151
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Strausberg RL, Simpson AJG, Wooster R. Sequence-based cancer genomics: progress, lessons and opportunities. Nat Rev Genet 2003; 4:409-18. [PMID: 12776211 DOI: 10.1038/nrg1085] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Technologies that provide a genome-wide view offer an unprecedented opportunity to scrutinize the molecular biology of the cancer cell. The information that is derived from these technologies is well suited to the development of public databases of alterations in the cancer genome and its expression. Here, we describe the synergistic efforts of research programmes in Brazil, the United Kingdom and the United States towards building integrated databases that are widely accessible to the research community, to enable basic and applied applications in cancer research.
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Affiliation(s)
- Robert L Strausberg
- National Cancer Institute, 31 Center Drive, Room 10A07, Bethesda, Maryland 20892, USA.
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152
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Abstract
Large segmental duplications (SDs) constitute at least 3.6% of the human genome and have increased its size, complexity, and diversity. SDs can mediate ectopic sequence exchange resulting in gross chromosomal rearrangements that could contribute to speciation and disease. We have identified and evaluated a subset of human SDs that harbor an 88-member subfamily of olfactory receptor (OR)-like genes called the 7Es. At least 92% of these genes appear to be pseudogenes when compared to other OR genes. The 7E-containing SDs (7E SDs) have duplicated to at least 35 regions of the genome via intra- and interchromosomal duplication events. In contrast to many human SDs, the 7E SDs are not biased towards pericentromeric or subtelomeric regions. We find evidence for gene conversion among 7E genes and larger sequence exchange between 7E SDs, supporting the hypothesis that long, highly similar stretches of DNA facilitate ectopic interactions. The complex structure and history of the 7E SDs necessitates extension of the current model of large-scale DNA duplication. Despite their appearance as pseudogenes, some 7E genes exhibit a signature of purifying selection, and at least one 7E gene is expressed.
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Affiliation(s)
- Tera Newman
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
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153
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Abstract
As the complete sequences of human and other mammalian genomes become available we are faced with the challenge of understanding how variation in sequence and gene expression contributes to neurological and psychiatric disorders. DNA microarrays, or DNA chips, provide the means to measure simultaneously where and when thousands of genes are expressed. Microarrays are changing the way that researchers approach work at the bench and have already yielded new insights into brain tumours, multiple sclerosis, acute neurological insults such as stroke and seizures, and schizophrenia. The study of disease-related changes in gene expression is the first step in the long process in translation of genome research to the clinic. Eventually, the changes observed in microarray studies will need to be independently confirmed and we wil need to understand how gene expression changes translate into functional effects at the cellular level in the nervous system. Progress in these studies will translate into array-based disease classification schemes and help optimise therapy for individual patients based on gene expression patterns or their genetic background.
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154
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Stankiewicz P, Shaw CJ, Dapper JD, Wakui K, Shaffer LG, Withers M, Elizondo L, Park SS, Lupski JR. Genome architecture catalyzes nonrecurrent chromosomal rearrangements. Am J Hum Genet 2003; 72:1101-16. [PMID: 12649807 PMCID: PMC1180264 DOI: 10.1086/374385] [Citation(s) in RCA: 144] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2002] [Accepted: 01/16/2003] [Indexed: 11/03/2022] Open
Abstract
To investigate the potential involvement of genome architecture in nonrecurrent chromosome rearrangements, we analyzed the breakpoints of eight translocations and 18 unusual-sized deletions involving human proximal 17p. Surprisingly, we found that many deletion breakpoints occurred in low-copy repeats (LCRs); 13 were associated with novel large LCR17p structures, and 2 mapped within an LCR sequence (middle SMS-REP) within the Smith-Magenis syndrome (SMS) common deletion. Three translocation breakpoints involving 17p11 were found to be located within the centromeric alpha-satellite sequence D17Z1, three within a pericentromeric segment, and one at the distal SMS-REP. Remarkably, our analysis reveals that LCRs constitute >23% of the analyzed genome sequence in proximal 17p--an experimental observation two- to fourfold higher than predictions based on virtual analysis of the genome. Our data demonstrate that higher-order genomic architecture involving LCRs plays a significant role not only in recurrent chromosome rearrangements but also in translocations and unusual-sized deletions involving 17p.
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Affiliation(s)
- Paweł Stankiewicz
- Departments of Molecular and Human Genetics and Pediatrics and Interdepartmental Program in Cell and Molecular Biology, Baylor College of Medicine, and Texas Children's Hospital, Houston
| | - Christine J. Shaw
- Departments of Molecular and Human Genetics and Pediatrics and Interdepartmental Program in Cell and Molecular Biology, Baylor College of Medicine, and Texas Children's Hospital, Houston
| | - Jason D. Dapper
- Departments of Molecular and Human Genetics and Pediatrics and Interdepartmental Program in Cell and Molecular Biology, Baylor College of Medicine, and Texas Children's Hospital, Houston
| | - Keiko Wakui
- Departments of Molecular and Human Genetics and Pediatrics and Interdepartmental Program in Cell and Molecular Biology, Baylor College of Medicine, and Texas Children's Hospital, Houston
| | - Lisa G. Shaffer
- Departments of Molecular and Human Genetics and Pediatrics and Interdepartmental Program in Cell and Molecular Biology, Baylor College of Medicine, and Texas Children's Hospital, Houston
| | - Marjorie Withers
- Departments of Molecular and Human Genetics and Pediatrics and Interdepartmental Program in Cell and Molecular Biology, Baylor College of Medicine, and Texas Children's Hospital, Houston
| | - Leah Elizondo
- Departments of Molecular and Human Genetics and Pediatrics and Interdepartmental Program in Cell and Molecular Biology, Baylor College of Medicine, and Texas Children's Hospital, Houston
| | - Sung-Sup Park
- Departments of Molecular and Human Genetics and Pediatrics and Interdepartmental Program in Cell and Molecular Biology, Baylor College of Medicine, and Texas Children's Hospital, Houston
| | - James R. Lupski
- Departments of Molecular and Human Genetics and Pediatrics and Interdepartmental Program in Cell and Molecular Biology, Baylor College of Medicine, and Texas Children's Hospital, Houston
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155
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Cheng Z, Buell CR, Wing RA, Jiang J. Resolution of fluorescence in-situ hybridization mapping on rice mitotic prometaphase chromosomes, meiotic pachytene chromosomes and extended DNA fibers. Chromosome Res 2003; 10:379-87. [PMID: 12296520 DOI: 10.1023/a:1016849618707] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Fluorescence in-situ hybridization (FISH) is a quick and affordable approach to map DNA sequences to specific chromosomal regions. Although FISH is one of the most important physical mapping techniques, research on the resolution of FISH on different cytological targets is scarce in plants. In this study, we report the resolution of FISH mapping on mitotic prometaphase chromosomes, meiotic pachytene chromosomes and extended DNA fibers in rice. A majority of the FISH signals derived from bacterial artificial chromosome (BAC) clones separated by approximately 1 Mb of DNA cannot be resolved on mitotic prometaphase chromosomes. In contrast, the relative positions of closely linked or even partially overlapping BAC clones can be resolved on a euchromatic region of rice chromosome 10 at the early pachytene stage. The resolution of pachytene FISH is dependent on early or late pachytene stages and also on the location of the DNA probes in the euchromatic or heterochromatic regions. We calibrated the fiber-FISH technique in rice using seven sequenced BAC clones. The average DNA extension was 3.21 kb/microm among the seven BAC clones. Fiber-FISH results derived from a BAC contig that spanned 1 Mb DNA matched remarkably to the sequencing data, demonstrating the high resolution of this technique in cytological mapping.
