3.9 Molecular genetics LOINC naming

3.9.1 Introduction

Molecular pathology testing can be used for many purposes. In infectious disease testing to identify organisms and mutations in organisms; in genetic analysis to identify mutations including substitutions, deletions/insertions, frame shifts and trinucleotide repeats; to identify specific chromosomal translocation and clonality in leukemia and lymphomas; to identify various tumor associated genes and gene deletions; in paternity testing to determine the probability that a person is the parent of a child; and in forensic testing to determine the probability that a criminal is associated with genetic material he/she left as evidence.[[^25]]

LOINC term names follow the recommendations and nomenclature of other standards. As molecular genetic testing expands, we are evolving our naming conventions. Existing terms are being reviewed for compatibility with current naming conventions. An overall description of LOINC’s approach to naming molecular genetics tests can be found in the Deckard et al[[^26]] paper.

3.9.2 Brief review of molecular genetics terminology

For clarity, here we provide a brief introduction to some key genetics terminology. DNA consists of a series of nucleotides, nucleotides encode amino acids, and a string of amino acids forms a protein. There are four types of nucleotides (adenine, guanine, cytosine and thymine), and a sequence of three nucleotides that codes for one amino acid is called a codon. Codons are numbered from the first codon participating in the protein (in humans the codon for Methionine) starting with codon number 1. Locus refers to a specific DNA (or RNA) codon or the corresponding amino acid produced by this codon.

The string of DNA that codes for a protein is usually interrupted by DNA segments called introns, which do not contribute to the protein definition. The coding sequences of DNA between the introns are called exons. Linked together, the exons provide the instructions for creating the specific protein. Exons may be numbered e.g., exon 1, exon 2, etc. Exon numbers sometimes appear in the names of DNA mutations, but for a number of reasons, identifying codon locations relative to an exon is unreliable and we will try to avoid such nomenclature when possible in LOINC names.

The term “mutation” is usually applied to a genetic variant that causes a functional change in the gene and results in disease. Genetic changes that occur during the life of the patient such as tumor mutation are called somatic and those that are inherited are referred to as germ line. The nature of the specimen and the testing usually distinguishes these two, so it is not necessary to include this distinction in the test names.

Alleles refer to different forms of a gene and are distinguished at the phenotype level. The term allele is usually applied to a genetic variant that does not cause a disease.

3.9.3 Background on molecular genetics testing methods

The main laboratory methods used are Southern Blot, which applies hybridization to selected DNA “chopped up” by restriction enzymes, Northern Blot, which applies hybridization to all cellular RNA (which comes naturally in smaller segments), and Restriction Fragment Length Polymorphism (RFLP). RFLP depends on the Variable Number of Tandem Repeats (VNTR), which are normal, but specific variants of each person’s DNA. Southern Blot may be combined with RFLP to target mutations whose exact gene molecular chemistry is not known. For completeness sake, we mention Western Blot, which applies an analogous blot method to protein analysis.

In situ hybridization is a method that applies probes to intact tissue. The cellular patterns of the homologies can then be read microscopically. There are a variety of methods for detecting such in situ probes. One popular method is Fluorescent In-Situ Hybridization (FISH). This technique is analogous to an immune stain except that the molecular binding is based on DNA/RNA homologies instead of antigen-antibody binding.

DNA chips provide a radical new way to identify DNA and RNA sequences. In the patented AFYMETRIX® technique, the nucleoside chains are grown using lithography-like methods. Target DNA is tagged with a detector and “washed” over the chip in steps. The locations of the tags on the chip identify the DNA (RNA) in the sample.

Identity testing is used to identify relationships among people and has special complexity. In paternity testing, it can be helpful to have DNA from the child, the putative father and the mother when possible to distinguish the alleles that come from the father.

Forensic testing has special requirements of stringency and often mixes blood antigen testing with RFLP testing. The results are usually reported as a probability.

