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2. Getting Started
This section describes patient data and knowledge data used to drive the operations. You can experiment with predefined queries (see postman collection) or create your own queries based on available data.
Representative patients are listed in the following table. Not all patients have genetic testing data. Several patients (e.g. HG00403, HG00406) have whole exome sequencing data; many patients (e.g. ABC456, HCC1143) have been studied for structural variants; some patients (e.g. HCC1143) have somatic data; there are patients with PGx star alleles (e.g. XYZ123) and HLA haplotypes (e.g. NB6TK328). Patient NA19238 is the mother, and patient NA19239 is the father of patient NA19240. Some patient data is based on build37 (e.g. HG02657), and some is based on build38 (e.g. CA12345). The find-study-metadata operation can be used to see what types of testing a patient has had.
To add a table, use three or more hyphens (---) to create each column’s header, and use pipes (|) to separate each column. For compatibility, you should also add a pipe on either end of the row.
| patientID | Sex | patientID | Sex | patientID | Sex |
|---|---|---|---|---|---|
| ABC123 | M | m123 | M | NA19240 | F |
| ABC456 | M | NA18498 | M | NA19247 | F |
| ABC789 | F | NA18499 | F | NA19256 | M |
| CA12345 | M | NA18870 | F | NB6TK328 | F |
| HCC1143 | F | NA18871 | M | NB6TK329 | F |
| HG00403 | M | NA19190 | F | XYZ123 | F |
| HG00406 | M | NA19210 | M | XYZ234 | F |
| HG02657 | M | NA19238 | F | XYZ345 | F |
| huC30902 | M | NA19239 | M | --- | --- |
Knowledge data is used to dynamically compute diagnostic and therapeutic implications of genetic variants.
Clinvar knowledge is based on a Nov 2021 extract. The Clinvar snapshop is limited to ACMG genes. Conditions are coded with Medgen codes (codeSystem='https://www.ncbi.nlm.nih.gov/medgen')
PharmGKB knowledge is based on a Dec 2021 extract. The PharmKGB snapshot is limited to CPIC Level A star alleles in CYP2B6, CYP2C9, CYP2C19, CYP2D6, CYP3A5, NUDT15, SLCO1B1, TPMP, UGT1A1. Medications are coded with RxNorm ingredient codes (codeSystem='http://www.nlm.nih.gov/research/umls/rxnorm')
CIViC knowledge is based on a Dec 2021 extract. The CIViC snapshot is limited to simple variants. Conditions are coded with Disease Ontology codes (codeSystem='https://disease-ontology.org'). Medications are coded with RxNorm ingredient codes (codeSystem='http://www.nlm.nih.gov/research/umls/rxnorm')
This section describes additional APIs provided as part of the reference implementation that are not part of FHIR Genomics Operations.
This utility returns genomic feature coordinates and other annotations. All data are from NCBI Human Genome Resources. For chromosomes, build 37 and build 38 reference sequences are returned. For genes, genomic coordinates are returned, along with a list of transcripts. MANE transcript is flagged. For transcripts, genomic coordinates are returned, along with the gene name and composite exons, along with exon coordinates. For proteins, the corresponding transcript is returned.