web-based tools for bioinformatics; a (free) introduction

Web-based tools for Bioinformatics; A (free) introduction to (freely available) NCBI, MUSC and World-wide. When and Where---Wednesdays 1pm-2pm Room 426 Library Admin Building Beginning September 10, 2003.

Overview Spectral Karyotyping Tools. January 7, 2004

Introduction/Scope

SKY, M-FISH and CGH

Spectral Karyotyping (SKY), Multiplex Fluorescence In Situ Hybridization (M-FISH) and Comparative Genomic Hybridization (CGH) are complementary fluorescent molecular cytogenetic techniques. SKY/M-FISH permits the simultaneous visualization of each human or mouse chromosome in a different color, facilitating the identification of chromosomal aberrations. CGH utilizes the hybridization of differentially labeled tumor and reference DNA to generate a map of DNA copy number changes in tumor genomes.

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1/7/2004http://people.musc.edu/~hazards/WebBioInformatics/SKY_CGH.htm

Here is a nice summary PDF about SKY methods. Molecular cytogeneticists use SKY methods to allow unique simultaneous in vitro color coding of each chromosome. Properly executed, this allows the researcher to visually identify chromosomal rearrangements, steming from breakpoint or translocations.

In CGH, gains, losses and amplifications in chromosomal DNA during metaphase. In tumor cells the chromosomal copy number can change and CGH methods can detect such differences in a single experiment.

The NCBI SKY/MFISH CGH site is designed to allow users of these methods to share their results with one another and the general Scientific community.

Users of the NCBI site may search by the following means:

Submitter, by last name (Access to public SKY and CGH database for current list of submitters) Case name Cell line, by name Whole chromosome, chromosome arm, or chromosome breakpoint Diagnosis (morphology), using ICD-0-3** classification terminology or code number Site of disease (topography), using ICD-0-3** classification terminology or code number Specific types of treatment (e.g., drugs) Specific hereditary disorder Mouse strain and genotype Media type and media selection

NCI has a useful Metathesaurus browser



The Browse link on the left gives you access to a term browser which is a popup JAVA application window. This can give you hints for terms to search with.



The Search window allows querys with phrases or terms. Here are the matches founds with "clear cell adenocarcinoma" as query.



The link "Clear cell adenocarcinoma" opens this next page which shows some definitions and some further links.



The View Neighborhood in menu allows you to pick for example "ICD03". Clicking OK then displays the ICD03 code number corresponding to "clear cell adenocarcinoma". The "8310/3" code may be used as a query for searching SKY/CGH database for clear cell adenocarcinoma.

Why Bother with metathesaurus searches to locate say an ICD03 code? Well cancer types often have multiple name/synonyms and text searches can become inefficient. Locating the codes can provide some specificity.

Here's a PDF guide for using the Metathesaurus.

Connect to the NCBI Sky database to perform a "Quick Search" with the clear cell adenocarcinoma code 8310/3 and press go.



The following page shows case specific results for the code including both SKY/M-FISH and CGH results as well as case specific information.



Here is the case information for the last entry. Note the code entry.



From the cases page when you select the SKY/M-FISH button you see the following. Click the SKYGRAM button to see the ideograms.

A graphical summary of the identified changes and normal condition of chromosomes is depicted in the following screen shot. Text summary is available from the indicated button.



Here is what the text summary looks like. There are no normal Chromosome 1s in any of the studied cells from this case; the details provide a description of the aberations..



Following the CGH link for this case shows the following. In these images green represents a gain and red a loss. The relative thickness of thered/green bands is semi-quantitative indicator of the degree of gain or loss.



The CGH data in table form for this case shows:



Automatic Karyotype to SKYGRAM Convertor Available from SKY/CGH main page for registered case submitters.

This tool will automatically convert the short form karyotype into a SKYGRAM image (the full ideogram of a cell or clone, with each chromosome displayed in a different color, with band overlay). The program will also incorporate the number of cells for each structural abnormality which is displayed in brackets.

CGH Case Comparison Tool (Public Cases) http://www.ncbi.nlm.nih.gov/sky/webcghdrawing.cgi

Results from the comparison tool searching for 11pter[loss].

Results table



Selecting a case



dbMHC

Data related to the human Major Histocompatibility Complex . Note the TOOLS in the left side panel.

