{ "resourceType": "CodeSystem", "id": "genomicstudy-methodtype", "meta": { "lastUpdated": "2023-03-25T23:21:02-05:00", "profile": [ "http://hl7.org/fhir/StructureDefinition/shareablecodesystem" ] }, "text": { "status": "generated", "div": "

This code system http://hl7.org/fhir/genomicstudy-methodtype defines the following codes:

CodeDisplay
biochemical-genetics Biochemical Genetics
cytogenetics Cytogenetics
molecular-genetics Molecular Genetics
analyte Analyte
chromosome-breakage-studies Chromosome breakage studies
deletion-duplication-analysis Deletion/duplication analysis
detection-of-homozygosity Detection of homozygosity
enzyme-assay Enzyme assay
fish-interphase FISH-interphase
fish-metaphase FISH-metaphase
flow-cytometry Flow cytometry
fish Fluorescence in situ hybridization (FISH)
immunohistochemistry Immunohistochemistry
karyotyping Karyotyping
linkage-analysis Linkage analysis
methylation-analysis Methylation analysis
msi Microsatellite instability testing (MSI)
m-fish Multicolor FISH (M-FISH)
mutation-scanning-of-select-exons Mutation scanning of select exons
mutation-scanning-of-the-entire-coding-region Mutation scanning of the entire coding region
protein-analysis Protein analysis
protein-expression Protein expression
rna-analysis RNA analysis
sequence-analysis-of-select-exons Sequence analysis of select exons
sequence-analysis-of-the-entire-coding-region Sequence analysis of the entire coding region
sister-chromatid-exchange Sister chromatid exchange
targeted-variant-analysis Targeted variant analysis
udp Uniparental disomy study (UPD)
aspe Allele-specific primer extension (ASPE)
alternative-splicing-detection Alternative splicing detection
bi-directional-sanger-sequence-analysis Bi-directional Sanger Sequence Analysis
c-banding C-banding
cia Chemiluminescent Immunoassay (CIA)
chromatin-immunoprecipitation-on-chip Chromatin Immunoprecipitation on ChIP
comparative-genomic-hybridization Comparative Genomic Hybridization
damid DamID
digital-virtual-karyotyping Digital / Virtual karyotyping
digital-microfluidic-microspheres Digital microfluidic microspheres
enzymatic-levels Enzymatic levels
enzyme-activity Enzyme activity
elisa Enzyme-Linked Immunosorbent Assays (ELISA)
fluorometry Fluorometry
fusion-genes-microarrays Fusion genes microarrays
g-banding G-banding
gc-ms Gas chromatography–mass spectrometry (GC-MS)
gene-expression-profiling Gene expression profiling
gene-id GeneID
gold-nanoparticle-probe-technology Gold nanoparticle probe technology
hplc High-performance liquid chromatography (HPLC)
lc-ms Liquid chromatography mass spectrometry (LC-MS)
lc-ms-ms Liquid chromatography-tandem mass spectrometry (LC-MS/MS)
metabolite-levels Metabolite levels
methylation-specific-pcr Methylation-specific PCR
microarray Microarray
mlpa Multiplex Ligation-dependent Probe Amplification (MLPA)
ngs-mps Next-Generation (NGS)/Massively parallel sequencing (MPS)
ola Oligonucleotide Ligation Assay (OLA)
oligonucleotide-hybridization-based-dna-sequencing Oligonucleotide hybridization-based DNA sequencing
other Other
pcr PCR
pcr-with-allele-specific-hybridization PCR with allele specific hybridization
pcr-rflp-with-southern-hybridization PCR-RFLP with Southern hybridization
protein-truncation-test Protein truncation test
pyrosequencing Pyrosequencing
q-banding Q-banding
qpcr Quantitative PCR (qPCR)
r-banding R-banding
rflp RFLP
rt-lamp RT-LAMP
rt-pcr RT-PCR
rt-pcr-with-gel-analysis RT-PCR with gel analysis
rt-qpcr RT-qPCR
snp-detection SNP Detection
silver-staining Silver staining
sky Spectral karyotyping (SKY)
t-banding T-banding
ms-ms Tandem mass spectrometry (MS/MS)
tetra-nucleotide-repeat-by-pcr-or-southern-blot Tetra-nucleotide repeat by PCR or Southern Blot
tiling-arrays Tiling Arrays
trinucleotide-repeat-by-pcr-or-southern-blot Trinucleotide repeat by PCR or Southern Blot
