MORGAM Manual

Data transfer format - DNA transfer request Form: 40 Version: 2 Date: 2007-05-21

© National Institute for Health and Welfare and the MORGAM Project investigators Last updated: 2009-10-09 For more information, please contact Ari Haukijärvi (firstname.lastname@thl.fi) or Kari Kuulasmaa (firstname.lastname@thl.fi)

The purpose of this transfer format is to provide an exact format for the MORGAM Data Centre (MDC) to transfer the identification of the subjects on whom DNA are expected to the MORGAM Participating Centre (MPC) and the DNA Extraction Laboratory in the National Institute for Health and Welfare Finland (THL). Data in the format specified here should be submitted by the MDC for every member of the MORGAM cohorts concerned, which has been selected for the genetic case-cohort substudy. The selection of these members is described in section "Instructions for MORGAM case and subcohort selections" and in "Instructions for DNA requests". The data should be sent via e-mail.

Contents

• Format specification
• General instructions
• Specific instructions for each item
• Data transfer instructions
• 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 a computer file for the data transfer from the MDC to MPC and MEL.

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Number 40 indicates the "Data transfer format: DNA transfer request".

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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.

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Enter appropriate code of MORGAM DNA Extraction Laboratory from the list of MORGAM centres for DNA transfer

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From the list of MORGAM centres for DNA transfer select appropriate code of the MORGAM Participating centre for which DNA transfer request will be sent.

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This is a primary key, identifying individual in MORGAM study. Enter value of Centre code as characters 1-2, value of Reporting Unit code as characters 3-4, value of Cohort code as characters 5-6 and value of Serial number as characters 7-12.

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KEY2 is a primary key, identifying DNA sample in MORGAM. 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.

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Item GENGROUP makes it possible for the laboratory to place the baseline cases for a separate plate that can be genotyped later than the rest of the case-cohort set.

Enter here the date when requests for DNA transfers were sent to MEL and MPC. Format is yyyymmdd (date ANSI, 8 characters, year day month).

Data transfer Instructions

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:

MPCXX_YYYYMMDD_N.CSV, where:

• F40 - identifies the data are from Form 40
• 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 40 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