Precision Local MAB (Precision_Local_MAB)

Version:
Status: active
Unique ID: VCF identifier
How to create a CSV file for this data collection?

Start date: 16/06/2021

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

1 Identification

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

Mapping of the clinical building blocks (indicative only)

Concept:

be.en.hd.Patient

Data element:

PatientIdentificationNumber

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

Length:

Required:

false

Stable:

true

Mapping of the clinical building blocks (indicative only)

Concept:

be.en.hd.Patient

Data element:

PatientIdentificationNumber

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

Last Name

Help

The prefix is included in the last name. 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

Length:

Required:

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

Stable:

true

Mapping of the clinical building blocks (indicative only)

Concept:

be.en.hd.Patient

Data element:

LastName

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

Length:

Required:

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

Stable:

true

Mapping of the clinical building blocks (indicative only)

Concept:

be.en.hd.Patient

Data element:

FirstNames

date

Date of birth

Technical specs

Format:

DD/MM/YYYY

CSV column name:

patient_id|date_of_birth

Required:

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

Stable:

true

Mapping of the clinical building blocks (indicative only)

Concept:

be.en.hd.Patient

Data element:

DateOfBirth

Validation

Date of birth cannot be in the future (error)

choice

Sex

Technical specs

CSV column name:

patient_id|sex

Required:

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

Stable:

true

Options

Label	Value
Female	F
Male	M
Unknown	U

Mapping of the clinical building blocks (indicative only)

Concept:

be.en.hd.Patient

Data element:

Gender

text

Place of residence

Technical specs

CSV column name:

patient_id|place_of_residence

Length:

Reference list:

POSTAL_CODE

Required:

true

Stable:

true

Mapping of the clinical building blocks (indicative only)

Concept:

be.en.hd.Patient

Data element:

Place of residence

boolean

Deceased?

Technical specs

CSV column name:

patient_id|deceased

Required:

true

Stable:

true

Mapping of the clinical building blocks (indicative only)

Concept:

be.en.hd.Patient

Data element:

DeathIndicator

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:

true

Stable:

true

Mapping of the clinical building blocks (indicative only)

Concept:

be.en.hd.Patient

Data element:

DateOfDeath

Validation

Date of death cannot be in the future (error)

text

RIZIV/INAMI-code of the responsible physician

Technical specs

CSV column name:

responsible_physician

Length:

100

Reference list:

PHYSICIAN

Required:

true

Mapping of the clinical building blocks (indicative only)

Concept:

be.en.hd.HealthProfessional

Data element:

HealthProfessionalIdentificationNumber

text

VCF identifier

Technical specs

CSV column name:

vcf_identifier

Length:

100

Required:

false

2 Advice

2.1 Medical Information

text

Primary tumor type and histology

Technical specs

CSV column name:

CD_ICDO_MORPH

Reference list:

ICDO_MORPH_3.2.0

Required:

true

Mapping of the clinical building blocks (indicative only)

Concept:

be.en.hd.Problem

Data element:

ProblemName

2.2 Sample information

choice

Patient registration is linked with

Technical specs

CSV column name:

CD_PAT_REGN

Required:

true

Options

Label	Value
GeNeo	1
BALLETT	2
No study	99

text

FMI-Order ID (primary lab)

Technical specs

CSV column name:

TX_SAMPLE_ID_PRM_LAB

Only when:

Required:

true

Mapping of the clinical building blocks (indicative only)

Concept:

be.en.hd.LaboratoryTestResult

Data element:

SpecimenID

text

XML NGS report file name

Technical specs

CSV column name:

TX_ATT_FILENAME

Only when:

Required:

true

date

Sampling date

Technical specs

Format:

DD/MM/YYYY

CSV column name:

DT_SAMPLING

Required:

true

Mapping of the clinical building blocks (indicative only)

Concept:

be.en.hd.LaboratoryTestResult

Data element:

CollectionDateTime

choice

Sample tumoral stage

Technical specs

CSV column name:

CD_SAMPLE_TUMOR_STG

Required:

true

Options

Label	Value
Primary	86049000
Metastasis	14799000

Mapping of the clinical building blocks (indicative only)

Concept:

be.en.hd.FunctionalorMentalStatus

Data element:

StatusValue

text

Sample anatomic site

Technical specs

CSV column name:

CD_ANATCL_SITE

Reference list:

ICDO

Required:

true

Mapping of the clinical building blocks (indicative only)

Concept:

be.en.hd.LaboratoryTestResult

Data element:

AnatomicalLocation

choice

Sample acquisition

Technical specs

CSV column name:

CD_SAMPLE_ACQST

Required:

true

Options

Label	Value
Excision	65801008
Biopsy	86273004
Collection of fluid specimen	764928002
Aspiration	14766002
Trephine biopsy	50590007
Other	PR9999

Mapping of the clinical building blocks (indicative only)

Concept:

be.en.hd.Procedure

Data element:

ProcedureType

text

Please specify

Technical specs

CSV column name:

TX_SAMPLE_ACQST_OTH

Only when:

Required:

true

text

Sample types

Technical specs

CSV column name:

CD_SAMPLE_TPE

Reference list:

PITTER_SAMPLE_TYPE

Required:

true

Mapping of the clinical building blocks (indicative only)

Concept:

be.en.hd.LaboratoryTestResult

Data element:

SpecimenMaterial

number

Neoplastic cells (%)

Technical specs

CSV column name:

MS_CEL_NEOPLC

Length:

4.1

Required:

true

Mapping of the clinical building blocks (indicative only)

Concept:

be.en.hd.LaboratoryTestResult

Data element:

TestResult

Validation

The inserted value for Neoplastic cells (%) may contain maximum 1 decimal (error)

2.2.1 Variant information

list

Variant information

This is a container for multiple answers. See the reference documentation for more details. Below you can find the information about the fields of the container

Element conditions

Message	Expression
The read depth needs to be an integer	typeof $.MS_READ_DEPTH === 'number'?$.MS_READ_DEPTH*1 % 1===0:true
The inserted value for Allelic frequency may contain maximum 1 decimal	(typeof $.MS_ALLC_FREQ=== 'number' && $. MS_ALLC_FREQ.toString().indexOf('.') !== -1)?($. MS_ALLC_FREQ.toString().trim().length - $. MS_ALLC_FREQ.toString().trim().indexOf('.') - 1

List items

text

Gene name

Technical specs

CSV column name:

variant_information|0|TX_GENE_NAM

Required:

true

Mapping of the clinical building blocks (indicative only)

Concept:

be.en.hd.LaboratoryTestResult

Data element:

TestResult

text

NM_ref

Technical specs

CSV column name:

variant_information|0|TX_NM_REF

Required:

true

text

cDNA position

Technical specs

CSV column name:

variant_information|0|TX_CDNA_POSTN

Required:

true

Mapping of the clinical building blocks (indicative only)

Concept:

be.en.hd.LaboratoryTestResult

Data element:

TestResult

text

Protein position

Technical specs

CSV column name:

variant_information|0|TX_PROTE_POSTN

Required:

true

Mapping of the clinical building blocks (indicative only)

Concept:

be.en.hd.LaboratoryTestResult

Data element:

TestResult

choice

Biological classes

Technical specs

CSV column name:

variant_information|0|CD_BIOL_CLASS

Required:

false

Options

Label	Value
Pathogenic	1
Probably pathogenic	2
VUS	3

Mapping of the clinical building blocks (indicative only)

Concept:

be.en.hd.LaboratoryTestResult

Data element:

ResultInterpretation

number

Allelic frequency

Technical specs

CSV column name:

variant_information|0|MS_ALLC_FREQ

Length:

4.1

Required:

true

Mapping of the clinical building blocks (indicative only)

Concept:

be.en.hd.LaboratoryTestResult

Data element:

TestResult

number

Read depth

Technical specs

CSV column name:

variant_information|0|MS_READ_DEPTH

Length:

10.0

Required:

true

Mapping of the clinical building blocks (indicative only)

Concept:

be.en.hd.LaboratoryTestResult

Data element:

choice

Clinical classes

Technical specs

CSV column name:

variant_information|0|CD_CLIN_CLASS

Required:

false

Options

Label	Value
Tier I: Strong clinical significance	1
Tier II: Potential clinical significance	2
Tier III: Unknown clinical significance	3

Mapping of the clinical building blocks (indicative only)

Concept:

be.en.hd.LaboratoryTestResult

Data element:

ResultInterpretation