A 6.9-Mb High-Resolution BAC/PAC Contig of Human 4p15.3–p16.1, a Candidate Region for Bipolar Affective Disorder

Evans, Kathryn; Hellard, Stéphanie Le; Morris, Stewart W.; Lawson, Diane; Whitton, Claire; Semple, Colin A.; Fantes, Judith A.; Torrance, Helen S.; Malloy, M. P.; Maule, John; Humphray, Sean; Ross, Mark T.; Muir, Walter; Blackwood, Douglas; Porteous, David J.

doi:10.1006/geno.2000.6432

Cited by 12 publications

(12 citation statements)

References 28 publications

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“…More recently, Evans et al have reported the building of a 6.9-Mb high-resolution BAC/PAC contig of this region and the identification of 57 expressed sequence tags (ESTs) and nine known genes. Resequencing of candidate genes and construction of a high-density SNP map of the region will facilitate linkage disequilibrium (LD) mapping across the putative risk region (55).…”

Section: Chromosome 4p15-16mentioning

confidence: 99%

LINKAGEANALYSIS INPSYCHIATRICDISORDERS: The Emerging Picture

Sklar

2002

Annu. Rev. Genom. Hum. Genet.

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Gene finding in genetically complex diseases has been difficult as a result of many factors that have diagnostic and methodologic considerations. For bipolar disorder and schizophrenia, numerous family, twin, and adoption studies have identified a strong genetic component to these behavioral psychiatric disorders. Despite difficulties that include diagnostic differences between sample populations and the lack of statistical significance in many individual studies, several promising patterns have emerged, suggesting that true susceptibility loci for schizophrenia and bipolar disorder may have been identified. In this review, the genetic epidemiology of these disorders is covered as well as linkage findings on chromosomes 4, 12, 13, 18, 21, and 22 in bipolar disorder and on chromosomes 1, 6, 8, 10, 13, 15, and 22 in schizophrenia. The sequencing of the human genome and identification of numerous single nucleotide polymorphisms (SNP) should substantially enhance the ability of investigators to identify disease-causing genes in these areas of the genome.

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Section: Chromosome 4p15-16mentioning

confidence: 99%

LINKAGEANALYSIS INPSYCHIATRICDISORDERS: The Emerging Picture

Sklar

2002

Annu. Rev. Genom. Hum. Genet.

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“…The region between these two BACs is spanned by 56 other BAC se- Evans et al (2001) also supported the presence of these 58 BAC sequences in the region. In addition, all BACs were found to contain chromosome 4 STS sequences from the region using e-PCR (Schuler 1997).…”

Section: Methods Sequence Retrievalmentioning

confidence: 71%

Computational Comparison of Human Genomic Sequence Assemblies for a Region of Chromosome 4

Semple¹,

Morris

Porteous³

et al. 2002

Genome Res.

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Much of the available human genomic sequence data exist in a fragmentary draft state following the completion of the initial high-volume sequencing performed by the International Human Genome Sequencing Consortium (IHGSC) and Celera Genomics (CG). We compared six draft genome assemblies over a region of chromosome 4p (D4S394-D4S403), two consecutive releases by the IHGSC at University of California, Santa Cruz (UCSC), two consecutive releases from the National Centre for Biotechnology Information (NCBI), the public release from CG, and a hybrid assembly we have produced using IHGSC and CG sequence data. This region presents particular problems for genomic sequence assembly algorithms as it contains a large tandem repeat and is sparsely covered by draft sequences. The six assemblies differed both in terms of their relative coverage of sequence data from the region and in their estimated rates of misassembly. The CG assembly method attained the lowest level of misassembly, whereas NCBI and UCSC assemblies had the highest levels of coverage. All assemblies examined included <60% of the publicly available sequence from the region. At least 6% of the sequence data within the CG assembly for the D4S394-D4S403 region was not present in publicly available sequence data. We also show that even in a problematic region, existing software tools can be used with high-quality mapping data to produce genomic sequence contigs with a low rate of rearrangements.[All sequence accessions for the genomic sequence assemblies analyzed and the data sets used to assess coverage and rates of misassembly are available from http://www.ed.ac.uk/∼csemple.]

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“…A consensus map was created using all the available marker information. Firstly, the order of the nine markers was determined from separate linkage analysis on the Scottish and USA data sets, and subsequently, these data sets were jointly analyzed, constraining the marker order to that of a known physical map [Evans et al, 2001] if those orders were not significantly worse than the best order. Finally, the Danish data was added to create an overall consensus map.…”

Section: Methodsmentioning

confidence: 99%

Joint multi‐population analysis for genetic linkage of bipolar disorder or “wellness” to chromosome 4p

Visscher

Haley

Ewald

et al. 2004

American J of Med Genetics Pt B

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To test the hypothesis that the same genetic loci confer susceptibility to, or protection from, disease in different populations, and that a combined analysis would improve the map resolution of a common susceptibility locus, we analyzed data from three studies that had reported linkage to bipolar disorder in a small region on chromosome 4p. Data sets comprised phenotypic information and genetic marker data on Scottish, Danish, and USA extended pedigrees. Across the three data sets, 913 individuals appeared in the pedigrees, 462 were classified, either as unaffected (323) or affected (139) with unipolar or bipolar disorder. A consensus linkage map was created from 14 microsatellite markers in a 33 cM region. Phenotypic and genetic data were analyzed using a variance component (VC) and allele sharing method. All previously reported elevated test statistics in the region were confirmed with one or both analysis methods, indicating the presence of one or more susceptibility genes to bipolar disorder in the three populations in the studied chromosome segment. When the results from both the VC and allele sharing method were considered, there was strong evidence for a susceptibility locus in the data from Scotland, some evidence in the data from Denmark and relatively less evidence in the data from the USA. The test statistics from the Scottish data set dominated the test statistics from the other studies, and no improved map resolution for a putative genetic locus underlying susceptibility in all three studies was obtained. Studies reporting linkage to the same region require careful scrutiny and preferably joint or meta analysis on the same basis in order to ensure that the results are truly comparable.

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A 6.9-Mb High-Resolution BAC/PAC Contig of Human 4p15.3–p16.1, a Candidate Region for Bipolar Affective Disorder

Cited by 12 publications

References 28 publications

LINKAGEANALYSIS INPSYCHIATRICDISORDERS: The Emerging Picture

LINKAGEANALYSIS INPSYCHIATRICDISORDERS: The Emerging Picture

Computational Comparison of Human Genomic Sequence Assemblies for a Region of Chromosome 4

Joint multi‐population analysis for genetic linkage of bipolar disorder or “wellness” to chromosome 4p

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