3.9.4 General molecular genetics naming rules

LOINC’s approach to naming tests makes use of established conventions. For naming genetic tests that target specific genetic variations, LOINC uses the Human Genome Organization (HUGO) Gene Nomenclature Committee’s (HGNC) terminology to name the gene(s) and Human Genome Variation Society’s (HGVS) syntax to name the variation(s) of interest.

HGVS provides seven types of prefixes to identify the difference types of reference sequences used in naming gene defects as described in the following table. As of LOINC release 2.66, LOINC has terms for the first four (p., c., g., m.).

The HGVS recommendations have evolved over time. In our early approach, we used the extant protein-based naming convention to get the following name for the commonest mutation causing cystic fibrosis:

CFTR gene.p.F508del:PrThr:Pt:Bld/Tiss:Ord:Molgen

For clarity’s sake, HGVS now prefers the three letter amino acid abbreviations over the single letter amino acid abbreviations we used in the above example.

We embrace the HGVS naming style for naming mutations at the amino acid level, but the world has not been consistently quick to adopt it. The old style, perhaps because of its brevity, persists. As we update existing codes to harmonize with current HGVS guidelines, we will make it easy for users to find our test names by including the old style as synonyms for the new style. Under the current HGVS rules, the above name would be:

CFTR gene.p.Phe508del:PrThr:Pt:Bld/Tiss:Ord:Molgen

Where we still report variants at the amino acid level, we use the nomenclature for human gene mutations proposed by Beaudet[[^27]] in the Component or in the LOINC Answer when the mutation is reported as an answer. A list of single and three letter amino acid codes are given in the following table.

HGVS has made other changes in naming style. Overall they now prefer describing the variant at the coding DNA level as nucleotide changes rather than at the protein level as amino acid changes. The above cystic fibrosis mutation would have the following coding DNA-based name:

CFTR gene.c.1521_1523del:PrThr:Pt:Bld/Tiss:Ord:Molgen

For the nucleotide changes, they have adjusted the syntax for representing a change from one nucleotide string to another as # String1>String2 rather than String1 # String2, where # is an integer representing the nucleotide position of the variation.

Another common cause of cystic fibrosis is a mutation that at the amino acid level would be named p.Gly551Asp with the new protein based naming convention, c.G1652A with the old DNA naming convention and c.1652G>A with the new coding DNA naming convention. (Realize, of course, that more than one nucleotide-level variation name can correspond to a single amino acid variation name.)

If clear guidelines are not in place for a given variant when a LOINC code is created, the familiar or common variant name may be used. LOINC will resort to using the disease name only when the gene has no name and/or the genetic defect is not yet fully specified. We will include the genetic disease name in the RELATEDNAMES2 field of the database when the disease name is not part of the Component. This allows users to easily find the LOINC term by the disease name as well.

3.9.4.1 Specimens in molecular genetics

Blood is the most common specimen for molecular pathology studies. Leukocytes, bone marrow, tumors, products of conception and forensic specimens also contain DNA and are important specimens. The System (specimen) used in the LOINC name for genetic testing will usually be Bld/Tiss since the distinction between these two specimens is rarely important to the result of a molecular pathology test. We have split this further to accommodate fetal specimens (Tiss^fetus). Other specimens include amniotic fluid, CVS, bone marrow, fixed tissue, and CSF.

3.9.4.2 Methods in molecular genetics

In general, we do not create separate variables for each kind of molecular genetics method (e.g., Southern Blot Northern Blot, PCR, restriction fragment length polymorphism (RFLP)) because the different methods do not provide significantly different results. Moreover, there are a plethora of minor method variants, and we would not be able to keep up with their proliferation. Therefore, instead we use a generic Method of Molgen (for molecular genetics method) to indicate that a result of the analysis is based on a molecular genetics method rather than some chemical or antigen method.

