MORGAM Manual

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Data transfer format - DNA Extraction Inventory

  • Form: 43
  • Version: 1
  • Date: 2005-10-15
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© National Institute for Health and Welfare and the MORGAM Project investigators
Last updated: 31 October 2007
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 DNA Extraction Laboratory (MEL) to transfer data on the extracted 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).

Contents


Format specification

NAME SPECIFICATION AND CODES FORMAT or Value
FORM Form number I2 |4|3|
VERSION Version of this form I1 1
KEY2 Sample identificaton C7 |_|_|_|_|_|_|_|
Receiving of whole blood
REC_DATE Date when whole blood was received at DNA extraction laboratory (date ANSI)
YYYYMMDD (year month day)		 C8 |_|_|_|_||_|_||_|_|
REC_COMM Comments on received blood C100 free text
Extraction of DNA
DNA_DATE Date when DNA extraction was performed at DNA extraction laboratory (date ANSI)
YYYYMMDD (year month day)		 C8 |_|_|_|_||_|_||_|_|
AB260 Absorbance value at 260 nm F5.3 |_|.|_|_|_|
AB280 Absorbance value at 280 nm F5.3 |_|.|_|_|_|
CONC Concentration of DNA (µg/ml)
Concentration: AB260 x DILUTION x 50 =µg/ml		 F7.2 |_|_|_|_|.|_|_|
PURITY Purity (ratio AB260 / AB280) |_|.|_|_|_| 3 decimal points
VOL Amount of liquid left in the tube (µl) |_|_|_|.|_| 1 decimal point
DILUTION Coefficient by which the sample was diluted |_|_|_|  
METHOD DNA extraction method:
1=phenol-chloroform
2=salt precipitation
3=other
9=unknown		 char(1) |_|
DNA_BUFF Type of buffer in which DNA was dissolved:
1=dH2O
2=1xTE
3=other
9=unknown		 char(1) |_|
 
DNA_EXTR Amount of DNA extracted (µg) |_|_|_|_|_|.|_|_| 2 decimal points
COMMENTS Comments on DNA extraction char(100) 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 from the GLAB to the MDC.

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FORM Form number char(2)

|4|3|

Number 43 indicates the "Data transfer format: DNA Extraction Inventory".

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VERSION Version of this form char(1)

|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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KEY2 Sample identification char(7)

|_|_|_|_|_|_|_|

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.

Receiving of whole blood

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REC_DATE Date when whole blood was received at MEL (date ANSI)
YYYYMMDD (year month day)		 char(8) |_|_|_|_||_|_||_|_|

Enter here a date when whole blood sample was received at MEL. Format is yyyymmdd (date ANSI, 8 characters, year day month).

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REC_COMM Comments on received blood char(100) free text

Enter coments here (if any).

Extraction of DNA

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DNA_DATE Date when DNA extraction was performed at MEL (date ANSI)
YYYYMMDD (year month day)		 char(8) |_|_|_|_||_|_||_|_|

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

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AB260 Absorbance value at 260 nm (3 decimal points) char(4) |_|.|_|_|_|

...

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AB280 Absorbance value at 280 nm (3 decimal points) char(4) |_|.|_|_|_|

...

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CONC Concentration of DNA:
Concentration: AB260 x DILUTION x 50 =µg/ml (1 decimal point)		 char(5) |_|_|_|_|.|_|

...

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PURITY Purity (ratio AB260 / AB280): (3 decimal points) char(4) |_|.|_|_|_|

...

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VOL Amount of liquid left in the tube (µl):  (1 decimal point) char(4) |_|_|_|.|_|

...

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DILUTION Coefficient by which the sample was diluted: char(3) |_|_|_|

...

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METHOD DNA extraction method:
1=phenol-chloroform
2=salt precipitation
3=other
9=unknown		 char(1) |_|

Code here a method of extraction of DNA.

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DNA_BUFF Type of buffer in which DNA was dissolved:
1=dH2O
2=1xTE
3=other
9=unknown		 char(1) |_|

Code here a type of bugffer in which DNA was dissolved.

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DNA_EXTR Amount of DNA extracted (µg): (2 decimal points) char(6) |_|_|_|_|.|_|_|

...

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COMMENTS Comments on DNA extraction char(100) free text


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:

F43_MPCXX_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 43 ASCII comma-delimited data file:

form;version;key2;rec_date;rec_comm;dna_date;ab260;ab280;conc;purity;vol;dilution;method;dna_buff;dna_extr;comments
43;1;1231234;20040706;volume of blood received 1 ml;20040706;0.064;0.041;256;1.561;490;80;1;2;125.4;re-extracted with salt precipitation
43;1;10123123;20040802;volume of blood received 1.5 ml;20040802;0.035;0.036;140;0.972;490;80;1;2;68.6;

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.