• Case Summaries List
• Case Details Entry Form, Human
• Case Details Entry Form, Mouse

• SKY/M-FISH Data Entry Form I (Karyotype Information)
• SKY/M-FISH Data Entry Form II (Number of Normal/Abnormal Chromosomes)
• SKY/M-FISH Data Entry Form III (Abnormal Chromosome Details)

LOG-ON

1. Select "Log-on" from Home page to reach your public AND private cases in the database.
2. Enter your Name and Password. Press "Enter."
3. Arrive at the Case Summaries List page.

ENTER A NEW CASE

A. Case Summaries List

1. Select the number of cases you want displayed per page.
2. Select page you want displayed.
3. Press "Add New Cases" to bring you to the first blank row of fields for a new case.
4. Enter information or select from pull-down menu for the following fields:
   • Ignore Case Number, which is an internal number generated by the computer.
   • Select either public or private. Public cases can be read (only) by all viewers while private cases can be accessed only by the submitter.
   • Enter a Case Name.
   • Select Yes or No for cell line.
   • Select Organism: Human or Mouse.
   • For diagnosis and site, enter ICD-0-3 terms. If the specific term is unknown, click Myeloid/Lymphoid for hematologic terms; for all other terms, click on "Diagnosis" or "Site" to enter the NCI Metathesaurus system. See "Use NCI Metathesaurus to Find ICD-0-3 Terms," below.
5. Press "Submit." This saves the information and adds active buttons for "Case Details," "SKY/M-FISH," and "CGH."
   Note: The above information will be displayed in a one-line case summary on all pages.

B. Case Details Entry Form (Human)

1. Press "Case Details" in the Case Summaries List.

• Case Summary

1. Information from the previous screen is repeated here.
2. Changes made at either location will automatically be made by the computer in both places.
3. However, the "Organism" field can only be changed in the Case Summaries List page.

• Clinical Data

1. Fill in all appropriate fields.
2. 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.

• Cytogenetic Data

1. Fill in any relevant cytogenetic data,including FISH (chromosomal and interphase).

• Cell Line Data

1. Fill in as appropriate.

• Reference

1. Fill in the reference information using Index Medicus abbreviations for Journal Name.
2. Press "Submit" and the PubMed ID number will be added automatically, linked to the abstract.
3. Return to the "Case Summaries List" page to add new SKY/M-FISH and/or CGH data.

Note: Any information about an existing case may be edited either on the "Case Summaries List" page or the "Case Details page." After changes are made, press "Submit."

    2. Return to Case Summaries List.

C. Case Details Entry Form (Mouse)

1. Fill in all appropriate fields (see instructions for B, above).
2. Enter specific Mouse Information regarding strain, genotype, and additional information.
3. Return to Case Summaries List.

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ENTER SKY/M-FISH DATA

A. SKY/M-FISH Data Entry Form I (Karyotype Information)

1. Press the "SKY/M-FISH" button on the Case Summaries List page to bring up the SKY/M-FISH Data Entry Form I (Karyotype Information) page.
2. Fill in the following fields:
   • Karyotype: Write out karyotype.
   • Modal Chrom. Number: Enter a number.
   • Source/imagefile: Enter the location of your SKY/M-FISH 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.
3. Press "Submit."
4. The SKY/M-FISH Data Entry Form I (Karyotype Information) page reappears with the addition of several new buttons.
   • "Continue with Manual Data Entry " button: This brings up SKY/M-FISH Data Entry Forms II or III.
   • "Auto-Convert Karyotype" button: This automatically converts the karyotype text into an initial SKYGRAM image.
   • "Edit Clone/Cell" button: Add new SKY/M-FISH data or edit existing data.
   • "Copy Data" button: Check this button when the next Clone/Cell is similar to the current one and press "Submit"; this copies the data into the next available empty Clone/Cell section where is can be edited as required.
   • "Delete Data" button: Check this button and press "Submit" to remove the Clone/Cell section.

   Note: The "Date Created" information appears automatically in the colored heading for each Clone/Cell.

5. Continue entering information for other clones/cells in this case, as necessary.If the information is very similar to a previous cell use the "Copy Data" operation described above.

B. SKY/M-FISH Data Entry Form II (Number of Normal/Abnormal Chromosomes Input)

Complete the "Number of Normal and Abnormal Chromosomes" table, as follows:

1. Adjust the number of normal chromosomes.
2. 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.
3. Maximum number of segments:
   • 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.
4. Press "Submit" to get to the SKY/M-FISH Data Entry Form III (Abnormal Chromosome Details).

C. SKY/M-FISH Data Entry Form III (Abnormal Chromosome Details)

1. The table from the previous screen is repeated.
2. Below the chromosome table, each abnormal chromosome is listed separately. To advance quickly to each abnormal chromosome segment section, press the link for that chromosome.

   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.

