Genetic Tests And Technologies

Question 1

Types of genetic test

Answer 1

Testing for genetic conditions

Testing to clarify familial relationships

Genetic testing to determine identity

Question 2

Testing for genetic conditions

Answer 2

offered in Clinical Genetics

• Diagnostic
• Carrier
• Predictive
• Prenatal tests incl.NIPT

Question 3

Testing to clarify familial relationships

Answer 3

usually done in private sector or a forensic
laboratory

• Paternity testing

Question 4

Genetic testing to determine identity

Answer 4

usually done in a forensic laboratory

Genetic finger printing

Question 5

Role of genetic testing

Answer 5

• To confirm a clinical diagnosis

•To give information about prognosis

•To inform management

•Allow pre-symptomatic/predictive testing in close relatives

•Carrier testing

•To give accurate recurrence risks

•Prenatal diagnosis

Question 6

Sanger sequencing

Answer 6

Developed by Frederick Sanger in 1977

Uses PCR to amplify regions of interest followed by sequencing of products

Useful for single gene testing

Question 7

Next generation sequencing

Answer 7

High throughput or massively parallel sequencing

Can sequence whole human genome in one day

Multi-gene panels, whole exome/genomes

Question 8

Sanger

Answer 8

Single start point (primer)

Single DNA fragment sequenced

High cost per gene

Time consuming

Simple analysis (read the sequence)

Very accurate

The gold standard

Question 9

NGS

Answer 9

Library of DNA fragments

Massively parallel sequencing

Low cost per gene

Fast

Huge amounts of raw data to interpret

Moderately accurate

Question 10

NGS Data Analysis

Answer 10

• 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 11

Every genome contains many rare, potentially functional variants

Answer 11

– 500 rare missense variants
– 100 Loss of Function variants: ~20 homozygous, ~20 rare
– 100 rare variants in known disease genes
– 5-10 recessive disease-causing mutations
– 1-2 de novo coding mutations
– sequencing errors

Question 12

Interpretation

Answer 12

Pathogenic variant

Variant of unknown significance (VUS)

Normal variation

Question 13

Unclassified variants- require more
work

Answer 13

• 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 14

Incidental/secondary findings

Answer 14

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

Question 15

Examples of incidental/secondary findings

Answer 15

• Non-paternity on examination of a family trio

• Variant known to confer high risk of adult-onset disease

• Variants of uncertain clinical significance, possibly requiring further investigation

Question 16

When looking at incidental/secondary findings

Answer 16

• Need to consider whether and when to disclose

• Importance of full and informed consent prior to test

• Use of clinical judgement

Question 17

Targeted Panels

Answer 17

Select specific genes to select

Less noise

Fewer variants of uncertain significance

But panels need to be updated

Question 18

Comparisons of tests

Answer 18

Slide 21

Question 19

Summary

Answer 19

• Newest genetic technology opens new avenues in genetic diagnosis
•Challenges of variant interpretation and secondary findings
•In the near-future exome/genome sequencing may well become feasible for all inherited disorders
•Thorough clinical examination, medical history and family history remain extremely valuable and complementary to genetic testing
•Genetic counselling and informed consent will be more important than ever