Table 1.

Regression models for detecting ancestry-associated molecular correlates

Alternative hypothesis	Method	Example model
Somatic alteration is associated with local ancestry	Logistic Regression	somatic alteration ~ local ancestry + percentage of EUR ancestry + percentage of AFR ancestry
Ancestry is associated with arm-level SCNA	Logistic Regression	ancestry ~ arm-level SCNA + aneuploidy + genome doubling + age + gender + subtype
Ancestry is associated with TMB, aneuploidy, and IMS	Logistic Regression	ancestry ~ aneuploidy + TMB + IMS + age + gender + subtype
DNA methylation is associated with ancestry	Linear Regression	DNA methylation level (β value) ~ ancestry + tumor purity + age + gender + subtype
mRNA expression is associated with ancestry	Linear Regression	log2(RPM) ~ ancestry + TCGA plate number + subtype
miRNA expression is associated with ancestry	Linear Regression	log2(RPM+1) ~ ancestry + subtype
Pathway activity is associated with ancestry	Linear Regression	IPL ~ ancestry + subtype

RPM: Read Per Million. IPL: Integrated Pathway Level.