Clinical Genomic Testing - Week 4 Flashcards
Genomic testing
testing DNA at a large scale
Typically single gene testing for
patients with a strong suspicion of given syndrome
what type of testing do you use for single gene testing?
typically Sanger sequencing
What is the advantage of Next generation sequencing in this context?
able to scale up and look at more genes i.e. through gene panel sequencing i.e. patient with monogenic diabetes (20-30 genes know to cause monogenic diabetes) gene panel most cost effective way of genetic testing for these patients rather than single gene testing
For who would you use next generation sequencing
• Patients with intellectual disabilities, dysmorphic features, developmental delay we would like to look at a bigger target = next generation sequencing to look at thousands of genes to cause the phenotype. Clinical exome = 5,000-6,000 genes. • Can go broader by doing whole exome sequencing – sequence all 20,000 human genes
Vision
whole genome sequencing – looking not only at the protein coding regions of the genes but looking at the whole genome including deep intronic regions and non-coding regulatory regions of the genome
Who should be having genomic testing?
- Usually focus on patients likely to have a monogenic/Mendelian disorder (caused by a single gene) i.e depilepsis, progressive neuromuscular disorders and metabolic disorders
- Also testing patients who don’t have clinical phenotype (feel well) but have strong family history of rare genetic disorder
Why test people?
- Testing to look for diagnosis (if they are affected)
- Diagnosis can inform on clinical management and treatment decisions
- If patient’s don’t have clinical presentation but family history then its predictive testing (not diagnostic testing)
- Test patients, to use the results for reproductive decisions – prenatal diagnosis and pre-implantation genetic testing
Sequencing the human exome (whole exome sequencing), when would this method be applicable?
- Patients who have heterogenous presentation likely to be caused by any of the genes in the genome and no strong clinical suspicion of given syndrome
- So look at exome which represents 1.2-1.4% of the genome, it can be enriched (captured) from genomic DNA by hybridisation
- Around 80-85% of disease causing variants are located within protein coding regions (exons) of the genome
- Sequencing all the exons = exome sequencing
- Small target but chances of identifying genetic cause are quite high in exome sequencing
How many disease causing variants are located within the protein coding regions?
80-85%
Different family structures - who should be sequenced in exome sequencing
Singleton analysis, parental analysis, Sib pair analysis, trio analysis
Singleton analysis
sequence only the child affected
parental analysis
sequence only the parents if no DNA on affected foetuses
sib pair analysis
If 2 affected children on consanguineous family then you might sequence both affected and compare their rare variants
trio analysis
sequence affected proband and both unaffected parents (sequence all 20,000 genes and when analysing the variants tend to focus on the rare variants that would fit with the different modes of inheritance (autosomal dominant de novo, autosomal recessive, X linked recessive, X linked dominant and mitochondrial) this is refereed to gene agnostic (looking at all 20,000 genes) and inheritance based (as filtering rare variants that would fit with different modes of inheritance and that’s possible as we have the genotypes of the parents as well as the child so can compare and do analysis.)
