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SKY and CGH Techniques Quick Search SKY SKY CGH SKY/CGH for Help Home NCI Sites CGAP CCAP Ried Lab Metaphrase (ICD-0-3) Chromosome Databases Mitelman Database Recurrent Aberrations FISH Mapped Clone High Resolution: CCAP Human BAC Resource Other NCBI sites Mapview Locuslink OMIM Pubmed Related sites Charité Atlas of Genetic and Cytogenetics in Oncology and Haematology Comparative Genomic Hybridization Literature Database Progenetix Cytogenetic and Molecular Genetic Laboratory Jackson Laboratory Instructions for SKY and CGH data submission Logon Enter a New Case Enter SKY Data Enter CGH Data Use Metaphrase LOG_ON Select'Log_on'from Home_page to reach your public AND private cases in the database. Enter your Name and Password. Press'Enter.''Arrive_at the Case List Input Screen. ENTER A NEW CASE A. Case List Input Screen Select the number of cases you want displayed per page. Enter page_number and press'Go'to advance to other pages, if desired. Press'Add New Cases'to bring you to the first blank row of fields for a new case. Enter information or select from pull_down menu for the following fields: Ignore Case Number, which is an internal number generated by the computer. Enter a Case Name Select Yes or No for cell line Select Human or Mouse Select one of the following genders: U nknown M ale F emale O ther Enter ICD-0-3 morphology term for the diagnosis . If you do not know the specific term, click on'Diagnosis'to enter the Metaphrase system. See'Use Metaphrase to Find ICD-0-3 Terms,'below. Enter ICD-0-3 topography term for site. If you do not know the specific term, click on'Site.''Select one of the following tissues: Unknown Bonemarrow Fluid such_as ascites, pleural, CSF Lymph_node Organ-Derived Peripheral Blood Tumor T/Met for metastatic_tumor. Press'Submit.''This saves the information to the screen and adds active buttons for'Case Details,''SKY,'and'CGH.''Note: The above information will_be_displayed in a one-line case summary on all pages, except in the Case Details Entry Form. B. Case Details Entry Form Press'Case Details'to bring_up the form, which has three parts: Case Name/Species/Cell Line Information Clinical Data Reference Note: Information from the previous screen is_repeated here. Changes made at either location will automatically be_made by the computer in both places. However, the'organism'field can only be_changed in the Case List page. Case Name/Species/Cell Line Information Case Number: Automatically assigned Case Name: Repeated from Case List Input page Species: If mouse was_selected: Press'Addn Info for Mouse'to bring_up the'Nonhuman Species Information Screen.''Enter animal strain, genotype, and comments. Press'Submit'and review the data. Press'Go'to return to the Case Detail Screen. Clinical Data Fill_in all appropriate fields. If you have_completed the diagnosis and site fields with proper ICD-0-3 terms, the ICD-0-3 code numbers for both will_be_displayed automatically. Select either public or private. Reference Fill_in the reference information using Index Medicus abbreviations for Journal Name. Press'Submit'and the Pubmed ID number will_be_added automatically, linked to the abstract. Return to the'Case List Input Screen'to add new SKY and/or CGH data. Note: Any information about an existing case may_be_edited either on the'Case List Input Screen'or the'Case Details Screen.''After changes are_made, press'Submit.''Back to Top ENTER SKY DATA A. Karyotype Input Screen Press the'SKY'button on the Case List Input Screen to bring_up the Karyotype Input Screen. Fill_in the following fields: Karyotype: Write_out karyotype. Modal Chrom. Number: Enter a number. Source/imagefile: Enter the location of your SKY data_files. Clone?:Select Yes, No, or Composite from the pull_down menu. Ploidy: Select from pull_down-menu. Cell Cnt.:Enter the number of cells with this karyotype. Max Segs: Determine the maximum number of segments in the most complicated chromosome in the karyotype and enter it in_this field. Note: A new segment begins each_time you use:: in the ISCN chromosome description. Count the number of segments from top_to_bottom of the chromosome. Press'Submit.''The Karyotype Input Screen reappears with the addition of several new fields.''Edit Sky'button: Add new SKY data or edit existing data. Copy cell: Click the check box to copy the information entered for this clone/cell, including the karyotype, into the corresponding fields for the_next clone/cell where it can be_revised as_required. Delete Cell: Check to delete all_the information entered for that clone/cell. Create Date: Added automatically. SKY"View