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1.
Oncogene ; 26(5): 683-700, 2007 Feb 01.
Article in English | MEDLINE | ID: mdl-16878154

ABSTRACT

We had previously defined by allele loss studies a minimal region at 6q27 (between D6S264 and D6S297) to contain a putative tumour suppressor gene. The p90 ribosomal S6 kinase-3 gene (p90 Rsk-3, RPS6KA2) maps in this interval. It is a serine-threonine kinase that signals downstream of the mitogen-activated protein kinase pathway. It is expressed in normal ovarian epithelium, whereas reduced or absent in tumours or cell lines. We show that RPS6KA2 is monoallelically expressed in the ovary suggesting that loss of a single expressed allele is sufficient to cause complete loss of expression in cancer cells. Further, we have identified two new isoforms of RPS6KA2 with an alternative start codon. Homozygous deletions were identified within the RPS6KA2 gene in two cell lines. Re-expression of RPS6KA2 in ovarian cancer cell lines suppressed colony formation. In UCI101 cells, the expression of RPS6KA2 reduced proliferation, caused G1 arrest, increased apoptosis, reduced levels of phosphorylated extracellular signal-regulated kinase and altered other cell cycle proteins. In contrast, small interfering RNA against RPS6KA2 showed the opposite effect in 41M cells. The above results suggest that RPS6KA2 is a putative tumour suppressor gene to explain allele loss at 6q27.


Subject(s)
Chromosomes, Human, Pair 6/genetics , Genes, Tumor Suppressor/physiology , Neoplasms, Glandular and Epithelial/genetics , Ovarian Neoplasms/genetics , Ribosomal Protein S6 Kinases, 90-kDa/metabolism , Adenocarcinoma, Clear Cell/genetics , Adenocarcinoma, Clear Cell/metabolism , Adenocarcinoma, Clear Cell/pathology , Adenocarcinoma, Mucinous/genetics , Adenocarcinoma, Mucinous/metabolism , Adenocarcinoma, Mucinous/pathology , Amino Acid Sequence , Apoptosis , Carcinoma, Endometrioid/genetics , Carcinoma, Endometrioid/metabolism , Carcinoma, Endometrioid/pathology , Cell Cycle , Cell Proliferation , Chromosome Deletion , Chromosome Mapping , Cystadenocarcinoma, Serous/genetics , Cystadenocarcinoma, Serous/metabolism , Cystadenocarcinoma, Serous/pathology , DNA Methylation , DNA, Neoplasm/genetics , DNA, Neoplasm/metabolism , Female , Gene Expression Regulation, Neoplastic , Humans , Immunoprecipitation , Loss of Heterozygosity , MAP Kinase Signaling System/genetics , Mitogen-Activated Protein Kinases , Molecular Sequence Data , Neoplasms, Glandular and Epithelial/metabolism , Neoplasms, Glandular and Epithelial/pathology , Ovarian Neoplasms/metabolism , Ovarian Neoplasms/pathology , Polymerase Chain Reaction , Polymorphism, Single-Stranded Conformational , RNA Interference , Ribosomal Protein S6 Kinases, 90-kDa/genetics , Sequence Homology, Amino Acid , Transfection , Tumor Cells, Cultured
2.
Oncogene ; 25(8): 1261-71, 2006 Feb 23.
Article in English | MEDLINE | ID: mdl-16205629

ABSTRACT

Deletions of chromosome 6 are a common abnormality in diverse human malignancies including astrocytic tumours, suggesting the presence of tumour suppressor genes (TSG). In order to help identify candidate TSGs, we have constructed a chromosome 6 tile path microarray. The array contains 1,780 clones (778 P1-derived artificial chromosome and 1,002 bacterial artificial chromosome) that cover 98.3% of the published chromosome 6 sequences. A total of 104 adult astrocytic tumours (10 diffuse astrocytomas, 30 anaplastic astrocytomas (AA), 64 glioblastomas (GB)) were analysed using this array. Single copy number change was successfully detected and the result was in general concordant with a microsatellite analysis. The pattern of copy number change was complex with multiple interstitial deletions/gains. However, a predominance of telomeric 6q deletions was seen. Two small common and overlapping regions of deletion at 6q26 were identified. One was 1,002 kb in size and contained PACRG and QKI, while the second was 199 kb and harbours a single gene, ARID1B. The data show that the chromosome 6 tile path array is useful in mapping copy number changes with high resolution and accuracy. We confirmed the high frequency of chromosome 6 deletions in AA and GB, and identified two novel commonly deleted regions that may harbour TSGs.


