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Comparative analysis of human genome assemblies reveals genome-level differences.

Shuyu Li1, Jiayu Liao, Gene Cutler

  • 1Tularik, Inc. Two Corporate Drive, South San Francisco, California 94080, USA.

Genomics
|August 6, 2002
PubMed
Summary

Differences in human genome assemblies from the International Human Genome Sequencing Consortium (HGSC) and Celera Genomics, not just prediction methods, explain gene set disparities. Analysis revealed significant transcriptome differences, impacting gene set predictions.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Comparative Genomics

Background:

  • Comparative analysis identified significant discrepancies in predicted gene sets between the International Human Genome Sequencing Consortium (HGSC) and Celera Genomics.
  • The source of these discrepancies, whether genomic sequence differences or varied gene prediction methodologies, remained unclear.

Purpose of the Study:

  • To investigate the root causes of the gene set prediction disparities between HGSC and Celera Genomics human genome assemblies.
  • To determine if differences in genome assemblies or gene prediction algorithms were primarily responsible for the observed variations.

Main Methods:

  • Both HGSC and Celera Genomics human genome assemblies were analyzed in parallel.
  • The GENSCAN gene prediction algorithm was employed to generate comparable predicted transcriptomes.

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  • BLAST-based comparisons and Protein Family (PFAM) domain analyses were conducted to assess genomic and transcriptomic differences.

    • Main Results:

    • GENSCAN analysis revealed substantial differences, with 20-30% variation between the predicted transcriptomes of the two genome assemblies.
    • Protein domain (PFAM) analyses further highlighted significant differences between the underlying genomic sequences of HGSC and Celera Genomics.
    • These findings indicate that inherent variations in the genome assemblies contribute significantly to the discrepancies.

    Conclusions:

    • Fundamental differences in the human genome assemblies produced by HGSC and Celera Genomics are the primary drivers of the observed disparities in predicted gene sets.
    • The study underscores the importance of consistent genome assembly quality and methodology in comparative genomics.
    • Future gene set predictions should account for potential variations stemming from different genome assembly versions and characteristics.