Version 2.78

Status Information

Status
TRIAL

Term Description

The method used for analyzing chromosome structural variation, such as FISH, arrCGH, sequencing, and MLPA.
Source: Regenstrief LOINC

Fully-Specified Name

Component
Structural variant analysis method
Property
Type
Time
Pt
System
^Patient
Scale
Nom
Method
*

Additional Names

Short Name
Struct var analysis method
Display Name
Structural variant analysis method Nom
Consumer Name Alpha Get Info
Structural variant analysis method

Example Answer List: LL4048-6

Source: National Center for Biotechnology Information (NCBI) ClinVar
Answer Code Score Answer ID
Sequencing

Usually refers to high-throughput, next-generation sequencing methods, although can also refer to traditional capillary-based Sanger sequencing. Advantages: a lot of data at little cost. Disadvantages: short read length; high error rates. Next-Gen Sequencing is currently the most popular method for generating genetic data in general, and for detecting both single-nucleotide and structural variation.

LA26398-0
Oligo aCGH

The use of dense arrays of oligonucleotides deposited on glass slides, subjected to fluorescent Comparative Genomic Hybridization. Probe Intensity Analysis (see Analysis Types below) use test:reference ratios to detect copy number changes. Advantages: one can "scan" an entire genome very rapidly; high sensitivity. Disadvantages: cannot detect inversions or complex rearrangements; cannot determine genomic location of copy number gains (and in some cases losses); resolution not as high as sequencing. Another very popular method for detecting structural variation.

LA26399-8
SNP array

Originally designed to genotype single nucleotide variation in a massively parallel manner, SNP arrays have many of the same advantages and disadvantages as oligonucleotide arrays. However, they have the added benefit of enabling statistical analysis of allelic inhertance patterns between samples from related individuals, thus adding to their ability to detect and describe de novo structural variation events.

LA26400-4
BAC aCGH

BAC arrays pre-date oligo arrays and use as probes replicated bacterial artificial chromosome DNA (average insert length ~150 kilobases) and comparative genomic hybridization between a reference and a test sample. Disadvantages: labor-intensive to produce; very low resolution. Not typically in current use.

LA26401-2
Curated

The manual aggregation and curation of independently reported structural variants from several online resources. These often clinically important variants would not otherwise find their way into a public catalogue of important structural variation. Examples include variants sporadically reported in the scientific literature, or stored in clinically-oriented online resources (e.g., OMIM) or in locus-specific databases (LSDBs).

LA26402-0
Digital array

The use of microfluidics and highly parallel real-time PCR to digitally count copy number in a sample. Similarly to other array-based techniques, uses comparative genomic hybridization. Rarely used, usually as a validation method.

LA26403-8
FISH

The use of multiple, differentially colored fluorescently-labeled probes (usu. fosmids, cosmids, or BACs) hybridized to a chromosome spread to detect copy number and position of target loci. Advantages: gives unambiuous relative positional information, can detect balanced and unbalanced translocations. Disadvantages: very low resolution, low throughput, labor intensive.

LA26404-6
Gene expression array

Similar to other array-based methods, except probes represent transcribed regions rather than the entire genome; therefore, subsequent intensity analysis reflects changes in gene expression which do not necessarily reflect changes in genomic DNA. Advantages: good for identifying possible gene deletions as a by-product of a gene expression experiment. Disadvantages: reduction or loss of signal does not necessarily indicate gene deletion - results must be followed up with more experiments.

LA26405-3
Karyotyping

May refer to any of several methods involving preparation of chromosome spreads and capable of detecting cytogenetic changes under a microscope. Examples are G-banding and fluorescence-based FISH, or chromosome "painting."

LA26406-1
MAPH

Multiplex Amplifiable Probe Hybridization; based on the quantitative recovery of short amplifiable probes after hybridization to genomic DNA. Advantages: good at detecting specific deletions in clinical samples; potential for high throughput. Rarely used.

