A systematic, high-resolution linkage of the cytogenetic and physical maps of the human genome

Identification of large-scale genomic variation in cancer genomes using in silico reference models

Identifying large-scale structural variation in cancer genomes continues to be a challenge to researchers. Current methods rely on genome alignments based on a reference that can be a poor fit to highly variant and complex tumor genomes. To address this challenge we developed a method that uses available breakpoint information to generate models of structural variations. We use these models as references to align previously unmapped and discordant reads from a genome. By using these models to align unmapped reads, we show that our method can help to identify large-scale variations that have been previously missed.

A short introduction to cytogenetic studies in mammals with reference to the present volume

Genome diversity has long been studied from the comparative cytogenetic perspective. Early workers documented differences between species in diploid chromosome number and fundamental number. Banding methods allowed more detailed descriptions of between-species rearrangements and classes of differentially staining chromosome material. The infusion of molecular methods into cytogenetics provided a third revolution, which is still not exhausted. Chromosome painting has provided a global view of the translocation history of mammalian genome evolution, well summarized in the contributions to this special volume. More recently, FISH of cloned DNA has provided details on defining breakpoint and intrachromosomal marker order, which have helped to document inversions and centromere repositioning. The most recent trend in comparative molecular cytogenetics is to integrate sequencing information in order to formulate and test reconstructions of ancestral genomes and phylogenomic hypotheses derived from comparative cytogenetics. The integration of comparative cytogenetics and sequencing promises to provide an understanding of what drives chromosome rearrangements and genome evolution in general. We believe that the contributions in this volume, in no small way, point the way to the next phase in cytogenetic studies.

Comparative genomic hybridization to detect variation in the copy number of large DNA segments

Array comparative genomic hybridization (CGH) is an excellent tool to scan the genome for copy number variations (CNVs) when used conscientiously. This article is intended to provide an understanding of the basic principles of array CGH and the different options available to the user to design their array CGH experiments. Specifically, the six subsections discuss the different array platforms available, test and reference DNA preparation, reference DNA choice, the basics of hybridization, data processing, and our current understanding of CNVs in the human genome.

The analysis of inconsistencies between cytogenetic annotations and sequence mapping by defining the imprecision zones of cytogenetic banding

MOTIVATION

In current databases, there are many genes with inconsistent mapping positions between their cytogenetic annotations and sequence map positions. However, not all inconsistencies are the same. Some of them may be problematic which should be corrected in the future; while others may result from the imprecise nature of chromosomal banding which may be tolerable. It is important to stratify the cytogenetic position information into different confidence groups with the recognition of the impreciseness of cytogenetic banding.

RESULTS

When plotting their cytogenetic annotations against sequence map positions on a 2D plane, the consistent genes tend to have a compact linear distribution; while genes with inconsistent positions are more scattered. The overlapping areas between these two groups are defined as the tolerable imprecision zones by linear regression and distance analysis. The system was implemented using sequence information from NCBI Map Viewer Build 36.3 and cytogenetic annotations from NCBI Entrez Gene. The genes' position information is classified into five confidence groups: inconsistent-intolerable, inconsistent-tolerable, consistent-imprecise, consistent-precise and consistent-rough. Using information from NCBI Map Viewer Build 36.3 and NCBI Entrez Gene, the percentages of these confidence groups are 1.4%, 7.0%, 54.0%, 35.4% and 2.2%, respectively. Using information from NCBI Map Viewer Build 36.3 and NCBI online Mendelian inheritance in man (OMIM), the percentages are 3.7%, 16.9%, 49.0%, 19.0% and 11.4%, respectively. Combining these two results, a confidence table of genes' position information was constructed.

AVAILABILITY

The detailed results are accessible over the Internet at http://centrallab.hosp.ncku.edu.tw/imz.

Comparative genomic hybridization (CGH)--detection of unbalanced genetic aberrations using conventional and micro-array techniques

This unit presents comparative genomic hybridization (CGH), a genome-wide screening technique for genetic aberrations in tumor samples. Specific emphasis is placed on recent applications to the analysis of murine model systems for human cancer. CGH is an invaluable tool for identifying the characteristic genetic rearrangements in these models. The authors discuss an exciting new method currently being developed, array CGH, which results in a tremendous increase in resolution. Oncogene amplifications and deletions of tumor-suppressor genes are detected on a single-gene level. Detailed protocols are supplied for CGH analysis of both human and mouse chromosomes.

