Physical Mapping of Chromosome 6: A Strategy for the Rapid Generation of Sequence-Ready Contigs

Mungall, Andrew J.; Edwards, Carol A.; Ranby, A. S.; Humphray, J. S.; Heathcott, W. R.; Clee, C.; East, L. C.; Holloway, Eric; Butler, Paul; Langford, F.; Gwilliam, Rhian; Rice, M. K.; Maslen, G.; Carter, P. N.; Ross, Tristen; Deloukas, Panos; Bentley, R.; Dunham, Ian

doi:10.3109/10425179609015647

Cited by 7 publications

(5 citation statements)

References 3 publications

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“…Contig construction was based on the strategy described by Mungall et al 10 Using the existing contig information held within the Sanger Institute's FingerPrint Contig (FPC) database, 11 STS markers were designed from BAC end sequences positioned at contig ends. These STSs were then used to screen the RPCI-11 BAC library 12 to isolate new chromosome 6-specific BACs.…”

Section: Physical Mapping (Contig Extension)mentioning

confidence: 99%

β-1,3-Glucuronyltransferase-1 gene implicated as a candidate for a schizophrenia-like psychosis through molecular analysis of a balanced translocation

et al. 2003

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We have mapped and sequenced both chromosome breakpoints of a balanced t(6;11)(q14.2;q25) chromosome translocation that segregates with a schizophrenia-like psychosis. Bioinformatics analysis of the regions revealed a number of confirmed and predicted transcripts. No confirmed transcripts are disrupted by either breakpoint. The chromosome 6 breakpoint region is gene poor, the closest transcript being the serotonin receptor 1E (HTR1E) at 625 kb telomeric to the breakpoint. The chromosome 11 breakpoint is situated close to the telomere. The closest gene, b-1,3-glucuronyltransferase (B3GAT1 or GlcAT-P), is 299 kb centromeric to the breakpoint. B3GAT1 is the key enzyme during the biosynthesis of the carbohydrate epitope HNK-1, which is present on a number of cell adhesion molecules important in neurodevelopment. Mice deleted for the B3GAT1 gene show defects in hippocampal long-term potentiation and in spatial memory formation. We propose that the translocation causes a positional effect on B3GAT1, affecting expression levels and making it a plausible candidate for the psychosis found in this family. More generally, regions close to telomeres are highly polymorphic in both sequence and length in the general population and several studies have implicated subtelomeric deletions as a common cause of idiopathic mental retardation. This leads us to the hypothesis that polymorphic or other variation of the 11q telomere may affect the activity of B3GAT1 and be a risk factor for schizophrenia and related psychoses in the general population.

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Section: Physical Mapping (Contig Extension)mentioning

confidence: 99%

β-1,3-Glucuronyltransferase-1 gene implicated as a candidate for a schizophrenia-like psychosis through molecular analysis of a balanced translocation

et al. 2003

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“…Any amplifiable single-copy sequence can therefore be placed in a RH map. The RH mapping technique has been used for the construction of high-resolution gene maps using ESTs (Schuler et al, 1996;Deloukas et al, 1998) and has also been used to supplement the construction of chromosome physical maps via sequence-tagged site (STS) localization (Mungall et al, 1996).…”

Section: Radiation Hybrid Mappingmentioning

confidence: 99%

Genomics and Bioinformatics

Stenger

Gregory

2005

Genetic Analysis of Complex Diseases

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“…The availability of a high-resolution landmark framework has allowed the assembly of sequence-ready bacterial clone contigs over ∼18 Mb (75%-90%) of Xq23-q26.1 (see http://www.sanger.ac.uk/HGP/ChrX). The RPCI1, RPCI3, RPCI4, RPCI5, RPCI6, RPCI11, and RPCI13 PAC and BAC libraries (kindly provided by Pie t e r d e J o n g a n d J o e C a t a n e s e ; s e e h t t p : / / bacpac.med.buffalo.edu/) were used as a source of clones, and contigs were assembled by a combination of restriction fingerprinting and landmark content (Mungall et al 1996). Where necessary, the YAC end probes from the framework map are being converted into STSs for this purpose (see Fig.…”

Section: Use Of the Framework Map In Sequence-ready Mappingmentioning

confidence: 99%

“…DNA from PAC clones identified by STS screening (see Mungall et al 1996) was prepared using a standard alkaline-lysis protocol. DNA was labeled with biotin-16-dUTP or digoxigenin-11-dUTP (Boehringer Mannheim) by nick translation.…”

Section: Fluorescence In Situ Hybridizationmentioning

confidence: 99%

High-Resolution Landmark Framework for the Sequence-Ready Mapping of Xq23–q26.1

Steingruber¹,

Coffey²,

Clegg³

et al. 1999

Genome Res.

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We have established a landmark framework map over 20–25 Mb of the long arm of the human X chromosome using yeast artificial chromosome (YAC) clones. The map has approximately one landmark per 45 kb of DNA and stretches from DXS7531 in proximal Xq23 to DXS895 in proximal Xq26, connecting to published framework maps on its proximal and distal sides. There are three gaps in the framework map resulting from the failure to obtain clone coverage from the YAC resources available. Estimates of the maximum sizes of these gaps have been obtained. The four YAC contigs have been positioned and oriented using somatic-cell hybrids and fluorescence in situ hybridization, and the largest is estimated to cover ∼15 Mb of DNA. The framework map is being used to assemble a sequence-ready map in large-insert bacterial clones, as part of an international effort to complete the sequence of the X chromosome. PAC and BAC contigs currently cover 18 Mb of the region, and from these, 12 Mb of finished sequence is available.

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Physical Mapping of Chromosome 6: A Strategy for the Rapid Generation of Sequence-Ready Contigs

Cited by 7 publications

References 3 publications

β-1,3-Glucuronyltransferase-1 gene implicated as a candidate for a schizophrenia-like psychosis through molecular analysis of a balanced translocation

β-1,3-Glucuronyltransferase-1 gene implicated as a candidate for a schizophrenia-like psychosis through molecular analysis of a balanced translocation

Genomics and Bioinformatics

High-Resolution Landmark Framework for the Sequence-Ready Mapping of Xq23–q26.1

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