LA26407-9
MALDI-TOF

MALDI-TOF mass spectroscopy of allele-specific primer extension products. Can be used to determine allele dosage ratios at specific loci in samples with heterozygous genotypes. Used rarely, as a validation method.

LA26408-7
Merging LA26808-8
Multiple complete digestion

Fosmids or other library inserts are fully digested with multiple restriction enzymes, and the resulting restriction pattern is compared to what is expected based on a reference. Used rarely, as a validation method.

LA26414-5
MLPA

Multiplex Ligation-dependent Probe Amplification; fluorescence- and capillary-based detection of copy number changes at specific loci using multiplex PCR. Advantages: low cost; not labor-intensive; excellent for detecting specific small copy number changes like exon duplications and deletions.

LA26415-2
Optical mapping

An integrated set of methods and analyses which involve stretching DNA into a single filament, immobilizing it on a charged surface, complete digestion with a single restriction enzyme, optical observation of the resulting restriction pattern, and comparison of results against the expected restriction pattern based on a reference genome. Advantages: ability to detect location and nature of insertions, deletions, and inversions. Disadvantages: highly specialized; cannot alone determine the sequence content or genomic origin of abberant events.

LA26417-8
PCR

The use of polymerase chain reaction technology to determine the presence or absence of a specified genomic locus. Advantages: easy; quick; inexpensive. Disadvantages: low throughput; low resolution. Typically used to genotype specific loci of interest.

LA26418-6
qPCR (real-time PCR)

Similar to PCR but fluorescence-based and able to detect copy number with some degree of accuracy.

LA26419-4
ROMA

Representational Oligonucleotide Microarray Analysis. Same as oligo aCGH except restriction digest and PCR amplification are applied to samples to reduce genomic complexity and thereby increase hybridization efficiency.

LA26420-2
Denaturing high-pressure liquid chromatography (DHPLC) LA26809-6
DNA hybridization LA26810-4
Computational analysis LA26811-2
Single-stranded conformational polymorphism (SSCP) LA26812-0
Restriction fragment length polymorphism (RFLP) LA26813-8

Basic Attributes

Class
MOLPATH
Type
Laboratory
First Released
Version 2.56
Last Updated
Version 2.58
Order vs. Observation
Observation

Member of these Panels

LOINC Long Common Name
81247-9 Master HL7 genetic variant reporting panel

Language Variants Get Info

Tag Language Translation
es-ES Spanish (Spain) Métodos de análisis de la variante estrucutral:Tipo:Punto temporal:^paciente:Nom:*
es-MX Spanish (Mexico) Método de análisis de variantes estructurales:Tipo:Punto temporal:^ Paciente:Nominal:*
fr-FR French (France) Variant structurel méthode d'analyse:Type:Ponctuel:Patient:Résultat nominal:
it-IT Italian (Italy) Metodo di analisi della variante strutturale:Tipo:Pt:^Paziente:Nom:*
Synonyms: Metodo di analisi Patologia molecolare paziente Punto nel tempo (episodio)
zh-CN Chinese (China) 结构变异分析方法:类型:时间点:^患者:名义型:*
Synonyms: 分子病理学;分子病理学试验 分类型应答;分类型结果;名义性;名称型;名词型;名词性;标称性;没有自然次序的名义型或分类型应答 医疗服务对象;客户;病人;病患;病号;超系统 - 病人 型 方;法;办法;方式 时刻;随机;随意;瞬间 结构性变异;结构性遗传性变异(遗传变异、基因变异、传性变型、遗传变异体、基因变异体) 结构性变异分析方法;结构性遗传性变异(遗传变异、基因变异、传性变型、遗传变异体、基因变异体)分析方法

LOINC Terminology Service (API) using HL7® FHIR® Get Info

CodeSystem lookup
https://fhir.loinc.org/CodeSystem/$lookup?system=http://loinc.org&code=81304-8