Subject(s)
Astrocytoma/genetics , Chromosome Deletion , Chromosomes, Human, Pair 6/genetics , Glioblastoma/genetics , Nucleic Acid Hybridization , Oligonucleotide Array Sequence Analysis , Astrocytoma/pathology , Brain Neoplasms/genetics , Brain Neoplasms/pathology , Chromosomes, Artificial, Bacterial , DNA, Neoplasm/analysis , Gene Dosage , Glioblastoma/pathology , Humans , Microsatellite Repeats , Telomere/genetics
3.
Nature ; 428(6982): 522-8, 2004 Apr 01.
Article in English | MEDLINE | ID: mdl-15057823

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.


Subject(s)
Chromosomes, Human, Pair 13/genetics , Genes/genetics , Physical Chromosome Mapping , Chromosome Mapping , Genetics, Medical , Humans , Pseudogenes/genetics , RNA, Untranslated/genetics , Sequence Analysis, DNA
4.
Mol Psychiatry ; 8(7): 654-63, 2003 Jul.
Article in English | MEDLINE | ID: mdl-12874601

ABSTRACT

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, beta-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.


Subject(s)
Chromosomes, Human, Pair 11/genetics , Chromosomes, Human, Pair 6/genetics , Glucuronosyltransferase/genetics , Psychotic Disorders/genetics , Telomere/ultrastructure , Translocation, Genetic , Base Sequence , Chromosome Breakage , Chromosome Mapping/methods , Chromosomes, Human, Pair 11/ultrastructure , Chromosomes, Human, Pair 6/ultrastructure , Depression/genetics , Expressed Sequence Tags , Female , Glucuronosyltransferase/physiology , Humans , Male , Molecular Sequence Data , Pedigree , Psychotic Disorders/epidemiology , Risk Factors , Sequence Deletion , Suicide , Suicide, Attempted
6.
Genome Res ; 11(7): 1290-5, 2001 Jul.
Article in English | MEDLINE | ID: mdl-11435412

ABSTRACT

The near-completion of the sequence for chromosome 22q revolutionizes map integration. We describe a sequence-based integrated map containing 968 loci including 516 known or predicted gene sequences, 317 STSs not included in these sequences, and 135 nonexpressed multinucleotide polymorphisms. The published sequence spans 34.6 Mb, inclusive of gaps estimated to total 1.1 Mb, compared with a top-down estimate of 43 Mb. This discrepancy is discussed, but will not be resolved until more of the genome is analyzed. The radiation hybrid map has 5% error in order and 34% error in location exceeding 1 Mb. The utility of a composite location based on evidence other than sequence is limited to regions not yet sequenced. A genetic map conditional on sequence order was constructed from pairwise lods. Its length of 74.8 cM in males and 80.2 cM in females is slightly less than the previous estimate not constrained by sequence order. Five recombination hot spots are detected, with differences in location between the sexes. Male recombination correlates with repetitive DNA, whereas female recombination does not. It remains to be seen whether this is true for other human chromosomes. An algorithm to improve the fit of cytogenetic bands sequence location reduces the discrepancies in cytogenetic assignment from 61 to 38. This sequence-based integrated map is represented in the genetic location database (LDB2000), which is available at http://cedar.genetics.soton.ac.uk/public_html/LDB2000.html.


Subject(s)
Base Sequence/genetics , Chromosomes, Human, Pair 22/genetics , Physical Chromosome Mapping/methods , Databases, Factual , Female , Gene Order/genetics , Genetic Markers/genetics , Humans , Internet , Male , Polymorphism, Genetic/genetics , Sex Factors
7.
Nature ; 409(6822): 860-921, 2001 Feb 15.
Article in English | MEDLINE | ID: mdl-11237011

ABSTRACT

The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human genome. We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence.


Subject(s)
Genome, Human , Human Genome Project , Sequence Analysis, DNA , Animals , Chromosome Mapping , Conserved Sequence , CpG Islands , DNA Transposable Elements , Databases, Factual , Drug Industry , Evolution, Molecular , Forecasting , GC Rich Sequence , Gene Duplication , Genes , Genetic Diseases, Inborn , Genetics, Medical , Humans , Mutation , Private Sector , Proteins/genetics , Proteome , Public Sector , RNA/genetics , Repetitive Sequences, Nucleic Acid , Sequence Analysis, DNA/methods , Species Specificity
8.
Nature ; 409(6822): 942-3, 2001 Feb 15.
Article in English | MEDLINE | ID: mdl-11237015

ABSTRACT

We constructed maps for eight chromosomes (1, 6, 9, 10, 13, 20, X and (previously) 22), representing one-third of the genome, by building landmark maps, isolating bacterial clones and assembling contigs. By this approach, we could establish the long-range organization of the maps early in the project, and all contig extension, gap closure and problem-solving was simplified by containment within local regions. The maps currently represent more than 94% of the euchromatic (gene-containing) regions of these chromosomes in 176 contigs, and contain 96% of the chromosome-specific markers in the human gene map. By measuring the remaining gaps, we can assess chromosome length and coverage in sequenced clones.


