QTDT - Quantitative TDT 2.2.1 (c) 1998-2001 Goncalo Abecasis (goncalo@well.ox.ac.uk) This program implements tests described by Abecasis et al, Am J Hum Genet 66:279-292 (2000) Abecasis et al, Eur J Hum Genet 8:545-551 (2000) and others The following parameters are in effect: QTDT Data File : keavney.dat (-dname) QTDT Pedigree File : keavney.ped (-pname) QTDT IBD Status File : merlin.ibd (-iname) Missing Value Code : -99.999 (-xname) Covariates : USER SPECIFIED (-c{p|s|u|-|}) Association Model : ORTHOGONAL (-a[a|d|f|m|o|p|r|t|w|-]) Full Model Variances : NOT MODELLED (-v{e|c|g|n|t|a|d|-|}) Null Model Variances : NON SHARED (-w{e|c|g|n|t|a|d|-|}) & POLYGENIC & ADDITIVE Parent of Origin Effects : NONE (-o[f|t|m|p|-]) Monte-Carlo Permutations : 0 (-m9999) Numeric Minimizer : NELDER AND MEAD (-n[n|p]) Transmission Scoring : FULL PEDIGREE (-t[n|p]) Additional Options --dominance, --snp, --multi-allelic, --references, --exclude-founder-phenotypes Online documentation http://www.well.ox.ac.uk/asthma/QTDT Comments, bugs: goncalo@well.ox.ac.uk The following models will be evaluated... NULL MODEL Means = Mu + B Variances = Ve + Vg + Va FULL MODEL Means = Mu + B + W Variances = Ve + Vg + Va Testing trait: Angiotensin ============================================= Testing marker: t-5491c --------------------------------------------- Allele df(0) LnLk(0) df(T) LnLk(T) ChiSq p 1 : 387 498.43 386 476.81 43.25 5e-11 ( 186/392 probands) 2 : 387 498.43 386 476.81 43.25 5e-11 ( 186/392 probands) Testing marker: a-5466c --------------------------------------------- Allele df(0) LnLk(0) df(T) LnLk(T) ChiSq p 1 : 385 496.28 384 476.57 39.44 3e-10 ( 190/390 probands) 2 : 385 496.28 384 476.57 39.44 3e-10 ( 190/390 probands) Testing marker: t-3892c --------------------------------------------- Allele df(0) LnLk(0) df(T) LnLk(T) ChiSq p 1 : 392 504.91 391 476.20 57.43 4e-14 ( 214/397 probands) 2 : 392 504.91 391 476.20 57.43 4e-14 ( 214/397 probands) Testing marker: a-240t --------------------------------------------- Allele df(0) LnLk(0) df(T) LnLk(T) ChiSq p 1 : 393 510.94 392 487.95 45.98 1e-11 ( 196/398 probands) 2 : 393 510.94 392 487.95 45.98 1e-11 ( 196/398 probands) Testing marker: t-93c --------------------------------------------- Allele df(0) LnLk(0) df(T) LnLk(T) ChiSq p 1 : 384 500.85 383 477.77 46.17 1e-11 ( 188/389 probands) 2 : 384 500.85 383 477.77 46.17 1e-11 ( 188/389 probands) Testing marker: t-1237c --------------------------------------------- Allele df(0) LnLk(0) df(T) LnLk(T) ChiSq p 1 : 369 473.17 368 446.30 53.75 2e-13 ( 199/374 probands) 2 : 369 473.17 368 446.30 53.75 2e-13 ( 199/374 probands) Testing marker: g2215a --------------------------------------------- Allele df(0) LnLk(0) df(T) LnLk(T) ChiSq p 1 : 364 459.87 363 424.37 71.01 4e-17 ( 200/369 probands) 2 : 364 459.87 363 424.37 71.01 4e-17 ( 200/369 probands) Testing marker: i/d --------------------------------------------- Allele df(0) LnLk(0) df(T) LnLk(T) ChiSq p 1 : 393 494.61 392 457.65 73.92 8e-18 ( 216/398 probands) 2 : 393 494.61 392 457.65 73.92 8e-18 ( 216/398 probands) Testing marker: g2350a --------------------------------------------- Allele df(0) LnLk(0) df(T) LnLk(T) ChiSq p 1 : 360 454.49 359 418.62 71.74 2e-17 ( 187/365 probands) 2 : 360 454.49 359 418.62 71.74 2e-17 ( 187/365 probands) Testing marker: 4656ct --------------------------------------------- Allele df(0) LnLk(0) df(T) LnLk(T) ChiSq p 1 : 382 475.62 381 441.21 68.82 1e-16 ( 215/387 probands) 2 : 382 475.62 381 441.21 68.82 1e-16 ( 215/387 probands)