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Data transfer format - SNP genotypic data transfer to MDC - for special situations

  • Form: 47
  • Version: 3
  • Date: 2012-10-17
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© National Institute for Health and Welfare and the MORGAM Project investigators
Last updated: 2012-10-17
For more information, please contact Ari Haukijärvi (firstname.lastname@thl.fi) or Kari Kuulasmaa (firstname.lastname@thl.fi)

This data transfer format is an alternative to Form 46, and should be used only in special situations, after consultation with the MDC. In this data transfer format, Key2 is replaced with Key0 and Key1. The primary format for the transfer of genotypic data to the MDC is Form 46.

(NOTE: Version 1 of Form 47, named "SNP data transfer inventory", had a different purpose, which has become redundant.)

Contents


Specification of the data items

VARIABLE NAME SPECIFICATION FORMAT AND VALUE
FORM Form number I2 |4|7|
VERSION Form version I1 |2|
GLAB Genotyping Laboratory code, selected from the list of genotyping laboratories I3 |_|_|_|
SHIPMENT Shipment number given by the Genotyping Laboratory I3 |_|_|_|
SHIPDATE Date of this shipment
YYYYMMDD (year month day)		 C8 |_|_|_|_||_|_||_|_|
KEY1 Identification of individual in MORGAM study:
CENTRE + RUNIT + COHORT + SERIAL		 C12 |_|_||_|_||_|_||_|_|_|_|_|_|
KEY0 Local key identifying DNA sample in the Genotyping Laboratory C20 free text
DNA_DUPL Type of the DNA sample
0 = primary
1 = duplicate		 I1 |_|
MARKER SNP / polymorphism name (abbreviation) as used locally C30 free text
METHOD Method of genotyping I1 |_|
GENOTYPE Genotype C256 free text
STATUS Genotyping status I1 |_|
GENODATE Genotyping analysis run date or reading date
YYYYMMDD (year month day)		 C8 |_|_|_|_||_|_||_|_|
COMMENTS Comments for this genotype data row (if any) C256 free text

General instructions

VARIABLE NAME
Name used for the data item in the MDC.
SPECIFICATION
Specification of the variable. More details can be found in the section "Specific instructions for each item" below, or by following the hyperlink in column VARIABLE NAME.
FORMAT AND VALUE
Specifies the format in which the value should be presented in the transferred data set. In the cases where the value of the variable is fixed, the value is also given in this column.

FORMAT Type Code Example Comments
C Character C8 20090205 Used for dates, leading zeroes are obligatory in days and months.
I Integer I3 200
5		 Leading zeroes should not be used.

Instructions for making corrections to data that have already been sent to the MDC are given in section Data communication between the Participating Centres and the MDC.
Please contact the MDC for instructions if you can not provide information as specified in this document or if you have any problems with the interpretation of the coding for any specific items.


Specific instructions for each data item

The detailed definition for each variable and instructions for their use are given below. Follow these instructions when creating a file for genotype data transfer from the Genotyping Laboratory to the MDC.


