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. 1998 Nov;8(11):1216-27.
doi: 10.1101/gr.8.11.1216.

Quality assessment of whole genome mapping data in the refined familial spastic paraplegia interval on chromosome 14q

C Paternotte  1 , D Rudnicki, C Fizames, C S Davoine, D Mavel, A Dürr, D Samson, C Marquette, D Muselet, N Vega-Czarny, N Drouot, T Voit, B Fontaine, G Gyapay, G Auburger, J Weissenbach, J Hazan
Affiliations

Quality assessment of whole genome mapping data in the refined familial spastic paraplegia interval on chromosome 14q

C Paternotte et al. Genome Res. 1998 Nov.

Abstract

Autosomal dominant familial spastic paraplegia (AD-FSP) is a genetically heterogeneous neurodegenerative disorder characterized by progressive spasticity of the lower limbs. Three loci on chromosome 14q (SPG3), 2p (SPG4), and 15q (SPG6) were shown to be responsible for AD-FSP. Analysis of recombination events in three SPG3-linked families allowed us to narrow the critical interval from 9 to 5 cM. An approximately 5-Mb YAC contig comprising 32 clones and 90 STSs was built from D14S301 to D14S991, encompassing this region of 14q21. Fifty-six ESTs assigned previously to this region with radiation hybrid (RH) panels Genebridge 4 and G3 were precisely localized on the YAC contig. The 90 STSs positioned on the contig were tested on the TNG RH panel to compare our YAC-based map with an RH map at a high level of resolution. Comparison between our map and the whole genome mapping data on this interval of chromosome 14q is discussed.

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Figures

Figure 1
Figure 1
Pedigrees of families C, W, and 014. Affected individuals are represented by black symbols and unaffected family members by open symbols. Boxes indicate disease chromosomes. Critical recombination events in patients are marked with an arrow. (A) Family C; (B) family W; (C) family 014.
Figure 1
Figure 1
Pedigrees of families C, W, and 014. Affected individuals are represented by black symbols and unaffected family members by open symbols. Boxes indicate disease chromosomes. Critical recombination events in patients are marked with an arrow. (A) Family C; (B) family W; (C) family 014.
Figure 1
Figure 1
Pedigrees of families C, W, and 014. Affected individuals are represented by black symbols and unaffected family members by open symbols. Boxes indicate disease chromosomes. Critical recombination events in patients are marked with an arrow. (A) Family C; (B) family W; (C) family 014.
Figure 2
Figure 2
YAC contig map of the SPG3 region. The 90 STSs, including polymorphic markers and ESTs for which GenBank accession numbers are indicated in italics, are listed along the second line at top. The two thick black lines surrounding loci D14S259 and D14S1018 represent the proximal and distal borders of the SPG3 interval, respectively. Polymorphic markers appearing on the last version of Généthon genetic map are framed with a thicker line. Each of the 32 YAC clones is depicted by dark grey rectangles with its name given to the left and to the right. Presence or absence of an STS in the corresponding YAC clone is indicated by dark or light grey squares. RH mapping data using the TNG panel are presented at top: The 22 linkage groups defined by a pairwise lod score above 4 are indicated on the first line, a 0 is used to describe STSs that did not amplify on TNG, and the colors along the second line correspond to the 11 linkage groups containing more than one STS. Positions of ESTs H68092 and H99050, which generate an internal deletion in YAC 965B6, were those defined by TNG RH mapping data.
Figure 2
Figure 2
YAC contig map of the SPG3 region. The 90 STSs, including polymorphic markers and ESTs for which GenBank accession numbers are indicated in italics, are listed along the second line at top. The two thick black lines surrounding loci D14S259 and D14S1018 represent the proximal and distal borders of the SPG3 interval, respectively. Polymorphic markers appearing on the last version of Généthon genetic map are framed with a thicker line. Each of the 32 YAC clones is depicted by dark grey rectangles with its name given to the left and to the right. Presence or absence of an STS in the corresponding YAC clone is indicated by dark or light grey squares. RH mapping data using the TNG panel are presented at top: The 22 linkage groups defined by a pairwise lod score above 4 are indicated on the first line, a 0 is used to describe STSs that did not amplify on TNG, and the colors along the second line correspond to the 11 linkage groups containing more than one STS. Positions of ESTs H68092 and H99050, which generate an internal deletion in YAC 965B6, were those defined by TNG RH mapping data.
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