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Multiple haplotype-resolved genomes reveal population patterns of gene and protein diplotypes

Author

Listed:
  • Margret R. Hoehe

    (Max Planck Institute for Molecular Genetics)

  • George M. Church

    (Harvard Medical School)

  • Hans Lehrach

    (Max Planck Institute for Molecular Genetics)

  • Thomas Kroslak

    (Max Planck Institute for Molecular Genetics)

  • Stefanie Palczewski

    (Max Planck Institute for Molecular Genetics)

  • Katja Nowick

    (University of Leipzig)

  • Sabrina Schulz

    (Max Planck Institute for Molecular Genetics)

  • Eun-Kyung Suk

    (Max Planck Institute for Molecular Genetics)

  • Thomas Huebsch

    (Max Planck Institute for Molecular Genetics)

Abstract

To fully understand human biology and link genotype to phenotype, the phase of DNA variants must be known. Here we present a comprehensive analysis of haplotype-resolved genomes to assess the nature and variation of haplotypes and their pairs, diplotypes, in European population samples. We use a set of 14 haplotype-resolved genomes generated by fosmid clone-based sequencing, complemented and expanded by up to 372 statistically resolved genomes from the 1000 Genomes Project. We find immense diversity of both haploid and diploid gene forms, up to 4.1 and 3.9 million corresponding to 249 and 235 per gene on average. Less than 15% of autosomal genes have a predominant form. We describe a ‘common diplotypic proteome’, a set of 4,269 genes encoding two different proteins in over 30% of genomes. We show moreover an abundance of cis configurations of mutations in the 386 genomes with an average cis/trans ratio of 60:40, and distinguishable classes of cis- versus trans-abundant genes. This work identifies key features characterizing the diplotypic nature of human genomes and provides a conceptual and analytical framework, rich resources and novel hypotheses on the functional importance of diploidy.

Suggested Citation

  • Margret R. Hoehe & George M. Church & Hans Lehrach & Thomas Kroslak & Stefanie Palczewski & Katja Nowick & Sabrina Schulz & Eun-Kyung Suk & Thomas Huebsch, 2014. "Multiple haplotype-resolved genomes reveal population patterns of gene and protein diplotypes," Nature Communications, Nature, vol. 5(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:5:y:2014:i:1:d:10.1038_ncomms6569
    DOI: 10.1038/ncomms6569
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