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Affiliation(s)
- Zhukuan Cheng
- Department of Horticulture, University of Wisconsin-Madison, 53706, USA
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156
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Abstract
Linkage studies of mental illness have provided suggestive evidence of susceptibility loci over many broad chromosomal regions. Pinpointing causative gene mutations by conventional linkage strategies alone is problematic. The breakpoints of chromosomal abnormalities occurring in patients with mental illness may be more direct pointers to the relevant gene locus. Publications that describe patients where chromosomal abnormalities co-exist with mental illness are reviewed along with supporting evidence that this may amount to an association. Chromosomal abnormalities are considered to be of possible significance if (a) the abnormality is rare and there are independent reports of its coexistence with psychiatric illness, or (b) there is colocalisation of the abnormality with a region of suggestive linkage findings, or (c) there is an apparent cosegregation of the abnormality with psychiatric illness within the individual's family. Breakpoints have been described within many of the loci suggested by linkage studies and these findings support the hypothesis that shared susceptibility factors for schizophrenia and bipolar disorder may exist. If these abnormalities directly disrupt coding regions, then combining molecular genetic breakpoint cloning with bioinformatic sequence analysis may be a method of rapidly identifying candidate genes. Full karyotyping of individuals with psychotic illness especially where this coexists with mild learning disability, dysmorphism or a strong family history of mental disorder is encouraged.
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Affiliation(s)
- D J MacIntyre
- Department of Psychiatry, University of Edinburgh, Scotland, UK
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157
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158
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Strausberg RL, Camargo AA, Riggins GJ, Schaefer CF, de Souza SJ, Grouse LH, Lal A, Buetow KH, Boon K, Greenhut SF, Simpson AJG. An international database and integrated analysis tools for the study of cancer gene expression. THE PHARMACOGENOMICS JOURNAL 2003; 2:156-64. [PMID: 12082587 DOI: 10.1038/sj.tpj.6500103] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2002] [Revised: 02/21/2002] [Accepted: 02/27/2002] [Indexed: 11/10/2022]
Abstract
Researchers working collaboratively in Brazil and the United States have assembled an International Database of Cancer Gene Expression. Several strategies have been employed to generate gene expression data including expressed sequence tags (ESTs), serial analysis of gene expression (SAGE), and open reading-frame expressed sequence tags (ORESTES). The database contains six million gene tags that reflect the gene expression profiles in a wide variety of cancerous tissues and their normal counterparts. All sequences are deposited in the public databases, GenBank and SAGEmap. A suite of informatics tools was designed to facilitate in silico analysis of the gene expression datasets and are available through the NCI Cancer Genome Anatomy Project web site (http://cgap.nci.nih.gov).
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159
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Gray JW, Suzuki S, Kuo WL, Polikoff D, Deavers M, Smith-McCune K, Berchuck A, Pinkel D, Albertson D, Mills GB. Specific keynote: genome copy number abnormalities in ovarian cancer. Gynecol Oncol 2003; 88:S16-21; discussion S22-4. [PMID: 12586079 DOI: 10.1006/gyno.2002.6677] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Joe W Gray
- University of California, Los Angeles, USA
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160
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Li J, Jiang T, Bejjani B, Rajcan-Separovic E, Cai WW. High-resolution human genome scanning using whole-genome BAC arrays. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2003; 68:323-9. [PMID: 15338633 DOI: 10.1101/sqb.2003.68.323] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Affiliation(s)
- J Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
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161
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Karolchik D, Baertsch R, Diekhans M, Furey TS, Hinrichs A, Lu YT, Roskin KM, Schwartz M, Sugnet CW, Thomas DJ, Weber RJ, Haussler D, Kent WJ. The UCSC Genome Browser Database. Nucleic Acids Res 2003; 31:51-4. [PMID: 12519945 PMCID: PMC165576 DOI: 10.1093/nar/gkg129] [Citation(s) in RCA: 1159] [Impact Index Per Article: 55.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The University of California Santa Cruz (UCSC) Genome Browser Database is an up to date source for genome sequence data integrated with a large collection of related annotations. The database is optimized to support fast interactive performance with the web-based UCSC Genome Browser, a tool built on top of the database for rapid visualization and querying of the data at many levels. The annotations for a given genome are displayed in the browser as a series of tracks aligned with the genomic sequence. Sequence data and annotations may also be viewed in a text-based tabular format or downloaded as tab-delimited flat files. The Genome Browser Database, browsing tools and downloadable data files can all be found on the UCSC Genome Bioinformatics website (http://genome.ucsc.edu), which also contains links to documentation and related technical information.
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Affiliation(s)
- D Karolchik
- Genome Bioinformatics Group, The University of California Santa Cruz (UCSC), School of Engineering, 1156 High Street, Santa Cruz, CA 95064-1077, USA.
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162
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Bussey KJ, Kane D, Sunshine M, Narasimhan S, Nishizuka S, Reinhold WC, Zeeberg B, Weinstein JN. MatchMiner: a tool for batch navigation among gene and gene product identifiers. Genome Biol 2003; 4:R27. [PMID: 12702208 PMCID: PMC154578 DOI: 10.1186/gb-2003-4-4-r27] [Citation(s) in RCA: 121] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2002] [Revised: 12/20/2002] [Accepted: 02/28/2003] [Indexed: 11/10/2022] Open
Abstract
MatchMiner is a freely available program package for batch navigation among gene and gene product identifier types commonly encountered in microarray studies and other forms of 'omic' research. The user inputs a list of gene identifiers and then uses the Merge function to find the overlap with a second list of identifiers of either the same or a different type or uses the LookUp function to find corresponding identifiers.
