Contig Assembly of Bacterial Artificial Chromosome Clones through Multiplexed Fluorescence-Labeled Fingerprinting

Ding, Yan; Johnson, Michelle D.; Colayco, R.; Chen, Y.J.; Melnyk, James M.; Schmitt, Holger; Shizuya, Hiroaki

doi:10.1006/geno.1998.5734

Cited by 44 publications

(33 citation statements)

References 15 publications

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“…To address these problems, a set of new methods has been developed, known collectively as high-informationcontent fingerprinting (HICF; see Ding et al, 1999Ding et al, , 2001Luo et al, 2003). These methods emerged from the acrylamide-based methods of Coulson et al (1986) and Brenner and Livak (1989), with further adaptations to take advantage of automated sequencing technology, leading to substantial increases in both the throughput and sensitivity of fingerprinting.…”

mentioning

confidence: 99%

Whole-Genome Validation of High-Information-Content Fingerprinting

Bharti²,

et al. 2005

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Fluorescent-based high-information-content fingerprinting (HICF) techniques have recently been developed for physical mapping. These techniques make use of automated capillary DNA sequencing instruments to enable both high-resolution and high-throughput fingerprinting. In this article, we report the construction of a whole-genome HICF FPC map for maize (Zea mays subsp. mays cv B73), using a variant of HICF in which a type IIS restriction enzyme is used to generate the fluorescently labeled fragments. The HICF maize map was constructed from the same three maize bacterial artificial chromosome libraries as previously used for the whole-genome agarose FPC map, providing a unique opportunity for direct comparison of the agarose and HICF methods; as a result, it was found that HICF has substantially greater sensitivity in forming contigs. An improved assembly procedure is also described that uses automatic end-merging of contigs to reduce the effects of contamination and repetitive bands. Several new features in FPC v7.2 are presented, including shared-memory multiprocessing, which allows dramatically faster assemblies, and automatic end-merging, which permits more accurate assemblies. It is further shown that sequenced clones may be digested in silico and located accurately on the HICF assembly, despite size deviations that prevent the precise prediction of experimental fingerprints. Finally, repetitive bands are isolated, and their effect on the assembly is studied.

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confidence: 99%

Whole-Genome Validation of High-Information-Content Fingerprinting

Bharti²,

et al. 2005

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“…To provide confirmation of overlap and information to merge contigs, the Sanger Centre traditionally has used markers with fingerprints (e.g., see Mungall et al 1997;Soderlund et al 1998). An alternative approach by Ding et al (1999) uses three separate sets of fingerprints to increase the sensitivity of overlap calculation. In the spring of 1999, the Genome Sequencing Center (GSC) in St. Louis started mass-fingerprinting BACs from the RPCI-11 male library constructed at Roswell Park Cancer Institute (Buffalo NY) (see http:// genome.wustl.edu/gsc and http://www.chori.org/ bacpac, respectively).…”

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confidence: 99%

Contigs Built with Fingerprints, Markers, and FPC V4.7

Soderlund

Humphray²,

French³

2000

Genome Research

305

299

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Contigs have been assembled, and over 2800 clones selected for sequencing for human chromosomes 9, 10 and 13. Using the FPC (FingerPrinted Contig) software, the contigs are assembled with markers and complete digest fingerprints, and the contigs are ordered and localised by a global framework. Publicly available resources have been used, such as, the 1998 International Gene Map for the framework and the GSC Human BAC fingerprint database for the majority of the fingerprints. Additional markers and fingerprints are generated in-house to supplement this data. To support the scale up of building maps, FPC V4.7 has been extended to use markers with the fingerprints for assembly of contigs, new clones and markers can be automatically added to existing contigs, and poorly assembled contigs are marked accordingly. To test the automatic assembly, a simulated complete digest of 110 Mb of concatenated human sequence was used to create datasets with varying coverage, length of clones, and types of error. When no error was introduced and a tolerance of 7 was used in assembly, the largest contig with no false positive overlaps has 9534 clones with 37 out-of-order clones, that is, the starting coordinates of adjacent clones are in the wrong order. This paper describes the new features in FPC, the scenario for building the maps of chromosomes 9, 10 and 13, and the results from the simulation.

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“…Many restriction enzymes could be used simultaneously to generate more bands and thus detect 20% overlaps. This strategy could be an alternative to the strategy of Ding et al [13]. However, these authors suggest that too many bands (∼100 bands) could be troublesome for FPC to handle.…”

Section: Discussionmentioning

confidence: 99%

“…Therefore, to provide reliable data, all samples were manually checked and edited if necessary before exporting to FPC. As described in [13], we submited fragment sizes as ×10 in order to deal with some limitations of FPC: we could thus set the TOL value at 5 to take into account the fact that the standard deviation of fragment size measurements was less than one base.…”

Section: Data Analysis and Cleanupmentioning

confidence: 99%

A first generation bovine BAC-based physical map

et al. 2004

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-A first generation clone-based physical map for the bovine genome was constructed combining, fluorescent double digestion fingerprinting and sequence tagged site (STS) marker screening. The BAC clones were selected from an Inra BAC library (105 984 clones) and a part of the CHORI-240 BAC library (26 500 clones). The contigs were anchored using the screening information for a total of 1303 markers (451 microsatellites, 471 genes, 127 EST, and 254 BAC ends). The final map, which consists of 6615 contigs assembled from 100 923 clones, will be a valuable tool for genomic research in ruminants, including targeted marker production, positional cloning or targeted sequencing of regions of specific interest.cattle / physical map / BAC

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Contig Assembly of Bacterial Artificial Chromosome Clones through Multiplexed Fluorescence-Labeled Fingerprinting

Cited by 44 publications

References 15 publications

Whole-Genome Validation of High-Information-Content Fingerprinting

Whole-Genome Validation of High-Information-Content Fingerprinting

Contigs Built with Fingerprints, Markers, and FPC V4.7

A first generation bovine BAC-based physical map

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