A new platform linking chromosomal and sequence information

We have tested whether a direct correlation of sequence information and staining properties of chromosomes is possible and whether this combined information can be used to precisely map any position on the chromosome. Despite huge differences of compaction between the naked DNA and the DNA packed in chromosomes we found a striking correlation when visualizing the GGCC density on both levels. Software was developed that allows one to superimpose chromosomal fluorescence intensity profiles generated by chromolysin A3 (CMA3) staining with GGCC density extracted from the Ensembl database. Thus, any position along the chromosome can be defined in megabase pairs (Mb) besides the cytoband information, enabling direct alignment of chromosomal information with the sequence data. The mapping tool was validated using 13 different BAC clones, resulting in a mean difference from Ensembl data of 2 Mb (ranging from 0.79 to 3.57 Mb). Our results indicate that the sequence density information and information gained with sequence-specific fluorochromes are superimposable. Thus, the visualized GGCC motif density along the chromosome (sequence bands) provides a unique platform for comparing different types of genomic information.

Linking the human cytogenetic map with nucleotide sequence: the CCAP clone set

We present the completed dataset and clone repository of the Cancer Chromosome Aberration Project (CCAP), an initiative developed and funded through the intramural program of the U.S. National Cancer Institute, to provide seamless linkage of human cytogenetic markers with the primary nucleotide sequence of the human genome. Spaced at 1-2 Mb intervals across the human genome, 1,339 bacterial artificial chromosome (BAC) clones have been localized to chromosomal bands through high-resolution fluorescence in situ hybridization (FISH) mapping. Of these clones, 99.8% can be positioned on the primary human genome sequence and 95% are placed at or close to their precise nucleotide starts and stops. This dataset can be studied and manipulated within generally available public Web sites. The clones are available from a commercial repository. The CCAP BAC clone set provides anchors for the interrogation of gene and sequence involvement in oncogenic and developmental disorders when the starting point is the recognition of a structural, numerical, or interstitial chromosomal aberration. This dataset also provides a current view of the quality and coherence of the available genome sequence and insight into the nucleotide and three-dimensional structures that manifest as Giemsa light and dark chromosomal banding patterns.

The interactive online SKY/M-FISH & CGH database and the Entrez cancer chromosomes search database: linkage of chromosomal aberrations with the genome sequence

To catalog data on chromosomal aberrations in cancer derived from emerging molecular cytogenetic techniques and to integrate these data with genome maps, we have established two resources, the NCI and NCBI SKY/M-FISH & CGH Database and the Cancer Chromosomes database. The goal of the former is to allow investigators to submit and analyze clinical and research cytogenetic data. It contains a karyotype parser tool, which automatically converts the ISCN short-form karyotype into an internal representation displayed in detailed form and as a colored ideogram with band overlay, and also has a tool to compare CGH profiles from multiple cases. The Cancer Chromosomes database integrates the SKY/M-FISH & CGH Database with the Mitelman Database of Chromosome Aberrations in Cancer and the Recurrent Chromosome Aberrations in Cancer database. These three datasets can now be searched seamlessly by use of the Entrez search and retrieval system for chromosome aberrations, clinical data, and reference citations. Common diagnoses, anatomic sites, chromosome breakpoints, junctions, numerical and structural abnormalities, and bands gained and lost among selected cases can be compared by use of the "similarity" report. Because the model used for CGH data is a subset of the karyotype data, it is now possible to examine the similarities between CGH results and karyotypes directly. All chromosomal bands are directly linked to the Entrez Map Viewer database, providing integration of cytogenetic data with the sequence assembly. These resources, developed as a part of the Cancer Chromosome Aberration Project (CCAP) initiative, aid the search for new cancer-associated genes and foster insights into the causes and consequences of genetic alterations in cancer.

A precise and scalable method for querying genes in chromosomal banding regions based on cytogenetic annotations

MOTIVATION

Staining the human metaphase chromosomes reveals characteristic banding patterns known as cytogenetic bands or cytobands. Using technologies based on metaphase chromosomes, researchers have accumulated much knowledge about the correlations between human diseases and specific cytoband aberrations, indicating the presence of disease-associated genes in those bands. With the progress of human genome project and techniques such as fluorescent in situ hybridization, many genes have been assigned to the cytobands and annotated in public databases, making it possible to find all genes in the disease-related cytobands through database queries. However, finding genes in cytobands remains an imprecise process, partly due to the insufficiency of current methods for cytoband queries, especially for those based on cytogenetic annotations.