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Affiliation(s)
- Kimberly J Bussey
- Genomics and Bioinformatics Group, Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH Building 37, Bethesda, MD 20892-4255, USA
| | - David Kane
- SRA International Inc., 4300 Fair Lakes CT, Fairfax, VA 22033, USA
| | - Margot Sunshine
- SRA International Inc., 4300 Fair Lakes CT, Fairfax, VA 22033, USA
| | - Sudar Narasimhan
- SRA International Inc., 4300 Fair Lakes CT, Fairfax, VA 22033, USA
| | - Satoshi Nishizuka
- Genomics and Bioinformatics Group, Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH Building 37, Bethesda, MD 20892-4255, USA
| | - William C Reinhold
- Genomics and Bioinformatics Group, Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH Building 37, Bethesda, MD 20892-4255, USA
| | - Barry Zeeberg
- Genomics and Bioinformatics Group, Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH Building 37, Bethesda, MD 20892-4255, USA
| | - John N Weinstein
- Genomics and Bioinformatics Group, Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH Building 37, Bethesda, MD 20892-4255, USA
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163
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Cowell JK, Nowak NJ. High-Resolution Analysis of Genetic Events in Cancer Cells Using Bacterial Artificial Chromosome Arrays and Comparative Genome Hybridization. Adv Cancer Res 2003; 90:91-125. [PMID: 14710948 DOI: 10.1016/s0065-230x(03)90003-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Chromosome analysis of cancer cells has been one of the primary means of identifying key genetic events in the development of cancer. The relatively low resolution of metaphase chromosomes, however, only allows characterization of major genetic events that are defined at the megabase level. The development of the human genome-wide bacterial artificial chromosome (BAC) libraries that were used as templates for the human genome project made it possible to design microarrays containing these BACs that can theoretically span the genome uninterrupted. Competitive hybridization to these arrays using tumor and normal DNA samples reveals numerical chromosome abnormalities (deletions and amplifications) that can be accurately defined depending on the density of the arrays. At present, we are using arrays with 6,000 BACs, which provide an average resolution of less than 700 kb. Analysis of tumor DNA samples using these arrays reveals small deletions and amplifications that were not detectable by chromosome analysis and provides a global view of these genetic changes in a single hybridization experiment in 24 hours. The extent of the genetic changes can then be determined precisely and the gene content of the affected regions established. These arrays have widespread application to the analysis of cancer patients and their tumors and can detect constitutional abnormalities as well. The availability of these high-density arrays now provides the opportunity to classify tumors based on their genetic fingerprints, which will assist in staging, diagnosis, and even prediction of response to therapy. Importantly, subtle genetic changes that occur consistently in tumor cell types may eventually be used to stratify patients for clinical trials and to predict their response to custom therapies.
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Affiliation(s)
- John K Cowell
- Roswell Park Cancer Institute, Department of Cancer Genetics, Elm and Carlton Streets, Buffalo, New York 14263, USA
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164
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Strausberg RL, Buetow KH, Greenhut SF, Grouse LH, Schaefer CF. The cancer genome anatomy project: online resources to reveal the molecular signatures of cancer. Cancer Invest 2002; 20:1038-50. [PMID: 12449737 DOI: 10.1081/cnv-120005922] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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165
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Abstract
Genomic rearrangements play a major role in the pathogenesis of human genetic diseases. Nonallelic homologous recombination (NAHR) between low-copy repeats (LCRs) that flank unique genomic segments results in changes of genome organization and can cause a loss or gain of genomic segments. These LCRs appear to have arisen recently during primate speciation via paralogous segmental duplication, thus making the human species particularly susceptible to genomic rearrangements. Genomic disorders are defined as a group of diseases that result from genomic rearrangements, mostly mediated by NAHR. Molecular investigations of genomic disorders have revealed genome architectural features associated with susceptibility to rearrangements and the recombination mechanisms responsible for such rearrangements. The human genome sequence project reveals that LCRs may account for 5% of the genome, suggesting that many novel genomic disorders might still remain to be recognized.
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Affiliation(s)
- Ken Inoue
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.
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166
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Wendl MC, Waterston RH. Generalized gap model for bacterial artificial chromosome clone fingerprint mapping and shotgun sequencing. Genome Res 2002; 12:1943-9. [PMID: 12466299 PMCID: PMC187573 DOI: 10.1101/gr.655102] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
We develop an extension to the Lander-Waterman theory for characterizing gaps in bacterial artificial chromosome fingerprint mapping and shotgun sequencing projects. It supports a larger set of descriptive statistics and is applicable to a wider range of project parameters. We show that previous assertions regarding inconsistency of the Lander-Waterman theory at higher coverages are incorrect and that another well-known but ostensibly different model is in fact the same. The apparent paradox of infinite island lengths is resolved. Several applications are shown, including evolution of the probability density function, calculation of closure probabilities, and development of a probabilistic method for computing stopping points in bacterial artificial chromosome shotgun sequencing.
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Affiliation(s)
- Michael C Wendl
- Washington University School of Medicine, St. Louis, Missouri 63108, USA.
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167
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Timblin B, Rehli M, Skidgel RA. Structural characterization of the human carboxypeptidase D gene and its promoter. Int Immunopharmacol 2002; 2:1907-17. [PMID: 12489804 DOI: 10.1016/s1567-5769(02)00149-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Human carboxypeptidase D (CPD) is a 180-kDa type I membrane protein with three tandem active site domains. CPD is a B-type (or kininase I-type) carboxypeptidase that cleaves C-terminal basic residues from proteins and peptides, such as Arg9 from bradykinin. The human carboxypeptidase D (CPD) gene was found to encompass approximately 88.3 kb of genomic sequence, containing 21 exons ranging in size from 65 to 1813 bp, and 21 introns ranging in size from 112 bp to 35.6 kb. Although CPD and CPM belong to the same metallocarboxypeptidase subfamily, their intron/exon structures differ significantly. Multiple transcription start sites were found in the CPD gene within a GC-rich sequence lacking the typical TATA box, but containing three GC boxes. Luciferase reporter assays with various size constructs containing the promoter region upstream of the start sites showed that it was active in three different cell lines, especially in the human hepatoma cell line HepG2 and the human monocytic cell line THP-1, which have high constitutive expression of CPD.
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Affiliation(s)
- Barbara Timblin
- Department of Pharmacology, College of Medicine, University of Illinois, Chicago, IL 60612, USA
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168
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Affiliation(s)
- Matthew Hurles
- Molecular Genetics Laboratory, McDonald Institute for, Archaeological Research, University of Cambridge, Cambridge, CB2 3ER, UK
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169
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Church D, Pruitt KD. Accessing the human genome. CURRENT PROTOCOLS IN HUMAN GENETICS 2002; Chapter 6:Unit 6.9. [PMID: 18428332 DOI: 10.1002/0471142905.hg0609s34] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The majority of the sequence for the human genome is now available. Regardless of the researcher's area of interest, it is quite likely that they will want to use some aspect of this data. This unit helps researchers achieve that goal. It presents the gene models available at NCBI, the UCSC Genome Browser, and Ensembl. It reviews the features and options available from the three web sites to query, display, and download the data. In addition, the unit illustrates how to query each of the databases in order to identify information, such as the genomic location of a novel cDNA, a BAC clone that contains a particular gene, and homologous human genes to a particular protein sequence from a different organism.
