What is a proxy rsid#?Updated 4 months ago

A proxy rsid# is a surrogate or stand in for a rsid# that fails to meet quality control and/or cannot be successfully called by the microarray. A proxy rsid# is detectable by the array and has extremely high linkage disequilibrium (D prime) as well as very high R2 value approaching 1.0. For example: a proxy with both D' and R2 of .98 or better essentially "calls" or identifies the original rsid# with 98% accuracy. Proxies are a common fallback measure in research when scientists are unable to accurately call the rsid# alleles they are interested in due to technological difficulties or an array design that may have omitted the intended rsid# altogether.
Original MPO rs2333227; new MPO proxy: rs2243828 D' =1 and R2 = 1 for CEU (this means it is a perfect match for Caucasians) and D' = 0.997 and R2 = 0.9852 for all populations or 98.52% accurate match for any ethnicity.
Original MTR rs1131450; new MTR proxy: rs3768142 D'=0.9775 and R2 = 0.8951 for CEU.
This proxy has lower accuracy for other ethnicities which can be determined here: https://ldlink.nci.nih.gov/?tab=ldproxy
Original PEMT rs12325817; new PEMT proxy: rs3760188 . D' = 0.9978 and R'2 = 0.99 for all populations or 99% accurate match for any ethnicity.