uni-directional-sanger-sequencing Uni-directional Sanger sequencing
" }, "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-wg", "valueCode": "cg" }, { "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status", "valueCode": "trial-use" }, { "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fmm", "valueInteger": 1 } ], "url": "http://hl7.org/fhir/genomicstudy-methodtype", "identifier": [ { "system": "urn:ietf:rfc:3986", "value": "urn:oid:2.16.840.1.113883.4.642.4.1979" } ], "version": "5.0.0", "name": "GenomicStudyMethodType", "title": "Genomic Study Method Type", "status": "active", "experimental": true, "date": "2022-08-16T16:49:24-05:00", "publisher": "HL7 (FHIR Project)", "contact": [ { "telecom": [ { "system": "url", "value": "http://hl7.org/fhir" }, { "system": "email", "value": "fhir@lists.hl7.org" } ] } ], "description": "The method type of the GenomicStudy analysis. These method types and relevant codes were pulled from [National Library of Medicine-Genetic Testing Registry](https://www.ncbi.nlm.nih.gov/gtr/) (NCBI-GTR) values of describing different testing methods on various levels: [major method category](https://ftp.ncbi.nlm.nih.gov/pub/GTR/standard_terms/Major_method_category.txt), [method category](https://ftp.ncbi.nlm.nih.gov/pub/GTR/standard_terms/Method_category.txt), and [primary methodology](https://ftp.ncbi.nlm.nih.gov/pub/GTR/standard_terms/Primary_test_methodology.txt)", "jurisdiction": [ { "coding": [ { "system": "http://unstats.un.org/unsd/methods/m49/m49.htm", "code": "001", "display": "World" } ] } ], "caseSensitive": true, "valueSet": "http://hl7.org/fhir/ValueSet/genomicstudy-methodtype", "content": "complete", "concept": [ { "code": "biochemical-genetics", "display": "Biochemical Genetics" }, { "code": "cytogenetics", "display": "Cytogenetics" }, { "code": "molecular-genetics", "display": "Molecular Genetics" }, { "code": "analyte", "display": "Analyte" }, { "code": "chromosome-breakage-studies", "display": "Chromosome breakage studies" }, { "code": "deletion-duplication-analysis", "display": "Deletion/duplication analysis" }, { "code": "detection-of-homozygosity", "display": "Detection of homozygosity" }, { "code": "enzyme-assay", "display": "Enzyme assay" }, { "code": "fish-interphase", "display": "FISH-interphase" }, { "code": "fish-metaphase", "display": "FISH-metaphase" }, { "code": "flow-cytometry", "display": "Flow cytometry" }, { "code": "fish", "display": "Fluorescence in situ hybridization (FISH)" }, { "code": "immunohistochemistry", "display": "Immunohistochemistry" }, { "code": "karyotyping", "display": "Karyotyping" }, { "code": "linkage-analysis", "display": "Linkage analysis" }, { "code": "methylation-analysis", "display": "Methylation analysis" }, { "code": "msi", "display": "Microsatellite instability testing (MSI)" }, { "code": "m-fish", "display": "Multicolor FISH (M-FISH)" }, { "code": "mutation-scanning-of-select-exons", "display": "Mutation scanning of select exons" }, { "code": "mutation-scanning-of-the-entire-coding-region", "display": "Mutation scanning of the entire coding region" }, { "code": "protein-analysis", "display": "Protein analysis" }, { "code": "protein-expression", "display": "Protein expression" }, { "code": "rna-analysis", "display": "RNA analysis" }, { "code": "sequence-analysis-of-select-exons", "display": "Sequence analysis of select exons" }, { "code": "sequence-analysis-of-the-entire-coding-region", "display": "Sequence analysis of the entire coding region" }, { "code": "sister-chromatid-exchange", "display": "Sister chromatid exchange" }, { "code": "targeted-variant-analysis", "display": "Targeted variant analysis" }, { "code": "udp", "display": "Uniparental disomy study (UPD)" }, { "code": "aspe", "display": "Allele-specific primer