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Affiliation(s)
- Deanna Church
- National Center for Biotechnology Information, NIH, Bethesda, MaryLand, USA
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170
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Martin CL, Waggoner DJ, Wong A, Uhrig S, Roseberry JA, Hedrick JF, Pack SD, Russell K, Zackai E, Dobyns WB, Ledbetter DH. "Molecular rulers" for calibrating phenotypic effects of telomere imbalance. J Med Genet 2002; 39:734-40. [PMID: 12362030 PMCID: PMC1734978 DOI: 10.1136/jmg.39.10.734] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
Abstract
As a result of the increasing use of genome wide telomere screening, it has become evident that a significant proportion of people with idiopathic mental retardation have subtle abnormalities involving the telomeres of human chromosomes. However, during the course of these studies, there have also been telomeric imbalances identified in normal people that are not associated with any apparent phenotype. We have begun to scrutinize cases from both of these groups by determining the extent of the duplication or deletion associated with the imbalance. Five cases were examined where the telomere rearrangement resulted in trisomy for the 16p telomere. The size of the trisomic segment ranged from approximately 4-7 Mb and the phenotype included mental and growth retardation, brain malformations, heart defects, cleft palate, pancreatic insufficiency, genitourinary abnormalities, and dysmorphic features. Three cases with telomeric deletions without apparent phenotypic effects were also examined, one from 10q and two from 17p. All three deletions were inherited from a phenotypically normal parent carrying the same deletion, thus without apparent phenotypic effect. The largest deletion among these cases was approximately 600 kb on 17p. Similar studies are necessary for all telomeric regions to differentiate between those telomeric rearrangements that are pathogenic and those that are benign variants. Towards this goal, we are developing "molecular rulers" that incorporate multiple clones at each telomere that span the most distal 5 Mb region. While telomere screening has enabled the identification of telomere rearrangements, the use of molecular rulers will allow better phenotype prediction and prognosis related to these findings.
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Affiliation(s)
- C L Martin
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
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171
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Affiliation(s)
- Laird Jackson
- Department of Obstetrics and Gynecology, MCP Hahnemann University, Philadelphia, Pennsylvania 19107, USA.
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172
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Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D. The human genome browser at UCSC. Genome Res 2002; 12:996-1006. [PMID: 12045153 PMCID: PMC186604 DOI: 10.1101/gr.229102] [Citation(s) in RCA: 6744] [Impact Index Per Article: 306.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
As vertebrate genome sequences near completion and research refocuses to their analysis, the issue of effective genome annotation display becomes critical. A mature web tool for rapid and reliable display of any requested portion of the genome at any scale, together with several dozen aligned annotation tracks, is provided at http://genome.ucsc.edu. This browser displays assembly contigs and gaps, mRNA and expressed sequence tag alignments, multiple gene predictions, cross-species homologies, single nucleotide polymorphisms, sequence-tagged sites, radiation hybrid data, transposon repeats, and more as a stack of coregistered tracks. Text and sequence-based searches provide quick and precise access to any region of specific interest. Secondary links from individual features lead to sequence details and supplementary off-site databases. One-half of the annotation tracks are computed at the University of California, Santa Cruz from publicly available sequence data; collaborators worldwide provide the rest. Users can stably add their own custom tracks to the browser for educational or research purposes. The conceptual and technical framework of the browser, its underlying MYSQL database, and overall use are described. The web site currently serves over 50,000 pages per day to over 3000 different users.
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Affiliation(s)
- W James Kent
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Cruz, CA 95064, USA.
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173
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Rauen KA, Albertson DG, Pinkel D, Cotter PD. Additional patient with del(12)(q21.2q22): further evidence for a candidate region for cardio-facio-cutaneous syndrome? AMERICAN JOURNAL OF MEDICAL GENETICS 2002; 110:51-6. [PMID: 12116271 DOI: 10.1002/ajmg.10478] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cardio-facio-cutaneous (CFC) syndrome is characterized by a distinct facial appearance, cardiac defects, ectodermal anomalies and developmental delay. Recently, we reported a 19-month-old girl with phenotypic manifestations consistent with the CFC syndrome who had an interstitial deletion of the long arm of chromosome 12, del(12)(q21.2q22), implicating a possible locus for CFC syndrome. Here, we report an additional patient with a cytogenetically identical interstitial deletion: 47,XYY,del(12)(q21.2q22). To further characterize this deletion we used microarray-based comparative genomic hybridization (array CGH). Array CGH confirmed both the deletion and the second Y chromosome. The deletion on chromosome 12q spanned at least 14 Mb as indicated by the positions on the genome sequence of the 4 BAC clones included in the deletion. While the proband did not have the classic features of CFC, he had some dysmorphic craniofacial characteristics, ectodermal anomalies and moderate developmental delay which were suggestive of CFC syndrome; however, this patient did not have classical CFC. The phenotypic differences between the two del(12)(q21.2q22) patients may be due to variability in the expression of the syndrome, or this deletion may present as a syndrome with overlapping features. Alternatively, the phenotypic differences may result from discordance at the molecular level, which may yield a critical minimal region of deletion for CFC. The region 12q21.2 --> q22 remains a possible candidate region for CFC syndrome. Additional characterization of these and other CFC patients may confirm and further refine this candidate region.
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Affiliation(s)
- Katherine A Rauen
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, California, USA.
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174
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Abstract
Molecular studies of unstable regions in the human genome have identified region-specific low-copy repeats (LCRs). Unlike highly repetitive sequences (e.g. Alus and LINEs), LCRs are usually of 10-400 kb in size and exhibit > or = 95-97% similarity. According to computer analyses of available sequencing data, LCRs may constitute >5% of the human genome. Through the process of non-allelic homologous recombination using paralogous genomic segments as substrates, LCRs have been shown to facilitate meiotic DNA rearrangements associated with disease traits, referred to as genomic disorders. In addition, this LCR-based complex genome architecture appears to play a major role in both primate karyotype evolution and human tumorigenesis.
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Affiliation(s)
- Pawel Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Room 604B, One Baylor Plaza, and Texas Children Hospital, Houston, Texas 77030-3498, USA
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175
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Abstract
As vertebrate genome sequences near completion and research refocuses to their analysis, the issue of effective genome annotation display becomes critical. A mature web tool for rapid and reliable display of any requested portion of the genome at any scale, together with several dozen aligned annotation tracks, is provided at http://genome.ucsc.edu. This browser displays assembly contigs and gaps, mRNA and expressed sequence tag alignments, multiple gene predictions, cross-species homologies, single nucleotide polymorphisms, sequence-tagged sites, radiation hybrid data, transposon repeats, and more as a stack of coregistered tracks. Text and sequence-based searches provide quick and precise access to any region of specific interest. Secondary links from individual features lead to sequence details and supplementary off-site databases. One-half of the annotation tracks are computed at the University of California, Santa Cruz from publicly available sequence data; collaborators worldwide provide the rest. Users can stably add their own custom tracks to the browser for educational or research purposes. The conceptual and technical framework of the browser, its underlying MYSQL database, and overall use are described. The web site currently serves over 50,000 pages per day to over 3000 different users.