RESULTS

By transforming the cytoband annotations into numerical segments, a new query method is developed that is able to accurately define any cytogenetic ranges in human chromosomes. A query system (designated cytoband query sys CQS) is implemented using cytogenetic annotations in the public domain. Judged by a performance test, CQS executed as accurately as expected using cytogenetic annotations from NCBI Map Viewer. The new method is scalable and can be applied to genomes from other species.

AVAILABILITY

The CQS is freely accessible over the Internet at http://moris.csie.ncku.edu.tw/cqs/

CONTACT

clh9@mail.ncku.edu.tw

SUPPLEMENTARY INFORMATION

http://moris.csie.ncku.edu.tw/cqs/

Uprobe: a genome-wide universal probe resource for comparative physical mapping in vertebrates

Interspecies comparisons are important for deciphering the functional content and evolution of genomes. The expansive array of >70 public vertebrate genomic bacterial artificial chromosome (BAC) libraries can provide a means of comparative mapping, sequencing, and functional analysis of targeted chromosomal segments that is independent and complementary to whole-genome sequencing. However, at the present time, no complementary resource exists for the efficient targeted physical mapping of the majority of these BAC libraries. Universal overgo-hybridization probes, designed from regions of sequenced genomes that are highly conserved between species, have been demonstrated to be an effective resource for the isolation of orthologous regions from multiple BAC libraries in parallel. Here we report the application of the universal probe design principal across entire genomes, and the subsequent creation of a complementary probe resource, Uprobe, for screening vertebrate BAC libraries. Uprobe currently consists of whole-genome sets of universal overgo-hybridization probes designed for screening mammalian or avian/reptilian libraries. Retrospective analysis, experimental validation of the probe design process on a panel of representative BAC libraries, and estimates of probe coverage across the genome indicate that the majority of all eutherian and avian/reptilian genes or regions of interest can be isolated using Uprobe. Future implementation of the universal probe design strategy will be used to create an expanded number of whole-genome probe sets that will encompass all vertebrate genomes.

Generic features of tertiary chromatin structure as detected in natural chromosomes

Knowledge of tertiary chromatin structure in mammalian interphase chromosomes is largely derived from artificial tandem arrays. In these model systems, light microscope images reveal fibers or beaded fibers after high-density targeting of transactivators to insertional domains spanning several megabases. These images of fibers have lent support to chromonema fiber models of tertiary structure. To assess the relevance of these studies to natural mammalian chromatin, we identified two different approximately 400-kb regions on human chromosomes 6 and 22 and then examined light microscope images of interphase tertiary chromatin structure when the regions were transcriptionally active and inactive. When transcriptionally active, these natural chromosomal regions elongated, yielding images characterized by a series of adjacent puncta or "beads", referred to hereafter as beaded images. These elongated structures required transcription for their maintenance. Thus, despite marked differences in the density and the mode of transactivation, the natural and artificial systems showed similarities, suggesting that beaded images are generic features of transcriptionally active tertiary chromatin. We show here, however, that these images do not necessarily favor chromonema fiber models but can also be explained by a radial-loop model or even a simple nucleosome affinity, random-chain model. Thus, light microscope images of tertiary structure cannot distinguish among competing models, although they do impose key constraints: chromatin must be clustered to yield beaded images and then packaged within each cluster to enable decondensation into adjacent clusters.

Multiple reciprocal translocations in salivary gland mucoepidermoid carcinomas

Mucoepidermoid carcinoma, the most common human malignant salivary gland tumor, can arise from both major and minor salivary glands, including sites within the pulmonary tracheobronchial tree. We performed comparative genomic hybridization (CGH) and spectral karyotyping (SKY) on two tumor cell lines: H3118, derived from tumor originating in the parotid gland, and H292, from tumor in the lung. In both cell lines, CGH showed a partial gain within the short arm of chromosome 7 and SKY revealed the presence of the previously reported reciprocal translocation t(11;19)(q21;p12). Additional chromosomal rearrangements were found in both cell lines, including three more reciprocal translocations in cell line H292 [t(1;16), t(6;8)x2] and three other reciprocal translocations in cell line H3118 [t(1;7), t(3;15), and t(7;15)]. A review of the literature of other reported cases of mucoepidermoid carcinomas analyzed with standard G-banding techniques, as well as distinct benign salivary gland tumors, such as pleomorphic adenomas and Warthin tumor, confirmed the presence of a karyotype dominated by reciprocal translocations. Four chromosomal bands were involved in chromosomal translocations in both cell lines: 1q32, 5p15, 7q22, and 15q22. Fluorescence in situ hybridization studies showed that the breakpoints in these four bands were often within a few megabases of each other. The involvement of similar chromosomal bands in breakpoints in these two cell lines suggests that these regions may be predisposed or selected for chromosomal rearrangements in this tumor type. The presence of multiple reciprocal translocations in both benign and malignant salivary gland tumors may also suggest a particular mechanism within mucous or serous glands mediating chromosomal rearrangements.