Subject(s)
Chromosomes, Human, Pair 10 , Chromosomes, Human, Pair 13 , Chromosomes, Human, Pair 1 , Chromosomes, Human, Pair 20 , Chromosomes, Human, Pair 6 , Contig Mapping , Genome, Human , X Chromosome , Humans
9.
Genome Res ; 11(1): 170-8, 2001 Jan.
Article in English | MEDLINE | ID: mdl-11156626

ABSTRACT

The recent publication of the complete sequence of human chromosome 22 provides a platform from which to investigate genomic sequence variation. We report the identification and characterization of 12,267 potential variants (SNPs and other small insertions/deletions) of human chromosome 22, discovered in the overlaps of 460 clones used for the chromosome sequencing. We found, on average, 1 potential variant every 1.07 kb and approximately 18% of the potential variants involve insertions/deletions. The SNPs have been positioned both relative to each other, and to genes, predicted genes, repeat sequences, other genetic markers, and the 2730 SNPs previously identified on the chromosome. A subset of the SNPs were verified experimentally using either PCR-RFLP or genomic Invader assays. These experiments confirmed 92% of the potential variants in a panel of 92 individuals. [Details of the SNPs and RFLP assays can be found at http://www.sanger.ac.uk and in dbSNP.]


Subject(s)
Chromosomes, Human, Pair 22/genetics , Polymorphism, Single Nucleotide/genetics , Base Composition , Chromosome Deletion , Chromosome Mapping , Chromosomes, Human, Pair 22/chemistry , DNA Transposable Elements/genetics , Genetic Variation , Genome, Human , Humans , Reproducibility of Results
10.
Am J Hum Genet ; 67(6): 1544-54, 2000 Dec.
Article in English | MEDLINE | ID: mdl-11078480

ABSTRACT

The design and feasibility of whole-genome-association studies are critically dependent on the extent of linkage disequilibrium (LD) between markers. Although there has been extensive theoretical discussion of this, few empirical data exist. The authors have determined the extent of LD among 38 biallelic markers with minor allele frequencies >.1, since these are most comparable to the common disease-susceptibility polymorphisms that association studies aim to detect. The markers come from three chromosomal regions-1,335 kb on chromosome 13q12-13, 380 kb on chromosome 19q13.2, and 120 kb on chromosome 22q13.3-which have been extensively mapped. These markers were examined in approximately 1,600 individuals from four populations, all of European origin but with different demographic histories; Afrikaners, Ashkenazim, Finns, and East Anglian British. There are few differences, either in allele frequencies or in LD, among the populations studied. A similar inverse relationship was found between LD and distance in each genomic region and in each population. Mean D' is.68 for marker pairs <5 kb apart and is.24 for pairs separated by 10-20 kb, and the level of LD is not different from that seen in unlinked marker pairs separated by >500 kb. However, only 50% of marker pairs at distances <5 kb display sufficient LD (delta>.3) to be useful in association studies. Results of the present study, if representative of the whole genome, suggest that a whole-genome scan searching for common disease-susceptibility alleles would require markers spaced < or = 5 kb apart.


Subject(s)
Chromosome Mapping , Genetic Predisposition to Disease/genetics , Linkage Disequilibrium/genetics , Phylogeny , Africa/ethnology , Alleles , Chromosome Mapping/methods , Chromosomes, Human, Pair 13/genetics , Chromosomes, Human, Pair 19/genetics , Chromosomes, Human, Pair 22/genetics , Demography , Finland/ethnology , Gene Frequency/genetics , Genetic Markers/genetics , Genotype , Humans , Jews/genetics , Polymorphism, Genetic/genetics , United Kingdom/ethnology
11.
Yeast ; 17(3): 218-24, 2000 Sep 30.
Article in English | MEDLINE | ID: mdl-11025532

ABSTRACT

A recent flurry of publications and media attention has revived interest in the question of how many genes exist in the human genome. Here, I review the estimates and use genomic sequence data from human chromosomes 21 and 22 to establish my own prediction.


