An STS Content Map of Human Chromosome 11: Localization of 910 YAC Clones and 109 Islands

Quackenbush, John; Davies, Christopher; Bailis, Julie M.; Khristich, Jason V.; Diggle, Karin; Marchuck, Yelena; Tobin, Joshua M.; Clark, Stephen P.; Rodkins, Annie; Marcano, Stewart; Churukian, Allan C.; Hutchinson, J; Probst, Shane; Romberg, Lori; Wei, Yalin H.; Nowak, Norma J.; Garner, Harold R.; Smith, Michael W.; Selleri, Licia; Evans, Glen A.

doi:10.1006/geno.1995.9974

Cited by 15 publications

(14 citation statements)

References 3 publications

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“…The primer sequences and the PCR conditions were obtained by searching the Genome Data Base (GDB), On-line Mendelian Inheritance in Man (OMIM), GenBank, and the scientific literature (Smith et al 1993;Ambrose et al 1994;van Heyningen & Little 1995;Quackenbush et al 1995).…”

Section: Dna Markersmentioning

confidence: 99%

“…Many genome-wide physical maps have been constructed in the last few years. They are generally based on a few tens of thousands of STSs (sequence tagged sites) dispersed in the genome by radiation hybrid (RH) mapping ( James et al 1994), STS-content YAC mapping (Chumakov et al 1995;Quackenbush et al 1995;Qin et al 1996) or both (Hudson et al 1995). RH mapping is particularly useful for determining the longrange order of markers, and STS-content YAC mapping has been accepted as an efficient method for constructing fine and precise physical maps.…”

Section: Introductionmentioning

confidence: 99%

“…RH mapping is particularly useful for determining the longrange order of markers, and STS-content YAC mapping has been accepted as an efficient method for constructing fine and precise physical maps. However, these maps are subject to inherent defects, since biological sensitivity to radiation varies between chromosomes (Hudson et al 1995) and regions (Holmquist 1992), and specific genomic regions of YACs are subject to a high degree of instability (Chumakov et al 1995;Quackenbush et al 1995;Hudson et al 1995). Linking-clone mapping (Poustka & Lehrach 1986) is a method for constructing a macro-restriction map which provides accurate physical distances in kb and a precise order of markers.…”

Section: Introductionmentioning

confidence: 99%

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A complete Not I restriction map covering the entire long arm of human chromosome 11

et al. 1997

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Section: Dna Markersmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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A complete Not I restriction map covering the entire long arm of human chromosome 11

et al. 1997

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“…This general approach, called YAC-based STScontent mapping (Green and Olson 1990a;Green and Green 1991), has been used to map numerous targeted regions of the human genome. This strategy has also been used to construct physical maps of whole human chromosomes (Chumakov et al 1992a;Foote et al 1992;Vollrath et al 1992;Bell et al 1995;Collins et al 1995;Hudson et al 1995;Krauter et al 1995;Quackenbush et al 1995;Qin et al 1996;Nagaraja et al 1997).…”

mentioning

confidence: 99%

A Physical Map of Human Chromosome 7: An Integrated YAC Contig Map with Average STS Spacing of 79 kb

Bouffard¹,

Idol²,

Braden³

et al. 1997

Genome Res.

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The construction of highly integrated and annotated physical maps of human chromosomes represents a critical goal of the ongoing Human Genome Project. Our laboratory has focused on developing a physical map of human chromosome 7, a ∼170-Mb segment of DNA that corresponds to an estimated 5% of the human genome. Using a yeast artificial chromosome (YAC)-based sequence-tagged site (STS)-content mapping strategy, 2150 chromosome 7-specific STSs have been established and mapped to a collection of YACs highly enriched for chromosome 7 DNA. The STSs correspond to sequences generated from a variety of DNA sources, with particular emphasis placed on YAC insert ends, genetic markers, and genes. The YACs include a set of relatively nonchimeric clones from a human-hamster hybrid cell line as well as clones isolated from total genomic libraries. For map integration, we have localized 260 STSs corresponding to Genethon genetic markers and 259 STSs corresponding to markers ordered by radiation hybrid (RH) mapping on our YAC contigs. Analysis of the data with the program SEGMAP results in the assembly of 22 contigs that are ''anchored'' on the Genethon genetic map, the RH map, and/or the cytogenetic map. These 22 contigs are ordered relative to one another, are (in all but 3 cases) oriented relative to the centromere and telomeres, and contain >98% of the mapped STSs. The largest anchored YAC contig, accounting for most of 7p, contains 634 STSs and 1260 YACs. An additional 14 contigs, accounting for ∼1.5% of the mapped STSs, are assembled but remain unanchored on either the genetic or RH map. Therefore, these 14 ''orphan'' contigs are not ordered relative to other contigs. In our contig maps, adjacent STSs are connected by two or more YACs in >95% of cases. With 2150 mapped STSs, our map provides an average STS spacing of ∼79 kb. The physical map we report here exceeds the goal of 100-kb average STS spacing and should provide an excellent framework for systematic sequencing of the chromosome.

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“…A number of factors distinguish these two maps from others that have been published previously (Foote et al 1992;Ashworth et al 1995;Bell et al 1995;Chumakov et al 1995;Collins et al 1995;Crollius et al 1996;Doggett et al 1995;Hudson et al 1995;Krauter et al 1995;Quackenbush et al 1995;Qin et al 1996): First, the significant size of chromosomes X and 7 is estimated at 160 and 170 Mb, respectively; the next largest chromosome-specific map, for chromosome 11, is 130 Mb. Second, the high density of STS markers on these maps averages 80 kb in both cases, which is better than the 100 kb goal set by the Human Genome Project and comparable to the best of the chromosome-specific maps (e.g., chromosomes 11 and 22).…”

mentioning

confidence: 78%

The Mappers’ Torch Song

Wong²

1997

Genome Res.

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An STS Content Map of Human Chromosome 11: Localization of 910 YAC Clones and 109 Islands

Cited by 15 publications

References 3 publications

A complete Not I restriction map covering the entire long arm of human chromosome 11

A complete Not I restriction map covering the entire long arm of human chromosome 11

A Physical Map of Human Chromosome 7: An Integrated YAC Contig Map with Average STS Spacing of 79 kb

The Mappers’ Torch Song

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