Clinical Genomics Resource Incubator
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Clinical Genomics Resource Incubator, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 0.1.0-ci-build built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/cg-incubator/ and changes regularly. See the Directory of published versions

CodeSystem: Genomic Study Method Type (Experimental)

Official URL: http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-methodtype Version: 0.1.0-ci-build
Standards status: Draft Draft as of 2022-08-16 Maturity Level: 1 Computable Name: GenomicStudyMethodType
Other Identifiers: OID:2.16.840.1.113883.4.642.4.1979

The method type of the GenomicStudy analysis. These method types and relevant codes were pulled from National Library of Medicine-Genetic Testing Registry (NCBI-GTR) values of describing different testing methods on various levels: major method category, method category, and primary methodology

This Code system is referenced in the definition of the following value sets:

Last updated: 2022-08-16 16:49:24-0500

Profile: Shareable CodeSystem

This case-sensitive code system http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-methodtype defines the following codes:

CodeDisplayDefinition
biochemical-genetics Biochemical Genetics Analysis of biochemical compounds and pathways to detect genetic metabolic disorders.
cytogenetics Cytogenetics Study of chromosome structure and number using microscopy-based methods.
molecular-genetics Molecular Genetics Analysis of DNA and genes using molecular techniques to identify variations and mutations.
analyte Analyte Analysis of biological analytes to detect genetic disorders.
chromosome-breakage-studies Chromosome breakage studies Tests to assess chromosome stability and fragility, often used to detect DNA repair disorders.
deletion-duplication-analysis Deletion/duplication analysis Detection of deletions and duplications in DNA sequences.
detection-of-homozygosity Detection of homozygosity Identification of homozygous regions in the genome.
enzyme-assay Enzyme assay Measurement of enzyme activity to detect genetic metabolic disorders.
fish-interphase FISH-interphase Fluorescence in situ hybridization performed during interphase of the cell cycle.
fish-metaphase FISH-metaphase Fluorescence in situ hybridization performed during metaphase of the cell cycle.
flow-cytometry Flow cytometry Analysis of cells using flow cytometry to assess genetic disorders.
fish Fluorescence in situ hybridization (FISH) Visualization of specific DNA sequences using fluorescent probes.
immunohistochemistry Immunohistochemistry Detection of antigens in tissue samples using antibodies.
karyotyping Karyotyping Visual analysis of chromosome structure and number in metaphase cells.
linkage-analysis Linkage analysis Analysis of genetic markers to identify disease-associated variants in families.
methylation-analysis Methylation analysis Detection of DNA methylation patterns to assess epigenetic modifications.
msi Microsatellite instability testing (MSI) Detection of microsatellite instability to assess DNA mismatch repair function.
m-fish Multicolor FISH (M-FISH) Multiple fluorescent in situ hybridization using multiple probes and colors simultaneously.
mutation-scanning-of-select-exons Mutation scanning of select exons Screening for mutations in specific exons of targeted genes.
mutation-scanning-of-the-entire-coding-region Mutation scanning of the entire coding region Comprehensive screening for mutations throughout the entire coding region of a gene.
protein-analysis Protein analysis Analysis of protein structure and function to detect genetic disorders affecting protein.
protein-expression Protein expression Measurement of protein expression levels to assess genetic effects on protein production.
rna-analysis RNA analysis Analysis of RNA sequences and expression to detect genetic disorders.
sequence-analysis-of-select-exons Sequence analysis of select exons DNA sequencing of specific exons to identify mutations.
sequence-analysis-of-the-entire-coding-region Sequence analysis of the entire coding region Comprehensive DNA sequencing of the entire coding region of a gene.
sister-chromatid-exchange Sister chromatid exchange Assessment of sister chromatid exchange as an indicator of DNA damage and repair.
targeted-variant-analysis Targeted variant analysis Sequencing or genotyping of specific, pre-selected genetic variants.
udp Uniparental disomy study (UPD) Detection of regions where both chromosomes are inherited from a single parent.
aspe Allele-specific primer extension (ASPE) Genotyping method using allele-specific primers to identify genetic variants.
alternative-splicing-detection Alternative splicing detection Detection and analysis of alternative splicing patterns in RNA.
bi-directional-sanger-sequence-analysis Bi-directional Sanger Sequence Analysis DNA sequencing using Sanger method in both forward and reverse directions.
c-banding C-banding Chromosome banding technique visualizing constitutive heterochromatin.
cia Chemiluminescent Immunoassay (CIA) Immunoassay detecting antigens using chemiluminescent reaction.
chromatin-immunoprecipitation-on-chip Chromatin Immunoprecipitation on ChIP ChIP-on-chip analysis combining chromatin immunoprecipitation with microarray.
comparative-genomic-hybridization Comparative Genomic Hybridization Detection of copy number variations by comparison of test and control DNA.