Karyotype"button: Not active until the_next screen (Number of Normal/Abnormal Chromosomes Input Screen) is_completed. Continue entering information for other clones/cells in_this case, as necessary. If the information is very similar to a previous cell: Click'Copy Cell'on_that line Click'Submit, 'and the_next available empty line will_be_filled. Make changes as_required. If there_are no other clones/cells for this case, press'Edit SKY'to enter SKY data on the Number of Normal/Abnormal Chromosome Input Screen. B. Number of Normal/Abnormal Chromosomes Input Screen There_are two tables on this screen. The Case Summary Table is for review and the Chromosome Table is to be_completed, as_follows: Adjust the number of normal chromosomes. Enter the number of abnormal chromosomes: For rcp translocations, enter both chromosomes as abnormal. For derivatives, only enter chromosome contributing centromere. If there_is more_than one centromere, pick the chromosome you want the derivative displayed with in the karyotype. The maximum number of abnormal segments can be_changed here, if necessary. Press'Submit'to get_to the SKY Chromosome Input Screen. C. SKY Chromosome Input Screen The same two tables are_repeated from the previous screen. The'Text 'and'Image'buttons are not active until all_the SKY data has_been_entered and submitted.. Below the chromosome table, each chromosome is_listed separately and each one has the complete list of linked chromosome numbers in a horizontal line to allow you to go quickly from one to the other.''T'returns you to the chromosome table.''U'advances you to the end of the page. Click on an abnormal chromosome, marked with an asterisk), (*to obtain the segment section. Note: If you forgot to list a chromosome as abnormal in the chromosome table, return to the table, make the change, and press'Submit'to obtain a segment section for that chromosome. For each structurally abnormal chromosome, complete the following fields: Structural abnormality Highlight a relevant structural abnormality from the pull_down menu. Press'Copy Structure Info'to have it appear in the field to the right. Repeat to add more abnormalities as necessary. To remove all structure info, press'Clear All Structure Info 'or highlight an individual abnormality and press'Delete'on your keyboard. Place this chromosome with: Check for correctness. Changing the number, using the pull_down menu, from the default number will alter the location of the abnormal chromosome in the karyotype display. Number of cells in which aberrant chromosome found: Enter a number. Number of copies of aberrant chromosome found in_this cell: Enter a number. Proceed to describe each abnormal chromosome, segment by segment, working from the top to the bottom of the chromosome: Parent Chrom.:Select from pull_down menu Seg. Start: e_g.,pter Seg. Stop: e_g.,q31 hsr?: Select yes or no Centromere: Added automatically as 1 or 0; refers to_that particular segment. Size Estimate: Estimate size of hsr as%of normal parent. When the parent chromosome is unknown, use%of chr 1. It is usually necessary to experiment a little to get the hsr to the desired size. Gene: Fill_in if relevant. Delete Frag: Delete as appropriate. Press'Submit.''The SKY Chromosome Input Screen returns with the following features: An active'Text'button to view written karyotype. An active'Image'button to view written karyotype and full colored ideogram. Each abnormally described chromosome in SKY colors and with band overlay. If an error messge appears in_place of the colored ideogram, you may_have_used an improper band designation (e_g.,, if a band is_divided into q11. 1 and q11. 2, the use of q11 would be incorrect.''FISH'link to bring_up Map View with_that chromosomal breakpoint highlighted. Repeat SKY Chromosome Input Screen for each clone/cell in your case. Back to Top ENTER CGH DATA Press the CGH button on the Case List Input Screen to bring you to the CGH File Data/Manual Selection Screen. Data may_be_entered or edited, either automatically or manually. A. Automatic Entry (using Leica QCGH Software*in QPD/SLD format) To enter a new case: Press'Browse.''Go_to your own files. Open CGH folder. Go_to file with QPD/SLD format for that case. Select'all files'in'Files of type'field. Choose file for that case and press'open 'and your file name will_be_displayed in the form. If the file name is correct, check box_in'Confirm CGH File.''Scroll down to'CGH Action to Perform, 'select'Load New File'and press'Continue.''This brings up the CGH Input Screen, which displays the losses (in red) and gains (in green) for each chromosome with an abnormal CGH profile. To view the complete profile for this case, press'View CGH Profile.'