MORGAM Manual

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Data transfer format: Inventory of transfer of DNA from a MORGAM Laboratory

  • Form: 45
  • Version: 1
  • Date: 2005-11-07
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© National Institute for Health and Welfare and the MORGAM Project investigators
Last updated: 2008-06-04
For more information, please contact Päivi Laiho (firstname.lastname@thl.fi) or Ari Haukijärvi (firstname.lastname@thl.fi)

This data transfer format is used by the MORGAM Central Laboratory (MCL) (or some other MORGAM Laboratory (ML)) when transferring DNA to another MORGAM Laboratory (ML) or MORGAM Participating Centre (MPC). It provides the receiving Centre and the MORGAM Data Centre (MDC) with relevant information on the DNA transfer.

Data in the format specified here should be provided for every DNA sample transferred. The data should be sent through e-mail.

This form should not be used for transferring DNA from a MPC Centre to the MCL. Form42, Form48 or Form49 should be used for such transfer.

Contents


Format specification

NAME SPECIFICATION AND CODES FORMAT or Value
FORM Form number I2

|4|5|
VERSION Version of this form I1

|1|
FROM The sender of the sample material I3

|_|_|_|
TO The receiver of the sample material I3

|_|_|_|
KEY2 Identification of the DNA sample:
enter text 'EMPTY' if cell is empty		 C7 |_|_|_|_|_|_|_|
MDTA Serial number of the Material and Data Transfer Agreement:
777 = return of DNA to the MPC. No signed MDTA to the transfer of the DNA.
999 = irrelevant, i.e. transfer of DNA inside KTL between DNA extraction unit and genotyping laboratory
(In this case code FROM = 901 and TO = 911.) 		I3

|_|_|_|
DATE_SENT Date of transfer of the DNA (date ANSI)
YYYYMMDD (year month day)		 C8 |_|_|_|_||_|_||_|_|
AMOUNT_SENT Amount of DNA transferred (µg) F8.2 |_|_|_|_|_|.|_|_|
CONCENTRATION Concentration of this aliquot (ng/µl, with 2 decimals)
7777 = irrelevant, return of DNA to the MPC.
8888 = irrelevant (KEY2='EMPTY')		 F5.2

|_|_|.|_|_|
VOLUME Amount of liquid in the tube (µl):
7777 = irrelevant, return of DNA to the MPC.
8888 = irrelevant (KEY2='EMPTY)		 I4 |_|_|_|_|
PLATE_TYPE Type of plate:
1 = matrix deep well rack (96 wells)
leave empty if return of DNA to the MPC.		 I1 |_|
PLATE_ID Identification of the plate
e.g. MPC20_V2_P1
leave empty if return of DNA to the MPC.		 C40 free text
COORDINATES Co-ordinates of the sample in the plate:
e.g. B12, G05, D10
leave empty if return of DNA to the MPC.		 C3 |_|_|_|
COMMENTS Comments on this sample:
enter text 'EMPTY' if cell is empty		 C100 free text


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:

FORMAT Type Format Example Comments
C Character C8 19991210 Used for dates, trailing zeroes are obligatory
C20 "B 17 E" Location of sample in a box, surrounded with double quotes (") if contains spaces. Free text, maximum 20 characters is allowed for this variable.
C3 -80 Storage temperature, includes leading '-' sign
F Float F5.2 13.1
2.18		 Variable must include a decimal point (.). Leading and trailing zeroes are not obligatory.
I Integer I3 1
15
180		 Leading zeroes are not obligatory

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.

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FORM Form number I2

|4|5|

Number 45 indicates the "Data transfer format: inventory of transfer of DNA from a MORGAM Laboratory".

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VERSION Version of this form I1

|1|

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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FROM The sender of the sample material I3

|_|_|_|

Enter appropriate code of the MORGAM Centre, which is sending the DNA, from the list of MORGAM centres for DNA transfer.

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TO The receiver of the sample material I3

|_|_|_|

Enter appropriate code of MORGAM DNA Extraction Laboratorty (MEL) from the list of MORGAM centres for DNA transfer

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KEY2 Identification of the DNA sample:
enter text 'EMPTY' if cell is empty		 C7 |_|_|_|_|_|_|_|

KEY2 is a primary key, identifying DNA sample in MORGAM. KEY2 does not include any of the components of KEY1 (identifying the individual or Centre in the MORGAM Project). KEY2 sample identification code is generated in the MDC and its relation with KEY1 is kept in the MDC. The labels used for transferring the DNA samples should include only KEY2.

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MDTA Serial number of the Material and Data Transfer Agreement
777 = return of DNA to the MPC. No signed MDTA to the transfer of the DNA.
999 = irrelevant (transfer of DNA inside KTL between DNA extraction unit and genotyping laboratory), code FROM=901, TO=911 in this case		 I3

|_|_|_|

MTDA gives the serial number of the Material and Data Transfer Agreement (M&DTA) covering this transfer of DNA. A copy of the M&DTA and its serial number can be found in the internal MORGAM web site.

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DATE_SENT Date of transfer of the DNA (date ANSI)
YYYYMMDD (year month day)		 C8 |_|_|_|_||_|_||_|_|

Enter here a date of transfer of DNA. Format is yyyymmdd (date ANSI, 8 characters, year day month).

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AMOUNT_SENT Amount of DNA transferred (µg) F8.2 |_|_|_|_|_|.|_|_|

Enter here the amount of DNA which will be transferred to the receiving centre.

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CONCENTRATION Concentration of this aliquot (ng/µl, with 2 decimals)
7777 = irrelevant, return of DNA to the MPC.
8888 = irrelevant (KEY2='EMPTY)		 F5.2

|_|_|.|_|_|

Enter here a concentration of the aliquot.

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VOLUME Amount of liquid in the tube (µl):
7777 = irrelevant, return of DNA to the MPC.
8888 = irrelevant (KEY2='EMPTY)		 I4 |_|_|_|_|

Enter here the amount of liquid in the tube.

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PLATE_TYPE Type of plate:
1 = matrix deep well rack (96 wells)
leave empty if return of DNA to the MPC.		 I1 |_|

Enter here a type of the plate.

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PLATE_ID Identification of the plate
e.g. MPC20_V2_P1
leave empty if return of DNA to the MPC.		 C40 free text

Enter here identification of the plate with DNA samples.

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COORDINATES Co-ordinates of the sample in the plate:
e.g. B12, G05, D10
leave empty if return of DNA to the MPC.		 C3 |_|_|_|

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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COMMENTS Comments on this sample:
enter text 'EMPTY' if cell is empty		 C100 free text

You can add here any relevant comments concerning this sample.


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:

F45_FROM_TO_YYYYMMDD_N.CSV, where:

To avoid possible errors in variable naming use the first row from the example below containing variable names. Example of Form 47 ASCII comma-delimited data file:

form;version;from:to;key2;mtda;date_sent;amount_sent;concentration;volume;plate_type;plate_id;coordinates;comments
45;1;901;911;1234567;999;20030722;2.50;2.50;1000;1;MG_P35;C15;
45;1;901;911;1012345;999;20030722;0.10;5;20;1;MPC84_WGA_P2;D17;

The data files should be archived (ZIP) before sending them to the receiver of DNA material. 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 file 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.