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. 2003;4(4):R25.
doi: 10.1186/gb-2003-4-4-r25. Epub 2003 Mar 17.

Genome-wide detection of segmental duplications and potential assembly errors in the human genome sequence

Joseph Cheung  1 , Xavier Estivill, Razi Khaja, Jeffrey R MacDonald, Ken Lau, Lap-Chee Tsui, Stephen W Scherer
Affiliations

Genome-wide detection of segmental duplications and potential assembly errors in the human genome sequence

Joseph Cheung et al. Genome Biol. 2003.

Abstract

Background: Previous studies have suggested that recent segmental duplications, which are often involved in chromosome rearrangements underlying genomic disease, account for some 5% of the human genome. We have developed rapid computational heuristics based on BLAST analysis to detect segmental duplications, as well as regions containing potential sequence misassignments in the human genome assemblies.

Results: Our analysis of the June 2002 public human genome assembly revealed that 107.4 of 3,043.1 megabases (Mb) (3.53%) of sequence contained segmental duplications, each with size equal or more than 5 kb and 90% identity. We have also detected that 38.9 Mb (1.28%) of sequence within this assembly is likely to be involved in sequence misassignment errors. Furthermore, we have identified a significant subset (199,965 of 2,327,473 or 8.6%) of single-nucleotide polymorphisms (SNPs) in the public databases that are not true SNPs but are potential paralogous sequence variants.

Conclusion: Using two distinct computational approaches, we have identified most of the sequences in the human genome that have undergone recent segmental duplications. Near-identical segmental duplications present a major challenge to the completion of the human genome sequence. Potential sequence misassignments detected in this study would require additional efforts to resolve.

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Figures

Figure 1
Figure 1
Intrachromosomal segmental duplications identified in the human genome. Three panels of results are displayed for each chromosome. Left, graphical views of the paralogous relationships between recent segmental duplications (graphics produced using GenomePixelizer [29,30]; each line represents a duplicated module; coloring scheme, red = 99% to 100% sequence identity, purple = 96% to 98%, green = 93% to 95%, and blue = 90% to 92%). Middle panel: segmental duplications as detected by BLAST analysis (size of duplication in kb plotted against the length of chromosome in Mb). Right panel: ambSNPs density plot (number of ambSNPs plotted against the length of chromosome in Mb). All analyses were done using the June 2002 human genome sequence assembly.
Figure 2
Figure 2
An example of sequence misassignment error as indicated by e-PCR analysis. AC121339 is incorrectly mapped to 3q13.13 in the June 2002 human genome assembly as shown by a consensus number of chromosome X STS markers.
See this image and copyright information in PMC

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