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Affiliation(s)
- W James Kent
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Cruz, CA 95064, USA.
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176
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Vázquez-Gundín F, Rivero MT, Gosálvez J, Luis Fernández J. Radiation-induced DNA breaks in different human satellite DNA sequence areas, analyzed by DNA breakage detection-fluorescence in situ hybridization. Radiat Res 2002; 157:711-20. [PMID: 12005551 DOI: 10.1667/0033-7587(2002)157[0711:ridbid]2.0.co;2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Human blood leukocytes were exposed to X rays to analyze the initial level of DNA breakage induced within different satellite DNA sequence areas and telomeres, using the DNA breakage detection-FISH procedure. The satellite DNA families analyzed comprised alphoid sequences, satellite 1, and 5-bp classical satellite DNA sequences from chromosome 1 (D1Z1 locus), from chromosome 9 (D9Z3 locus), and from the Y chromosome (DYZ1 locus). Since the control hybridization signal was quite different in each of the DNA targets, the relative increase in whole fluorescence intensity with respect to unirradiated controls was the parameter used for comparison. Irradiation of nucleoids obtained after protein removal demonstrated that the alkaline unwinding solution generates around half the amount of signal when breaks are present in the 5-bp classical DNA satellites as when the same numbers of breaks are present the genome overall, whereas the signal is slightly stronger when the breaks are within the alphoids or satellite 1 sequences. After correction for differences in sensitivity to the alkaline unwinding-renaturation, DNA housed in chromatin corresponding to 5-bp classical satellites proved to be more sensitive to breakage than the overall genome, whereas DNA in the chromatin corresponding to alphoids or satellite 1 showed a sensitivity similar to that of the whole genome. The minimum detectable dose was 0.1 Gy for the whole genome, 0.2 Gy for alphoids and satellite 1, and 0.4 Gy for the 5-bp classical satellites. Telomeric DNA sequences appeared to be maximally labeled in unirradiated cells. Thus telomeric ends behave like DNA breaks, constituting a source of background in alkaline unwinding assays.
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Affiliation(s)
- Fernando Vázquez-Gundín
- Laboratorio de Genética Molecular y Radiobiología, Centro Oncológico de Galicia, Avda de Montserrat s/n 15009, La Coruña, Spain
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177
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Veltman JA, Schoenmakers EFPM, Eussen BH, Janssen I, Merkx G, van Cleef B, van Ravenswaaij CM, Brunner HG, Smeets D, van Kessel AG. High-throughput analysis of subtelomeric chromosome rearrangements by use of array-based comparative genomic hybridization. Am J Hum Genet 2002; 70:1269-76. [PMID: 11951177 PMCID: PMC447601 DOI: 10.1086/340426] [Citation(s) in RCA: 160] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2001] [Accepted: 02/25/2002] [Indexed: 12/08/2022] Open
Abstract
Telomeric chromosome rearrangements may cause mental retardation, congenital anomalies, and miscarriages. Automated detection of subtle deletions or duplications involving telomeres is essential for high-throughput diagnosis, but impossible when conventional cytogenetic methods are used. Array-based comparative genomic hybridization (CGH) allows high-resolution screening of copy number abnormalities by hybridizing differentially labeled test and reference genomes to arrays of robotically spotted clones. To assess the applicability of this technique in the diagnosis of (sub)telomeric imbalances, we here describe a blinded study, in which DNA from 20 patients with known cytogenetic abnormalities involving one or more telomeres was hybridized to an array containing a validated set of human-chromosome-specific (sub)telomere probes. Single-copy-number gains and losses were accurately detected on these arrays, and an excellent concordance between the original cytogenetic diagnosis and the array-based CGH diagnosis was obtained by use of a single hybridization. In addition to the previously identified cytogenetic changes, array-based CGH revealed additional telomere rearrangements in 3 of the 20 patients studied. The robustness and simplicity of this array-based telomere copy-number screening make it highly suited for introduction into the clinic as a rapid and sensitive automated diagnostic procedure.
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Affiliation(s)
- Joris A Veltman
- Department of Human Genetics, University Medical Center Nijmegen, Nijmegen, The Netherlands.
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178
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Rowen L, Young J, Birditt B, Kaur A, Madan A, Philipps DL, Qin S, Minx P, Wilson RK, Hood L, Graveley BR. Analysis of the human neurexin genes: alternative splicing and the generation of protein diversity. Genomics 2002; 79:587-97. [PMID: 11944992 DOI: 10.1006/geno.2002.6734] [Citation(s) in RCA: 144] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The neurexins are neuronal proteins that function as cell adhesion molecules during synaptogenesis and in intercellular signaling. Although mammalian genomes contain only three neurexin genes, thousands of neurexin isoforms may be expressed through the use of two alternative promoters and alternative splicing at up to five different positions in the pre-mRNA. To begin understanding how the expression of the neurexin genes is regulated, we have determined the complete nucleotide sequence of all three human neurexin genes: NRXN1, NRXN2, and NRXN3. Unexpectedly, two of these, NRXN1 ( approximately 1.1 Mb) and NRXN3 ( approximately 1.7 Mb), are among the largest known human genes. In addition, we have identified several conserved intronic sequence elements that may participate in the regulation of alternative splicing. The sequences of these genes provide insight into the mechanisms used to generate the diversity of neurexin protein isoforms and raise several interesting questions regarding the expression mechanism of large genes.
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Affiliation(s)
- Lee Rowen
- Institute for Systems Biology, 1441 North 34th Street, Seattle, Washington 98103, USA
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179
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Kim JS, Childs KL, Islam-Faridi MN, Menz MA, Klein RR, Klein PE, Price HJ, Mullet JE, Stelly DM. Integrated karyotyping of sorghum by in situ hybridization of landed BACs. Genome 2002; 45:402-12. [PMID: 11962637 DOI: 10.1139/g01-141] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The reliability of genome analysis and proficiency of genetic manipulation are increased by assignment of linkage groups to specific chromosomes, placement of centromeres, and orientation with respect to telomeres. We have endeavored to establish means to enable these steps in sorghum (Sorghum bicolor (L.) Moench), the genome of which contains ca. 780 Mbp spread across n = 10 chromosomes. Our approach relies on fluorescence in situ hybridization (FISH) and integrated structural genomic resources, including large-insert genomic clones in bacterial artificial chromosome (BAC) libraries. To develop robust FISH probes, we selected sorghum BACs by association with molecular markers that map near the ends of linkage groups, in regions inferred to be high in recombination. Overall, we selected 22 BACs that encompass the 10 linkage groups. As a prelude to development of a multiprobe FISH cocktail, we evaluated BAC-derived probes individually and in small groups. Biotin- and digoxygenin-labeled probes were made directly from the BAC clones and hybridized in situ to chromosomes without using suppressive unlabelled C0t-1 DNA. Based on FISH-signal strength and the relative degree of background signal, we judged 19 BAC-derived probes to be satisfactory. Based on their relative position, and collective association with all 10 linkage groups, we chose 17 of the 19 BACs to develop a 17-locus probe cocktail for dual-color detection. FISH of the cocktail allowed simultaneous identification of all 10 chromosomes. The results indicate that linkage and physical maps of sorghum allow facile selection of BAC clones according to position and FISH-signal quality. This capability will enable development of a high-quality molecular cytogenetic map and an integrated genomics system for sorghum, without need of chromosome flow sorting or microdissection. Moreover, transgeneric FISH experiments suggest that the sorghum system might be applicable to other Gramineae.
