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Inconsistencies between human genetic cytolocations and those derived using genomic sequence.

A J Cuticchia1, R D Kulkarni, W E Parris

  • 1Research Triangle Institute, Research Triangle Park, NC 27709, USA. ajc@rti.org

Cytogenetic and Genome Research
|November 9, 2005
PubMed
Summary
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The human genome sequence enables gene mapping but creates discrepancies between genetic references and computational locations. 18% of gene records show differing cytogenetic band locations, impacting biological database utility.

Area of Science:

  • Genomics
  • Bioinformatics
  • Human Genetics

Background:

  • The publication of the human genome sequence allows for gene identification via genomic positioning.
  • This has led to a divergence between traditional genetic references and computationally derived gene locations.
  • Discrepancies exist in the cytogenetic band assignments for human genes.

Purpose of the Study:

  • To quantify the extent of discrepancies between published cytolocations and computationally derived genomic locations for human genes.
  • To assess the impact of these data inconsistencies on the usability of integrated biological databases.

Main Methods:

  • Comparison of gene records from Mendelian Inheritance in Man (MIM) and Ensembl.
  • Analysis focused on records sharing HUGO gene symbols.

Related Experiment Videos

  • Identification of differences in cytogenetic band locations between the two datasets.

    • Main Results:

    • A total of 6,830 gene records with shared HUGO gene symbols were analyzed.
    • 18% of these records exhibited a discrepancy of at least one cytogenetic band.
    • This highlights a significant level of discordance between genetic and genomic data sources.

    Conclusions:

    • The frequency of discrepancies between cytogenetic and genomic gene locations is substantial.
    • These inconsistencies pose a significant challenge to the utility and integration of biological databases.
    • Standardization efforts are needed to reconcile differing gene location data.