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An evaluation of the draft human genome sequence

Nature Genetics volume 29, pages 88–91 (2001)Cite this article

Abstract

The completed draft version of the human genome, comprised of multiple short contigs encompassing 85% or more of euchromatin, was announced in June of 2000 (ref. 1). The detailed findings of the sequencing consortium were reported several months later2. The draft sequence has provided insight into global characteristics, such as the total number of genes and a more accurate definition of gene families. Also of importance are genome positional details such as local genome architecture, regional gene density and the location of transcribed units that are critical for disease gene identification. We carried out a series of mapping and computational experiments using a nonredundant collection of 925 expressed sequence tags (ESTs) and sections of the public draft genome sequence that were available at different timepoints between April 2000 and April 2001. We found discrepancies in both the reported coverage of the human genome and the accuracy of mapping of genomic clones, suggesting some limitations of the draft genome sequence in providing accurate positional information and detailed characterization of chromosomal subregions.

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Figure 1: EST mapping to a monochromosomal hybrid panel.
Figure 2: Outline of the strategy used to evaluate the mapping accuracy of human genomic sequence.
Figure 3: Mapping discrepancy calculations on the 17 April and 17 September versions of the draft human genome sequence.
Figure 4: Discrepancies between the electronically-inferred mapping positions of BACs matching the same EST.

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Acknowledgements

We thank Z. Yang for expert programming assistance and A. Beaudet and A. Bradley for critical review. This work was supported by the National Eye Institute, NIH, grants EY12666 to N.K. and K.C.W. and EY11780 to J.R.L. and by the Foundation Fighting Blindness.

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Authors and Affiliations

  1. Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Room 604B, Houston, 77030, Texas, USA

    Nicholas Katsanis, Kim C. Worley & James R. Lupski

  2. Department of Pediatrics, Baylor College of Medicine, One Baylor Plaza, Room 604B, Houston, 77030, Texas, USA

    James R. Lupski

  3. The Texas Children's Hospital, Baylor College of Medicine, One Baylor Plaza, Room 604B, Houston, 77030, Texas, USA

    James R. Lupski

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  1. Nicholas Katsanis
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  2. Kim C. Worley
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  3. James R. Lupski
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Correspondence to James R. Lupski.

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Katsanis, N., Worley, K. & Lupski, J. An evaluation of the draft human genome sequence. Nat Genet 29, 88–91 (2001). https://doi.org/10.1038/ng0901-88

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