FORM Form number I2 |4|7||
The form number 47 indicates the "Data transfer format : SNP genotype data transfer to the MDC". In this form both KEY1 and KEY0 will be used in the MDC to identify each individual and genotyping sample instead of using normal KEY2 identification (see Form46 definition).
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VERSION Version of this form I1 |2|
Current version of this data transfer format. If the version number of the data transfer format which you are using is not "2", these instructions do not correspond to the format you are using. Version number changes if some major changes are introduced in the form, for example adding and/or deleting data items that need to be included.
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GLAB Genotyping Laboratory code I3 |_|_|_|
Enter the appropriate code of your MORGAM Genotyping Laboratory from the list of MORGAM Genotyping Laboratories:
  • 911 = Genotyping laboratory in THL, Helsinki
  • 912 = Genotyping laboratory in INSERM, Paris
  • 913 = Genotyping laboratory in RSCI (Royal College of Surgeons in Ireland), Dublin
  • 914 = Genotyping laboratory in QUB (Queen's University), Belfast
  • 915 = Genotyping laboratory in FIMM (Institute for Molecular Medicine Finland), Helsinki
  • 916 = Genotyping laboratory in Helmholz-Münich
If the genotypic data are sent from an MPC instead of a MORGAM laboratory, enter here the MPC code.
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SHIPMENT Shipment number given by the Genotyping Laboratory (GLAB) I3 |_|_|_|
This is the shipment number from the Genotyping Laboratory to the MDC. Usually this is a sequential number of shipments from GLAB to the MDC. If you are not using this kind of general sequential number, please enter the number of shipment to the MDC on that particular day.
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SHIPDATE Date of this shipment
YYYYMMDD (year month day)		 C8 |_|_|_|_||_|_||_|_|
The date of this shipment (the date when you completed this data form). The date format is YYYYMMDD (date ANSI, 8 characters, year month day).
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KEY1 Identification of individual in MORGAM study (CENTRE + RUNIT + COHORT + SERIAL) C12 |_|_|_|_||_|_||_|_|
This is the primary key identifying individual in the MORGAM study. The first 2 characters correspond to the CENTRE, the next 2 characters to the RUNIT, the next 2 to the COHORT and the last 6 characters to the SERIAL on MORGAM Form 20 ("Data transfer format: MONICA survey data"). Please make sure that the codes are identical with those used for the same persons there. It is important that there are no misprints in this entry to ensure connecting the result with the correct person.
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KEY0 Local key identifying DNA sample in the Genotyping Laboratory (GLAB) C20 free text
This is a local key identifying the DNA sample in the Genotyping Laboratory. It is important that there are no misprints in this entry. The KEY2 sample identification code which is used in the MORGAM study will be generated in the MDC, based on the KEY1 and KEY0 information delivered here.
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DNA_DUPL Type of the DNA sample:
  • 0 = Primary
  • 1 = Duplicate
 I1 |_|
Enter here the type of the sample whether it is a primary sample or a duplicate sample for quality control. The MDC will create the 7-character MORGAM KEY2 for the samples for all KEY0s.
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MARKER SNP / polymorphism name (abbreviation) as used locally C30 free text
Enter here the SNP / polymorphism name, as it is recorded in your local database.
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METHOD Method of genotyping I1 |_|
Enter appropriate code for the genotyping method from the following list:
  • 1 = Chip
  • 2 = MassSpec
  • 3 = Amplifuor
  • 4 = Taqman
  • 5 = Agarose (fragment analysis on agarose)
  • 6 = KASPar
  • 7 = Fluorescent fragment analysis on ABI Sequencer
Please contact the MDC if method used in the Genotyping Laboratory is not included in this list.
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GENOTYPE Genotype C256 free text
Enter here alleles in capital letters (A, C, T, G) in alphabetical order, from both chromosomes, separated by slash ( / ).
Deletions should be marked as D, unknown genotype as N, for example:
  • A/A
  • C/D
  • N/N
  • A/N
  • D/G
The reason for an unknown genotype should be given in variable STATUS.
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STATUS Genotyping status I1 |_|
Enter the code for either successful genotyping or the reason for an unknown genotype. Use codes 1 ... 4 to specify the reason for unknown genotype if code N was used for GENOTYPE. Use code 5 if both alleles were coded using A, C, T, G or D.
  • 1 = Sample lost
  • 2 = Not genotyped because no DNA left
  • 3 = Sample available but not genotyped
  • 4 = Genotyping unsuccsessful
  • 5 = Successfully genotyped
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GENODATE Genotyping analysis run date or reading date
YYYYMMDD (year month day)		 C8 |_|_|_|_||_|_||_|_|
Enter here the analysis run date or reading date of this genotype. The date format is YYYYMMDD (date ANSI, 8 characters, year month day).
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COMMENTS Comments for this genotype data row (if any) C256 free text
Enter here comments for this data row (if any). Maximum 256 characters is allowed for this variable.
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Data transfer Instructions

The data should be prepared in ASCII format using semicolon (;) as a delimiter, with the names of data items (i.e. variables) in the first row. If data contains text with delimiter (semicolon) used inside the text, the value should be surrounded by double quotes ("). A dot (.) shold be used as a decimal point.

To simplify the tracing of data transfers the files should be named as: F47_GLAB_YYYYMMDD_N.CSV, where

To avoid possible errors in variable naming use the first row from the example below containing the variable names.

Example: Form 47 ASCII comma-delimited data file

FORM;VERSION;GLAB;SHIPMENT;SHIPDATE;KEY1;KEY0;DNA_DUPL;MARKER;METHOD;GENOTYPE;STATUS;GENODATE;COMMENTS
47;2;916;1;20090525;260301700002;1111222;0;RS2689216;2;A/G;5;20090420;
47;2;916;1;20090525;260301700008;2222333;1;RS4756356;2;C/C;5;20090420;

The data files should be archived in ZIP format before sending to the MDC. The archive name should be the same as the file name above. Please send the archived data file to the MDC (to Ari Haukijarvi, firstname.lastname@thl.fi) as an attachment to an e-mail message. Please make sure to save a copy of the transferred files in the sending MPC or laboratory.

After the data are received in the MDC, an acknowledgement will be sent to the sender. The data will be checked for consistency and quality, and after any problems have been resolved, they will be entered into the MORGAM database.


Updates

Date Update
2009-05-19 Form 47 (version 2): "Data transfer format - SNP genotype data transfer to MDC" was created.
This replaces the old Form 47 (version 1): "Data transfer format - SNP data transfer Inventory".
2012-10-17 Form 47 (version 3): Item TYPE was replaced with the DNA_DUPL. The meaning of the variable is unchanged, but the codes were changed from1 and 2 to 0 and 1.
   
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