A bacterial artificial chromosome library for sequencing the complete human genome

Abstract

A 30-fold redundant human bacterial artificial chromosome (BAC) library with a large average insert size (178 kb) has been constructed to provide the intermediate substrate for the international genome sequencing effort. The DNA was obtained from a single anonymous volunteer, whose identity was protected through a double-blind donor selection protocol. DNA fragments were generated by partial digestion with EcoRI (library segments 1--4: 24-fold) and MboI (segment 5: sixfold) and cloned into the pBACe3.6 and pTARBAC1 vectors, respectively. The quality of the library was assessed by extensive analysis of 169 clones for rearrangements and artifacts. Eighteen BACs (11%) revealed minor insert rearrangements, and none was chimeric. This BAC library, designated as "RPCI-11," has been used widely as the central resource for insert-end sequencing, clone fingerprinting, high-throughput sequence analysis and as a source of mapped clones for diagnostic and functional studies.

Figure 1

Size distribution of the RPCI-11 library. A total of 483, 246, 299, 308, and 212 clones from each of segments 1–5 was picked randomly and analyzed with a CHEF apparatus after NotI digestion. The horizontal axis refers to the size range of insert DNA, and the vertical axis indicates percentage of clones corresponding to each size range. Purple, pink, yellow, blue, and green bars correspond to segment 1, 2, 3, 4, and 5, respectively.

Figure 2

Analysis of BAC clones containing α-satellite sequence. Thirty-seven α-satellite positive BAC clones were isolated and digested with NotI or EcoRI. (A) The NotI-digested DNA was separated using CHEF with the Low Range PFG Marker loaded on both sides, and the sizes of the markers are indicated with arrows. (B) The EcoRI-digested DNA was fractionated with standard agarose gel electrophoresis with the 1-kb DNA ladder (outside) and the λ DNA/HindIII fragments (inside) loaded on both sides. Vector bands that are indicated by arrows are observed at 8.8 kb in both panels. False-positive clones that contain intact vector are shown in lanes 5 and 39 in both panels. Stronger intensity of the vector bands is due to the high copy number of plasmid derived from pUC19-stuffer fragment. A variety of EcoRI repetitive blocks are observed in B and indicated with vertical arrows.

Figure 2

Analysis of BAC clones containing α-satellite sequence. Thirty-seven α-satellite positive BAC clones were isolated and digested with NotI or EcoRI. (A) The NotI-digested DNA was separated using CHEF with the Low Range PFG Marker loaded on both sides, and the sizes of the markers are indicated with arrows. (B) The EcoRI-digested DNA was fractionated with standard agarose gel electrophoresis with the 1-kb DNA ladder (outside) and the λ DNA/HindIII fragments (inside) loaded on both sides. Vector bands that are indicated by arrows are observed at 8.8 kb in both panels. False-positive clones that contain intact vector are shown in lanes 5 and 39 in both panels. Stronger intensity of the vector bands is due to the high copy number of plasmid derived from pUC19-stuffer fragment. A variety of EcoRI repetitive blocks are observed in B and indicated with vertical arrows.

Figure 3

A 1.5-Mb BAC contig map localized on chromosome 14q24.3. A total of 169 BAC clones were identified from the RPCI-11 BAC library. The contig has been assembled according to the hybridization results using SEGMAP. The deduced markers are depicted with a black circle along the top, and each short horizontal line with black circles represents a BAC clone. Combination of the plate number and well position represents the clone name from the RPCI-11 library. For example, 1035K4 is found in plate 1035 at well position K4. The markers derived from the T7 or SP6 vector end are condensed as −T or −S after the clone name. The size of each clone is indicated in kilobases in parentheses. Markers have arbitrarily been assigned even spacing for diagrammatic purposes, and the length of the horizontal lines does not accurately represent the insert size. Only 121 markers derived from BAC ends are shown in this figure. Note that seven markers (between 289P13-S and 466E15-T) are overlapping in two contiguous figures. BACs derived from MboI library section (segment 5) are shown in red.

Figure 3

A 1.5-Mb BAC contig map localized on chromosome 14q24.3. A total of 169 BAC clones were identified from the RPCI-11 BAC library. The contig has been assembled according to the hybridization results using SEGMAP. The deduced markers are depicted with a black circle along the top, and each short horizontal line with black circles represents a BAC clone. Combination of the plate number and well position represents the clone name from the RPCI-11 library. For example, 1035K4 is found in plate 1035 at well position K4. The markers derived from the T7 or SP6 vector end are condensed as −T or −S after the clone name. The size of each clone is indicated in kilobases in parentheses. Markers have arbitrarily been assigned even spacing for diagrammatic purposes, and the length of the horizontal lines does not accurately represent the insert size. Only 121 markers derived from BAC ends are shown in this figure. Note that seven markers (between 289P13-S and 466E15-T) are overlapping in two contiguous figures. BACs derived from MboI library section (segment 5) are shown in red.

Figure 4

This picture shows clonal heterogeneity that is derived from the same clone. (M) Marker lane that contains a mixture of two commercially available markers as described in Methods. The DNAs shown in lanes A and B were isolated from different single colonies that are derived from the same clone. (Arrows) Inconsistent EcoRI fragments between the clones. Some of the marker sizes are indicated. The fingerprints show rearrangements that took place during cell duplication.