GRR - Background Information
How are pedigree errors identified?
- Pairs of different classes of relatives and non-relatives can be
characterised by a unique distribution of allele sharing across the
genome. For instance, full siblings are expected to share a higher
proportion of alleles than half siblings, and parent-offspring pairs are
expected to share the same number of alleles, on average, as sibling pairs,
but their variability in allele sharing is much lower than that of sibling
pairs. Pairs of unrelated individuals should share fewer alleles on
average than half siblings. Finally, MZ twins should share alleles at
all loci (provided there is no genotyping error).
How does GRR use IBS allele sharing to identify pedigree errors?
- By computing the average allele sharing for any pair of individuals in a
sample, across all available markers, along with the standard deviation in
genome-wide IBS and plotting this mean against the standard deviation, we
readily characterise full-sib from half-sib pairs, parent-offspring pairs
from siblings, and unrelated individuals from relatives. Each relative
class will form a distinct cluster on these plots and outliers from these
clusters will represent likely pedigree errors. When including all
pairings in a sample, not just pairings within families, we can further
detect problems such as sample duplications or perhaps related individuals
who have been presumed to be unrelated.