High-Throughput BAC Fingerprinting

Schein, Jacqueline E.; Kucaba, Tamara A.; Sekhon, Mandeep; Smailus, Duane E.; Waterston, Robert H.; Marra, Marco A.

doi:10.1385/1-59259-752-1:143

Cited by 33 publications

(38 citation statements)

References 8 publications

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“…All clone sequences were analyzed computationally to generate "in silico" fingerprints. The actual clones were recovered from our local copy of the RPCI-11 library (Osoegawa et al 2001) and fingerprinted using our standard protocols (Schein et al 2003). The resulting fingerprinting gels were analyzed by BandLeader version 2.3.3, and the BandLeader-identified restriction fragments were compared to the corresponding in silico restriction fragments.…”

Section: Methodsmentioning

confidence: 99%

“…nlm.nih.gov), that had been sequenced completely and accurately (i.e., were "finished") at Washington University Genome Sequencing Center, the Whitehead Institute for Biomedical Research Sequencing Center, or at the Sanger Institute. We generated HindIII fingerprints of the BACs using our standard laboratory conditions (Schein et al 2003). The resulting gel images were analyzed with BandLeader, and the bandcall data compared to the "in silico" fingerprints identified by computer analysis of the sequenced BACs (see Methods).…”

Section: Assessment Of Bandleader Performancementioning

confidence: 99%

“…These end-labeled fragments represent typically only a portion of the DNA contained within the clone. This is in contrast to the agarose method employed currently by ourselves (Marra et al 1997;Schein et al 2003) and others, in which all of the restriction fragments derived from a clone are visualized by postelectrophoretic staining of agarose gels with SYBR green (Molecular Probes). Indeed, this methodological difference has made possible our bandcalling approach, which aims to identify all of the restriction fragments and, in the case of comigrating restriction fragments, their copy number (or "multiplicity").…”

mentioning

confidence: 96%

“…Schein, I. Bosdet, and M. Marra, unpubl.). Starting with a sufficiently redundant largeinsert library of genomic DNA, the fingerprinting process (Schein et al 2003) involves purification of DNA from clones, treatment of the DNA with restriction enzymes to produce restriction fragments, resolution of the restriction fragments on agarose gels, identification of the restriction fragments to produce a fingerprint, comparison of the fingerprints to each other to generate contigs (clusters of overlapping clones representing the genomic regions from which the clones were derived), and finally verification of clone ordering within every contig. Even using clones containing very large inserts (i.e., bacterial artificial chromosome [BAC] clones; Shizuya et al 1992), hundreds of thousands of fingerprints may be required to accurately represent a large (i.e., mammalian-sized) genome in large contigs.…”

mentioning

confidence: 99%

“…Currently the BandLeader software is completely dependent upon the gel and data format presently in use at the British Columbia Cancer Agency (BCCA) Genome Sciences Centre. Detailed protocols for the production of fingerprints suitable for analysis by BandLeader have been described (Schein et al 2003). Briefly, each gel consists of 25 marker lanes and 96 "data lanes" containing large-insert clone fingerprints.…”

mentioning

confidence: 99%

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Software for Automated Analysis of DNA Fingerprinting Gels

Fuhrmann¹,

Krzywinski²,

Chiu³

et al. 2003

Genome Res.

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Here we describe software tools for the automated detection of DNA restriction fragments resolved on agarose fingerprinting gels. We present a mathematical model for the location and shape of the restriction fragments as a function of fragment size, with model parameters determined empirically from “marker” lanes containing molecular size standards. Automated identification of restriction fragments involves several steps, including: image preprocessing, to put the data in a form consistent with a linear model; marker lane analysis, for determination of the model parameters; and data lane analysis, a procedure for detecting restriction fragment multiplets while simultaneously determining the amplitude curve that describes restriction fragment amplitude as a function of mobility. In validation experiments conducted on fingerprinted and sequenced Bacterial Artificial Chromosome (BAC) clones, sensitivity and specificity of restriction fragment identification exceeded 96% on restriction fragments ranging in size from 600 base pairs (bp) to 30,000 bp. The integrated suite of software tools, written in MATLAB and collectively called BandLeader, is in use at the BC Cancer Agency Genome Sciences Centre (GSC) and the Washington University Genome Sequencing Center, and has been provided to the Wellcome Trust Sanger Institute and the Whitehead Institute. Employed in a production mode at the GSC, BandLeader has been used to perform automated restriction fragment identification for more than 850,000 BAC clones for mouse, rat, bovine, and poplar fingerprint mapping projects

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Section: Methodsmentioning

confidence: 99%

Section: Assessment Of Bandleader Performancementioning

confidence: 99%

mentioning

confidence: 96%

mentioning

confidence: 99%

mentioning

confidence: 99%

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Software for Automated Analysis of DNA Fingerprinting Gels

Fuhrmann¹,

Krzywinski²,

Chiu³

et al. 2003

Genome Res.

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Strategies for Large‐Insert Cloning and Analysis

Smith¹,

Moir

2005

CP Human Genetics

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This revised introduction provides an up‐to‐date overview of available resources and methods for identifying, mapping, manipulating, and analyzing large‐insert (BAC, YAC, PAC, and P1) clones from the human genome or from other genomes. The table listing available libraries and clone resources has been updated, emphasizing widely used resources that are readily available and that were also used to map and sequence the human genome. Mapping references have been updated, along with links to web sites that provide online access to integrated mapping and sequencing resources. Additional information is included on restriction endonuclease fingerprinting approaches and on transformation‐associated recombination (TAR) cloning methods for rescue of genes or genomic segments from specific cell types or individuals.

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