!QTL analysis via Pihat method !Using marker1 !Using MZ and DZ twins !Analysis of platelet count !Twelve year olds #define nvar 1 ! different for multivariate #define nsib 2 ! number of siblings #NGroups 3 G1: Parameter Estimates Calculation Begin Matrices; X Lower nvar nvar Free !genetic background W Lower nvar nvar Free !dominance Z Lower nvar nvar Free !unique environment L Full nvar 1 Free !QTL effect M Full nsib nvar Free !means H Full 1 1 R Full 1 1 End Matrices; Specify M 10 10 Matrix H .5 Matrix R .25 Begin Algebra; A= X*X'; !additive genetic variance D= W*W'; !dominance variance E= Z*Z'; !unique environmental variance Q= L*L'; !variance due to QTL V= A+Q+D+E; !total variance T= A|Q|D|E; !parameters in one matrix for standardizing S= T@V~; !standardized variance component estimates End Algebra; Labels Row S standest Labels Col S a^2 q^2 d^2 e^2 Labels Row T unstandest Labels Col T a^2 q^2 d^2 e^2 End G2: Monozygotic twins Data NInput=13 Rectangular File=marker1.dat Labels famid indid1 indid2 pibd0 pibd1 pibd2 zygosity plt11 plt12 plt13 plt21 plt22 plt23 Select if zygosity <3; Select plt11 plt21; Begin Matrices = Group 1; Means M; Covariance A+D+Q+E | A+D+Q _ A+D+Q | A+D+Q+E; End G3: Dizygotic twins Data NInput=13 Rectangular File=marker1.dat Labels famid indid1 indid2 pibd0 pibd1 pibd2 zygosity plt11 plt12 plt13 plt21 plt22 plt23 Select if zygosity >2; Select pibd0 pibd1 pibd2 plt11 plt21; Definition pibd0 pibd1 pibd2; Begin Matrices = Group 1; K Full 3 1 !IBD probabilities (from Genehunter) F Full 1 3 !coefficients 0,0.5,1 for pihat End Matrices; Specify K pibd0 pibd1 pibd2 Matrix F 0. 0.5 1.0 Begin Algebra; P= F*K; !estimate of pihat End Algebra; Means M; Covariance A+D+Q+E | H@A+R@D+P@Q _ H@A+R@D+P@Q | A+D+Q+E; Start 1 All Start 2.8 M 1 1 1 Option NDecimals=3 Option Iterations=5000 Option Multiple Issat End ! Test significance of QTL effect Drop L 1 1 1 End