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Affiliation(s)
- Jeong-Soon Kim
- Department of Soil and Crop Sciences, Texas A&M University, College Station 77843, USA
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180
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Martin CL, Wong A, Gross A, Chung J, Fantes JA, Ledbetter DH. The evolutionary origin of human subtelomeric homologies--or where the ends begin. Am J Hum Genet 2002; 70:972-84. [PMID: 11875757 PMCID: PMC379127 DOI: 10.1086/339768] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2001] [Accepted: 01/17/2002] [Indexed: 11/04/2022] Open
Abstract
The subtelomeric regions of human chromosomes are comprised of sequence homologies shared between distinct subsets of chromosomes. In the course of developing a set of unique human telomere clones, we identified many clones containing such shared homologies, characterized by the presence of cross-hybridization signals on one or more telomeres in a fluorescence in situ hybridization (FISH) assay. We studied the evolutionary origin of seven subtelomeric clones by performing comparative FISH analysis on a primate panel that included great apes and Old World monkeys. All clones tested showed a single hybridization site in Old World monkeys that corresponded to one of the orthologous human sites, thus indicating the ancestral origin. The timing of the duplication events varied among the subtelomeric regions, from approximately 5 to approximately 25 million years ago. To examine the origin of and mechanism for one of these subtelomeric duplications, we compared the sequence derived from human 2q13--an ancestral fusion site of two great ape telomeric regions--with its paralogous subtelomeric sequences at 9p and 22q. These paralogous regions share large continuous homologies and contain three genes: RABL2B, forkhead box D4, and COBW-like. Our results provide further evidence for subtelomeric-mediated genomic duplication and demonstrate that these segmental duplications are most likely the result of ancestral unbalanced translocations that have been fixed in the genome during recent primate evolution.
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Affiliation(s)
- Christa Lese Martin
- Department of Human Genetics, University of Chicago, Chicago; and Medical Genetics Section, Department of Medical Sciences, University of Edinburgh, Edinburgh
| | - Andrew Wong
- Department of Human Genetics, University of Chicago, Chicago; and Medical Genetics Section, Department of Medical Sciences, University of Edinburgh, Edinburgh
| | - Alyssa Gross
- Department of Human Genetics, University of Chicago, Chicago; and Medical Genetics Section, Department of Medical Sciences, University of Edinburgh, Edinburgh
| | - June Chung
- Department of Human Genetics, University of Chicago, Chicago; and Medical Genetics Section, Department of Medical Sciences, University of Edinburgh, Edinburgh
| | - Judy A. Fantes
- Department of Human Genetics, University of Chicago, Chicago; and Medical Genetics Section, Department of Medical Sciences, University of Edinburgh, Edinburgh
| | - David H. Ledbetter
- Department of Human Genetics, University of Chicago, Chicago; and Medical Genetics Section, Department of Medical Sciences, University of Edinburgh, Edinburgh
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181
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Abstract
An increasing number of human diseases are recognized to result from recurrent DNA rearrangements involving unstable genomic regions. These are termed genomic disorders, in which the clinical phenotype is a consequence of abnormal dosage of gene(s) located within the rearranged genomic fragments. Both inter- and intrachromosomal rearrangements are facilitated by the presence of region-specific low-copy repeats (LCRs) and result from nonallelic homologous recombination (NAHR) between paralogous genomic segments. LCRs usually span approximately 10-400 kb of genomic DNA, share >or= 97% sequence identity, and provide the substrates for homologous recombination, thus predisposing the region to rearrangements. Moreover, it has been suggested that higher order genomic architecture involving LCRs plays a significant role in karyotypic evolution accompanying primate speciation.
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Affiliation(s)
- Paweł Stankiewicz
- Dept Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030-3498, USA
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182
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Niimura Y, Gojobori T. In silico chromosome staining: reconstruction of Giemsa bands from the whole human genome sequence. Proc Natl Acad Sci U S A 2002; 99:797-802. [PMID: 11792839 PMCID: PMC117385 DOI: 10.1073/pnas.022437999] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2001] [Indexed: 11/18/2022] Open
Abstract
Giemsa staining has been used for identifying individual human chromosomes. Giemsa-dark and -light bands generally are thought to correspond to GC-poor and GC-rich regions; however, several experiments showed that the correspondence is quite poor. To elucidate the precise relationship between GC content and Giemsa banding patterns, we developed an "in silico chromosome staining" method for reconstructing Giemsa bands computationally from the whole human genome sequence. Here we show that 850-level Giemsa bands are best correlated with the difference in GC content between a local window of 2.5 megabases and a regional window of 9.3 megabases along a chromosome. The correlations are of strong statistical significance for almost all 43 chromosomal arms. Our results clearly show that Giemsa-dark bands are locally GC-poor regions compared with the flanking regions. These findings are consistent with the model that matrix-associated regions, which are known to be AT-rich, are present more densely in Giemsa-dark bands than in -light bands.
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Affiliation(s)
- Yoshihito Niimura
- Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, 1111, Yata, Mishima, Shizuoka 411-8540, Japan
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183
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Abstract
Initial human genome sequence analysis has revealed large segments of nearly identical sequence in particular chromosomal regions. The recent origin of these segments and their abundance (approximately 5%) has challenged investigators to elucidate their underlying mechanism and role in primate genome evolution. Although the precise fraction is unknown, some of these duplicated segments have recently been shown to be associated with rapid gene innovation and chromosomal rearrangement in the genomes of man and the great apes.
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Affiliation(s)
- Rhea Vallente Samonte
- Department of Genetics and Center for Human Genetics, School of Medicine and University Hospitals of Cleveland, Case Western Reserve University, Cleveland, Ohio 44106, USA.
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184
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Abstract
An estimated 5% of the human genome consists of interspersed duplications that have arisen over the past 35 million years of evolution. Two categories of such recently duplicated segments can be distinguished: segmental duplications between nonhomologous chromosomes (transchromosomal duplications) and duplications mainly restricted to a particular chromosome (chromosome-specific duplications). Many of these duplications exhibit an extraordinarily high degree of sequence identity at the nucleotide level (>95%) and span large genomic distances (1-100 kb). Preliminary analyses indicate that these same regions are targets for rapid evolutionary turnover among the genomes of closely related primates. The dynamic nature of these regions because of recurrent chromosomal rearrangement, and their ability to create fusion genes from juxtaposed cassettes suggest that duplicative transposition was an important force in the evolution of our genome.
