genetic tests and technologies

Question 1

role of genetic testing

Answer 1

confirm a clinical diagnosis
give information about prognosis
inform management

Question 2

testing for genetic conditions - offered in clinical genetics

Answer 2

diagnostic
carrier
predictive
prenatal tests incl. NIPT

Question 3

sanger sequencing

Answer 3

Developed by Frederick Sanger in 1977, uses PCR to amplify regions of interest followed by sequencing of products, useful for single gene testing
single start point, single DNA fragment , high cost and time per gene, very accurate

Question 4

Next generation sequencing (NGS)

Answer 4

High throughput or massively parallel sequencing, can sequence whole human genome in one day, multi-gene panels, whole exome/genomes
fast, low cost, moderately accurate

Question 5

NGS data analysis

Answer 5

• NGS generates millions of short DNA fragments (reads) the need to be filtered for quality and aligned to a reference sequence
• Reference genome
• Identify variants
• Interpret variants
• Insilico tools (bioinformatics)

Question 6

interpretation

Answer 6

• Pathogenic variant
• Variant of unknown significance (VUS)
• Normal variation
• Has the variant previously been reported? (in the literature, present on variant or reference databases
• Type of mutation – nonsense, frame shift, splice site, missense etc

Question 7

unclassified variants

Answer 7

• Type of mutation
• Population frequency
• Literature search
• Evolutionary conservation – domain context
• Severity of amino acid substitution
• Splice site prediction
• Functional studies – protein and/ or mRNA analysis
• Genotype-phenotype correlation – importance of clinical assessment
• Family studies – analysis of affected and unaffected individuals
• De-novo variant

Question 8

incidental/ secondary findings

Answer 8

• Additional findings concerning a patient or research participant that may, or may not, have potential health implications and clinical significance, that are discovered during the course of a clinical or research investigation, but are beyond the aims of the original test or investigation
• Importance of full and informed consent prior to test
• Use of clinical judgement

Question 9

targeted panels

Answer 9

• Select specific genes to sequence
• Less noise
• Fewer variants of uncertain significance
• But panels need to be updated

Question 10

pick up rate

Answer 10

• Chromosome analysis <1%
• Fragile-X syndrome «1%
• Microarrays 15%
• Whole exomes 30%
• Whole genomes?