Intramural Research
Online Research Resources
Human Chromosome 7
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YAC-Based STS-Content Maps
A total of 2150 chromosome 7 STSs were mapped relative to 3892 YACs. The data was then analyzed using the program SEGMAP, resulting in the construction of 36 contigs. The YAC-based STS-content analysis allowed 90% of the mapped STSs to be uniquely ordered within each contig. Furthermore, >95% of adjacent STS pairs are connected by two or more YACs (i.e., double-linked), thereby providing strong evidence for their close proximity on chromosome 7.
Of the 36 contigs, 22 are 'anchored' in place relative to the Genethon genetic, radiation hybrid (RH), and/or cytogenetic maps. These 22 anchored contigs account for >98% of the mapped STSs. Each of the 22 anchored YAC contigs has been assigned two names: one given by SEGMAP that reflects the lowest-numbered STS in the contig and one indicating its long-range position relative to the other anchored contigs (A through V, respectively). Within the first and last anchored contigs, A (sWSS1361) and V (sWSS25), are 7p and 7q telomere-containing YACs, respectively. In addition to establishing the relative order for most of the anchored contigs, the Genethon genetic and RH maps allow the relative orientation to be determined for all but a few contigs. In total, 19 of the anchored YAC contigs, containing just under 98% of the mapped STSs, are both ordered and oriented.
- View Table Summarizing Properties of Anchored YAC Contigs
- View Global Positioning of Anchored YAC Contigs
Despite our rigorous attempts, 14 unanchored (i.e., 'orphan') contigs remain that either have no YAC-based connections to an anchored contig or cannot be consistently placed within an anchored contig by SEGMAP. Examination of these 14 contigs reveals a number of features. First, the orphan contigs are small, containing an average of 2.4 STSs and 2.9 YACs each (compared to an average of 96 STSs and 175 YACs for the anchored contigs). In fact, five of the orphan contigs contain a single STS. Second, the STSs mapping to orphan contigs are, in general, poorly represented in our YAC collection, with an average of 2.7 positive YACs per STS (compared to an average of 9.9 positive YACs per STS for all contigs). A disproportionate number of the STSs in orphan contigs correspond to genes and ESTs [12 of 33 (36%)]. In fact, 8 of the 14 orphan contigs contain at least one gene- or EST-specific STS. These findings suggest that many (or most) of the orphan contigs likely correspond to gene-rich regions of the chromosome that are GC-rich and difficult to clone in YACs. Supporting this theory is the fact that the average GC content of the STSs in the anchored contigs is 40%, whereas the average GC content of the STSs in the unanchored contigs and those failing to identify a positive YAC is 47%.
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