Subject(s)
Genes , Genome, Human , Genomics , Base Sequence , Chromosomes, Human, Pair 21/genetics , Chromosomes, Human, Pair 22/genetics , Computational Biology , CpG Islands , Expressed Sequence Tags , Humans
12.
Trends Genet ; 16(10): 456-61, 2000 Oct.
Article in English | MEDLINE | ID: mdl-11050332

ABSTRACT

The end of the beginning of the Human Genome Project was announced on 26 June when the working draft or first assembly was announced. Here, Ian Dunham who led the group at the Sanger Centre that produced the first complete sequence of a human chromosome reflects on how it felt to be with the genome project from the beginning.


Subject(s)
Genomics , Human Genome Project/history , Chromosomes, Human, Pair 22/genetics , England , Forecasting , History, 20th Century , Humans , Publishing , Research Personnel , Sequence Analysis, DNA/history
13.
Nature ; 407(6803): 516-20, 2000 Sep 28.
Article in English | MEDLINE | ID: mdl-11029003

ABSTRACT

The human genome sequence will provide a reference for measuring DNA sequence variation in human populations. Sequence variants are responsible for the genetic component of individuality, including complex characteristics such as disease susceptibility and drug response. Most sequence variants are single nucleotide polymorphisms (SNPs), where two alternate bases occur at one position. Comparison of any two genomes reveals around 1 SNP per kilobase. A sufficiently dense map of SNPs would allow the detection of sequence variants responsible for particular characteristics on the basis that they are associated with a specific SNP allele. Here we have evaluated large-scale sequencing approaches to obtaining SNPs, and have constructed a map of 2,730 SNPs on human chromosome 22. Most of the SNPs are within 25 kilobases of a transcribed exon, and are valuable for association studies. We have scaled up the process, detecting over 65,000 SNPs in the genome as part of The SNP Consortium programme, which is on target to build a map of 1 SNP every 5 kilobases that is integrated with the human genome sequence and that is freely available in the public domain.


Subject(s)
Chromosomes, Human, Pair 22 , Polymorphism, Single Nucleotide , Sequence Analysis, DNA/methods , Cell Line , Chromosome Mapping/methods , Evaluation Studies as Topic , Gene Library , Genome, Human , Humans , Sequence Alignment
15.
Genomics ; 64(3): 264-76, 2000 Mar 15.
Article in English | MEDLINE | ID: mdl-10756094

ABSTRACT

Genetic studies have previously assigned a quantitative trait locus (QTL) for hemoglobin F and F cells to a region of approximately 4 Mb between the markers D6S408 and D6S292 on chromosome 6q23. An initial yeast artificial chromosome contig of 13 clones spanning this region was generated. Further linkage analysis of an extended kindred refined the candidate interval to 1-2 cM, and key recombination events now place the QTL within a region of <800 kb. We describe a high-resolution bacterial clone contig spanning 3 Mb covering this critical region. The map consists of 223 bacterial artificial chromosome (BAC) and 100 P1 artificial chromosome (PAC) clones ordered by sequence-tagged site (STS) content and restriction fragment fingerprinting with a minimum tiling path of 22 BACs and 1 PAC. A total of 194 STSs map to this interval of 3 Mb, giving an average marker resolution of approximately one per 15 kb. About half of the markers were novel and were isolated in the present study, including three CA repeats and 13 single nucleotide polymorphisms. Altogether 24 expressed sequence tags, 6 of which are unique genes, have been mapped to the contig.


Subject(s)
Chromosomes, Human, Pair 6/genetics , Contig Mapping , Fetal Hemoglobin/genetics , Quantitative Trait, Heritable , Base Sequence , Chromosomes, Artificial, Yeast , Expressed Sequence Tags , Female , Genetic Linkage , Haplotypes , Humans , Male , Molecular Sequence Data , Pedigree , Polymerase Chain Reaction , Polymorphism, Restriction Fragment Length
16.
Eur J Hum Genet ; 8(3): 209-14, 2000 Mar.
Article in English | MEDLINE | ID: mdl-10780787