3. For each structurally abnormal chromosome, complete the following fields:
   • Enter number of cells in which this aberrant chromosome found.
   • Enter number of copies of this aberrant chromosome found in this cell.
   • Check if the chromosome is a ring structure.
   • Check the placement of the abnormal chromosome. To change from the default setting, select another chromosome from the pull-down menu. This will alter the location of the abnormal chromosome in the karyotype display.
4. 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.
   • Band Drawn: Each start and stop band can be displayed in one of three ways (pulldown menu): the full band, half the band, or no band; the default setting is half band for all bands except pter and qter, which are listed as whole bands.
   • Seg. Stop: e.g., q31.
   • Band Drawn: Similar to above for the Seg.Start.
   • Centromere: Added automatically as 1 or 0; refers to that particular segment.
   • Size Estimate: Estimate size of unknown segment (unknown band or unknown chromosome) or 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 correct size. If the chromosome origin is unknown, the segment will be drawn in a color different from other classification colors.
   • hsr?: Select yes or no.
   • Gene: Fill in if relevant.
   • Delete Segment: Delete as appropriate.
5. Press "Submit."
6. The SKY/M-FISH Data Entry Form III (Abnormal Chromosome Details) returns with the following features:
   • Each described abnormal chromosome in classification colors and with band overlay. If an error message 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.
7. Repeat SKY/M-FISH Data Entry Form III (Abnormal Chromosome Details) page for each clone/cell in your case.

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ENTER CGH DATA

Press the CGH button on the Case Summaries List page to bring you to the CGH Data Entry Form I . Data may be entered or edited, either automatically or manually.
A. Automatic Entry* (using Leica QCGH Software in QPD/SLD format, Applied Imaging or MetaSystems Isis Software)

• To enter a new case:
  1. Press "Browse."
  2. Go to your own files.
     • Open CGH folder.
     • Choose file for case to be loaded;
       Note:file must have one of the following file extensions.
       • .qpd (Old Lieca system)
       • .sld (New Lieca system)
       • .pro or .ai (Applied Imaging)
       • .CGH (MetaSystems)
     • Press "open" and your file name will be displayed in the form.
  3. If the file name is correct, check box in "Confirm CGH File."
  4. Scroll down to "CGH Action to Perform," select "Load New File" and press "Continue."
  5. This brings up the CGH Data Entry Form II, which displays the losses (in red) and gains (in green) for each chromosome with an abnormal CGH profile.
  6. To view the complete profile for this case, press "View CGH Profile."
• To view and edit a previously entered case:
  1. The file name will appear in the field "Previously Loaded File."
  2. Press "View Existing Profile."
  3. To edit existing profile, return to CGH Data Entry Form I.
  4. 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 page).
  5. Scroll down to "CGH Action to Perform," select "Edit Previous Data," and press "Continue."
  6. This brings you to the CGH Data Entry Form II, 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 Data Entry Form II page for Manual Submission of CGH Data," below.

B. Manual Entry

• To enter a new case:
  1. Scroll down to "CGH Action to Perform, " select "Manual Submission," and press "Continue."
  2. This will bring you to the "CGH Data Entry Form II page for Manual Transmission" (see instructions below).

• To view and edit a previously entered case:
  1. Proceed to "CGH Action to Perform," select "Edit Previously Loaded File," and press "Continue."
  2. This will bring you to the CGH Data Entry Form II, 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 Data Entry Form II page for Manual Submission of CGH Data," below.

C. CGH Data Entry Form II for Manual Submission
Note: To advance quickly to a particular chromosome, click on that chromosome number in the horizontal list of chromosome numbers.

1. 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.
2. 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.
3. 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.
     

4. The form re-appears with each chromosome for which data has been entered displayed at the left of the data entry fields.
5. 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.

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USE NCI'S METATHESAURUS 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/M-FISH/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 NCI Metathesaurus^TM, a medical terminology search engine developed by the National Cancer Institute (NCI).
A. Diagnosis (morphology)

1. Go to NCI Metathesaurus.
2. 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).
3. Enter the morphology term or concept in the text box and press "Search."
4. Click on the best match in the list "Matching Concepts" in the left panel.
5. Scroll down through the right panel to the heading "Sources."
6. Search the Sources for ICD-0-3.
7. 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.
8. Enter into the SKY/M-FISH/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:

1. Select ICD-O-3 in the sources box on the left panel.
2. Type breast adenocarcinoma in the box. You get two matches, "breast" and "adenocarcinoma."
3. Click on "breast," then go to the right panel and scroll down to "Sources."
4. 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.
5. Go back to left panel and click on "adenocarcinoma," then go to the right panel and scroll down to "Sources."
6. Click on ICD-O-3. You will see the ICD-O-3 code for Adenocarcinoma, NOS (8140/3).
7. 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

1. 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 NCI Metathesaurus.
2. 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.
3. 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.
4. 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/M-FISH/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 NCI Metathesaurus

NCI Metathesaurus was developed by Apelon Inc. (formerly Lexical Technologies Inc.) and adapted for use by the National Cancer Institute. It is based on the Unified Medical Language System (UMLS) published by the National Library of Medicine and adds NCI vocabulary and other standard vocabularies useful to NCI.The NCI Metathesaurus 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

1. 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 .
2. 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.

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