MORGAM Manual

Data transfer format - DNA sex determination Form: 44 Version: 2 Date: 2007-01-16

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 the sex determination from DNA to the MORGAM Data Centre (MDC). 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 should be placed on KTL network drive.

Contents

• Format specification
• General instructions
• Specific instructions for each item
• Data transfer instructions
• Updates to this form

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 MCL to the MDC.

Number 45 indicates the "Data transfer format: DNA Extraction Inventory".

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.

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.

Sex determination from DNA

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

...

Method of sex determination:
1 = PCR and agarose electroforesis
2 = PCR and ABI fragment analysis
3 = Paternity testing kit. ABI fragment analysis with paternity testing panel of markers analysed by NPHI paternity testing laboratory.
4 = Heterozygosity of X-chromosome genotypes. This code is based on the Metabochip genotyping quality control at Sanger institute.
8 = irrelevant (SEX_DNA = 4)

...

Item CONTYPE1 ... CONTYPE3: Contamination of the sample

...

...

...

Enter additional comments describing a problem in DNA sex determination

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:

F44_MPCXX_YYYYMMDD_N.CSV, where:

• F44 - identifies the data are from Form 44
• 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 44 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