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breast_mutation_BRCA_Details

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					breast-mutation-
details Data
Dictionary
Table Description:
Table Background:




Primary Key:


Foreign Key(s):

Table Transmission
Requirements:

Module name:
 Implementation date:

Data Item/Field Name


Official field/item name to be used in the Data Dictionary




PERSON_ID




CENTER_NO
GENE_NAME
VARIANT_NUMBER
CENTER_VARIANT_NAME
STANDARD_VARIANT_NAME
VARIANT_CID
HGVS_GENOMIC
HGVS_PROTEIN
Detailed mutation data for BRCA1 and BRCA2
Breast_mutation_Details table should contain detail data for all
personID’s with a 2, 3, or 4 for BRCA1_person_status or
BRCA2_person_status from the breast_mutation table.

person_id, gene_name, varient_number (note: while center_no
may be important for querying the data, it is not necessary to
uniquely identify the row.
person_id --> individual
center_no --> individual
Required


breast-mutation



Description                                                                                              CIS   Type
                                                                                                         Requi
                                                                                                         red:
Description or definition of the field/item and its use. Note: There should be one row per field/item.   Indicates     Indicates the length and
                                                                                                         whether or    characteristic of the data
                                                                                                         not this      item/field.
                                                                                                         item/field    A = Alphabetic only with
                                                                                                         must be       or without blanks.
                                                                                                         reported to   N = Numeric only.
                                                                                                         the Central   X = May include
                                                                                                         Informatics   alphabetic, numeric,
                                                                                                         System        and/or special characters.
                                                                                                         (CIS).        Please list any characters
                                                                                                         - Yes/No      that are not alphanuberic.




CFR Unique ID for Person                                                                                 yes           number(12)




CFR Unique ID for Center                                                                                 yes           string(2)
BRCA 1 or 2 (HGVS symbol), part of pk                                      yes    string(30)
                                                                           yes
Person could have multiple variants, so give each sequential number, part of pk   integer(2N)
Varient name currently used by the Center                                  yes    string(30)
like BIC name to be assigned by Br-AWG lookup table                        yes    string(30)
Centers variant/mutation Identifier                                        no     string(30)
HGVS genomic designation assigned by Br-AWG lookup table                   no     string(30)
HGVS protein designation assigned by Br-AWG lookup table                   no     string(30)

Note: we are requiring one item from the lookup table, as it is not done,
this may change by proposal in the future if table is not completed in
time..
Allowable Values:                                         Validation Strategy


Acceptable codes for this item/field and the codes’       The edits will check the consistency between two or
descriptions. For numeric data,where applicable, the      more data items within the same record.
allowable ranges. Both codes and ranges can be used for a
single item/field




01 Philadelphia - Breast
02 New York - Breast
03 Utah - Breast
04 Australia - Breast
05 Ontario - Breast
06 Northern California -
Breast
07 Southern California -
Breast                                                    1) allowable-values check
BRCA1
BRCA2   1) allowable-values check
1-99    1) allowable-values check
Table Description:                        Summary mutation data for BRCA1 and BRCA2
Table Background:
Primary Key:                              person_id (note: while center_no may be important for
                                          querying the data, it is not necessary to uniquely identify
                                          the row.
Foreign Key(s):                           person_id --> individual
                                          center_no --> individual
Table Transmission                        Optional
Requirements:
Module name:                              breast-mutation
Implementation date:                      Aug 2010, apprioved by doodle poll July 20 2010

Data Item/Field Name                      Description

Official field/item name to be used in the Description or definition of the field/item and its use. Note: There should be
Data Dictionary                            one row per field/item.
CENTER_NO




PERSON_ID
BRCA1_PERSON_STATUS   BRCA1 Status - The over all status of BRCA1 variants. If multiple
                      varients exist the status of the highest ranking variant 4 > 3 > 2 > 1
                      is recorded here. Details on individual variants will be captured in
                      the 'details' table. It is likely that initially it may not be possible to
                      classify option 2=benign rare variant/LCL, this may happen later.
                      For now use option 3=Variant of uncertain significance (VUS)



BRCA2_PERSON_STATUS   BRCA2 Status - The over all status of BRCA2 variants. If multiple
                      varients exist the status of the highest ranking variant 4 > 3 > 2 > 1
                      is recorded here. Details on individual variants will be captured in
                      the 'details' table. It is likely that initially it may not be possible to
                      classify option 2=benign rare variant/LCL, this may happen later.
                      For now use option 3=Variant of uncertain significance (VUS)
BRCA1_PRI_METHOD   Primary Screening Method _BRCA1




BRCA2_PRI_METHOD   Primary Screening Method _BRCA2




BRCA1_LGR          Method of screening for large genomic rearrangements
BRCA2_LGR                           Method of screening for large genomic rearrangements




