wiki:Hicdep_1.70/TableLabRes

Version 2 (modified by ledergb, 4 years ago) (diff)

Added sentence that non-amplifiable tests need not be reported.

tblLAB_RES - Resistance testing

holds background information on the resistance test, laboratory, library, kit, software and type of test

Note: This table is tightly linked to tblLAB_RES_LVL_1, tblLAB_RES_LVL_2 and tblLAB_RES_LVL_3.

Resistance should be reported at lowest level of interpretation possible – so if the nucleotide sequence is available this should be reported rather than the list of mutations or resistance scores. However, the resistance test results should be captured if they have been part of the physician’s treatment decisions for the patient.

Non-amplifiable resistance tests should not be reported.

These four tables are designed to capture several possible formats the clinics and cohorts might have recorded resistance test data in. Once this data is gathered it should like all other tables be quality assessed.

Core fields

Note: Fields marked bold form the unique identifier for a record of the table.

Field name

Format

Description

PATIENT

character (or numeric if possible)

Code to identify patient (Cohort Patient ID)

TEST_ID

character (or numeric if possible)

An arbitrary value identifying a resistance test result

SAMPLE_D

yyyy-mm-dd

Date of the actual sample taken (NOT the test date)

SEQ_DT

yyyy-mm-dd hh:mm

Date and time when the sequencing was performed

LAB

character

Name of laboratory where the test was performed

LIBRARY

character

Library/algorithm used to identify resistance mutations

REFSEQ

character

Name/identifier of reference strain used to find mutations

KIT

character

Vendor and version/name of the kit used for the test

SOFTWARE

character

Software and version used to determine resistance

TESTTYPE

numeric:

  • 1 = Genotype
  • 2 = Phenotype
  • 9 = Other

Type of test

VIRUSTYPE

numeric:

  • 1 = HIV
  • 2 = HCV

Type of Virus

SUBTYPE

character

Subtype of HIV- or HCV-RNA

Additional fields

As shown with the core fields, the TEST_ID is the link between the 3 levels of data and the test background information table.

Some prior assessment of the assigned test identifiers has to be done in order to avoid duplicates.

In a running database the duplicate issues are easily resolved by adding a unique auto-generated key as the identifier between 3 levels of data and the test background information table.

Along with the TEST_ID it might be necessary to store the ID assigned to the sample at both the testing laboratory but also the centres laboratory in order to track the sample.

Field name

Format

Description

SAMP_LAB

character (or numeric if possible)

The assigned sample ID at the lab where the resistance test is preformed.

SAMP_INT

character (or numeric if possible)

The assigned sample ID from the centre.

QA Checks

Table Crosstable Error Code Description Study specific HICDEP?
AllTablesCrossTableATC001any date in database after DEATH_D in tblLTFUYES
AllTablesCrossTableATC002any date in database after DROP_D in tblLTFUYES
AllTablesCrossTableATC003any date in database before BIRTH_D in tblBASYES
AllTablesCrossTableATC004any date in database in the futureYES
AllTablesCrossTableATC005patients submitted previously who have been missed outYES
AllTablesCrossTableATC006Any fields not coded as coding lists on table definitionYES
tblLAB_RESWithinTableLRW001Duplicate records for same patient on same dateYES
tblLAB_RESWithinTableLRW002Missing PATIENTYES
tblLAB_RESWithinTableLRW003Missing TEST_IDYES
tblLAB_RESWithinTableLRW004Missing SAMPLE_DYES
tblLAB_RESWithinTableLRW005Missing SEQ_DTYES
tblLAB_RESWithinTableLRW006Missing LABYES
tblLAB_RESWithinTableLRW007Missing LIBRARYYES
tblLAB_RESWithinTableLRW008Missing REFSEQYES
tblLAB_RESWithinTableLRW009Missing KITYES
tblLAB_RESWithinTableLRW010Missing SOFTWAREYES
tblLAB_RESWithinTableLRW011Missing TESTTYPEYES
tblLAB_RESWithinTableLRW012Missing SUBTYPEYES
tblLAB_RESWithinTableLRW013SEQ_DT has no time partYES
tblLAB_RESWithinTableLRW014Missing VIRUSTYPEYES
tblLAB_RESCrossTableLRC001PATIENT has no record in tblBASYES
tblLAB_RESCrossTableLRC002This TEST_ID has both LVL_1 and LVL_2 recordsYES