| Literature DB >> 34427008 |
Margit Shah1,2,3, Arthavan Selvanathan4, Gareth Baynam5,6, Yemima Berman7,8, Tiffany Boughtwood9,10, Mary-Louise Freckmann7,11, Gayathri Parasivam12, Susan M White13,14, Natalie Grainger12, Edwin P Kirk1,15,16, Alan Sl Ma2,17, Rani Sachdev1,15.
Abstract
Monogenic rare disorders contribute significantly to paediatric morbidity and mortality, and elucidation of the underlying genetic cause may have benefits for patients, families and clinicians. Advances in genomic technology have enabled diagnostic yields of up to 50% in some paediatric cohorts. This has led to an increase in the uptake of genetic testing across paediatric disciplines. This can place an increased burden on paediatricians, who may now be responsible for interpreting and explaining test results to patients. However, genomic results can be complex, and sometimes inconclusive for the ordering paediatrician. Results may also cause uncertainty and anxiety for patients and their families. The paediatrician's genetic literacy and knowledge of genetic principles are therefore critical to inform discussions with families and guide ongoing patient care. Here, we present four hypothetical case vignettes where genomic testing is undertaken, and discuss possible results and their implications for paediatricians and families. We also provide a list of key terms for paediatricians.Entities:
Mesh:
Year: 2021 PMID: 34427008 PMCID: PMC9292248 DOI: 10.1111/jpc.15703
Source DB: PubMed Journal: J Paediatr Child Health ISSN: 1034-4810 Impact factor: 1.929
Fig 1Possible results of genomic testing. For variants of uncertain significance, the additional clinical/genetic correlation provided in expert multidisciplinary team review meetings provides the paediatrician with additional pathways for interpreting the variant, and possibly reclassifying as pathogenic or benign. Examples of these scenarios are provided in this paper (Adapted from Sachdev et al., with permission).
Common genetic terms
| Term | Meaning |
|---|---|
| > | A difference in the DNA sequence (at the indicated position) from the reference base on the left to the one on the right of the ‘>’ symbol. For instance, |
| ACMG criteria | A set of suggested criteria that are widely used to classify the pathogenicity of any variant identified (published by the ACMG) |
| Allele | A term describing the DNA sequence of one version of a gene |
| Autosomal dominant | A type of inheritance in which a pathogenic variant only needs to be on one copy of the chromosome to cause a phenotype |
| Autosomal recessive | A type of inheritance in which both copies of the chromosome need pathogenic variants to cause a phenotype |
| Benign | A variant that has been assessed with strong confidence (>99% likelihood) not to cause a Mendelian disease |
| c. | The position of a variant in the protein‐coding regions of a particular nominated version (transcript) of the gene (starting from the beginning of the start codon). For instance, NM_000492.3( |
| Canonical transcript | See transcript/transcription |
| Chromosome microarray | A genetic test that can detect copy number variants across the whole genome. The exact test specifications of the platform used determine the smallest size of copy number variation that can be detected |
| Controls | Individuals (often in a database) who do not have any evidence of disease |
| Copy number variant | A variant that is characterised by greater (duplication) or fewer (deletion) copies of a segment of the genetic code compared to the reference genome (for most of the genome, the reference copy number is 2, except for X and Y chromosomes in males) |
|
| Describes a variant that is not inherited from a parent, but is new in the patient. |
| Deletion | See copy number variant |
| Duplication | See copy number variant |
| Exon | The parts of a gene that code for the final mRNA (mostly protein‐coding sequence), which is used as the template to make a protein. Most disease‐causing variants that we currently understand are located in exons |
| Expressivity | The extent to which a phenotype is expressed by an individual with a genetic condition. Many genetic conditions have variable expressivity, whereby affected individuals may manifest with different clinical features and with differing degrees of severity |
| Functional domain | A region of the protein that has a specific role: variation from normal in a critically important functional domain may be more likely to cause disease than the one in a non‐functional domain |
| Functional studies | Investigations undertaken to assess the function of genes and the consequences of genetic variants (e.g. biochemical tests such as enzymology) |
| g. | The genomic position on the relevant chromosome (starting from the top of the short arm of the chromosome). For instance, ChrX:g.1 refers to the first nucleotide on the X chromosome |
| Gain‐of‐function variant | A variant that causes an increased level of function or activity of the gene product |
| Genomic testing | Genetic testing that sequences and then analyses all (or parts) of an individual's entire DNA sequence (genome). This can include WES (analysis of exons and exon–intron boundaries), WGS (analysis of the whole genome) or gene panels (analysis of a set of selected genes associated with the patient's specific phenotype) |
| Genotype | The genetic make‐up of an individual at a particular location or in a particular region |
| Germline | A variant that is present in all cells in the body, and occurred either in formation of germ cells, or immediately after conception or is inherited |
| gnomAD | A large database of individuals, derived from patients with ischaemic heart disease and mental health conditions, that is, depleted of individuals with severe childhood‐onset genetic conditions. This database is helpful for ruling out pathogenicity of common population variants |
| Gonadal mosaicism | The possible presence of mosaicism for a particular variant in the gonadal cells of an individual |
| Haploinsufficiency | A gene where reduction in functioning product by 50% is expected to cause a disease or phenotype (such as if one copy of the gene has a loss‐of‐function variant) |
| Hemizygous | Present in the only copy of the chromosome (e.g. variants in genes on X chromosome for a male) |