The Alignment viewer



The Probe/Primer Interface



Typing Kit Interface

Sequence Based Typing Interpretation



Viewer



dbMHCms page for comparing short tandem repeats in MHC locus



Clone Resources

Mammalian Gene Collection See Below for some details. Clone Registry See below for some details. Clone Finder This tool will allow you to identify mouse clones that contain an object, or that are contained within a particular genomic region. Human BAC Resource This resource provides genome-wide resource of large-insert clones that will help integrate cytogenetic, radiation-hybrid, linkage, and sequence maps of the human genome. The I.M.A.G.E. Consortium: large public collection of genes http://image.llnl.gov/image/ NIGMS Human Genetic Cell Repository http://locus.umdnj.edu/nigms/



Cancer Genome Anatomy Project - Tissues (cDNA Libraries & SNPs) http://cgap.nci.nih.gov/Tissues

Mammalian Gene Collection: The Mammalian Gene Collection is an effort by the NIH to generate full-length complementary DNA (cDNA) resources. These resources will be publicly accessible to the entire biomedical research community. The MGC project entails the production of cDNA libraries and sequences, database and repository development, as well as the support of research for improved library construction, sequencing, and analytic technologies, all of which are dedicated to the goal of obtaining a full set of human and other mammalian full-length (open reading frame) sequences and clones of expressed genes. Only the insert is available in the database. The goal of the Mammalian Gene Collection (MGC), a trans-NIH initiative, is to provide full-length open reading frame (FL-ORF) clones for human, mouse, and rat genes. All MGC sequences are deposited in GenBank and the clones can be purchased from distributors of the IMAGE consortium. For background information about the MGC, please read the Project Summary.

Searching MGC for our buddy CASP7:

Here's the Clone Registry page: The clone registry is a database used by participating human genome sequencing centers and mouse genome sequencing centers to record which clones have been selected for sequencing, which are currently in the pipeline, and which are finished and represented by sequence entries in GenBank. Includes BACs, PACs, cosmids, fosmids. Uses standardized clone names that represents a clone's microtitre plate address (plate number, row, and column) prefixed by a library abbreviation, to produce unique names. Includes clone ordering information. [NB: There may be some variation in names used early on. Standardized clone names were implemented quite a while after NCBI started receiving the high throughput genomic sequences.]



Here's the clone Library Browser page:



Searching for Canis familiaris gives a list of clones:



A worked Example

Sample Questions/Data Further Reading on Special Purpose Resources



dbMHC

Feolo M, Helmberg W, Sherry S, Maglott DR. NCBI genetic resources supporting immunogenetic research. Rev Immunogenet. 2000;2(4):461-7. [PubMed Abstract]

SKY/CGH

Knutsen T, Gobu V, Knaus R, Ried T, Sirotkin K. The SKY/CGH Database for Spectral Karyotyping and Comparative Genomic Hybridization Data. NCBI Handbook Available online: http://www.ncbi.nlm.nih.gov/books/data/handbook/pdfs/ch10d1.pdf

Knutsen T, Gobu V, Knaus R, Padilla-Nash H, Augustus M, Shenmen C, Greenhut S, Schrock E, Kriebel J, Plotkin J, Kirsch IR, Ostell J, Sirotkin K, Ried T. The NCI and NCBI interactive online database for chromosome aberrations detected by SKY/M-FISH and CGH. Proceedings of the AACR, Volume 44, 1st ed., March 2003. Available online: http://aacr03.agora.com/planner/

Knutsen T, Augustus M, Gobu V, Padilla-Nash H, Schröck E, Shenmen C, Plotkin J, Greenhut S, Kriebel J, Sirotkin K, Ried T. The NCI and NCBI SKY/CGH Interactive Online Database. Program number 299. American Society of Human Genetics 51st Annual Meeting, 2001. Available online: http://www.faseb.org/genetics/ashg/meet-2001/P-A/2001-archive.html

Knutsen T, Ried T. SKY: A comprehensive diagnostic and research tool.A review of the first 300 published cases. J Asso Genet Technol 26:3-15, 2000

Created by ESH 8-18-2003; updated 1-07-2004 11:30

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web-based tools for bioinformatics; a (free) introduction

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