Systematic generation of sequence-tagged sites for physical mapping of human chromosomes: Application to the mapping of human chromosome 7 using yeast artificial chromosomes

Green, Eric D.; Mohr, Rose M.; Idol, Jacquelyn R.; Jones, M. W.; Buckingham, Judy; Deaven, Larry L.; Moyzis, Robert K.; Olson, Maynard V.

doi:10.1016/0888-7543(91)90062-j

Cited by 77 publications

(27 citation statements)

References 20 publications

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“…In developing the corresponding set of STS-specific PCR assays, our efforts accounted for (1) both DNA sequence generation and PCR primer design for 66% of the STSs; (2) PCR primer design but not DNA sequence generation for 17%; and (3) neither DNA sequence generation nor PCR primer design for 17%. The development of virtually all of the STSs in the first two categories has been reported previously (Green et al 1991a;Bouffard et al 1997;Touchman et al 1997). Most of the STSs in the second and third categories correspond to markers that serve to integrate our physical map with the genetic, RH, and transcript (i.e., gene/EST) maps.…”

Section: Methods Chromosome 7 Stssmentioning

confidence: 91%

“…Of the 2150 mapped chromosome 7 STSs, 26% were developed from ''random'' chromosome 7 sequences (Green et al 1991a;Green 1993), whereas 37% were derived from YAC insert ends (Table 3). Genetic (i.e., microsatellite) markers were used to develop 20% of our STSs, with particular emphasis placed on generating STSs from the mapped Genethon (Weissenbach et al 1992;Gyapay et al 1994;Dib et al 1996), Cooperative Human Linkage Center (CHLC) (Murray et al 1994), and Utah (Utah Marker Development Group 1995) genetic markers.…”

Section: Methods Chromosome 7 Stssmentioning

confidence: 99%

“…l Presence of gene-and/or EST-specific STSs within the contig is indicated, along with the number of such STSs (in parenthesis). The chromosome 7-specific STSs can be broadly classified into four major categories: those derived from sequences corresponding to random segments of chromosome 7 DNA [e.g., isolated by flow-sorting, subcloning, or Alu-PCR amplification of human DNA from chromosome 7-containing monochromosomal hybrid cell lines (Green et al 1991a;Green 1993;Bouffard et al 1997)], YAC insert ends, genetic (microsatellite) markers, and genes and ESTs.…”

Section: Unanchored Contigsmentioning

confidence: 99%

“…Since the onset of the Human Genome Project, we have focused on constructing a detailed physical map of human chromosome 7 by a YAC-based STScontent mapping strategy (Green and Green 1991;Green et al 1991aGreen et al , 1994Green et al , 1995Bouffard et al 1997). Specifically, our goals included (1) mapping an STS, on average, every 100 kb across the chromosome [a programmatic goal of the U.S. Human Genome Project (Collins and Galas 1993)]; (2) integration of the YAC-based physical map with the cytogenetic, genetic, and RH maps of the chromosome; (3) construction of a map that covered the majority of the chromosome, that established an unique order for most of the mapped STSs, and that provided large, contiguous stretches of redundant clone coverage.…”

Section: Overview Of Projectmentioning

confidence: 99%

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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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Section: Methods Chromosome 7 Stssmentioning

confidence: 91%

Section: Methods Chromosome 7 Stssmentioning

confidence: 99%

Section: Unanchored Contigsmentioning

confidence: 99%

Section: Overview Of Projectmentioning

confidence: 99%

See 2 more Smart Citations

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.

Self Cite

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show abstract

“…This cell line contains a single chromosome 7 as its only human component (Jones et al, 1990;Ledbetter et al, 1990;Green et al, 1991). Chromosome preparation and fragile site induction were modi®ed from published procedures (Kuwano et al, 1990;Hirsch, 1991;Green et al, 1994).…”

Section: Production Of Chromosome Spreads and Induction Of Fra7gmentioning

confidence: 99%

FRA7G extends over a broad region: coincidence of human endogenous retroviral sequences (HERV-H) and small polydispersed circular DNAs (spcDNA) and fragile sites

Huang

Qian

Proffit³

et al. 1998

Oncogene

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FRA7G is an aphidicolin-inducible common fragile site at human chromosomal band 7q31.2. This region is frequently altered in a number of dierent tumor types including prostate, breast, and ovarian cancer. It has also been hypothesized that this region contains an important tumor suppressor gene which is mutated during the development of these cancers or an oncogene which is ampli®ed. We previously used a FISH-based approach to isolate YAC clones which spanned FRA7G. In this report, we describe the isolation and restriction endonuclease mapping of three overlapping P1 clones which cover FRA7G and the region frequently altered in the dierent cancers. FISH-based analysis of these clones reveals that aphidicolin-induced breakage in the FRA7G region occurs over a region of at least 300 Kb in length. We have also localized a previously sequenced BAC clone to this region. The sequence obtained from this clone reveals the presence of an endogenous retroviral sequence (HERV-H) in the midst of the FRA7G region as well as sequences with homology to small polydispersed circular DNAs (spcDNAs). Thus for the ®rst two cloned common fragile sites, FRA7G and FRA3B, there is an association with both spcDNAs and hot-spots for viral integration.

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Fish mapping of YAC clones at human chromosomal band 7q31.2: Identification of YACS spanning FRA7G within the common region of LOH in breast and prostate cancer

Huang

Qian

Jenkins

et al. 1998

Genes Chromosom. Cancer

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Systematic generation of sequence-tagged sites for physical mapping of human chromosomes: Application to the mapping of human chromosome 7 using yeast artificial chromosomes

Cited by 77 publications

References 20 publications

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

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

FRA7G extends over a broad region: coincidence of human endogenous retroviral sequences (HERV-H) and small polydispersed circular DNAs (spcDNA) and fragile sites

Fish mapping of YAC clones at human chromosomal band 7q31.2: Identification of YACS spanning FRA7G within the common region of LOH in breast and prostate cancer

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