| Table | Access (Site Only vs Node)[1] |
Data Originates From [2] | Mandatory | Field Name | Description | Data Type | Value Domain | Examples |
|---|---|---|---|---|---|---|---|---|
| Patient | Node | HVP Auto | Mandatory | HashCode | HVP Codified value of patient to hide patient identity | VARCHAR(255) | ||
| Patient | Node | Lab Extractor | Optional | ResearchHashCode | HVP Codified value of patient to allow de-identified linkage | VARCHAR(255) | ||
| (Patient) | Site only | Lab | Mandatory | PatientID | Internal ID used within the lab. Only exists within the lab | - | ||
| (Patient) | Site only | Clinic/Lab | Optional | FirstName | Only exists within the lab for Research hashcode (GRHANITE) | - | ||
| (Patient) | Site only | Clinic/Lab | Optional | LastName | Only exists within the lab for Research hashcode (GRHANITE) | - | ||
| (Patient) | Site only | Clinic/Lab | Optional | Gender | Only exists within the lab for Research hashcode (GRHANITE) | - | ||
| (Patient) | Site only | Clinic/Lab | Optional | DOB | Only exists within the lab for Research hashcode (GRHANITE) | - | ||
| (Patient) | Site only | Clinic/Lab | Optional | Postcode | Only exists within the lab for Research hashcode (GRHANITE) | - | ||
| (Patient) | Site only | Clinic/Lab | Optional | Digits 5-9 of the Medicare ID | Only exists within the lab for Research hashcode (GRHANITE) | - | ||
| VariantInstance | Node | HVP Auto | Mandatory | HashCode | De-identified code of the Test ID | VARCHAR(255) | ||
| VariantInstance | Node | HVP Auto | Mandatory | VariantID | The ID of the variant on HVP Node | INT32 | ||
| VariantInstance | Node | Lab | Mandatory | InstanceDate | Date instance was tested | DateTime | ||
| VariantInstance | Node | Lab | Optional | PatientAge | Age of patient when test was taken | INT32 | ||
| VariantInstance | Node | Lab | Optional | RefTestMethodID | Foreign key to TestMethod | INT32 | ||
| VariantInstance | Node | Lab | Optional | RefSampleTissueID | Foreign key to SampleTissue | INT32 | ||
| VariantInstance | Node | Lab | Optional | RefSampleSourceID | Foreign key to SampleSource | INT32 | ||
| VariantInstance | Node | Lab | Mandatory | RefPathogenicityID | Foreign key to estimated level of pathogenicity | INT32 | ||
| VariantInstance | Node | Lab | Optional | Justification | Justification by medical scientist | VARCHAR(65535) | ||
| VariantInstance | Node | Lab | Optional | PubMed | PubMed Identifier/Data Object Identifier | VARCHAR(255) | ||
| VariantInstance | Node | Lab | Optional | RecordedInDatabase | Whether it is recorded in disease specific or gene specific | Boolean | Yes/No | |
| VariantInstance | Node | Lab | Optional | SampleStored | Whether lab still has sample left | Boolean | Yes/No | |
| VariantInstance | Node | Clinic/Lab | Optional | PedigreeAvailable | Whether organisation has pedigree data | Boolean | Yes/No | |
| VariantInstance | Node | Lab | Optional | VariantSegregatesWithDisease | Whether pedigreee was consideed during diagnosis of pathogenicity | Boolean | Yes/No | |
| VariantInstance | Node | Lab | Optional | HistologyStored | Whether histograms are stored | Boolean | Yes/No | |
| VariantInstance | Node | HVP Auto | Mandatory | PatientID | The ID of the patient on HVP Node | INT32 | ||
| VariantInstance | Node | HVP Auto | Mandatory | Organisation_ID | The ID of the organisation on HVP Node | INT32 | ||
| (VariantInstance) | Site only | Lab | Mandatory | TestID | Internal to diagnostic lab | - | ||
| Variant | Node | HVP | Mandatory | ID | Internal ID for table | INT32 (auto) | ||
| Variant | Node | HVP | Mandatory | GeneID | The ID of the gene on HVP | INT32 | ||
| Variant | Node | Lab | Mandatory | cDNA | As cDNA | VARCHAR(255) | HGVS | c.128delGA |
| Variant | Node | Lab | Alternate cDNA | mRNA | As mRNA | VARCHAR(255) | HGVS | |