*'*Note: In_the_future, automatic entry will_be possible from other software_systems such_as Applied Imaging and Metasystems. To view and edit a previously entered case: The file name will appear in the field'Previously Loaded File.''If the file name is correct, check box_in'Confirm CGH File.''Press'View Existing Profile.''To edit existing profile, return to CGH File Data/Manual Selection Screen. Enter the number of segments you will_need to enter new data or to edit existing data for this profile (see note at_bottom of screen). Scroll down to'CGH Action to Perform, 'select'Edit Previous Data, 'and press'Continue.''This brings you to the CGH Input Screen, which displays the previously entered losses (in red) and gains (in green) for each chromosome with an abnormal CGH profile. To edit this data, see instructions for'CGH Input Screen for Manual Submission of CGH Data,'below. B. Manual Entry To enter a new case: Scroll down to'CGH Action to Perform,'select'Manual Submission, 'and press'Continue.''This will bring you to the'CGH Input Screen for Manual Transmission'(see instructions below. To view and edit a previously entered case: Proceed to'CGH Action to Perform, 'select'Edit Previously Loaded File, 'and press'Continue.''This will bring you to the CGH Input Screen, which displays the previously entered losses (in red) and gains (in green) for each chromosome with an abnormal CGH profile. To edit your data, see instructions for'CGH Input Screen for Manual Submission of CGH Data,'below. C. CGH Input Screen for Manual Submission Note: To advance quickly to a particular chromosome, click on_that chromosome number in the horizontal list of chromosome numbers. For each chromosome with a CGH abnormality, describe each segment*showing gain or loss, working from the top of the chromosome (pter. Select from the pull_down menu: high loss (both chromosomes), loss (one chromosome), normal, gain, or high gain (amplification). Enter the upper band number in the'start'field. Enter the lower band number in the'stop'field. Do not change the ratios since they are_computed automatically. If data has_been_entered incorrectly (e_g.,, entering a band number that does not exist in the ISCN), **an error message will appear in_place of the chromosome. To correct improperly entered data, do one of the following, whichever is appropriate: Delete the whole chromosome by checking the'Delete Chromosome'box. Make correction in appropriate segment. Check'Delete Row.''Note: When corrections are_done as part_of editing an already completed CGH profile, all_of the above must be_followed by pressing'Submit'at the bottom of the page. When data entry is complete, press'Submit'at the bottom of the page. The form reappears with each chromosome for which data has_been_entered displayed at the left of the data entry fields. To view the completed CGH profile, press'View CGH Profile'at the top of the page.**The total number of segments represents the total number of different gains and losses along the chromosome showing the greatest number of such variations. For_example, a chromosome with gain of the p arm, and both loss and gain along the q arm would have three (3) segments that would need to be_described.****If a band is_subdivided in the ISCN at the 400-band level, choose one of the subdivisions; e_g.,if the q11 band is_divided into q11. 1 and q11. 2, choose one of those sub-bands as q11 alone results in an error message. Back to Top USE METAPHRASE TO FIND ICD-0-3 TERMS Data submitters must use the same terminology for diagnosis (morphology) and organ site (topography) to permit comparison or combination of the data in the SKY/CGH database. From the many different disease classification_systems, we have_selected the International Classification of Diseases for Oncology, 3rd edition (ICD-0-3) as our standard. It contains a morphology tree and a topography tree. In most cases you must select one term from each tree to fully classify your case. To find and select the correct ICD-0-3 morphology and topography terms we refer the user to Metaphrase TM, a medical terminology search_engine developed by the National Cancer Institute (NCI). A. Diagnosis (morphology) Go_to Metaphrase. Select ICD-0-3 from the pull_down menu in the'Sources'field in the left panel (that way you only get potential matches that have an ICD-0-3 atom. Enter the morphology term or concept in the text box and press'Search.''Click on the best match in the list'Matching Concepts'in the left panel. Scroll down through the right panel to the heading'Sources.''Search the Sources for ICD-0-3. Click on ICD-0-3 to view the ICD-0-3 code number (highlighted in blue at the top of the right panel) and the various diagnostic terms that are_included under_that code number. Enter into the SKY/CGH database either the correct ICD-0-3 term or the code number. B. Site (topography) Follow the same procedure as for'Diagnosis,'above. Note: For all leukemias except myeloid sarcoma, the standard ICD-0-3 site is'Bone_marrow'(C42. 