However, when results for a given molecular pathology technique are significantly different, we will distinguish the method. Examples of specific molecular pathology Methods in LOINC include fluorescent in situ hybridization (FISH), sequencing, multiplex ligation probe amplification (MLPA), and microarray comparative genomic hybridization (Microarray). For the LOINC 2.68 release, we added a new Method for Mate pair sequencing. It is unclear at this time whether this new Method produces results that are significantly different from older sequencing methods, and we may update the Method for these terms in the future based on new information.

3.9.4.3 Narrative and document-level reporting in molecular genetics

Bulk narrative reports in molecular pathology are often used to provide results for mutation analyses, without reporting any discrete coded answers. We discourage the use of this approach because it is not useful for automated analyses. Since these kinds of results often include some structured elements, we will use the Property Find and Scale Doc beginning with version 2.54. The Scale of Doc represents a collection of information (e.g. results contained in a report) that are either structured or unstructured. To assist with structured reporting, we will attach to these terms specific associated observations that could be used to send data in a structured format. With this approach, labs will still have the flexibility to send text reports. However, we encourage them to also report key data as structured results using the associated observation variables so that it is more easily understood by computers. We plan to use this model for newly created terms for molecular pathology tests and are contemplating the best approach for transitioning existing terms to this format over time.

3.9.4.4 Inferred phenotype and genotype

Beginning in version 2.66, we have LOINC terms for genotype and phenotype results that are derived from their respective phenotype or genotype analysis. For such concepts we include the word “inferred” in the Component. One example is a blood banking panel that is used to report whether or not an RBC antigen is expected to be present in a patient or donor sample based on molecular analysis of the corresponding gene, such as the presence of K Ag based on analysis of the KEL gene, for which the Component is K Ag inferred phenotype. The reverse example is an assay that reports the genotype for the APOL1 gene based on analysis of apolipoprotein L1 isoforms; for this term, the Component is APOL1 inferred genotype.

3.9.5 Infectious diseases

For information about molecular genetics in the field of infectious diseases, see Section 3.4.3.

3.9.6 Genetic conditions

3.9.6.1 Diagnostic assays for mutation analysis

We currently have at least four different styles for mutation analyses in LOINC:

1. Single mutation analysis: Diagnostic assays for the detection of a specific mutation or variant
2. Targeted mutation analysis: Diagnostic assays for a fixed set of the most common or important mutations
3. Known mutation analysis: Diagnostic assays for one or more mutations that have been previously identified in an affected family member
4. Full gene mutation analysis: Diagnostic assays usually done by sequencing of the entire coding region of a gene

3.9.6.1.1 Diagnostic assays for the detection of a specific mutation or variant

When looking for one mutation, use LOINC’s single mutation style of gene name followed by the specification of the nomenclature (p, g, c, or m) and the mutation name. A dot will separate the gene name and the mutation identifier:

<gene name> gene.<mutation nomenclature>.<mutation and its location>

For example, Factor V Leiden mutation would be represented as F5 gene.p.R506Q. Where “F5” identifies the gene, “gene” is a fixed part, “p” identifies the kind of mutation nomenclature (protein) and “R506Q” indicates that the amino acid arginine (R) is replaced by glutamine (Q) (see Table 19) at codon #506.

Some examples of fully specified LOINC names for tests of specific mutation are:

F5 gene.p.R506Q:PrThr:Pt:Bld/Tiss:Ord:Molgen

Synonyms: Factor V Leiden, Factor V resistance, APC resistance gene

HFE gene.p.C282Y:PrThr:Pt:Bld/Tiss:Ord:Molgen

Synonyms: HLA-H gene, hemochromatosis gene

CFTR gene.p.F508 del:PrThr:Pt:Bld/Tiss:Ord:Molgen

Synonyms: Cystic Fibrosis Transmembrane Regulator

As mentioned above, HGVS now recommends the three letter amino acid abbreviations over the single letter amino acid abbreviations. As existing codes are updated, we will add synonyms for the old style to make it easy for users to find our test names.

