Allele-specific information is obtained from read counts at heterozygous SNPs.
Allelic-imbalance separates chromosomal regions by their allele constitution.
A diploid cell, which is the norm, will have one maternal and one paternal copy of a chromosome.
For each copy number there can be losses of segments to either of the
chromosomes as well as copies/gains. It is this allele-specific information that
allelic imbalance captures. It does not, however, discern the origin of a segment,
that is to say that two paternal copies have the same allelic imbalance ratio as two
maternal copies. Below is an attempt to explain the different possible allelic combinations
for a few copy numbers,
it is VERY important that you understand that from an allelic imbalance value point of view
it is the ratio between green and purple that
is important, not if purple/green is maternal/paternal.
is the same as
Possible chromosomal segment combinations
Here is a an example of a plot generated using TAPS where I have added the possible
allele combinations next to the clusters.
Log-ratio is calculated as log2(normalized intensity of sample / normalized intensity of reference sample or pool)
Sebastian DiLorenzo - sebastian.dilorenzo(at)medsci.uu.se
Markus Mayrhofer - markus.mayrhofer(at)medsci.uu.se
Anders Isaksson - anders.isaksson(at)medsci.uu.se