Genomics in general practice


Summary of genetic tests
☰ Table of contents


The following table provides information about genetic tests that may be encountered in general practice and the tests’ indications.

 

Genetic test

Indications

G-banded (conventional microscopic) karyotype – Chromosomes are stained to reveal patterns of alternating light and dark bands

Suspected chromosome rearrangement; investigate
multiple miscarriages

Fluorescent in situ hybridisation (FISH) – Using fluorescent dyes or tags specific to a chromosome, FISH can visualise chromosomes to identify abnormalities

Determine physical arrangement of chromosomal conditions or correct number of chromosomes (eg rapid method of aneuploidy screening in prenatal setting)

Chromosomal microarray (CMA) or molecular karyotype (eg single nucleotide polymorphism [SNP] microarray) – CMA uses a microchip-based platform to perform a genome-wide assay that looks for sub-microscopic copy number variants (CNVs). These variants are extra (duplications) or missing (deletions) segments of deoxyribonucleic acid (DNA). Many CNVs are common and benign, while some are pathogenic

Unexplained intellectual disability or developmental delay;
prenatal investigation of abnormality on ultrasound

Sanger sequencing – The exact order of base pairs A, G, T and C in an individual‘s genetic makeup is known as the DNA sequence. Sanger sequencing is old, low through-put, but reliable technology, and sequences just one gene at a time

Suspect condition with a known single-gene cause
(eg cystic fibrosis, thalassaemia)

Next generation sequencing (NGS) or massively parallel sequencing – NGS sequences millions of small DNA fragments, which are then mapped to a reference genome. NGS can sequence the entire genome, just the exome (coding genes)
or a panel of selected genes

Genome sequencing: A comprehensive approach that
captures the entire genome
Exome sequencing: A more cost-effective approach to
capture and analyse all known disease-causing genes
(eg rare childhood syndromes)
Panel sequencing: A more targeted approach focusing on a large number of key genes related to a clinical indication
(eg cancer, cardiac conditions)

SNP genotyping or genomic profiling or scan – Testing that analyses single nucleotide variations in the genome

Determine ability to metabolise certain drugs (eg CYP2D6, codeine), paternity testing, personal genomic testing (direct to consumer)

Polymerase chain reaction (PCR) – A method for amplifying DNA (ie making millions of copies of a particular sequence of DNA)

Disorders caused by triplet repeat expansions (eg Fragile X syndrome, Huntington’s disease)

Multiplex ligation-dependent probe amplification (MLPA) – A PCR method of detecting copy number variants and SNPs

Suspect disorder caused by large deletions or duplications of specific genes (eg Duchenne muscular dystrophy)

DNA methylation studies of specific chromosome region

Suspect disorder caused by abnormal gene methylation which affects gene expression (eg Beckwith–Wiedemann syndrome)

Maternal serum screening
Combined first trimester screening – Biochemical screening
of maternal blood combined with ultrasound
Second trimester serum screening – Biochemical screening
of maternal blood

 
First trimester: Screening at 11–13 weeks to estimate risk for trisomy 21, trisomy 18, trisomy 13
Second trimester: screening at 14–20 weeks to estimate risk for trisomy 21, trisomy 18 and neural tube defects

Non-invasive prenatal testing (NIPT) – Analysis of cell-free fetal DNA (cfDNA) in maternal plasma

Pregnancy screening from 10 weeks to detect evidence of trisomy 21, 18 or 13 in fetus with higher sensitivity and specificity than maternal serum screening

Adapted from Donoghue S, Downie L, Stutterd C. Advances in genomic testing. Aust Fam Physician 2017;46(4):200–05.  [Accessed 27 July 2017].


Genomics in general practice




 

 


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