Benefits and pitfalls of new genetic tests Amanda Krause Division of Human Genetics, NHLS and University of the Witwatersrand
Definition of Genetic Testing the analysis of human DNA, RNA, chromosomes, proteins and certain metabolites in order to detect heritable disease related genotypes, mutations, phenotypes or karyotypes for clinical purposes. Burke W. Genetic testing. NEJM 2002;347:1867-1875
Why Genetic Testing? People have major concerns about risks of occurrence and recurrence of genetic disorders Require accurate information Importance of appropriate genetic testing Genetic counselling important part of process
Uses of Genetic Testing Diagnostic Testing: Confirm or rule out a known or suspected genetic disorder in a symptomatic individual Predictive Testing: For asymptomatic individuals with a family history Carrier Testing: Identify individuals who carry autosomal or X-linked recessive mutations Prenatal Testing Performed during a pregnancy to assess the health status of the fetus
Development of Genetic Testing Chromosome analysis Singe gene analysis (10-50kb) MLPA analysis Gene panels (1Mb) Micro-array analysis Exome sequencing (50Mb) Genome sequencing (3000Mb)
Development of Next Generation Sequencing (NGS) Rapidly advancing technology Costs reducing rapidly (remain expensive) Platforms developing Increasing resolution Less hypothesis driven
Directed Single Gene Analysis Mutation Detection Traditional Testing for specific sequence changes Family specific Common mutations Sanger Sequencing Analyse genes one or two at a time High certainty of result Predictable outcome BUT: Costly, time-consuming Relative easy to compare labs and tests offered
Development of NGS - Benefits Increasing ability to make accurate diagnoses Ability to do multiple analyses simultaneously Identify mutations in rarer genes Identify disease modifiers Identify gene interactions Opportunities to identify new disease-associated genes Opportunity to characterise disease more precisely Improved family-risk assessment Improved understanding of genotype-phenotype relationships
Gene Panel Testing - NGS Gene panel Test to analyse multiple related genes simultaneously May be 2-100+ genes High yield if carefully selected Less ambiguous results Less unwanted results Useful if: Phenotype relatively distinct Muscular dystrophy Familial cancer Multiple genes known to cause similar phenotype Locus heterogeneity Cannot distinguish causative genes based on phenotype
Whole Exome Sequencing (WES) - NGS Sequence entire coding sequence of human genome (50Mb) Sequence exons No analysis of noncoding DNA Analyse 1-2% of the genome BUT: 85% of pathogenic mutations in exons
Whole Exome Sequencing (WES) NGS Consider if: Poorly defined phenotype Suspected new syndrome Negative panel? Likelihood of positive finding small Interpretation challenging Often generate new data New/rare syndrome Difficult to prove causation Clinical exome concept Subset of exome Genes with known clinical significance
Whole Genome Sequencing (WGS) -NGS Sequence all DNA of an individual (3000Mb) Massive data set Very large number of variants Analysis challenging Interpretation difficult May detect Deep intronic mutations Breakpoints Structural rearrangements Few clinical indications at present
NGS - Choices What Is Best For Patient? Single gene test vs panel vs exome vs genome Comparison of services very difficult Little information on technology, methodology, panel design, coverage, depth Consider: Costs Yield Diminishing returns
NGS - Choices What Is Best For Patient? Challenges: Information overload Comparison of different platforms Complex Information not easily accessible Difficult to assess laboratory competence Unexpected information
NGS: Is more always better? Importance of clinical assessment and information Aim to identify disease causing mutation NGS: Increased speed, capacity, reduced cost But: Single gene test could be better Uninterpretable findings Incidental findings Timing of testing Tests and interpretation of tests changing all the time Is reanalysis possible? How often should re-analysis be done
NGS-Challenges Large amount of data generated Analysis complex Requires expertise Interpretation of variants Influenced by experience Knowledge of individual genes Genetic complexity (heterogeneity) Gene mutations in different genes cause same disease Mutations in same gene cause different diseases Unexpected results Pathways modifiers
NGS-Challenges Variants of Unknown Significance May identify variants with unknown effect or pathogenicity Knowledge limitations Classification of variants complex Bioinformatic analysis Database knowledge Family segregation studies Follow in family Functional studies Laboratory studies Translation for patient? I got no information it felt like a huge waste of blood to get a giant question mark. https://www.theguardian.com/science/2017/jul/18
Genetic knowledge growing all the time Ability to re-analyse data Reclassification of variants New clinical issues NGS Challenges Reanalysis of Data
NGS Challenges - Reanalysis of Data Athena Diagnostics case: Dravet syndrome missed February 2016, Amy Williams filed a lawsuit against Athena Diagnostics, relating to the death of her son, Christian arguing diagnosis may have saved life Christian developed myoclonic epilepsy Identified VUS in SCN1A in 2007 treatment not altered 2014 Athena revised VUS to pathogenic when parents requested information for future family Confirmed diagnosis of Dravet syndrome Anti-epileptics may be toxic to children with Dravet https://www.theguardian.com/science/2017/jul/18/we-are-all-mutants-now-the-trouble-with-genetictesting
NGS Challenges Incidental findings Incidental or secondary findings Unrelated to the indication for testing May be of medical value for patient care Not part of reason for test Counselling issues When to inform Reportable/actionable variant 1% of tests have a reportable incidental variant ACMG list of 59 genes Pathogenic and likely pathogenic variants must be reported to patients eg inherited cancer, cardiomyopathy, familial hypercholesterolaemia, Marfan syndrome
NGS testing - Other Challenges Missing heritability Missed mutations Technical issues Larger rearrangements require testing methods other than NGS Epigenetic changes Other?
Conclusions People want genetic tests to be like pregnancy tests, You re either pregnant or you re not. Instead, they re more like a weather report. And most people aren t prepared to cope with the probabilities and uncertainties that entails. https://www.theguardian.com/science/2017/jul/18 Genetic knowledge growing all the time Genetic testing of increasing value Challenges remain Roles of geneticists/genetic counsellors in choice of tests and interpretation
How to Contact Genetics Secretary Janet Robbie 011 489 9223 janet.robbie@nhls.ac.za Bookings for all clinics Clinical requests Geneticist/Registrar/Counsellor on Call: 078 080 8841 human.genetics@nhls.ac.za Amanda Krause 011-489-9219 Amanda.krause@nhls.ac.za