ABSTRACT

Neurofibromatosis type 1 (NF1) is a frequent hereditary disorder that involves tissues derived from the embryonic neural crest. Besides the functional gene on chromosome arm 17q, NF1-related sequences (pseudogenes) are present on a number of chromosomes including 2, 12, 14, 15, 18, 21, and 22. We elucidated the complete nucleotide sequence of the NF1 pseudogene on chromosome 22. Only the middle part of the functional gene but not exons 21-27a, encoding the functionally important GAP-related domain of the NF1 protein, is presented in this pseudogene. In addition to the two known NF1 pseudogenes on chromosome 14 we identified two novel variants. A phylogenetic tree was constructed, from which we concluded that the NF1 pseudogenes on chromosomes 2, 14, and 22 are closely related to each other. Clones containing one of these pseudogenes cross-hybridised with the other pseudogenes in this subset, but did not reveal any in situ hybridisation with the functional NF1 gene or with NF1 pseudogenes on other chromosomes. This suggests that their hybridisation specificity is mainly determined by homologous sequences flanking the pseudogenes. Strong support for this concept was obtained by sequence analysis of the flanking regions, which revealed more than 95% homology. We hypothesise that during evolution this subset of NF1 pseudogenes initially arose by duplication and transposition of the middle part of the functional NF1 gene to chromosome 2. Subsequently, a much larger fragment, including flanking sequences, was duplicated and gave rise to the current NF1 pseudogene copies on chromosomes 14 and 22.


Subject(s)
Chromosomes, Human, Pair 2 , Proteins/genetics , Pseudogenes , Base Sequence , Chromosome Mapping , Chromosomes, Human, Pair 14 , Chromosomes, Human, Pair 22 , DNA/analysis , Evolution, Molecular , Humans , Molecular Sequence Data , Neurofibromin 1 , Nucleic Acid Hybridization , Phylogeny , Polymerase Chain Reaction , Sequence Homology, Nucleic Acid
18.
Nature ; 402(6761): 489-95, 1999 Dec 02.
Article in English | MEDLINE | ID: mdl-10591208

ABSTRACT

Knowledge of the complete genomic DNA sequence of an organism allows a systematic approach to defining its genetic components. The genomic sequence provides access to the complete structures of all genes, including those without known function, their control elements, and, by inference, the proteins they encode, as well as all other biologically important sequences. Furthermore, the sequence is a rich and permanent source of information for the design of further biological studies of the organism and for the study of evolution through cross-species sequence comparison. The power of this approach has been amply demonstrated by the determination of the sequences of a number of microbial and model organisms. The next step is to obtain the complete sequence of the entire human genome. Here we report the sequence of the euchromatic part of human chromosome 22. The sequence obtained consists of 12 contiguous segments spanning 33.4 megabases, contains at least 545 genes and 134 pseudogenes, and provides the first view of the complex chromosomal landscapes that will be found in the rest of the genome.


Subject(s)
Chromosomes, Human, Pair 22 , Human Genome Project , Sequence Analysis, DNA , Animals , Chromosome Mapping/methods , DNA , Gene Dosage , Humans , Mice , Molecular Sequence Data , Repetitive Sequences, Nucleic Acid , Species Specificity
20.
J Invest Dermatol ; 113(2): 162-9, 1999 Aug.
Article in English | MEDLINE | ID: mdl-10469298

ABSTRACT

Earlier studies of psoriatic and normal primary keratinocytes treated with phorbol 12-myristate-1-acetate identified two low-molecular-weight proteins, termed phorbolin-1 (20 kDa; pI 6.6) and phorbolin-2 (17.6 kDa; pI 6.5). As a first step towards elucidating the role of these proteins in psoriasis, we report here the molecular cloning and chromosomal mapping of phorbolin-1 and a related cDNA that codes for a protein exhibiting a similar amino acid sequence. The phorbolins were mapped to position 22q13 immediately centromeric to the c-sis proto-oncogene. Transient expression of the phorbolin-1 cDNA in COS cells and by in vitro transcription/translation, yielded polypeptides that comigrated with phorbolins-1 and -2. Comparative sequence analysis revealed 22% overall identity and a similarity of 44% of the phorbolins to apobec-1, the catalytic subunit of the mammalian apolipoprotein B mRNA editing enzyme; however, recombinant-expressed phorbolin-1 exhibited no cytidine deaminase activity, using either a monomeric nucleoside or apolipoprotein B cRNA as substrate, and failed to bind an AU-rich RNA template. Whereas the precise function of the phorbolins remains to be elucidated, the current data suggest that it is unlikely to include a role in the post-transcriptional modification of RNA in a manner analogous to that described for apobec-1.


Subject(s)
Cytidine Deaminase/physiology , Proteins/chemistry , Psoriasis/physiopathology , APOBEC-1 Deaminase , Amino Acid Sequence , Base Sequence , Binding Sites , Chromosome Mapping , Cloning, Molecular , Cytidine Deaminase/chemistry , Gene Library , Molecular Sequence Data , Proteins/genetics , Proto-Oncogene Mas , Sequence Homology, Amino Acid
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