One type of testing procedure identifies a single mutation using two DNA probes: one for the normal locus and the other for the abnormal locus. When only the normal probe reacts, the laboratory reports “no mutation” or “wild type”. When both the normal and mutation probes react, the laboratory reports “heterozygous”. When only the mutation probe reacts it reports “homozygous”. Consequently, such single mutation testing produces one of three ordinal “answers”:

1. no mutation (wild type)
2. heterozygous mutation (the mutation found in one gene)
3. homozygous mutation (the mutation was found in both genes in the gene pair)

Specific testing such as this is only possible when the molecular pathology of the gene is very well known and only one defect is being reported.

Both document-level (Scale is Doc) and ordinal (Scale is Ord) codes are available in the LOINC database for single variant tests. In cases where more than one variant is tested, a nominal (Nom) Scale will be used. As mentioned above, we encourage the use of document-level codes for the order and overall result report, which can be used in conjunction with additional LOINC codes for reporting the discrete results.

Results for specific mutations or variants may also be reported as two separate observations: one observation reports the kind of mutation (allele) found in the first chromosome and another for reporting the kind of mutation for the paired chromosome. In this case, the identity of the allele is reported in the answer. For example:

APOE gene allele 1:Prid:Pt:Bld/Tiss:Nom:Molgen

Answers: E2, E3, or E4

APOE gene allele 2:Prid:Pt:Bld/Tiss:Nom:Molgen

Answers: E2, E3, or E4

3.9.6.1.2 Targeted mutation analysis

LOINC’s approach to represent gene mutation analysis for many genetic variations within one or more genes has had the following form:

<gene name> gene targeted mutation analysis:Find:Pt:Bld/Tiss:Doc:Molgen

For example:

CFTR gene targeted mutation analysis:Find:Pt:Bld/Tiss:Doc:Molgen

Synonyms: Cystic fibrosis transmembrane regulator

BRCA1 gene targeted mutation analysis:Find:Pt:Bld/Tiss:Doc:Molgen

Synonyms: breast cancer risk gene

For each such targeted mutation analysis, we recommend reporting the mutations that were tested using an additional LOINC code, such as LOINC 36908-2 (Gene mutations tested for) or gene-specific companion LOINC observation codes with the words “mutations tested for”:

<Gene name or disease name> gene mutations tested for:Prid:Pt:Bld/Tiss:Nom:Molgen

For example:

CFTR gene mutations tested for:Prid:Pt:Bld/Tiss:Nom:Molgen

Example answers: “Delta F508”, “G542X”, “R553X”, “W1282X”, “N1303K”, etc.

The additional LOINC code is needed for reporting the mutation(s) that could have been found in a given analysis so that clinicians can know what was looked for when no abnormalities were found.

The above gene mutation analysis terms could be used for ordering or reporting the results of a given targeted mutation analysis. Both document-level (Scale is Doc) and nominal (Scale is Nom) codes are available in the LOINC database. As mentioned above, we encourage the use of document-level codes for the order and overall result report, which can be used in conjunction with additional LOINC codes for reporting the discrete results. Nominal results for such an analyses could be: 1) no pathologic mutations found or 2) a list of individual mutations/variations found. When reporting discrete mutations as results, we propose using the HGVS nomenclature and including (in parentheses) the historic versions of the mutation names when such names exist.

3.9.6.1.3 Known mutation analysis

The first two approaches are commonly called “targeted” mutation analyses, or looking for specific mutations within a given gene. Labs may offer testing for both targeted mutation analysis and analysis for known familial mutations. Known familial mutations are those previously identified within an affected family member. To distinguish these testing approaches, LOINC further defines testing for known familial mutations:

<Gene name> gene mutation analysis limited to known familial mutations:Find:Pt:Bld/Tiss:Doc:Molgen

For example:

TNFRSF13B gene mutation analysis limited to known familial mutations:Find:Pt:Bld/Tiss:Doc:Molgen

Since testing may involve more than one known mutation, especially for autosomal recessive conditions, LOINC uses the plural form of mutations in the Component. However, these terms also refer to testing for only one known familial mutation.

