MORGAM Manual

Data transfer format: DNA transfer inventory Form: 39 Version: 2 Date: 2008-02-29

© National Institute for Health and Welfare and the MORGAM Project investigators Last updated: 2009-05-13 For more information, please contact Päivi Laiho (firstname.lastname@thl.fi) or Ari Haukijärvi (firstname.lastname@thl.fi)

The purpose of this transfer format is to provide an exact and common format for the MORGAM Central Laboratory (MCL) at National Institute for Health and Welfare (THL) to transfer data on received DNA samples to the MORGAM Data Centre (MDC). The MDC can use this data to check which samples were actually received by the MCL from MPC.

Data in the format specified here should be submitted to the MORGAM Data Centre (MDC) for every subject on whom DNA was requested by the MDC (see Form 40). The data can be completed in the same excel-file along with the existing Form 40 and the data transfer data received from MPC: In case of "DNA aliquots" the excel-file will include the Form 49 data, in case of "stock DNA" the Form 48 data, and in case of "whole blood" the Form 49 data received from MPC.

The completed data should be placed in directory \\hkivms\mgdna\from_mlo.

Contents

• Format specification
• General instructions
• Specific instructions for each item
• Data transfer instructions and example
• Updates

Format specification

General Instructions

The item NAME on the document is a computer variable name used for the item by the MDC.

The item FORMAT specifies the format in which the value should be presented in the transfer data set:

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 cannot 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 item

Follow these instructions carefully when creating the computer file for the data transfer from the MPC to the MDC.

To the top of the form

Number 39 indicates the "Data transfer format: DNA transfer inventory - master list".

To the top of the form

Current version of this data transfer format. If the version number of the data transfer format which you are using is not "1", 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 / deleting some variables.

To the top of the form

Enter appropriate code of your MPC or laboratory from the list of MORGAM centres for DNA transfer. In most cases the sender will be the MPC, but in some cases the MPCs (or possibly many of them) are served by a separate laboratory (e.g. MPCs 34, 54, 55 and 59 are all served by laboratory 912 in Paris). If your laboratory is not directly connected to your MPC, and the laboratory is not listed in the list of MORGAM centres for DNA transfer, please contact the MDC for a code for your laboratory.

To the top of the form

This is the local key on the label fixed on the tube. If the local key includes a personal identification, additional measures should be taken to secure the confidentiality of the person, as specified in the subsection on section DNA Collection Procedure of the MORGAM Manual.

It is important that there are no misprints in this entry because otherwise the genotype derived from the sample will be lost or connected to a wrong individual's phenotypic data.

If the tube is not available then code 8888888.

To the top of the form

This is the primary key identifying the individual in the MORGAM study. The first 2 characters correspond to the Form 20 item CENTRE, the next 2 characters correspond to RUNIT, the next 2 to COHORT and the last 6 characters correspond to item SERIAL.

It is important that there are no misprints in this entry because otherwise the genotype derived from the sample will be lost or connected to a wrong individual's phenotypic data.

To the top of the form

KEY2 is a primary key, identifying DNA sample in MORGAM study. KEY2 does not include any of the components of KEY1 (identifying individual in MORGAM study). KEY2 sample identification code is generated in the MDC and it's relation with KEY1 is kept in the MDC. The labels used for transferring the DNA samples from the DNA storage unit in KTL to other MORGAM Genotyping Laboratories include only KEY2 codes.

To the top of the form

This form should be completed for every subject on whom DNA was requested by the MDC (see Form 40). Enter 1 if the sample for the subject was received in the MORGAM Central Laboratory (MCL), and enter 2 if it not.

To the top of the form

Code here a type of DNA which will be sent to Morgam Central Laboratory

To the top of the form

Enter here a date when this form was completed. Format is yyyymmdd (date ANSI, 8 characters, year day month).

Data transfer Instructions and example

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

To simplify the tracing of data transfers between the MPC and the MDC, the files should be named as follows:

F39_MPCXX_YYYYMMDD_N.CSV, where:

• F39 - identifies the data are from Form 39
• MPCXX - where XX is the MPC code (e.g. MPC54 for Toulouse)
• YYYYMMDD - the year, month and date when this file was created (e.g. 20031025)
• N - sequence number of the transfer from the MPC. The number is generated by the MPC, and should also be used for logging the data transfers locally.

To avoid possible errors in variable naming use the first row from the example below containing variable names. Example of Form 39 ASCII comma-delimited data file:

The data files should be archived (ZIP) before sending them to the MDC. The archive names should be the same as the file names. MORGAM data Error checking program will be used to prepare data (will be available later). The data should be sent to MDC (Zygimantas Cepaitis (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.

When the data are received in the MDC, an acknowledgement will be sent to the sender. Then 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