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Copy number variation

4 important questions on Copy number variation

How could aneuploidy cause cancer?

Because of random accident/damage by carcinogens to chromosome or mitogenic machinery, a dividing cell distributes its chromosomes unevenly between two daughter cells, leaving both aneuploid
Most resulting cells are not viable and die, but a surviving cell may continue proliferating. Low aneuploidy begins to affect internal functioning, but they are not yet multiplying excessively.

How do you see copy number variation in sequence output?

See schermopname 25 (nog invoegen)

What causes noise in copy number counting?

(random fragmentation --> variation, not much to do about that)
GC content

Proportion of Guanine and Cytosine basepairs
Affects binding affinity and enzymatic reactions
so you get more GC than AT since AT breaks down faster

Mappability

short read --> can go onto two places, eg two chromosomes. No way to tell where it come from.

Solution: you have reference genome: correct for mappability and GC simultaneously, by inferring parameters for ref genome (if GC content and mappability are different than random)
slightly improves this