MORGAM Manual

Data transfer format: DNA aliquots Form: 49 Version: 3 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 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 DNA samples to the MORGAM Central Laboratory (MCL). The transfer of the data should precede the transfer of DNA aliquots from the MPC to the MORGAM Central Laboratory (MCL). If you are transferring unextracted DNA (e.g. whole blood) or stock DNA, then you should use Form Form42 or Form48 instead of this form.

Data in the format specified here should be submitted for every subject on whom DNA aliquots 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 and example

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 49 indicates the "Data transfer format: DNA transfer inventory - DNA aliquots".

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 in MPC then code 8888888.

To the top of the form

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.

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 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.

To the top of the form

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.

To the top of the form

Enter the type of the material from which the DNA was extracted. If sample type is 'other' then check that full description of it was provided on Form41 DNA Sample Information Form, § 3.3-2.

To the top of the form

Enter the type of anticoagulant used for the sample. If anticoagulant is 'other' then check that full description of it was provided on Form41 DNA Sample Information Form, § 3.3-2.

To the top of the form

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).

To the top of the form

Enter kind of form in which sample was before extraction of DNA.

To the top of the form

Enter the temperature (in degrees Celsius) at which sample was stored before extraction of DNA. 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".

To the top of the form

Enter code for extraction method here. If the extraction method is 'other' then check that a full description of it was completed on Form41 DNA Sample Information Form, § 3.3-2.

To the top of the form

Enter the date when the extraction of the DNA was done. 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.

Items AB260..DILUTION

Data for items AB260...DILUTION refer usually to the stock DNA, from which this aliquot was derived. They are relevant if problems are encountered with the quality of the aliquots. However, if the absorbance values have also been measured from the aliquots, then these values are preferable to the stock DNA values.

To the top of the form

Give here the absorbance value at 260 nm of the aliquot, if measured. If it was not measured, give value from the original stock DNA, from which this aliquot was derived. If the value is not available (i.e. AB260 = 9999), your should provide data for the item PURITY below.

To the top of the form

Give here the absorbance value at 280 nm of the aliquot, if measured. If it was not measured, give value from the original stock DNA, from which this aliquot was derived. If the value is not available (i.e. AB280 = 9999), your should provide data for the item PURITY below.

To the top of the form

Enter the coefficient of dilution that was used to create the sample for the absorbance measurement for items AB260 and AB280.

To the top of the form

Enter 8 if there are insufficient data for all of the items AB260, AB280 and DILUTION.

To the top of the form

Purity of the DNA sample, calculated as the ratio of AB260 and AB280, with 3 decimal places. These data should be provided even if the absorbance values (AB260 and AB280) are unavailable.
Enter 88.888 (irrelevant) if AVAIL = 2. Enter 99.999 (unknown) if the sample is available (AVAIL = 1) but the value of purity is unknown. 

To the top of the form

Concentration of this aliquot.

To the top of the form

Enter here the amount of liquid in the tube.

To the top of the form

Enter the type of hydration buffer here.

To the top of the form

If BUFFER_TYPE was coded 3, describe here the type of the hydration buffer.

To the top of the form

Enter the temperature at which the DNA 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".

To the top of the form

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

To the top of the form

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

To the top of the form

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

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:

F49_MPCXX_YYYYMMDD_N.CSV, where:

• F49 - identifies the data are from Form 49
• 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 49 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. The data should be sent to MDC as an attachment to an e-mail message. Please make sure to save a copy of the transferred files in the 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.