Method for manufacturing whole-genome microarrays by rolling circle amplification

Comparative genomic hybridization (CGH) to metaphase chromosomes is a method for genome-wide detection of chromosomal aberrations in DNA samples. Recent advances in microarray technology have improved CGH by replacing metaphase chromosomes with a collection of mapped genomic clones placed on glass slides. However, it is quite expensive and labor-intensive to prepare DNA from the genomic clones for use in constructing genomic microarrays. Here we used strand-displacement rolling circle amplification (RCA) to manufacture whole-genome microarrays by using a collection of about 4,500 mapped RPCI-11 BAC clones that cover the human genome at approximately a 1-Mb resolution. These genomic microarrays detected all major chromosomal aberrations in cancer cells lines and in cell lines with aneuploidy. In this article, we discuss the advantages of using RCA for the manufacturing of large genomic microarrays.

Sequence-based cancer genomics: progress, lessons and opportunities

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.

An international database and integrated analysis tools for the study of cancer gene expression

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).

Genes, isochores and bands in human chromosomes 21 and 22

The recently available DNA sequences from chromosomes 21 and 22 enabled us to define the relationships of different band types with isochores and with gene concentration and to compare these relationships with previous results. We showed that chromosomal bands appear as Giemsa or Reverse bands depending not on their absolute GC level, but on the composition GC level relative to those of adjacent contiguous bands. We also demonstrated that the GC-richest, and gene-richest H3+ bands are characterized by a lower DNA compaction compared with the GC-poorest, gene-poorest L1+ bands. Moreover, our results indicate that the human genome contains about 30,000 genes.

The human genome browser at UCSC

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.

In silico analysis of cancer through the Cancer Genome Anatomy Project

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.

The Cancer Genome Anatomy Project: new resources for reading the molecular signatures of cancer

The Cancer Genome Anatomy Project (CGAP) has built informational, technological, and physical resources to interface genomics with basic and clinical cancer research. The CGAP web site (http://cgap.nci.nih.gov) provides informatics tools for in silico analysis of the CGAP datasets as well as information for accessing each of the CGAP resources. Published in 2001 by John Wiley & Sons, Ltd.

Spectral karyotyping and fluorescence in situ hybridization detect novel chromosomal aberrations, a recurring involvement of chromosome 21 and amplification of the MYC oncogene in acute myeloid leukaemia M2

Recurring chromosomal aberrations are of aetiological, diagnostic, prognostic and therapeutic importance in acute myeloid leukaemia (AML). However, aberrations are detected in only two thirds of AML cases at diagnosis and recurrent balanced translocations in only 50%. Spectral karyotyping (SKY) enables simultaneous visualization of all human chromosomes in different colours, facilitating the comprehensive evaluation of chromosomal abnormalities. Therefore, SKY was used to characterize 37 cases of newly diagnosed AML-M2, previously analysed using G-banding. In 15/23 patients it was possible to obtain metaphases from viably frozen cells; in 22 additional cases, fixed-cell suspensions were used. Of the 70 chromosomal aberrations identified by SKY, 30 aberrations were detected for the first time, 18 aberrations were redefined and 22 were confirmed. SKY detected two reciprocal translocations, t(X;3) and t(11;19). In five cases, eight structural aberrations resulted in partial gains of chromosome 21, six of which were undetected by G-banding. In 4/5 cases, these resulted in copy number increases for AML1. Amplification of MYC was detected in three cases. Using SKY and FISH, clonal aberrations were identified in 5/18 cases with a presumed normal karyotype; 3/5 aberrations were of known unfavourable prognostic significance. Karyotypes were entered into a custom-designed SKY database, which will be integrated with other cytogenetic and genomic databases.

