Genomics of Developmental Disorders Flashcards
What are some common phenotypes of DDDs?
Microencephaly Intellectual disability Behavioural problems Heart defects Deformities (cleft lip, extra fingers/toes) Abnormal growth of specific body parts Usually obvious shortly after birth Can be syndromic (many organs affected) or non-syndromic
Why is the range of phenotypes for DDDs so broad?
High genetic heterogeneity
Also diversity of the mutations types within the affected gene
How many variants dose each individual person normally have?
Out of 3.6 billion base pairs in the genome, an individual has about 4.5 million variants. The majority are SNVs.
Around 20,000 of these are within coding regions
Name the most common types of variants
SNVs Indels CNVs Translocations Inversions Chromosomal aneuploidy
Why might some genetic variation not cause disease?
Present in an intron
Present in an intergenic region (between genes)
The mutation is synonymous
The mutation might be in a gene that is not prone to haploinsufficiency
Why might genetic variation cause disease?
Leads to reduced or loss of function in a protein e.g. a nonsense mutations and nonsense mediated decay
Leads to gain of function in a protein, the protein gains a toxic function
What are the two ways in which a recessive condition can become presented in the phenotype?
Homozygous for the mutation
Compound heterozygous mutations
What is the most common genetic cause of DDDs?
80% are monogenic
Usually caused by de novo mutations
Leads to loss of function of a dominant gene. This causes haploinsufficiency (one functioning allele not sufficient - need two)
What are the two broad categories of genetic diagnostic testing?
Molecular genetics - have a ‘suspect gene’ based off the phenotype, then look for specific mutations or sequence specific genes to detect SNVs or small indels
Cytogenetics - look for large structural changes (aneuplodies, translocations, CNVs) across the genome using karyotyping, microarrays, FISH. No ‘suspect gene’ required
Which diagnostic test is usually used first for diagnosing DDDs?
Microarrays
What are the two possible approaches to filtering variants to identify which one is disease-causing?
Translation approach - look for the variants in genes that are known to be associated with DDDs
Research approach - look for new genetic causes that have not been identified yet, using a statistical approach
Once you have identified all the variants in a child with DDD’s exome, how do you filter these to identify which one is disease-causing?
- Exclude common variants that are present in lots of the population and known to not cause disease
- Exclude variants that do not affect protein production (synonymous, intergenic etc)
- Use a virtual panel to pick out genes that are already known to be associated with the child’s phenotype
- Carry out family trio sequencing to exclude benign inherited variants
Once you have just a handful of possible variants that could be disease-causing, how do you filter this down even further?
- Variants causing a big change (e.g. frameshift mutation) more likely to be disease-causing than those leading to a small change
- Do any of the variants lie in genes that are highly sensitive to haploinsufficiency?
If you have identified a de novo mutation in a child that you think might be disease causing, how could you prove this?
- Show that individuals without the phenotype do not have the variant
- Show that individuals with the phenotype have the variant (or have a different variant within the same gene)
- Sequence genome of any affected/unaffected family members to see if they have the variant
- Use in vitro or in vivo functional studies to find the effect of the variant e.g. animal models
- Statistical methods such as enrichment analysis
What is enrichment analysis?
Every gene has an expected number of mutations
Compare the expected number to the actual observed number of mutations
Provides a p value of how likely it is that certain mutations would occur if they were not linked to disease
What are the uses of trio exome sequencing?
- Exclusion of benign inherited variants
- Highlights de novo mutations
- Identification of homozygous or compound heterozygous variants
- Identification of new disease genes
What ethical issue should be considered before carrying out trio exome sequencing?
- Incidental findings e.g. cancer predisposition, paternity testing
- How will the data be stored and who will it be shared with
- Management of expectations - how likely it is to produce a diagnosis, and time-scale of getting results
- Implications for other related family members
- Capacity to give voluntary and informed consent
Why are DDDs difficult to diagnose?
- High heterogeneity - large possible numbers of affected genes
- Every genome has novel variation - which variation is disease causing?
- Most genetic variation is benign, lots of variants to filter out
- Similar phenotypes can be caused by different affected genes
- Inheritance patterns can vary between diseases
What is a deleterious variant?
A variant that confers susceptibility to a disease
Name some sources of genetic variation
Chemical agents UV radiation Hydrolysis of bases Deamination of methylated cytosine into uracil Base pair mismatch during replication Replication slippage Recombination errors Chromosome/chromatid segregation errors
Which type of variance is more common with increasing paternal age and why?
De novo mutations
Arise during replication errors during mitosis. As spermatogonia keep undergoing meiosis, there is more chance for mutations to accumulate over the years
Which type of variance is more common with increasing maternal age and why?
Aneuploidy
Arises due to non-disjunction of chromosomes during meiosis I, or chromatids during meiosis II (normally the former). Occurs because oogenesis is paused at meiosis I
What are the benefits of accurately molecularly diagnosing DDDs?
- Understanding how to manage the disease, if there are an possible treatments
- Easier to access special needs services
- Reproductive counselling
- Psychological benefit to understanding the cause
- Save healthcare systems money for future diagnostic tests
Why is NGS useful in diagnosing DDDs?
Agnostic approach - don’t need to know what you are looking for - so useful for discovering new disease genes
Can examine multiple genes at once
Can detect multiple types of variation
High throughput
Can be used for whole genome, exome sequencing or specific genes