1). Example: Select ICD-O-3 in the sources box on the left panel. Type breast adenocarcinoma in the box. You get two matches,'breast'and'adenocarcinoma.''Click on'breast,'then go_to the right panel and scroll down to'Sources.''Click on ICD-O-3. You will see the ICD-O-3 code for'Breast'(C50. 9) in the top blue colored bar. This indicates that the term is a legitimate ICD-0-3 term which can therefore be_used in the database. Use PT (preferred term), if possible. Go_back to left panel and click on'adenocarcinoma, 'then go_to the right panel and scroll down to'Sources.''Click on ICD-O-3. You will see the ICD-O-3 code for Adenocarcinoma, NOS (8140/3). If you get no matches using ICD-O-3 as the source in the left panel, change the Source to'All 'and resubmit the query. You will get more matches. Click on something that matches your query closely, and scroll down to related terms in the right panel. You may_be able to find a related concept that will_have an ICD-O-3 match. Clarifications Morphology terms have five-digit codes ranging from M-8000/0 to M-9989/3. The first four digits indicate the specific histologic term. The fifth digit after the slash(/)is a behavior code, which indicates whether a tumor is benign(/0), uncertain or unknown(/1), in_situ (2), malignant primary(/3), or malignant secondary(/6). To use this fifth digit appropriately, it may_be necessary to check the ICD-0-3 reference since this information is not available in Metaphrase . If the term entered in the search box does not have an ICD-0-3 Matching Concept, try searching for a slightly different term. For_example, 'acute_myeloid_leukemia M2'does not have an ICD-0-3 term; however, if you enter FAB M2, you will get an ICD-0-3 match. ICD-0-3 uses a non-pre-coordinated approach to classification where you have to choose both morphology (diagnosis) and topography (site). Therefore, ICD-0-3 does not have codes for all tumors by organ and you must describe the morphology and the site of that abnormal morphology separately, e_g.,Clear cell renal carcinoma is_entered as'clear cell adenocarcinoma, NOS'for morphology and'kidney'for site. If you enter clear cell renal carcinoma, you will only find renal cell carcinoma, not clear cell adenocarcinoma.)Breast_cancer is_entered as'adenocarcinoma'(8140/3) for morphology and'breast'(C50. 9) for site. See Table 13 in Ref. 1, pp. 16-18, for a concise list of ICD-0 Codes for hematopoietic and lymphoid neoplasms. About ICD-0-3 The ICD-0-3 was_developed as a joint project by the US National Cancer Institute and the World_health_organization (WHO) and published in 2000. This classification_system was_selected for the SKY/CGH database because: It is the most widely used throughout the world. It incorporates the new classifications for lymphomas and leukemias (Harris et_al. which includes subcategories of acute_myeloid_leukemia described according_to a combination of morphology and cytogenetic abnormalities. About Metaphrase Metaphrase was_developed by Apelon Inc. formerly Lexical Technologies Inc) . and adapted for use by the National Cancer Institute. It Is_unified based_on the Medical Language_system (UMLS) published by the National Library of Medicine and adds NCI vocabulary and other standard vocabularies useful to NCI. The Metaphrase tool facilitates mapping concepts from one vocabulary to other standard vocabularies. It contains two types of vocabularies: Pre-coordinated (contain more highly specific terminology), e_g.,, NCIPDQ (NCI Physicians Desk Query) and Meddra Not pre-coordinated, e_g.,, SNOMED International (produced by the College of American Pathologists) References International Classification of Diseases for Oncology, Third edition. Fritz A, Percy C, Jack A, Shanmugaratnam K, Sobin L, Parkin DM, Whelan S (eds. World_health_organization, Geneva, 2000. ISBN 92 4 154534 8. Harris NL, Jaffe ES, Diebold J, Flandrin G, Muller-Hermlink HK , Vardiman J, Lister TA, Bloomfield CD. World_health_organization classification of neoplastic diseases of the hematopoietic and lymphoid_tissues: Report of the clinical advisory committee_meeting--Airlie House, Virginia, November 1997. J Clin Oncol 17: 3835-3849,1999. Back to Top Questions and Comments: SKY/CGH Webmaster TITLE NLM NIH NCBI Help Disclaimer