Jumping translocations are common in solid tumor cell lines and result in recurrent fusions of whole chromosome arms

Jumping translocations (JTs) and segmental jumping translocations (SJTs) are unbalanced translocations involving a donor chromosome arm or chromosome segment that has fused to multiple recipient chromosomes. In leukemia, where JTs have been predominantly observed, the donor segment (usually 1q) preferentially fuses to the telomere regions of recipient chromosomes. In this study, spectral karyotyping (SKY) and FISH analysis revealed 188 JTs and SJTs in 10 cell lines derived from carcinomas of the bladder, prostate, breast, cervix, and pancreas. Multiple JTs and SJTs were detected in each cell line and contributed to recurrent unbalanced whole-arm translocations involving chromosome arms 5p, 14q, 15q, 20q, and 21q. Sixty percent (113/188) of JT breakpoints occurred within centromere or pericentromeric regions of the recipient chromosomes, whereas only 12% of the breakpoints were located in the telomere regions. JT breakpoints of both donor and recipient chromosomes coincided with numerous fragile sites as well as viral integration sites for human DNA viruses. The JTs within each tumor cell line promoted clonal progression, leading to the acquisition of extra copies of the donated chromosome segments that often contained oncogenes (MYC, ABL, HER2/NEU, etc.), consequently resulting in tumor-specific genomic imbalances. Published 2001 Wiley-Liss, Inc.

A high-resolution map of human chromosome 12

Our sequence-tagged site-content map of chromosome 12 is now integrated with the whole-genome fingerprinting effort. It provides accurate and nearly complete bacterial clone coverage of chromosome 12. We propose that this integrated mapping protocol serves as a model for constructing physical maps for entire genomes.

Integration of cytogenetic landmarks into the draft sequence of the human genome

We have placed 7,600 cytogenetically defined landmarks on the draft sequence of the human genome to help with the characterization of genes altered by gross chromosomal aberrations that cause human disease. The landmarks are large-insert clones mapped to chromosome bands by fluorescence in situ hybridization. Each clone contains a sequence tag that is positioned on the genomic sequence. This genome-wide set of sequence-anchored clones allows structural and functional analyses of the genome. This resource represents the first comprehensive integration of cytogenetic, radiation hybrid, linkage and sequence maps of the human genome; provides an independent validation of the sequence map and framework for contig order and orientation; surveys the genome for large-scale duplications, which are likely to require special attention during sequence assembly; and allows a stringent assessment of sequence differences between the dark and light bands of chromosomes. It also provides insight into large-scale chromatin structure and the evolution of chromosomes and gene families and will accelerate our understanding of the molecular bases of human disease and cancer.

GenMapDB: a database of mapped human BAC clones

GenMapDB (http://genomics.med.upenn.edu/genmapdb) is a repository of human bacterial artificial chromosome (BAC) clones mapped by our laboratory to sequence-tagged site markers. Currently, GenMapDB contains over 3000 mapped clones that span 19 chromosomes, chromosomes 2, 4, 5, 9-22, X and Y. This database provides positional information about human BAC clones from the RPCI-11 human male BAC library. It also contains restriction fragment analysis data and end sequences of the clones. GenMapDB is freely available to the public. The main purpose of GenMapDB is to organize the mapping data and to allow the research community to search for mapped BAC clones that can be used in gene mapping studies and chromosomal mutation analysis projects.

Genomics - the new rock and roll?

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.

Integration of cytogenetic data with genome maps and available probes: present status and future promise

The National Cancer Institute has established an initiative, called the Cancer Chromosome Aberration Project (Ccap), in order to link and integrate the physical and genetic maps of the human genome with cytogenetic data and the location of chromosomal rearrangements in human diseases. This goal will be achieved by high-resolution fluorescence in situ hybridization (FISH) mapping of colony-purified bacterial artificial chromosome (BAC) clones spaced at 1-to 2-Mb intervals across the entire genome. All BAC clones will be anchored on the physical map by the presence of a mapped sequence tagged site (STS). The generation of a publicly accessible clone repository will allow convenient distribution of these BACs. Ccap data can be correlated with other cancer-associated and genomic databases, such as the catalog of chromosomal aberrations in cancer and the emerging full genomic sequence. We anticipate that the use of Ccap clones will expedite and refine the mapping of chromosomal breakpoints. The eventual set of approximately 3,000 Ccap BACs should facilitate the production of BAC-containing DNA chips for assessing copy number of genomic segments by matrix comparative genomic hybridization. In addition, the repository will provide genome-wide tools for defining chromosomal aberrations in cytological specimens by interphase cytogenetics. The Ccap Web site illustrates goals and progress of this initiative (http://www.ncbi.nlm.nih.gov/CCAP/).