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Affiliation(s)
- E E Eichler
- Dept of Genetics and Center for Human Genetics, Case Western Reserve School of Medicine and University Hospitals of Cleveland, Cleveland, OH 44106, USA.
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185
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Strausberg RL, Greenhut SF, Grouse LH, Schaefer CF, Buetow KH. In silico analysis of cancer through the Cancer Genome Anatomy Project. Trends Cell Biol 2001. [DOI: 10.1016/s0962-8924(01)82370-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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186
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Snijders AM, Nowak N, Segraves R, Blackwood S, Brown N, Conroy J, Hamilton G, Hindle AK, Huey B, Kimura K, Law S, Myambo K, Palmer J, Ylstra B, Yue JP, Gray JW, Jain AN, Pinkel D, Albertson DG. Assembly of microarrays for genome-wide measurement of DNA copy number. Nat Genet 2001; 29:263-4. [PMID: 11687795 DOI: 10.1038/ng754] [Citation(s) in RCA: 695] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
We have assembled arrays of approximately 2,400 BAC clones for measurement of DNA copy number across the human genome. The arrays provide precise measurement (s.d. of log2 ratios=0.05-0.10) in cell lines and clinical material, so that we can reliably detect and quantify high-level amplifications and single-copy alterations in diploid, polyploid and heterogeneous backgrounds.
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Affiliation(s)
- A M Snijders
- Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94143, USA
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187
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Strausberg RL, Greenhut SF, Grouse LH, Schaefer CF, Buetow KH. In silico analysis of cancer through the Cancer Genome Anatomy Project. Trends Cell Biol 2001; 11:S66-71. [PMID: 11684445 DOI: 10.1016/s0962-8924(01)02104-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The Cancer Genome Anatomy Project (CGAP) was designed and implemented to provide public datasets, material resources and informatics tools to serve as a platform to support the elucidation of the molecular signatures of cancer. This overview of CGAP describes the status of this effort to develop resources based on gene expression, polymorphism identification and chromosome aberrations, and we describe a variety of analytical tools designed to facilitate in silico analysis of these datasets.
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188
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Zhao S, Shatsman S, Ayodeji B, Geer K, Tsegaye G, Krol M, Gebregeorgis E, Shvartsbeyn A, Russell D, Overton L, Jiang L, Dimitrov G, Tran K, Shetty J, Malek JA, Feldblyum T, Nierman WC, Fraser CM. Mouse BAC ends quality assessment and sequence analyses. Genome Res 2001; 11:1736-45. [PMID: 11591651 PMCID: PMC311142 DOI: 10.1101/gr.179201] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A large-scale BAC end-sequencing project at The Institute for Genomic Research (TIGR) has generated one of the most extensive sets of sequence markers for the mouse genome to date. With a sequencing success rate of >80%, an average read length of 485 bp, and ABI3700 capillary sequencers, we have generated 449,234 nonredundant mouse BAC end sequences (mBESs) with 218 Mb total from 257,318 clones from libraries RPCI-23 and RPCI-24, representing 15x clone coverage, 7% sequence coverage, and a marker every 7 kb across the genome. A total of 191,916 BACs have sequences from both ends providing 12x genome coverage. The average Q20 length is 406 bp and 84% of the bases have phred quality scores > or = 20. RPCI-24 mBESs have more Q20 bases and longer reads on average than RPCI-23 sequences. ABI3700 sequencers and the sample tracking system ensure that > 95% of mBESs are associated with the right clone identifiers. We have found that a significant fraction of mBESs contains L1 repeats and approximately 48% of the clones have both ends with > or = 100 bp contiguous unique Q20 bases. About 3% mBESs match ESTs and > 70% of matches were conserved between the mouse and the human or the rat. Approximately 0.1% mBESs contain STSs. About 0.2% mBESs match human finished sequences and > 70% of these sequences have EST hits. The analyses indicate that our high-quality mouse BAC end sequences will be a valuable resource to the community.
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Affiliation(s)
- S Zhao
- The Institute for Genomic Research, Rockville, Maryland 20850, USA.
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189
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Fauth C, Speicher MR. Classifying by colors: FISH-based genome analysis. CYTOGENETICS AND CELL GENETICS 2001; 93:1-10. [PMID: 11474168 DOI: 10.1159/000056937] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
In recent years a fascinating evolution of different multicolor fluorescence in situ hybridization (FISH) technologies could be witnessed. The various approaches to cohybridize multiple DNA probes in different colors opened new avenues for FISH-based automated karyotyping or the simultaneous analysis of multiple defined regions within the genome. These developments had a remarkable impact on microscopy design and the usage of highly sensitive area imagers. In addition, they led to the introduction of new fluorochromes with appropriate filter combinations, refinements of hybridization protocols, novel probe sets, and innovative software for automated chromosome analysis. This paper attempts to summarize the various multicolor approaches and discusses the application of the individual technologies.
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Affiliation(s)
- C Fauth
- Institut für Anthropologie und Humangenetik, Ludwig-Maximilians-Universität München, Goethestrasse 31, D-80336 Münich, Germany
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190
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Abstract
The data for the public working draft of the human genome contains roughly 400,000 initial sequence contigs in approximately 30,000 large insert clones. Many of these initial sequence contigs overlap. A program, GigAssembler, was built to merge them and to order and orient the resulting larger sequence contigs based on mRNA, paired plasmid ends, EST, BAC end pairs, and other information. This program produced the first publicly available assembly of the human genome, a working draft containing roughly 2.7 billion base pairs and covering an estimated 88% of the genome that has been used for several recent studies of the genome. Here we describe the algorithm used by GigAssembler.
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Affiliation(s)
- W J Kent
- Department of Biology, University of California at Santa Cruz, Santa Cruz, California 95064, USA.
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191
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Abstract
Recent spectacular advances in the technologies and strategies for DNA sequencing have profoundly accelerated the detailed analysis of genomes from myriad organisms. The past few years alone have seen the publication of near-complete or draft versions of the genome sequence of several well-studied, multicellular organisms - most notably, the human. As well as providing data of fundamental biological significance, these landmark accomplishments have yielded important strategic insights that are guiding current and future genome-sequencing projects.
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Affiliation(s)
- E D Green
- Genome Technology Branch and NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.
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192
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Abstract
The genome sequence of an organism is an information resource unlike any that biologists have previously had access to. But the value of the genome is only as good as its annotation. It is the annotation that bridges the gap from the sequence to the biology of the organism. The aim of high-quality annotation is to identify the key features of the genome - in particular, the genes and their products. The tools and resources for annotation are developing rapidly, and the scientific community is becoming increasingly reliant on this information for all aspects of biological research.