extension (ASPE)" }, { "code": "alternative-splicing-detection", "display": "Alternative splicing detection" }, { "code": "bi-directional-sanger-sequence-analysis", "display": "Bi-directional Sanger Sequence Analysis" }, { "code": "c-banding", "display": "C-banding" }, { "code": "cia", "display": "Chemiluminescent Immunoassay (CIA)" }, { "code": "chromatin-immunoprecipitation-on-chip", "display": "Chromatin Immunoprecipitation on ChIP" }, { "code": "comparative-genomic-hybridization", "display": "Comparative Genomic Hybridization" }, { "code": "damid", "display": "DamID" }, { "code": "digital-virtual-karyotyping", "display": "Digital / Virtual karyotyping" }, { "code": "digital-microfluidic-microspheres", "display": "Digital microfluidic microspheres" }, { "code": "enzymatic-levels", "display": "Enzymatic levels" }, { "code": "enzyme-activity", "display": "Enzyme activity" }, { "code": "elisa", "display": "Enzyme-Linked Immunosorbent Assays (ELISA)" }, { "code": "fluorometry", "display": "Fluorometry" }, { "code": "fusion-genes-microarrays", "display": "Fusion genes microarrays" }, { "code": "g-banding", "display": "G-banding" }, { "code": "gc-ms", "display": "Gas chromatography–mass spectrometry (GC-MS)" }, { "code": "gene-expression-profiling", "display": "Gene expression profiling" }, { "code": "gene-id", "display": "GeneID" }, { "code": "gold-nanoparticle-probe-technology", "display": "Gold nanoparticle probe technology" }, { "code": "hplc", "display": "High-performance liquid chromatography (HPLC)" }, { "code": "lc-ms", "display": "Liquid chromatography mass spectrometry (LC-MS)" }, { "code": "lc-ms-ms", "display": "Liquid chromatography-tandem mass spectrometry (LC-MS/MS)" }, { "code": "metabolite-levels", "display": "Metabolite levels" }, { "code": "methylation-specific-pcr", "display": "Methylation-specific PCR" }, { "code": "microarray", "display": "Microarray" }, { "code": "mlpa", "display": "Multiplex Ligation-dependent Probe Amplification (MLPA)" }, { "code": "ngs-mps", "display": "Next-Generation (NGS)/Massively parallel sequencing (MPS)" }, { "code": "ola", "display": "Oligonucleotide Ligation Assay (OLA)" }, { "code": "oligonucleotide-hybridization-based-dna-sequencing", "display": "Oligonucleotide hybridization-based DNA sequencing" }, { "code": "other", "display": "Other" }, { "code": "pcr", "display": "PCR" }, { "code": "pcr-with-allele-specific-hybridization", "display": "PCR with allele specific hybridization" }, { "code": "pcr-rflp-with-southern-hybridization", "display": "PCR-RFLP with Southern hybridization" }, { "code": "protein-truncation-test", "display": "Protein truncation test" }, { "code": "pyrosequencing", "display": "Pyrosequencing" }, { "code": "q-banding", "display": "Q-banding" }, { "code": "qpcr", "display": "Quantitative PCR (qPCR)" }, { "code": "r-banding", "display": "R-banding" }, { "code": "rflp", "display": "RFLP" }, { "code": "rt-lamp", "display": "RT-LAMP" }, { "code": "rt-pcr", "display": "RT-PCR" }, { "code": "rt-pcr-with-gel-analysis", "display": "RT-PCR with gel analysis" }, { "code": "rt-qpcr", "display": "RT-qPCR" }, { "code": "snp-detection", "display": "SNP Detection" }, { "code": "silver-staining", "display": "Silver staining" }, { "code": "sky", "display": "Spectral karyotyping (SKY)" }, { "code": "t-banding", "display": "T-banding" }, { "code": "ms-ms", "display": "Tandem mass spectrometry (MS/MS)" }, { "code": "tetra-nucleotide-repeat-by-pcr-or-southern-blot", "display": "Tetra-nucleotide repeat by PCR or Southern Blot" }, { "code": "tiling-arrays", "display": "Tiling Arrays" }, { "code": "trinucleotide-repeat-by-pcr-or-southern-blot", "display": "Trinucleotide repeat by PCR or Southern Blot" }, { "code": "uni-directional-sanger-sequencing", "display": "Uni-directional Sanger sequencing" } ] }