| Variant | Node | Lab | Alternate cDNA | Genomic | As genomic sequence | VARCHAR(255) | HGVS | |
| Variant | Node | Lab | Alternate cDNA | Protein | As protein sequence | VARCHAR(255) | HGVS | |
| Variant | Node | Lab | Optional | RefVariantClassID | Foreign key to VariantClass | INT32 | ||
| Variant | Node | Lab | Optional | Location | Exon or intron number | VARCHAR(255) | 1..3099 | |
| Variant | Node | HVP | Optional | Comments | By community consensus | VARCHAR(65535) | ||
| Variant | Node | HVP | Optional | RefPathogenicityID | By community consensus | INT32 | ||
| Gene | Node | HVP | Mandatory | ID | Internal ID for table | INT32 (auto) | ||
| Gene | Node | HVP | Mandatory | GeneName | Standard gene symbol used for gene in HVP system | VARCHAR(20) | MC1R | |
| Gene | Node | HVP | Mandatory | GeneDescription | Descriptive name for gene | VARCHAR(255) | melanocortin 1 receptor (alpha melanocyte stimulating hormone receptor) | |
| Gene | Node | HVP | Mandatory | RefSeqName | Name of reference sequence (NCBI's RefSeq project) | VARCHAR(20) | NM_002386 | |
| Gene | Node | HVP | Mandatory | RefSeqVer | Version of reference sequence (RefSeq) | VARCHAR(20) | 3 | |
| Gene | Node | HVP | Mandatory | RefSeqValidStart | Date range of when this version of sequence is valid (Start) | DateTime | 1/01/2010 | |
| Gene | RefSeqValidEnd | Date range of when this version of sequence is valid (End) | DateTime | 31/12/2010 | ||||
| Organisation | Node | HVP Auto | Mandatory | HashCode | De-identified code for organisation | VARCHAR(255) | ||
| (Organisation) | HVP Internal | Lab | Mandatory | Name | Name of diagnostic laboratory | VARCHAR(255) | ||
| (Organisation) | HVP Internal | Lab | Mandatory | Address | Address of diagnostic laboratory | VARCHAR(255) | ||
| (Organisation) | HVP Internal | Lab | Mandatory | Email of laboratory/main contact | VARCHAR(255) | |||
| (Organisation) | HVP Internal | Lab | Mandatory | Phone | Phone of laboratory/main contact | VARCHAR(255) | ||
| (Organisation) | HVP Internal | Lab | Mandatory | ContactPerson | Name of main contact person | VARCHAR(255) | ||
| RefVariantClass | Node | HVP | Mandatory | ID | Internal ID for table | INT32 (auto) | ||
| RefVariantClass | Node | HVP | Mandatory | VariantClass | The descript of the variant class | VARCHAR(20) | genomic, mitochrondrial | |
| RefTestMethod | Node | HVP | Mandatory | ID | Internal ID for table | INT32 (auto) | ||
| RefTestMethod | Node | HVP | Mandatory | TestMethod | The name of the test method used | VARCHAR(20) | DHPLC, PTT, CCM,… | |
| RefPathogenicity | Node | HVP | Mandatory | ID | Internal ID for table | INT32 (auto) | ||
| RefPathogenicity | Node | HVP | Mandatory | Pathogenicity | Level of pathogenicity | VARCHAR(20) | Class 1 - Certainly not Pathogenic Class 2 - Unlikely Pathogenic Class 3 - Unknown Class 4 - Likely Pathogenic Class 5 - Certainly Pathogenic |
|
| RefSampleTissue | Node | HVP | Mandatory | ID | Internal ID for table | INT32 (auto) | ||
| RefSampleTissue | Node | HVP | Mandatory | SampleTissue | Type of sample taken | VARCHAR(20) | Blood, tumour tissue... | |
| RefSampleSource | Node | HVP | Mandatory | ID | Internal ID for table | INT32 (auto) | ||
| RefSampleSource | Node | HVP | Mandatory | SampleSource | The source of the sample | VARCHAR(20) | DNA, g.DNA, RNA... |
Notes
- Site Only: Only the local site (lab/clinic) may see this data; Node: Visible at the Australian Node; HVP Internal: Held by HVP but not accessible via the Australian Node portal
- Lab: Data cames from the laboratory; Clinic: Data originally came from the clinic—however this may be a paper or electronic request which can be captured at the lab; HVP: Data that will be setup by the HVP organisers; HVP Auto: Data that is automatically generated by the system