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Affiliation(s)
- L Stein
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA.
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193
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Affiliation(s)
- S J O'Brien
- Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD 21702, USA.
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194
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Abstract
Last year we celebrated the sequencing of the entire long arm of human chromosome 21. This achievement now provides unprecedented opportunities to understand the molecular pathophysiology of trisomy 21, elucidate the mechanisms of all monogenic disorders of chromosome 21, and discover genes and functional sequence variations that predispose to common complex disorders. All these steps require the functional analysis of gene products and the determination of the sequence variation of this chromosome.
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Affiliation(s)
- S E Antonarakis
- Division of Medical Genetics, University of Geneva Medical School and University Hospitals, Geneva, Switzerland.
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195
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Bailey JA, Yavor AM, Massa HF, Trask BJ, Eichler EE. Segmental duplications: organization and impact within the current human genome project assembly. Genome Res 2001; 11:1005-17. [PMID: 11381028 PMCID: PMC311093 DOI: 10.1101/gr.gr-1871r] [Citation(s) in RCA: 513] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Segmental duplications play fundamental roles in both genomic disease and gene evolution. To understand their organization within the human genome, we have developed the computational tools and methods necessary to detect identity between long stretches of genomic sequence despite the presence of high copy repeats and large insertion-deletions. Here we present our analysis of the most recent genome assembly (January 2001) in which we focus on the global organization of these segments and the role they play in the whole-genome assembly process. Initially, we considered only large recent duplication events that fell well-below levels of draft sequencing error (alignments 90%-98% similar and > or =1 kb in length). Duplications (90%-98%; > or =1 kb) comprise 3.6% of all human sequence. These duplications show clustering and up to 10-fold enrichment within pericentromeric and subtelomeric regions. In terms of assembly, duplicated sequences were found to be over-represented in unordered and unassigned contigs indicating that duplicated sequences are difficult to assign to their proper position. To assess coverage of these regions within the genome, we selected BACs containing interchromosomal duplications and characterized their duplication pattern by FISH. Only 47% (106/224) of chromosomes positive by FISH had a corresponding chromosomal position by comparison. We present data that indicate that this is attributable to misassembly, misassignment, and/or decreased sequencing coverage within duplicated regions. Surprisingly, if we consider putative duplications >98% identity, we identify 10.6% (286 Mb) of the current assembly as paralogous. The majority of these alignments, we believe, represent unmerged overlaps within unique regions. Taken together the above data indicate that segmental duplications represent a significant impediment to accurate human genome assembly, requiring the development of specialized techniques to finish these exceptional regions of the genome. The identification and characterization of these highly duplicated regions represents an important step in the complete sequencing of a human reference genome.
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Affiliation(s)
- J A Bailey
- Department of Genetics and Center for Human Genetics, Case Western Reserve School of Medicine and University Hospitals of Cleveland, Cleveland, Ohio 44106, USA
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196
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Bailey JA, Yavor AM, Massa HF, Trask BJ, Eichler EE. Segmental Duplications: Organization and Impact Within the Current Human Genome Project Assembly. Genome Res 2001. [DOI: 10.1101/gr.187101] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Segmental duplications play fundamental roles in both genomic disease and gene evolution. To understand their organization within the human genome, we have developed the computational tools and methods necessary to detect identity between long stretches of genomic sequence despite the presence of high copy repeats and large insertion-deletions. Here we present our analysis of the most recent genome assembly (January 2001) in which we focus on the global organization of these segments and the role they play in the whole-genome assembly process. Initially, we considered only large recent duplication events that fell well-below levels of draft sequencing error (alignments 90%–98% similar and ≥1 kb in length). Duplications (90%–98%; ≥1 kb) comprise 3.6% of all human sequence. These duplications show clustering and up to 10-fold enrichment within pericentromeric and subtelomeric regions. In terms of assembly, duplicated sequences were found to be over-represented in unordered and unassigned contigs indicating that duplicated sequences are difficult to assign to their proper position. To assess coverage of these regions within the genome, we selected BACs containing interchromosomal duplications and characterized their duplication pattern by FISH. Only 47% (106/224) of chromosomes positive by FISH had a corresponding chromosomal position by BLAST comparison. We present data that indicate that this is attributable to misassembly, misassignment, and/or decreased sequencing coverage within duplicated regions. Surprisingly, if we consider putative duplications >98% identity, we identify 10.6% (286 Mb) of the current assembly as paralogous. The majority of these alignments, we believe, represent unmerged overlaps within unique regions. Taken together the above data indicate that segmental duplications represent a significant impediment to accurate human genome assembly, requiring the development of specialized techniques to finish these exceptional regions of the genome. The identification and characterization of these highly duplicated regions represents an important step in the complete sequencing of a human reference genome.
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Eichler EE. Segmental duplications: what's missing, misassigned, and misassembled--and should we care? Genome Res 2001; 11:653-6. [PMID: 11337463 DOI: 10.1101/gr.188901] [Citation(s) in RCA: 86] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- E E Eichler
- Department of Genetics and Center for Human Genetics, Case Western Reserve School of Medicine and University Hospitals of Cleveland, Cleveland, Ohio 44106, USA.
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198
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Weinberg RA. A question of strategy. Trends Biochem Sci 2001; 26:207-8. [PMID: 11295537 DOI: 10.1016/s0968-0004(01)01823-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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199
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Ratain MJ, Relling MV. Gazing into a crystal ball-cancer therapy in the post-genomic era. Nat Med 2001; 7:283-5. [PMID: 11231619 DOI: 10.1038/85414] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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200
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Osoegawa K, Mammoser AG, Wu C, Frengen E, Zeng C, Catanese JJ, de Jong PJ. A bacterial artificial chromosome library for sequencing the complete human genome. Genome Res 2001; 11:483-96. [PMID: 11230172 PMCID: PMC311044 DOI: 10.1101/gr.169601] [Citation(s) in RCA: 196] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2000] [Accepted: 01/09/2001] [Indexed: 01/20/2023]
Abstract
A 30-fold redundant human bacterial artificial chromosome (BAC) library with a large average insert size (178 kb) has been constructed to provide the intermediate substrate for the international genome sequencing effort. The DNA was obtained from a single anonymous volunteer, whose identity was protected through a double-blind donor selection protocol. DNA fragments were generated by partial digestion with EcoRI (library segments 1--4: 24-fold) and MboI (segment 5: sixfold) and cloned into the pBACe3.6 and pTARBAC1 vectors, respectively. The quality of the library was assessed by extensive analysis of 169 clones for rearrangements and artifacts. Eighteen BACs (11%) revealed minor insert rearrangements, and none was chimeric. This BAC library, designated as "RPCI-11," has been used widely as the central resource for insert-end sequencing, clone fingerprinting, high-throughput sequence analysis and as a source of mapped clones for diagnostic and functional studies.
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Affiliation(s)
- K Osoegawa
- Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, New York 14263, USA
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