enabling significant advancements.
  • However, its structure presents inherent constraints and limitations in data analysis.
  • Understanding these properties is crucial for interpreting genomic studies.

Purpose of the Study:

  • To review the history, characteristics, and drawbacks of the current human reference genome.
  • To analyze the impact of the reference genome on variant-calling methodologies.
  • To propose the adoption of a consensus human reference genome.

Main Methods:

  • Historical review of the human reference genome's development.
  • Analysis of the reference genome's properties and their implications.
  • Illustrative analyses focusing on variant-calling using the current reference.

Main Results:

  • The current reference genome, while beneficial, acts similarly to a 'type specimen', potentially limiting broader genomic representation.
  • Variant-calling analyses reveal specific challenges and biases associated with the existing reference.
  • The transition to a consensus reference is technically feasible.

Conclusions:

  • A consensus human reference genome offers significant advantages for genomic research and data interpretation.
  • Adopting a consensus reference is likely to enhance accuracy and reduce biases in analyses like variant-calling.
  • The benefits of a consensus reference outweigh the minimal disadvantages compared to the current system.