REMOVE ALL OTHER
VARIABLES

did not keep family ID because we
have person_id
2




    CIS                    Type                      Allowable Values:              Validation Strategy
    Required:
    Indicates whether or   Indicates the length      Acceptable codes for this      The edits will check the consistency
    not this item/field    and characteristic of     item/field and the codes’      between two or more data items within the
    must be reported to    the data item/field.      descriptions. For numeric      same record.
    the Central            A = Alphabetic only       data,where applicable, the
    Informatics System     with or without           allowable ranges. Both codes
    (CIS).                 blanks.                   and ranges can be used for a
    - Yes/No               N = Numeric only.         single item/field
                           X = May include
                           alphabetic, numeric,
                           and/or special
                           characters. Please list
                           any characters that
                           are not alphanuberic.
Yes   string(2)    01 Philadelphia - Breast   1) allowable-values check
                   02 New York - Breast
                   03 Utah - Breast
                   04 Australia - Breast
                   05 Ontario - Breast
                   06 Northern California -
                   Breast
                   07 Southern California -
                   Breast
                   11 Ontario - Colon
                   12 Los Angeles - Colon
                   13 Australia - Colon
                   14 Hawaii - Colon
                   15 Mayo Foundation - Colon
                   16 Seattle - Colon
                   17 Northern California -
                   Colon

Yes   number(12)
      number(1)    0=untested
                   1=wild-type/known
                   polymorphism
                   2=benign rare variant/LCL
                   3=Variant of uncertain
                   significance (VUS)          1) allowable-values check
Yes                4=pathogenic mutation       2) IF BRCA1_PRI_METHOD = 0 AND
                                               BRCA1_LGR = 0, must be 0

      number(1)    0=untested                  1) allowable-values check
                   1=wild-type/known           2) IF BRCA2_PRI_METHOD = 0 AND
                   polymorphism                BRCA2_LGR = 0, must be 0
                   2=benign rare variant/LCL
                   3=Variant of uncertain
                   significance (VUS)
Yes                4=pathogenic mutation
      number(2)   0 NOT TESTED                 1) allowable-values check
                  1 family specific mutation   2) If BRACA1=0, Then must be 0
                  2 AJ panel only
                  3 SSCP/CSGE
                  4 PTT cDNA + 3’&5’
                  sequencing                 5
Yes               PTT Genomic
                  6 PTT Genomic +
                  Seq/Heteroduplex
                  7 Heteroduplex
                  8 Full sequencing
                  9 other
                  10 2D GEL ELECTROPHORESIS
                  99 Unknown

      number(2)   0 NOT TESTED
                  1 family specific mutation
                  2 AJ panel only              1) allowable-values check
                  3 SSCP/CSGE                  2) If BRACA2=0, Then must be 0
                  4 PTT cDNA + 3’&5’
                  sequencing                 5
Yes               PTT Genomic
                  6 PTT Genomic +
                  Seq/Heteroduplex
                  7 Heteroduplex
                  8 Full sequencing
                  9 other
                  10 2D GEL ELECTROPHORESIS
                  99 Unknown

      number(2)   0 NOT TESTED for LGR         1) allowable-values check
                  1 MLPA                       2) If BRACA1=0, Then must be 0
                  2 Myriad Panel
                  3 Myriad BART
                  4 Specific Mutation (e.g.,
                  exon 13 dup)
Yes               5 Site Specific for family
                  members
                  99 Unknown
      number(2)   0 NOT TESTED for LGR
                  1 MLPA                       1) allowable-values check
                  2 Myriad Panel               2) If BRACA2=0, Then must be 0
                  3 Myriad BART
                  4 Specific Mutation (e.g.,
                  exon 13 dup)
Yes               5 Site Specific for family
                  members
                  99 Unknown
BRCA1 BRCA1    A summary of the BRCA1 status. Example               number(1)
      Status   0 = untested
               1 = willd-type or known polymorphism with no
               phenotype (known based on what criteria? What if it
               is an unknown polymorphism classify as #3?)
               2 = benign rare varient/LCL (criteria? what is LCL?)
               3 = Variant of uncertain significance (VUS) ( this
               should include any variation not covered by other
               options correct?)
               4 = pathogenic mutation. (anything know to be bad)




               if finding = null then BRCA1 status = 0
               if finding = 2 = no alterations detected then BRCA1
               status = 1
               if finding = 1 = alterations detected and Severity = 0 then
               BRCA1 status = 1 (or 0??)
               if finding = 1 = alterations detected and Severity = 1 then
               BRCA1 status = 4
               if finding = 1 = alterations detected and Severity = 3 then
               BRCA1 status = 3
               if finding = 1 = alterations detected and Severity = 4 then
               BRCA1 status = 3
0=untested
1=wild-type/known polymorphism 1) allowable-values check
2=benign rare variant/LCL           2) IF BRCA1_PRI_METHOD = 0 AND
3=Variant of uncertain significance BRCA1_LGR = 0, must be 0
(VUS)
4=pathogenic mutation

				
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