3.9.6.1.4 Full gene mutation analysis

To describe mutation analysis by sequencing of the entire coding (and possibly non-coding) region of the gene, we use:

TNFRSF13B gene full mutation analysis:Find:Pt:Bld/Tiss:Doc:Sequencing

Here, we include the Method of sequencing since this is a technique commonly used to identify mutations with the entire coding region of a gene.

3.9.6.2 Diagnostic assays for large deletions and/or duplications

Detection of larger (>50 bp) genomic duplications or deletions is done by various techniques, including multiplex ligation-dependent probe amplifications (MLPA) and array-based comparative genomic hybridization (arrCGH). MLPA and aarCGH techniques detect gene dosage. To describe testing for large deletions and/or duplications (insertions) within a gene, we use:

LDLR gene deletion+duplication:Find:Pt:Bld/Tiss:Doc:MLPA

In this case, we specify the Method of multiplex ligation-dependent probe amplification (MLPA). MLPA is a common technique used to detect gene dosage of genomic deletions and duplications (e.g. one or more entire exons) and determine gene copy number.

3.9.6.3 Trinucleotide repeats

A number of diseases, most of which manifest as neurologic disorders are caused by excessive repeats of specific trinucleotides, and the age of onset of the disease is inversely proportional to the number of excess repeats. Examples of these disorders include:

• Fragile X syndrome
• Huntington disease
• Spinocerebellar ataxia (SCA1)

We name the Component of these terms by the gene when the gene is well defined or the disease, and the name of the trinucleotide that repeats plus the word repeats.

<disease or gene name>.<trinucleotide> repeats

For example, Huntington disease would be represented as follows:

HTT gene.CAG repeats

Examples of some fully specified LOINC names are:

FRAXE gene.CGG repeats:PrThr:Pt:Bld/Tiss:Ord:Molgen

Synonym: Fragile x syndrome

HTT gene.CAG repeats:PrThr:Pt:Bld/Tiss:Ord:Molgen

Synonyms: Huntington Disease, It15, HD, Huntington Chorea

Spinocerebellar ataxia genes.CAG repeats:PrThr:Pt:Bld/Tiss:Ord:Molgen

DMPK gene.CTG repeats:PrThr:Pt:Bld/Tiss:Ord:Molgen

Synonym: Myotonic Dystrophy

These are usually reported “not expanded”, “indeterminate” or “expanded”, so the Scale is Ord.

When the actual number of trinucleotide repeats is reported, the Property is entitic number (EntNum) and the Scale is quantitative (Qn), and separate results are reported for each allele. Examples include:

HTT gene allele 1.CAG repeats:EntNum:Pt:Bld/Tiss:Qn:Molgen
HTT gene allele 2.CAG repeats:EntNum:Pt:Bld/Tiss:Qn:Molgen

DMPK gene allele 1.CTG repeats:EntNum:Pt:Bld/Tiss:Qn:Molgen
DMPK gene allele 2.CTG repeats:EntNum:Pt:Bld/Tiss:Qn:Molgen

3.9.6.4 Hematopathology gene re-arrangement

Immune cells have an innate genetic variability due to rearrangement. The unique rearrangement can be used to identify the development of a clone of one cell type as occurs in many lymph cell tumors (e.g., lymphoma). We use the following format to identify clonal excess.

Immunoglobulin heavy chain gene rearrangements:Arb:Pt:Bld/Tiss:Ord:Molgen

Immunoglobulin kappa light chain gene rearrangements:Arb:Pt:Bld/Tiss:Ord:Molgen

Immunoglobulin lambda light chain gene rearrangements:Arb:Pt:Bld/Tiss:Ord:Molgen

TCRB gene rearrangements:Arb:Pt:Bld/Tiss:Ord:Molgen

Synonym: T cell receptor beta chain

TCRD gene rearrangements:Arb:Pt:Bld/Tiss:Ord:Molgen

Synonym: T cell receptor delta chain

TCRG gene rearrangements:Arb:Pt:Bld/Tiss:Ord:Molgen

Synonym: T cell receptor gamma chain

These would be reported as “clonal” or “not clonal”.

