Human Chromosome 7 Mapping and Sequencing












Human Chromosome 7 Mapping and Sequencing Genome Technology Branch DIR Projects

Table 4
Characteristics of Different Sources of Mapped Chromosome 7 YACs

Hybrid Cell Line YACs^a CEPH YACs^b Other YACs^c Total

No. in Contigs^d 2200 1169 523 3892

Avg. Size (kb)^e 327 994 356 531

Avg. No. Positive YACs per STS^f 4.0 5.5 3.0 9.9

Avg. No. STSs per Positive YAC^g 3.7 9.1 4.7 5.5

Percent of STSs with Corresponding Positive YAC^h 95 90 37 99

Percent Contribution Based on Cumulative YAC Sizesⁱ 40 52 8 100

Percent Contribution Based on STS-YAC Hits^j 38 50 12 100

^aYACs constructed from the human chromosome 7-containing monochromosomal hybrid cell line GM10791, as described (Green et al. 1995a).

^bYACs isolated from the total human genomic CEPH YAC library (Albertsen et al. 1990; Dausset et al. 1992) on the basis of chromosome 7-specific Alu-PCR-based hybridization analysis (Chumakov et al. 1992b; Green et al. 1995a) and/or evidence that the YAC contains chromosome 7 DNA. The latter was assessed by the systematic examination of CEPH-Genethon mapping data (Cohen et al. 1993; Chumakov et al. 1995).

^cMiscellaneous YACs mostly isolated from the total human genomic Washington University YAC library (Burke et al. 1987; Brownstein et al. 1989; Imai and Olson 1990) as well as a small number of clones derived from the total human genomic ICI YAC library (Anand et al. 1989; Anand et al. 1990) and a human telomere-specific YAC library (Riethman et al. 1989).

^dTotal number of each source of YACs present in the contigs listed in Table 1.

^eAverage size of YACs (in kb) present in the contigs listed in Table 1, indicated for each source of YACs. The size of each YAC was measured by pulsed-field gel electrophoresis (Green et al. 1995a).

^fAverage number of positive YACs identified per STS, indicated for each source of YACs.

^gAverage number of STSs contained in each positive YAC, indicated for each source of YACs.

^hPercentage of the total set of screened chromosome 7 STSs that identified at least one positive YAC, indicated for each source of YACs.

ⁱRelative contribution (as a percentage) of each source of YACs within the contigs is indicated, as estimated by analyzing the measured sizes of the mapped YACs. For this analysis, chimerism-factored sizes of YACs from each source that mapped within the contigs listed in Table 1 were summed and the relative totals assessed. In an attempt to account for chimeric DNA segments, only 75% of the measured YAC size was considered for clones isolated from total genomic libraries (e.g., CEPH, Washington University, ICI), due to their estimated 40-60% chimerism rate (Green et al. 1991b). For the hybrid cell line-derived YACs, with their estimated 10-15% chimerism rate (Green et al. 1995a), 93% of the measured YAC size was considered. This calculation thus provides an estimate of the total amount of cloned chromosome 7 DNA accounted for by each YAC source as reflected by the size of the cloned inserts.

^jRelative contribution (as a percentage) of each source of YACs within the contigs is indicated, as estimated by analyzing the frequency of STS-YAC hits. The presence of an STS in a YAC represents a single STS-YAC hit. The total number of such hits encountered for the 2150 mapped STSs was calculated for each source of YACs and the relative totals assessed. This calculation thus provides an estimate of the total amount of cloned chromosome 7 DNA accounted for by each YAC source as reflected by the representation of STSs.

Human Chromosome 7 Physical Map

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