tblLAB_RES - Resistance testing

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

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)
SAMPLE_D_A character: see coding of date precision optional precision annotation for date of sample
SEQ_DT yyyy-mm-dd hh:mm Date and time when the sequencing was performed
SEQ_DT_A character: see coding of date precision optional precision annotation for date of sequencing
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 (e.g., GeneXpert, NAAT/LPA
  • 2 = Phenotype (e.g., culture)
  • 9 = Other
Type of test
PATHOGENTYPE character: MeSH terminology ​https://meshb.nlm.nih.gov/search Type of pathogen
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 Is HICDEP
AllTables CrossTable ATC001 any date in database after DEATH_D in tblLTFU Yes
AllTables CrossTable ATC002 any date in database after DROP_D in tblLTFU Yes
AllTables CrossTable ATC003 any date in database before BIRTH_D in tblBAS Yes
AllTables CrossTable ATC004 any date in database in the future Yes
AllTables CrossTable ATC005 patients submitted previously who have been missed out Yes
AllTables CrossTable ATC006 Any fields not coded as coding lists on table definition Yes
tblLAB_RES WithinTable LRW001 Duplicate records for same patient on same date Yes
tblLAB_RES WithinTable LRW002 Missing PATIENT Yes
tblLAB_RES WithinTable LRW003 Missing TEST_ID Yes
tblLAB_RES WithinTable LRW004 Missing SAMPLE_D Yes
tblLAB_RES WithinTable LRW005 Missing SEQ_DT Yes
tblLAB_RES WithinTable LRW006 Missing LAB Yes
tblLAB_RES WithinTable LRW007 Missing LIBRARY Yes
tblLAB_RES WithinTable LRW008 Missing REFSEQ Yes
tblLAB_RES WithinTable LRW009 Missing KIT Yes
tblLAB_RES WithinTable LRW010 Missing SOFTWARE Yes
tblLAB_RES WithinTable LRW011 Missing TESTTYPE Yes
tblLAB_RES WithinTable LRW012 Missing SUBTYPE Yes
tblLAB_RES WithinTable LRW013 SEQ_DT has no time part Yes
tblLAB_RES WithinTable LRW014 Missing VIRUSTYPE Yes
tblLAB_RES CrossTable LRC001 PATIENT has no record in tblBAS Yes
tblLAB_RES CrossTable LRC002 This TEST_ID has both LVL_1 and LVL_2 records Yes