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

Bouffard, Gerard G.; Idol, Jacquelyn R.; Braden, Valerie V.; Iyer, Leslie M.; Cunningham, Aimee; Weintraub, Lauren; Touchman, Jeffrey W.; Mohr-Tidwell, Rose M.; Peluso, Dale C.; Fulton, Robert S.; Ueltzen, Melinda S.; Weissenbach, Jean; Magness, Charles L.; Green, Eric D.

doi:10.1101/gr.7.7.673

Cited by 86 publications

(81 citation statements)

References 59 publications

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“…20,21 In addition, the chromosome 7-specific YAC library and the RPCI-11 BAC library were screened for marker-positive clones. At later stages, physical mapping incorporated STSs developed from available BACend sequence (TIGR Database; Table 1), as well as EST-derived STSs predicted to map to the SDS locus on GeneMap'99.…”

Section: Physical Mappingmentioning

confidence: 99%

“…At later stages, physical mapping incorporated STSs developed from available BACend sequence (TIGR Database; Table 1), as well as EST-derived STSs predicted to map to the SDS locus on GeneMap'99. 22 Based on integrated maps, 21,23,24 it was evident that the 2.7 cM SDS locus spanned the centromere of chromosome 7. As the interval was saturated with genetic markers, the question arose as to which markers flank the centromere on the p and the q arms.…”

Section: Physical Mappingmentioning

confidence: 99%

“…30,31 Furthermore, discrepancies were noted between genetic and physical maps. 20,21 Survey of genomic sequence available in GenBank for this region revealed poor coverage with high degree of discontinuity, insufficient to resolve the inconsistencies. This is not surprising given the complex organisation of pericentromeric regions, including that of chromosome 7.…”

Section: Mapping Of Sds At 7q11 and Exclusion Of Tpst1 M Popovic Et Amentioning

confidence: 99%

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Fine mapping of the locus for Shwachman-Diamond syndrome at 7q11, identification of shared disease haplotypes, and exclusion of TPST1 as a candidate gene

et al. 2002

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Shwachman-Diamond syndrome (SDS) is an autosomal recessive disorder characterised by exocrine pancreatic dysfunction, haematological and skeletal abnormalities. We have previously defined the SDS locus as a 2.7 cM interval spanning the centromere of chromosome 7. To facilitate additional analysis of this complex and poorly characterised region, a framework of ordered genetic markers at 7p11-q11, including six newly identified, has been constructed using somatic cell, radiation hybrid and STS-content mapping. We have identified shared disease haplotypes, that recur in unrelated families of common ethnic origin, and extend across the SDS locus. Detection of ancestral and intrafamilial recombination events in patients refined the SDS locus to a 1.9 cM interval at 7q11, which contains the tyrosylprotein sulfotransferase 1 (TPST1) gene. Patients with SDS were screened for mutations in TPST1 by sequencing of exons and intron ± exon junctions. Two single nucleotide polymorphisms, but no disease-causing mutations, were identified. In addition, Southern blot analysis yielded no evidence of large-scale mutations, and RT ± PCR analysis failed to detect alterations in expression. These results exclude TPST1 as the causative gene for SDS. The established map of the refined SDS locus will assist in the identification and characterisation of other candidate genes for SDS.

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Section: Physical Mappingmentioning

confidence: 99%

Section: Physical Mappingmentioning

confidence: 99%

Section: Mapping Of Sds At 7q11 and Exclusion Of Tpst1 M Popovic Et Amentioning

confidence: 99%

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Fine mapping of the locus for Shwachman-Diamond syndrome at 7q11, identification of shared disease haplotypes, and exclusion of TPST1 as a candidate gene

et al. 2002

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“…The primary concern is the presence of false-positive and false-negative PCR results as a possible source of errors in building YAC contigs (Bouffard et al 1997). To minimize this problem, any questionable PCR results, either positive or negative, were repeated to provide the most accurate data possible.…”

Section: Yac-sts Map Constructionmentioning

confidence: 99%

Integrated YAC Contig Map of the Prader–Willi/Angelman Region on Chromosome 15q11–q13 with Average STS Spacing of 35 kb

Christian

Bhatt²,

Martin³

et al. 1998

Genome Res.

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Prader-Willi syndrome and Angelman syndrome are associated with parent-of-origin-specific abnormalities of chromosome 15q11-q13, most frequently a deletion of an ∼4-Mb region. Because of genomic imprinting, paternal deficiency of this region leads to PWS and maternal deficiency to AS. Additionally, this region is frequently involved in other chromosomal rearrangements including duplications, triplications, or supernumerary marker formation. A detailed physical map of this region is important for elucidating the genes and mechanisms involved in genomic imprinting, as well as for understanding the mechanism of recurrent chromosomal rearrangments. An initial YAC contig extended from D15S18 to D15S12 and was comprised of 23 YACs and 21 STSs providing an average resolution of about one STS per 200 kb. To close two gaps in this contig, YAC screening was performed using two STSs that flank the gap between D15S18 and 254B5R and three STSs located distal to the GABRA5-149A9L gap. Additionally, we developed 11 new STSs, including seven polymorphic markers. Although several groups have developed whole-genome genetic and radiation hybrid maps, the depth of coverage for 15q11-q13 has been somewhat limited and discrepancies in marker order exist between the maps. To resolve the inconsistencies and to provide a more detailed map order of STSs in this region, we have constructed an integrated YAC STS-based physical map of chromosome 15q11-q13 containing 118 YACs and 118 STSs, including 38 STRs and 49 genes/ESTs. Using an estimate of 4 Mb for the size of this region, the map provides an average STS spacing of 35 kb. This map provides a valuable resource for identification of disease genes localized to this region as well as a framework for complete DNA sequencing.

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“…BAC selection: In order to construct a single fully contiguous series (contig) of BACs, we utilized the YAC based physical map of chromosome 7 previously reported by Bouffard, et al (1997). The entire region of interest, with boundaries at D7S522 and D7S677, is contained in a single YAC contig.…”

Section: Body a Experimental Proceduresmentioning

confidence: 99%

Identification and Cloning a Novel Tumor Suppressor Gene in Breast Cancer

Conti¹

1999

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

Cited by 86 publications

References 59 publications

Fine mapping of the locus for Shwachman-Diamond syndrome at 7q11, identification of shared disease haplotypes, and exclusion of TPST1 as a candidate gene

Fine mapping of the locus for Shwachman-Diamond syndrome at 7q11, identification of shared disease haplotypes, and exclusion of TPST1 as a candidate gene

Integrated YAC Contig Map of the Prader–Willi/Angelman Region on Chromosome 15q11–q13 with Average STS Spacing of 35 kb

Identification and Cloning a Novel Tumor Suppressor Gene in Breast Cancer

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