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. 1999 Aug;9(8):763-74.

A 12-Mb complete coverage BAC contig map in human chromosome 16p13.1-p11.2

Y Cao  1 , H L Kang, X Xu, M Wang, S H Dho, J R Huh, B J Lee, F Kalush, D Bocskai, Y Ding, J G Tesmer, J Lee, E Moon, V Jurecic, A Baldini, H U Weier, N A Doggett, M I Simon, M D Adams, U J Kim
Affiliations

A 12-Mb complete coverage BAC contig map in human chromosome 16p13.1-p11.2

Y Cao et al. Genome Res. 1999 Aug.

Abstract

We have constructed a complete coverage BAC contig map that spans a 12-Mb genomic segment in the human chromosome 16p13.1-p11.2 region. The map consists of 68 previously mapped STSs and 289 BAC clones, 51 of which-corresponding to a total of 7.721 Mb of genomic DNA-have been sequenced, and provides a high resolution physical map of the region. Contigs were initially built based mainly on the analysis of STS contents and restriction fingerprint patterns of the clones. To close the gaps, probes derived from BAC clone ends were used to screen deeper BAC libraries. Clone end sequence data obtained from chromosome 16-specific BACs, as well as from public databases, were used for the identification of BACs that overlap with fully sequenced BACs by means of sequence match. This approach allowed precise alignment of clone overlaps in addition to restriction fingerprint comparison. A freehand contig drawing software tool was developed and used to manage the map data graphically and generate a real scale physical map. The map we present here is approximately 3.5 x deep and provides a minimal tiling path that covers the region in an array of contigous, overlapping BACs.

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Figures

Figure 1
Figure 1
(A) An example of a digitized restriction fingerprint gel image obtained from a polyacrylamide-based slab gel. Image-2.1 was used for the analysis of the gel. Green lines superimposed on the gel image correspond to the gel bands (bars) detected by the software. (B) FPC-2.5 was used for the analysis and comparison of restriction fragment patterns.
Figure 2
Figure 2
Examples of end sequence matches with completely sequenced BACs.
Figure 2
Figure 2
Examples of end sequence matches with completely sequenced BACs.
Figure 3
Figure 3
A complete coverage, sequence-ready BAC contig in the chromosome 16p(13.1–11.2) region. The map is drawn to scale in AceDraw window; each map unit corresponds to 1 kb of DNA. Only the minimal set of confirmed BACs is shown. Fifty-one clones (orange) were sequenced completely; 183 clones (blue) were aligned with the completely sequenced clones by end sequence matches; 55 clones (green) were assembled into the contig based on restriction fingerprint analysis. All of the clones have been sized and fingerprinted. A total of 76 BACs (white diamond) within the clone boxes were FISH mapped and provided anchor points to ensure that BAC clusters are on the correct chromosomal loci.
Figure 3
Figure 3
A complete coverage, sequence-ready BAC contig in the chromosome 16p(13.1–11.2) region. The map is drawn to scale in AceDraw window; each map unit corresponds to 1 kb of DNA. Only the minimal set of confirmed BACs is shown. Fifty-one clones (orange) were sequenced completely; 183 clones (blue) were aligned with the completely sequenced clones by end sequence matches; 55 clones (green) were assembled into the contig based on restriction fingerprint analysis. All of the clones have been sized and fingerprinted. A total of 76 BACs (white diamond) within the clone boxes were FISH mapped and provided anchor points to ensure that BAC clusters are on the correct chromosomal loci.
Figure 4
Figure 4
Comparison of the order of STSs in the BAC-based physical map with the order of the same set of STSs in the previously constructed YAC-based map.
See this image and copyright information in PMC

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