Medical Genomics Flashcards
(41 cards)
When was the human genome mapped?
2003
When did next generation sequencing begin?
2010->
What is NGS?
Next generation sequencing
The rapidly advancing technology that makes it economically viable to sequence individuals rather than species
What % of the genome is the exome?
1%
What does studying the transcriptome RNA allow us to study?
Gene expression
Gene fusions
Splice variants
How many base pairs in a genome?
About 3200 million
How many base pairs in an exome?
5–70million
Negatives of exome sequencing
Only picks up 85% of disease causing variants
Requires additional sample prep
No assessment of non coding regions
Simple repeats, GC rich and highly homologous regions are poorly captured
Clinical exome develops over time
Negatives of genome sequencing
Much more expensive
Massive data (storage?)
Interpretation more expensive and difficult
Steps in exome sequencing
Genomic DNA Shotgun library-> fragments Rehybridisation Pull down and wash Captured DNA is sequenced Mapping, alignment and variant calling
What does variant calling rely on?
Accurate alignment to a reference sequence from the Human Genome Reference
No read is the full gene
Who should be sequenced?
Distantly related concordantly affected individuals (share very few mutations)
Closely related discordant individuals (very few differences)
What is a compound heterozygote?
The presence of two different mutant alleles at a particular gene locus, one on each chromosome of a pair
Different mutations in mum and dad but on same allele
Offspring has no functioning copies of that gene
What does consanguineous mean?
The quality of being descended from the same ancestor as another person.
What are the 6 main types of mutations?
Inherited (autosomal recessive, autosomal dominant, X linked recessive, consanguineous autosomal recessive)
De novo
Mosaic
What is needed for bioinformatics?
4Gb data for each sample
Biologists skilled in programming
IRIDIS4 supercomputer
What affects the quality of sequencing?
Read depths
Standard bias
PCR duplicates
What is tiered analysis?
Prioritised analysis on basis of clinical presentation
Use known targeted gene panels
Top candidate genes first then pathway, system, others
Minimises incidental findings
How can you filter data?
Mode of inheritance
Variant type
Concordance/discordance to affected relatives
Frequency in control populations
Give an example of an ‘in silico’ tool
Computerised predictors
Logit
Mutationtaster
Name 2 reference databases
UK10K, in-house, ESV
What do genetic libertarians believe about incidental findings in genome analysis?
“Return comprehensive data”
Patient has right to know
Return all data on known and unknown risk variants
What does the ACMG recommend about incidental findings in genome analysis?
“Return data on a limited number of conditions and genes”
20 diseases, 60 genes
What do genetic empiricists believe about incidental findings in genome analysis?
“Only return data that is truly significant”
Don’t create burden of ‘patient in waiting’
Penetrance for most variants is unknown
