MORGAM Manual

Data transfer format: Whole blood Form: 42 Version: 3 Date: 2008-10-28

© National Institute for Health and Welfare and the MORGAM Project investigators Last updated: 28 October 2008 For more information, please contact Päivi Laiho (firstname.lastname@thl.fi) or Kari Kuulasmaa (firstname.lastname@thl.fi)

The purpose of this transfer format is to provide an exact and common format for the MORGAM Participating Centres (MPCs) to transfer data on blood samples to the MORGAM Central Laboratory (MCL). The transfer of the data should precede the transfer of whole blood from the MPC to the MORGAM Central Laboratory (MCL). If you are transferring DNA which have already been extracted, then you should use Form48 or Form49 instead of this form.

Data in the format specified here should be submitted for every subject on whom whole blood will be sent to MORGAM Central Laboratory (see Form 40). These data should be submitted before or at the time of the shipment of the actual DNA material. The data in this form should be sent through e-mail. The MCL will share the data with the MORGAM Data Centre (MDC) .

Contents

• Format specification
• General instructions
• Specific instructions for each item
• Data transfer instructions

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 MPC to the MDC.

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Number 42 indicates the "Data transfer format: DNA transfer inventory - whole blood".

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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 "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 / deleting some variables.

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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.

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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.

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This is the primary key identifying the individual in the MORGAM database. 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.

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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 will be sent to the MORGAM Central Laboratory (MCL), and enter 2 if it not.

If AVAIL was coded as 2, the reason for the unavailability of the sample should be described in REASON. If there is a need to give more detailed information, report it to the MDC in a separate e-mail message.

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Describe here a reason why sample was unavailable. If there is a need to give more detailed information, report it to the MDC in a separate e-mail message.

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Enter the type of the sample being transferred. If you are transferring extracted DNA, then you should use Form48 or Form49 instead of this form.

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Enter the type of anticoagulant used for the sample. If anticoagulant is "other" then check that its full description was provided on Form 41: DNA Sample Information Form, § 3.3-2.

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Enter the date of drawing of the sample. If the exact date is unknown, an approximate date (e.g. the year) should be given if available. If only the month and year are known, enter 99 for the days. If only the year is known, enter 9999 for the month and the days.

This item can be coded as 77777777 if the date is the same as the date of examination given in the MONICA Survey data (item DEXAM of Form 20).

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Enter the temperature (in degrees Celsius) at which the sample was stored.  Enter the "-" in the first column to indicate a temperature below zero.
If the sample was stored at different temperatures, give here the highest temperature of a long term storage. E.g., if the sample was first stored for 5 years at -80ºC and the 2 years at  -20ºC, then enter here "-20".

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Enter here the volume of the sample that will be sent to the MCL.

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Enter the number written on the box in which the sample is sent to the MCL.

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Enter here the co-ordinates of the sample in the box. Make sure that the co-ordinates are also identifiable in the box.

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If you have any comments on the sample, please enter them here.

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:

• F42 - identifies the data are from Form 42
• 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 42 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 the 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.