Hi
I am working on cancer genomics. In studying copy number change of matched samples of pre and post chemotherapy from the same patient what does copy number states AA, AAB, AABB, AAA, and AAAA mean?
•
written
by
zizigolu
1 answer
The number of As and Bs stand for the number of alleles from each parent. Normal cells have one allele of each autosome from each parent, so the chromosomes 1-22, and all locations on those chromosomes are all AB.
Normally you don't know which allele came from the mother and which allele came from the father. You code any changes with more As than Bs.
A region with AAB is triploid, and still has alleles from both parents. Usually this has only moderate effects, if any. In general it takes amplification of a region (10 or more copies) for real dosage effects.
AABB is a doubling of both alleles, this can happen during cell division, in the G2 phase.
With states A, AA, AAA, and AAAA there is LOH, loss of heterozygosity, with varying amounts of duplication of the remaining allele. This can be used to determine tumor suppressor genes.
AA and BB are loss of heterozyosity, AB is the only normal state for autosomes
Log in to answer this question.
-
Matched samples in Deseq2
written by noodlejackson •
-
RNA-seq design advices
written by fmazzio1 •
-
A question in terms of definition
written by zizigolu
-
How do gene interaction studies manage multiallelic SNPs?
written by angus.gane •
-
Patient-derived DE to identify overexpression
written by bilodate •
-
Do tools doing clonal evolution analysis work on unmatched samples too
written by zizigolu
-
What is best tool for Cohort data of DNA?
written by 9521ljh •
-
Exome mean coverage for human
written by Omics data mining
-
Ploidy in copy number analysis
written by rahul.nahar •
-
Difference Between Allelic-Imbalance Copy Number Change And Allelic-Balance Copy Number Change
written by user1202664 •
Your organism is diploid by default. AA means that both alleles are A. AB means heterozygous allele (normal). BB means the same as AA but since there is no general rule how you denote alleles people write AA. AA is loss of heterozyosity. AAB = duplication. AABB = tetra ploidy (2 copies of one allele and 2 copies of another). And so on. Hope it is understandable :)
Are you able to see table 12.1?
Thank you @genomax, table gave me a very good intuition to start understanding