Sequence Ready—or Not?

Mcpherson, John Douglas

doi:10.1101/gr.7.12.1111

Cited by 9 publications

(3 citation statements)

References 14 publications

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“…www.nature.com/reviews/genetics R E V I E W S maps with highly redundant clone COVERAGE (for example, tenfold or greater) can be readily used for selecting suitable sets of clones for sequencing across most genomic regions 62 (hence, the name SEQUENCE-READY MAPS 64 (FIG. 2)).…”

Section: Clone-by-clone Shotgun Sequencingmentioning

confidence: 99%

Strategies for the systematic sequencing of complex genomes

Green

2001

Nat Rev Genet

163

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Recent spectacular advances in the technologies and strategies for DNA sequencing have profoundly accelerated the detailed analysis of genomes from myriad organisms. The past few years alone have seen the publication of near-complete or draft versions of the genome sequence of several well-studied, multicellular organisms - most notably, the human. As well as providing data of fundamental biological significance, these landmark accomplishments have yielded important strategic insights that are guiding current and future genome-sequencing projects.

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Section: Clone-by-clone Shotgun Sequencingmentioning

confidence: 99%

Strategies for the systematic sequencing of complex genomes

Green

2001

Nat Rev Genet

163

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“…As these goals have come to fruition (Cohen et al 1993;Dib et al 1996;Deloukas et al 1998), the primary emphasis has shifted to the determination of the complete nucleotide sequence of the more than 3000 Mb comprising the 24 different human chromosomes (Collins et al 1998). The predominant approach to sequence acquisition is the shotgun subcloning of fingerprinted DNA clones, generally BAC, PAC, and P1 clones of considerable size and stability (McPherson 1997;Rowen et al 1997; Sanger Centre and Washington University Genome Sequencing Center 1998), or, alternatively, whole genome shotgun sequencing (Weber and Myers 1997;Venter et al 1998). Inherent in this approach, however, is the realization and acceptance that a certain percentage of the genome is likely to be excluded from analysis, that is, regions containing large blocks of repetitive sequences that are therefore presumably of low sequence complexity (Collins et al 1998).…”

mentioning

confidence: 99%

Optical Mapping of BAC Clones from the Human Y Chromosome DAZ Locus

Giacalone¹,

Delobette²,

Gibaja³

et al. 2000

Genome Res.

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The accurate mapping of clones derived from genomic regions containing complex arrangements of repeated elements presents special problems for DNA sequencers. Recent advances in the automation of optical mapping have enabled us to map a set of 16 BAC clones derived from the DAZ locus of the human Y chromosome long arm, a locus in which the entire DAZ gene as well as subsections within the gene copies have been duplicated. High-resolution optical mapping employing seven enzymes places these clones into two contigs representing four distinct copies of the DAZ gene and highlights a number of differences between individual copies of DAZ.

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“…More recently, the problem of generating large-scale contigs as substrates for sequencing the human genome has framed much of the discussion of appropriate strategies for contig construction (McPherson 1997). The current application of genomic methods to a broad range of organisms, combined with the inevitable growth in DNA sequencing that will follow the successful completion of the human genomic sequence, make it likely that construction of large-scale contigs of bacterial clones will continue to be important in the future.…”

mentioning

confidence: 99%

A Sequence-Ready BAC Clone Contig of a 2.2-Mb Segment of Human Chromosome 1q24

Vollrath¹,

Jaramillo-Babb²

1999

Genome Res.

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Human chromosomal region 1q24 encodes two cloned disease genes and lies within large genetic inclusion intervals for several disease genes that have yet to be identified. We have constructed a single bacterial artificial chromosome (BAC) clone contig that spans over 2 Mb of 1q24 and consists of 78 clones connected by 100 STSs. The average density of mapped STSs is one of the highest described for a multimegabase region of the human genome. The contig was efficiently constructed by generating STSs from clone ends, followed by library walking. Distance information was added by determining the insert sizes of all clones, and expressed sequence tags (ESTs) and genes were incorporated to create a partial transcript map of the region, providing candidate genes for local disease loci. The gene order and content of the region provide insight into ancient duplication events that have occurred on proximal 1q. The stage is now set for further elucidation of this interesting region through large-scale sequencing.[The sequence data described in this paper have been submitted to GenBank under accession nos. G42259–G42312 and G42330–G42335.]

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Sequence Ready—or Not?

Cited by 9 publications

References 14 publications

Strategies for the systematic sequencing of complex genomes

Strategies for the systematic sequencing of complex genomes

Optical Mapping of BAC Clones from the Human Y Chromosome DAZ Locus

A Sequence-Ready BAC Clone Contig of a 2.2-Mb Segment of Human Chromosome 1q24

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