Dataset Information

The DNA sequence and analysis of human chromosome 13.

ABSTRACT: Chromosome 13 is the largest acrocentric human chromosome. It carries genes involved in cancer including the breast cancer type 2 (BRCA2) and retinoblastoma (RB1) genes, is frequently rearranged in B-cell chronic lymphocytic leukaemia, and contains the DAOA locus associated with bipolar disorder and schizophrenia. We describe completion and analysis of 95.5 megabases (Mb) of sequence from chromosome 13, which contains 633 genes and 296 pseudogenes. We estimate that more than 95.4% of the protein-coding genes of this chromosome have been identified, on the basis of comparison with other vertebrate genome sequences. Additionally, 105 putative non-coding RNA genes were found. Chromosome 13 has one of the lowest gene densities (6.5 genes per Mb) among human chromosomes, and contains a central region of 38 Mb where the gene density drops to only 3.1 genes per Mb.

SUBMITTER: Dunham A

PROVIDER: S-EPMC2665288 | biostudies-literature | 2004 Apr

REPOSITORIES: biostudies-literature

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The DNA sequence and analysis of human chromosome 13.

Dunham A A Matthews L H LH Burton J J Ashurst J L JL Howe K L KL Ashcroft K J KJ Beare D M DM Burford D C DC Hunt S E SE Griffiths-Jones S S Jones M C MC Keenan S J SJ Oliver K K Scott C E CE Ainscough R R Almeida J P JP Ambrose K D KD Andrews D T DT Ashwell R I S RI Babbage A K AK Bagguley C L CL Bailey J J Bannerjee R R Barlow K F KF Bates K K Beasley H H Bird C P CP Bray-Allen S S Brown A J AJ Brown J Y JY Burrill W W Carder C C Carter N P NP Chapman J C JC Clamp M E ME Clark S Y SY Clarke G G Clee C M CM Clegg S C M SC Cobley V V Collins J E JE Corby N N Coville G J GJ Deloukas P P Dhami P P Dunham I I Dunn M M Earthrowl M E ME Ellington A G AG Faulkner L L Frankish A G AG Frankland J J French L L Garner P P Garnett J J Gilbert J G R JG Gilson C J CJ Ghori J J Grafham D V DV Gribble S M SM Griffiths C C Hall R E RE Hammond S S Harley J L JL Hart E A EA Heath P D PD Howden P J PJ Huckle E J EJ Hunt P J PJ Hunt A R AR Johnson C C Johnson D D Kay M M Kimberley A M AM King A A Laird G K GK Langford C J CJ Lawlor S S Leongamornlert D A DA Lloyd D M DM Lloyd C C Loveland J E JE Lovell J J Martin S S Mashreghi-Mohammadi M M McLaren S J SJ McMurray A A Milne S S Moore M J F MJ Nickerson T T Palmer S A SA Pearce A V AV Peck A I AI Pelan S S Phillimore B B Porter K M KM Rice C M CM Searle S S Sehra H K HK Shownkeen R R Skuce C D CD Smith M M Steward C A CA Sycamore N N Tester J J Thomas D W DW Tracey A A Tromans A A Tubby B B Wall M M Wallis J M JM West A P AP Whitehead S L SL Willey D L DL Wilming L L Wray P W PW Wright M W MW Young L L Coulson A A Durbin R R Hubbard T T Sulston J E JE Beck S S Bentley D R DR Rogers J J Ross M T MT

Nature 20040401 6982

Chromosome 13 is the largest acrocentric human chromosome. It carries genes involved in cancer including the breast cancer type 2 (BRCA2) and retinoblastoma (RB1) genes, is frequently rearranged in B-cell chronic lymphocytic leukaemia, and contains the DAOA locus associated with bipolar disorder and schizophrenia. We describe completion and analysis of 95.5 megabases (Mb) of sequence from chromosome 13, which contains 633 genes and 296 pseudogenes. We estimate that more than 95.4% of the protein ...[more]

PMID: 15057823

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Project description:Our previous genome-wide linkage scan mapped five loci for caries experience. The purpose of this study was to fine map one of these loci, the locus 13q31.1, in order to identify genetic contributors to caries.Seventy-two pedigrees from the Philippines were studied. Caries experience was recorded and DNA was extracted from blood samples obtained from all subjects. Sixty-one single nucleotide polymorphisms (SNPs) in 13q31.1 were genotyped. Association between caries experience and alleles was tested. We also studied 1,481 DNA samples obtained from saliva of subjects from the USA, 918 children from Brazil, and 275 children from Turkey, in order to follow up the results found in the Filipino families. We used the AliBaba2.1 software to determine if the nucleotide changes of the associated SNPs changed the prediction of the presence of transcription-binding site sequences and we also analyzed the gene expression of the genes selected based on binding predictions. Mutation analysis was also performed in 33 Filipino individuals of a segment of 13q31.1 that is highly conserved in mammals.Statistically significant association with high caries experience was found for 11 markers in 13q31.1 in the Filipino families. Haplotype analysis also confirmed these results. In the populations used for follow-up purposes, associations were found between high caries experience and a subset of these markers. Regarding the prediction of the transcription-binding site, the base change of the SNP rs17074565 was found to change the predicted-binding of genes that could be involved in the pathogenesis of caries. When the sequence has the allele C of rs17074565, the potential transcription factors binding the sequence are GR and GATA1. When the subject carries the G allele of rs17074565, the potential transcription factor predicted to bind to the sequence is GATA3. The expression of GR in whole saliva was higher in individuals with low caries experience when compared to individuals with high caries experience (p =?0.046). No mutations were found in the highly conserved sequence.Genetic factors contributing to caries experience may exist in 13q31.1. The rs17074565 is located in an intergenic region and is predicted to disrupt the binding sites of two different transcription factors that might be involved with caries experience. GR expression in saliva may be a biomarker for caries risk and should be further explored.

Dataset Information

The DNA sequence and analysis of human chromosome 13.

Publications

The DNA sequence and analysis of human chromosome 13.

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