| Heterozygous | Present in one copy out of the two copies of the relevant chromosome |
| HGVS nomenclature | A standardised nomenclature guideline that is typically used to communicate genetic information, such as variant details and genetic test results (published by HGVS, an international collaborative group that aims to foster discovery and characterisation of genomic variants) |
| Homozygous | Present in both copies of the relevant chromosome |
| Hypomorphic allele | A variant that leads to reduced function of a gene product. Often used in connection with variants that are associated with mild or no phenotype |
|
| Also known as pathogenicity prediction software, these are computerised prediction tools using a variety of algorithms, which provide predictions as to whether some types of variants are likely to affect the function of a protein and therefore cause disease |
| Incidental finding | A variant, identified on genetic testing, which has health implications that are unrelated to the reason for doing the test |
| Intolerant of missense substitution | Regions of genetic code (or a whole gene) in which changes in the amino acid composition are assessed as more likely to significantly alter its function |
| Intron | The parts of a gene between exons. Introns are generally cut out in RNA processing and are not used as a template to make a protein. However, intronic segments may have other functions, and we do not completely understand these parts of the genetic code |
| Invariant | Genetic code (or the amino acid it codes) is identical across numerous species from simple to complex, suggesting a functional importance that is more likely to be disturbed by any variation |
| Likely benign | A variant that has been assessed as highly likely (>90% likelihood) not to cause a Mendelian disease |
| Likely pathogenic | A variant that has been assessed as highly likely (>90% likelihood) to cause a Mendelian disease |
| Loss‐of‐function variant | A variant that causes a complete absence of a gene product |
| Mendelian | Refers to inheritance in a pattern consistent with the principles laid out by Mendel – specifically autosomal recessive, autosomal dominant or X‐linked inheritance |
| Missense | A variant that corresponds to a different amino acid at that position compared to the reference |
| Mosaicism | The presence of two or more cell lines with different genetic composition |
| Mutation | Same as variant, although often used in connection with variants that are pathogenic or thought to be disease‐causing |
| Nonsense | A variant that introduces a stop codon earlier than usual and therefore leads to either no functional protein or a truncated protein being produced |
| Novel disease gene discovery | Identification of an association between pathogenic variants in a gene and a Mendelian disease |
| Null variant | A variant that causes a non‐functioning gene product, or that prevents translation to form any product at all |
| OMIM | A freely available database of human genes and associated phenotypes |
| p. | The protein (amino acid) position of the variant (starting from the first amino acid, the start codon). For instance, |
| Pathogenic | A variant that has been assessed with strong confidence (>99% likelihood) to cause a Mendelian disease |
| Penetrance | A quantitative measurement, describing the proportion of individuals carrying pathogenic variants in a gene that manifest signs or symptoms of the associated condition. Incomplete penetrance describes the state where there are individuals with pathogenic variants in a gene who do not manifest the condition |
| Phenotype | Observable clinical traits (symptoms, signs, biochemistry, radiology, etc.) in an individual |
| Preimplantation genetic diagnosis | Testing of embryos (conceived via |
| Prenatal testing | Invasive testing (often genetic) of a fetus during a pregnancy, usually from a chorionic villus sample or amniocentesis sample |
| Proband | The first family member where the possibility of a genetic condition is considered |
| Reference genome | A constructed reference of the ‘normal’ DNA sequence across all of a human genetic code |
| RefSeq | A repository that contains well‐annotated reference sequences of DNA, RNA transcripts and protein |
| Segregation | Assessing whether the variant(s) are present in family members in a pattern consistent with the expected inheritance pattern of disease. For instance, both parents being carriers for a child with compound heterozygous variants causing an autosomal recessive disorder |
| Single nucleotide polymorphism | A single base variation in the genetic code that is known to be present in many individuals (and so is unlikely to be causative of a disease phenotype) |
| Singleton testing | Sequencing and analysis of only the patient's DNA sequence |
| Somatic | A variant that occurred in dividing cells postnatally and is therefore only present in some cells in the body |
|
Transcript/transcription | The process of ‘reading’ DNA to RNA for subsequent processing to mature mRNA which is then translated to protein. Many genes can be transcribed in different ways, for example by using different transcription start sites, alternate splicing can also occur, with the resulting mRNA coding for different versions of a protein. The canonical transcript is generally the longest known transcript, although this may not always be the most biologically important transcript |
| Trio testing | Sequencing and analysis of the patient's and both biological parents' DNA sequence |
| Variant | A difference in the genetic code compared to the reference genome |
| Variant of uncertain significance | A variant for which there is insufficient evidence to determine if it causes a Mendelian phenotype or is a benign variation in the genetic code |
| WES | See genomic testing |
| WGS | See genomic testing |
| Wild type | The most common or usual version of any particular gene |
| X‐linked | A type of inheritance in which the phenotype is caused by pathogenic variants on the X chromosome |
ACMG, American College of Medical Genetics and Genomics; HGVS, Human Genome Variation Society; mRNA, messenger RNA; OMIM, Online Mendelian Inheritance in Man; WES, whole‐exome sequencing; WGS, whole‐genome sequencing.