damid DamID DNA Adenine Methyltransferase Identification for mapping protein-DNA interactions.
digital-virtual-karyotyping Digital / Virtual karyotyping Computer-based analysis of chromosome patterns and abnormalities.
digital-microfluidic-microspheres Digital microfluidic microspheres Microfluidic technology using digital control for genetic analysis.
enzymatic-levels Enzymatic levels Measurement of enzyme levels in biological samples.
enzyme-activity Enzyme activity Measurement of enzyme activity levels in biological samples.
elisa Enzyme-Linked Immunosorbent Assays (ELISA) Immunoassay for detecting antigens using enzyme-linked antibodies.
fluorometry Fluorometry Measurement of fluorescence intensity to quantify biological molecules.
fusion-genes-microarrays Fusion genes microarrays Microarray-based detection of gene fusion events.
g-banding G-banding Giemsa staining chromosome banding technique visualizing chromosome structure.
gc-ms Gas chromatography mass spectrometry (GC-MS) Technique combining gas chromatography with mass spectrometry for chemical compound separation and identification.
gene-expression-profiling Gene expression profiling Analysis of gene expression patterns using various molecular techniques.
gene-id GeneID Identification of genes through sequence comparison or database lookup.
gold-nanoparticle-probe-technology Gold nanoparticle probe technology Molecular detection technique using gold nanoparticles as probes.
hplc High-performance liquid chromatography (HPLC) Separation and analysis technique using high-pressure liquid chromatography.
lc-ms Liquid chromatography mass spectrometry (LC-MS) Combined technique using liquid chromatography followed by mass spectrometry.
lc-ms-ms Liquid chromatography-tandem mass spectrometry (LC-MS/MS) Laboratory technique using liquid chromatography with tandem mass spectrometry.
metabolite-levels Metabolite levels Measurement of metabolite concentrations in biological samples.
methylation-specific-pcr Methylation-specific PCR PCR-based technique detecting DNA methylation patterns at specific loci.
microarray Microarray Molecular technique using arrays of probes to detect DNA sequences or expression levels.
mlpa Multiplex Ligation-dependent Probe Amplification (MLPA) Technique for detecting copy number variations and point mutations.
ngs-mps Next-Generation (NGS)/Massively parallel sequencing (MPS) High-throughput sequencing technology for analyzing genetic variation.
ola Oligonucleotide Ligation Assay (OLA) DNA sequence detection method using complementary oligonucleotide ligation.
oligonucleotide-hybridization-based-dna-sequencing Oligonucleotide hybridization-based DNA sequencing DNA sequencing using hybridization with oligonucleotide probes.
other Other Other genetic testing method not listed in this code system.
pcr PCR Polymerase Chain Reaction for amplifying and detecting DNA sequences.
pcr-with-allele-specific-hybridization PCR with allele specific hybridization PCR technique combined with allele-specific probe hybridization for variant detection.
pcr-rflp-with-southern-hybridization PCR-RFLP with Southern hybridization Combination of PCR-RFLP and Southern blot analysis for genetic variation detection.
protein-truncation-test Protein truncation test Molecular technique detecting premature stop codons and truncated proteins.
pyrosequencing Pyrosequencing DNA sequencing method based on detection of pyrophosphate release during nucleotide incorporation.
q-banding Q-banding Quinacrine staining chromosome banding technique using fluorescent dye.
qpcr Quantitative PCR (qPCR) Real-time PCR technique for quantifying DNA or RNA sequences.
r-banding R-banding Reverse chromosome banding technique visualizing reverse of normal G-banding pattern.
rflp RFLP Restriction Fragment Length Polymorphism - technique detecting DNA variations via restriction mapping.
rt-lamp RT-LAMP Reverse transcription Loop-mediated Isothermal Amplification for RNA detection.
rt-pcr RT-PCR Reverse transcription PCR for detecting and amplifying RNA sequences.
rt-pcr-with-gel-analysis RT-PCR with gel analysis RT-PCR product analysis using gel electrophoresis for visualization and sizing.
rt-qpcr RT-qPCR Real-time reverse transcription PCR for quantitative RNA detection.
snp-detection SNP Detection Detection of single nucleotide polymorphisms through molecular testing.
silver-staining Silver staining Staining technique used in protein and DNA analysis for visualization.
sky Spectral karyotyping (SKY) Fluorescence in situ hybridization allowing simultaneous visualization of all chromosomes.
t-banding T-banding T-banding chromosome technique visualizing telomeres through staining.
ms-ms Tandem mass spectrometry (MS/MS) Tandem mass spectrometry technique for analyzing molecular structure and mass.
tetra-nucleotide-repeat-by-pcr-or-southern-blot Tetra-nucleotide repeat by PCR or Southern Blot Detection of tetra-nucleotide repeat expansions using PCR or Southern blot analysis.
tiling-arrays Tiling Arrays Microarray technology using overlapping probes to analyze genomic regions.
trinucleotide-repeat-by-pcr-or-southern-blot Trinucleotide repeat by PCR or Southern Blot Detection of trinucleotide repeat expansions using PCR or Southern blot analysis.
uni-directional-sanger-sequencing Uni-directional Sanger sequencing One-directional Sanger sequencing method for DNA sequence determination.

Description of the above table(s).