3.9.6.5 Chromosomal alterations: translocations, deletions, and inversions

LOINC nomenclature follows the International System for Human Cytogenetic Nomenclature (ISCN) guidelines when describing chromosomal alterations, including translocations, large deletions and inversions. Tests to detect fused genes or transcripts (RNA, cDNA) due to a chromosomal alteration are designated as follows:

t(<Chromosome of breakpoint gene 1>;<Chromosome of breakpoint gene 2>)(<Location on chromosome 1>; <Location on chromosome 2)(<gene1>,<gene2>) fusion transcript

For example:

t(9;22)(q34.1;q11)(ABL1,BCR) fusion transcript:Arb:Pt:Bld/Tiss:Ord:Molgen

Synonyms: Philadelphia chromosome, BCR1, chronic myeloid leukemia, CML

t(14;18)(q32;q21.3)(IGH,BCL2) fusion transcript:Arb:Pt:Bld/Tiss:Ord:Molgen

Synonyms: Follicular B cell lymphoma, oncogene B-cell leukemia 2, CLL, chronic lymphatic leukemia, follicular lymphoma

t(15;17)(q24.1;q21.1)(PML,RARA) fusion transcript:Arb:Pt:Bld/Tiss:Ord:Molgen

Synonyms: RAR, promyelocytic leukemia, myelogenous, retinoic acid receptor, acute promyelocytic leukemia, APL

For chromosomal deletions and inversion,‘t’ above would be replace with ‘del’ or ‘inv’, respectively:

del(1)(p32p32)(STIL,TAL1) fusion transcript:PrThr:Pt:Bld/Tiss:Ord:Molgen

Synonyms: SCL/TAL1 interrupting locus, T-cell acute lymphoblastic leukemia, ALL, T-ALL, TAL-1 deletions

inv(16)(p13.1;q22.1)(MYH11,CBFB) fusion transcript:Arb:Pt:Bld/Tiss:Ord:Molgen

Synonyms: inversion 16, AML, Acute myeloid leukemia

In some cases, testing may involve comparing the fused transcript to a control transcript and results may be reported as a number ratio (NRto), log number ratio (LnRto), or relative ratio (RelRto):

t(9;22)(q34.1;q11)(ABL1,BCR) fusion transcript/control transcript:NRto:Pt:Bld/Tiss:Ord:Molgen

t(9;22)(q34.1;q11)(ABL1,BCR) fusion transcript/control transcript:LnRto:Pt:Bld/Tiss:Ord:Molgen

t(9;22)(q34.1;q11)(ABL1,BCR) b3a2 fusion transcript/control transcript (International Scale):RelRto:Pt:Bld/Tiss:Ord:Molgen

To specify “major” or “minor” breakpoints, we use:

t(9;22)(q34.1;q11)(ABL1,BCR) fusion transcript major break points:Arb:Pt:Bld/Tiss:Ord:Molgen

t(9;22)(q34.1;q11)(ABL1,BCR) fusion transcript minor break points:Arb:Pt:Bld/Tiss:Ord:Molgen

To specify specific breakpoints, we use:

t(9;22)(q34.1;q11)(ABL1,BCR) b2a2+b3a2 fusion transcript:Arb:Pt:Bld/Tiss:Ord:Molgen

Synonyms: major breakpoints, p210, e13a2, e14a2

t(15;17)(q24.1;q21.1)(PML,RARA) bcr1 fusion transcript:Arb:Pt:Bld/Tiss:Ord:Molgen

Synonyms: breakpoint cluster region 1, long form

Translocation terms can also be expressed as a fraction of cells that have the rearrangement versus total cells of interest:

Cells.t(9;22)(q34.1;q11)(ABL1,BCR)/Cells.total:NFr:Pt:Bld/Tiss:Qn:Molgen

If specific partner genes are not known, we use the pattern:

CCND1 gene rearrangements:Arb:Pt:Bld/Tiss:Ord:Molgen

Synonym: Lymphoma 1

BCL2 gene rearrangements:Arb:Pt:Bld/Tiss:Ord:Molgen

Synonym: Lymphoma 2

3.9.7 Identity testing

The identity testers usually look at 4 genetic loci (each locus is polymorphic enough that any one match has a 10% error of being incorrect). The loci are independent so if all 4 probes match (including all exclusions and inclusions) the probability of an erroneously match is .0001 (one out of 10,000). They may use more than four depending upon the degree of confidence required by the circumstances of the testing. The forensic community chooses from a set of about 20 probes.

We propose two styles for reporting identity testing: atomic and pre-coordinated definitions.

3.9.7.1 Atomic style

This style uses a series of LOINC names to report the kind of index case, the kind of comparison case, the results of the identity testing, and all of the other separate components of the testing. It includes an observation for reporting the actual probes used, and another observation for reporting the population that the probes assume. The Method will be MOLGEN.IDENTITY.TESTING. For example:

DNA probes used:Prid:Pt:Index case^comparison case:Nom:Molgen.identity.testing

Population base:Prid:Pt:Probes:Nom:Molgen.identity.testing

Relationship:Type:Pt:index case:Nom:Molgen.identity.testing

Example Answers: child, victim, suspect

Relationship:Type:Pt:^comparison case:Nom:Molgen.identity.testing

Example Answers: mother, alleged mother, father, alleged father, evidence (external to victim)

Confidence of relationship:likelihood:Pt:Index case^comparison case:QN:Molgen.identity.testing

Comment: gives the statistical confidence in the conclusion

Conclusion:Imp:Pt:index case^comparison case:Nar:Molgen.identity.testing

Comment: gives a summary statement of the conclusion about identity of relatedness

3.9.7.2 Pre-coordinated definitions alternative

Some of the above atomic terms (e.g., DNA probes used) could also be reported with the pre-coordinated results.

Relationship:likelihood:child^alleged mother:Qn:Molgen.identity.testing

Synonym: maternity testing
Comment: gives the likelihood that the alleged mother is the mother of the index child

Relationship:likelihood:child^alleged father:Qn:Molgen.identity.testing

Synonym: paternity testing
Comment: gives the likelihood that the alleged father is the father of the index child

Relationship:likelihood:victim^suspect:Qn:Molgen.identity.testing

Comment: gives the likelihood that the genetic material on the victim is that of the suspect

Relationship:likelihood:suspect^victim:Qn:Molgen.identity.testing

Comment: gives the likelihood that the genetic material on the suspect is that of the victim

Identity:likelihood:evidence^suspect:Qn:Molgen.identity.testing

Comment: gives the likelihood that the genetic material on the evidence is that of the suspect

Identity:likelihood:evidence^victim:Qn:Molgen.identity.testing

Comment: gives the likelihood that the genetic material on the evidence is that of the victim

3.9.8 Tumor related genetics

Using the models described in this section, LOINC has terms for many genetic tests relevant to cancer, including tests related to tumor suppressor genes (e.g. BRCA1, BRCA2, and p53), oncogenes (e.g. HER2), and more.

[[^25]]: Antonarakis, SE, and the Nomenclature Working Group. Recommendations for a nomenclature system for human gene mutations. Human Mutation 1998;11:1-3. PubMed: 9450896.

[[^26]]: Deckard J, McDonald CJ, Vreeman DJ. Supporting interoperability of genetic data with LOINC. J Am Med Inform Assoc. 2015 May;22(3):621-7. PubMed: 25656513.

[[^27]]: Beaudet AL, Tsui LC. A suggested nomenclature for designating mutations. Human Mutation 1993;2 (4) :245-248. PubMed: 8401532.