HIV Sequence (HIV_Sequence)

Version:
Status: active
Unique ID: Patient ID + Codepat patient + Record name
How to create a CSV file for this data collection?

Start date: 18/05/2025

Full view CSV column names Validation rules Reference lists Computed expressions Additional information CSV extract

1 Patient identification

text

Codepat of the patient

Technical specs

CSV column name:

CODEPAT

Required:

true

patient identificator

National registry ID of the patient

Help

Please encode a social security identification number (SSIN). Please note that the patient ID is always pseudonymised before being transferred to Healthdata.

Technical specs

CSV column name:

patient_id

Required:

true

Validation

The validity of the national register number is checked with the mod97 check.

Fields

Section help

Please encode a social security identification number (SSIN). Please note that the patient ID is always pseudonymised before being transferred to Healthdata.

text

Internal patient ID

Help

This field can be used to enter an internal ID or reference number. It is available for internal use only and is not transferred to Healthdata. If there is an integration between HD4DP and your organisation's patient administration system, additional patient identification information such as date of birth, sex and SSIN can be automatically enriched based on this internal patient ID. Please do not encode the social security identification number (SSIN) in this field. The SSIN must be encoded in the field 'National registry ID of the patient'.

Technical specs

CSV column name:

patient_id|internal_patient_id

Required:

false

boolean

Generated

Help

The patient_id|generated column can be set to 'TRUE' for an automatically generated patient_id.This column should only be added in case the patient_id is empty. If the column is set to 'TRUE', a patient_id is automatically generated based on the name, first name, date of birth and sex of the patient.

Technical specs

CSV column name:

patient_id|generated

Required:

false

Options

Label	Value
Yes	TRUE
No	FALSE

text

Name

Help

The name of the patient is never transferred to Healthdata and is available for your information only.

Technical specs

CSV column name:

patient_id|name

Required:

noSSIN(Needed only if no national register number is entered)

text

First name

Help

The first name of the patient is never transferred and is available for your information only.

Technical specs

CSV column name:

patient_id|first_name

Required:

noSSIN(Needed only if no national register number is entered)

date

Date of birth

Technical specs

Format:

DD/MM/YYYY

CSV column name:

patient_id|date_of_birth

Required:

true

Validation

Date of birth should be after 1900. (error)
Date of birth should not be in the future. (error)
Sample date should not be before date of birth. (error)

choice

Sex

Technical specs

CSV column name:

patient_id|sex

Required:

true

Options

Label	Value
Female	F
Male	M
Unkown	U

text

Place of residence

Technical specs

CSV column name:

patient_id|place_of_residence

Reference list:

POSTAL_CODE

Only when:

Required:

false

boolean

Deceased?

Technical specs

CSV column name:

patient_id|deceased

Only when:

Required:

false

Options

Label	Value
Yes	TRUE
No	FALSE

date

Date of death

Technical specs

Format:

DD/MM/YYYY

CSV column name:

patient_id|date_of_death

Only when:

Required:

false

2 Health professional

Section help

Identification of the Lab director of the ARL.

text

Health professional identification value

Help

In case no NIHDI number is available, please use "99999999999.

Technical specs

CSV column name:

CD_HPIN_VAL

Length:

Reference list:

PHYSICIAN

Required:

true

3 Healthcare organization

text

Healthcare organization identification value

Help

Identification of the ARL.

Technical specs

CSV column name:

CD_HP_HCO_VAL

Length:

Reference list:

ARL

Required:

true

4 HIV sequence

text

Type of HIV

Technical specs

CSV column name:

CD_HIV_TPE

Length:

Reference list:

HIV_TYPE

Required:

true

text

Type of NA

Technical specs

CSV column name:

CD_NA_TPE

Length:

Reference list:

NA_TYPE

Required:

true

text

Test rationale

Technical specs

CSV column name:

CD_TST_REAS

Length:

Reference list:

TEST_REASON

Required:

true

text

Therapy

Technical specs

CSV column name:

CD_THERPY

Length:

Reference list:

THERAPY

Required:

true

text

Specimen type

Technical specs

CSV column name:

CD_SPECIM_TPE

Length:

Reference list:

SPECIMEN_MATERIAL_263

Required:

true

date

Sample date

Help

Unknown day: use the 15th of the month (e.g. ??/12/1999 becomes 15/12/1999);
Unknown month and day: use the 1st of July (e.g. ??/??/2020 becomes 01/07/2020);
If the date is completely unknown, use the fictive date 11/11/1911.

Technical specs

Format:

DD/MM/YYYY

CSV column name:

DT_SAMPLE

Required:

true

Validation

Sample date should not be in the future. (error)
Sample date should not be before date of birth. (error)

text

Type of sequence

Technical specs

CSV column name:

CD_SEQ_TPE

Length:

Reference list:

SEQUENCE_TYPE

Required:

true

text

Test method

Technical specs

CSV column name:

CD_TEST_METH

Length:

Reference list:

TEST_METHOD_263

Required:

true

number

Threshold NGS (%)

Help

Please report the percentage used as integer (. > 0 and . < 100). Report as -1 (minus one) when Sanger sequencing was used.

Technical specs

CSV column name:

MS_NGS_TRSH

Length:

3.0

Required:

true

Validation

Threshold NGS (%) must be an integer from 0 and smaller than or equal to 100 (or -1 when not applicable). (error)

date

Test date

Help

"Unknown day: use the 15th of the month (e.g. ??/12/1999 becomes 15/12/1999);
Unknown month and day: use the 1st of July (e.g. ??/??/2020 becomes 01/07/2020);
If the date is completely unknown, use the fictive date 11/11/1911."

Technical specs

Format:

DD/MM/YYYY

CSV column name:

DT_TEST

Required:

true

5 Linkage information

text

File name

Help

This field is used as the first key for linkage between the data sent through HD4DP1 (patient & sample data) and SFTP (nucleotide sequences data). This field must contain the same value for every row in both csv files that are uploaded. Please use this convention: ARL_yyyymmddHHMMSS (name of ARL and date-time stamp of the file, e.g. HSP_20240827092014). The name of the csv file with nucleotide sequences sent through SFTP must have this value in order to be linked with the patient & sample data (at file level), e.g. HSP_20240827092014.csv.

Technical specs

CSV column name:

TX_ATT

Length:

250

Required:

true

text

Record name

Help

This field is used as the second key for linkage between the data sent through HD4DP1 (patient & sample data) and SFTP (nucleotide sequences data). This field must contain a unique value for every row in the csv files that are uploaded (same set of unique values in both files). Please use this convention: ARL_yyyymmddHHMMSS_xxxxx (name of ARL, date-time stamp of the file and a unique 5-digit number, e.g. HSP_20240827092014_00001). The same values must occur in both files for correct linkage between the patient and nucleotide sequence data (at record level).

Technical specs

CSV column name:

TX_ATT_RECRD

Length:

250

Required:

true