Sequencing Data and Analysis of Rare Variants

Genotyping arrays can be obtained at pre-selected sites for each sample. Ex. Genotyping sites known to be polymorphic based on prior sequencing.

Sequencing is obtaining "every" base in the exome or genome for each sample. Most of the sequence is identical across samples. This is used to find locations that are polymorphic, or differ across samples.

Whole Genome Sequencing

Genome: ~3GB per individual

Advantage - whole genome coverage
Disadvantage - cost ~$1000 for 30x, limited interpretability

Whole "Exome" Sequencing

Exome: ~33MB per individual

Advantage: Covers protein coding regions, interpretable variation, cost ~$500
Disadvantage: Missing 99% genome coverage