MORGAM Manual

Data transfer format: Transfer of case and subcohort data from MDC Form: 66 Version: 1 Date: 2005-03-10

© National Institute for Health and Welfare and the MORGAM Project investigators Last updated: 2007-11-27 For more information, please contact Olli Saarela (firstname.lastname@thl.fi) or Kari Kuulasmaa (firstname.lastname@thl.fi)

 The purpose of this form is to provide a format for the transfer of data from the selection of cases and subcohort from the MDC to MORGAM Participating Centres (MPC) and Laboratories. Data in the format specified here accompanies the data on genotypes (see Form 64: Transfer of SNP genotype data from MDC). The data on this form are derived from Form 65: Case and subcohort selection data and Form 21: Additional Baseline Data, and the specific instructions have been targeted for those analyzing the MORGAM data.

The MORGAM case-cohort design is described in sections "Selection of cases and cohort subsample" and "Subsample selection after extension of follow-up" of the Manual.

Contents

• Format specification
• Specific comments on each item

Format specification

Columns of the format specification

ITEM NAME

name used for the item in the MDC.

SPECIFICATION AND CODES

specification and values of the variable. More details can be found in the section "Definitions of the variables" below, or by following the hyperlink in column ITEM NAME.

FORMAT OR VALUE

specifies the format in which the value should be presented in the transfer data set. In the cases where the value of the variable is fixed, the value is also given in this column.

FORMAT	Type	Format	Example	Comments
C	Character	C7	SWE-NSWa	RUA abbreviation used in MORGAM.
		C2	03	Cohort identification
F	Float	F5.2	13.1	Variable includes a decimal point (.).
R	Real number	R	0.24927345	Selection probability.
I	Integer	I5	221 10323

Specific comments on each item

The definitions of each variable and instructions for their use are given below.

Number 66 indicates the "Data transfer format: Transfer of case and subcohort data from MDC".

This indicates the version number of this data transfer format entitled "Data transfer format: Transfer of case and subcohort data from MDC".

These are key items used for identifying the record and merging it with other records of the same individual.

CENTRE is the official MORGAM Participating Centre code number, RUNIT the official MORGAM Reporting Unit code number and COHORT the official MORGAM Cohort code number as they appear in section "MORGAM Participating Centres and cohorts" of the MORGAM Manual.

SERIAL is the identification for the individual. It is unique within the combination of CENTRE, RUNIT and COHORT.

KEY1 is constructed from items CENTRE, RUNIT, COHORT and SERIAL by placing them one after the other. The purpose of this item is to facilitate the merging of different records of the same individual.

This is a unique sequence number which identifies the selection of cases and subcohorts from which these data were derived. For each selection, a report with the same SELECTION number is available in the internal MORGAM web site.

The selection of cases and subcohort may have been conducted in several phases, where earlier selections have been supplemented later, for example due to extension of the follow-up period of a MORGAM cohort.

This item indicates the latest phase of the case-cohort selection for the CENTRE/RUNIT/COHORT combination. The selection data in the data transfer set corresponds to combination of the latest and all earlier case and sub-cohort selections. General information on the selections is available in the internal MORGAM web site.

The first four numbers indicate the year, the next two the month and the last two the day of month of the latest phase of the selection.

This is the same as item ELIGSC of Form 65: Case and subcohort selection data. Briefly, the eligibility of the person to the subcohort requires that

• information on smoking, blood pressure and cholesterol are available,
• DNA are available, and
• there is consent for the use of DNA to study CHD and stroke.

It is possible that DNA are not available for a person eligible to the subcohort. This is because the availability of DNA was based on item Form 21, but after selection to the case-cohort set, the sample was not found or no DNA could be extracted from the sample. This is a rare situation in most cohorts, but common in those (e.g. PRIME) where the availability of DNA could be checked only after the selection of the case-cohort set.

This is the selection probability of the individual to the subcohort, i.e. the marginal probability on which the person is in the cohort subsample. The sampling weights for data analysis in the case-cohort design are derived from item PROB and the case status, which depends on the definition of the end-point for each analysis.

This item indicates whether the individual belongs to the subcohort or not.

This item indicates whether the individual was selected to the case-cohort set as a case or not. Note that here the term case covers the cases of all potential study endpoints, but only one or some of them are usually used for any single data analysis. Genotypic data are not necessarily available for all cases (see instructions for ELIGSC ... ELIGOD above). It is possible that DNA are not available for a person selected as a case. This is because at the time of selection of the case-cohort set, the availability of DNA was based on item DNAAV of Form 21, but after the selection, the sample was not found or no DNA could be extracted from the sample. This is a rare situation in most cohorts, but common in those (e.g. PRIME) where the availability of DNA could be checked only after the selection of the case-cohort set.

Item CASE is derived from items CASEDTH, CASECHD, CASESTR, CASETED, CASEAP, CASEBCHD and CASEBSTR of Form 65: Case and subcohort selection data:

• CASE has value 1, if any of these seven items has value 1. Then the person was selected to the case-cohort set with probability one;
• CASE has value 2, if all of these seven items have value 2. Then the person was selected to the case-cohort set with probability PROB;
• otherwise CASE has value 3. Then the person was selected to the case-cohort set with probability PROB. The reason for not selecting the person to the case-cohort set with probability one is described in the Case and subcohort selection report.

Items CONSCHD...CONSANY

These are the same as items CONSCHD, CONSSTR, CONSTED and CONSANY of Form 21: Additional baseline data.

The case-cohort set may include individuals for whom there is no consent to use the DNA for the study of some of the MORGAM end-points. Therefore, a person's data cannot be used to study:

• CHD unless CONSCHD = 1 or 2;
• stroke unless CONSSTR = 1 or 2;
• thrombo-embolic disease unless CONSTED = 1 or 2;
• other causes of death unless CONSANY = 1 or 2, or there is other confirmation from the MPC that there is a consent to study the specific cause of death.