Using Merlin in Rheumatoid Arthritis Analyses Wei V. Chen 05/05/2004

Rheumatoid Arthritis  Rheumatoid arthritis (RA) is an autoimmune/inflammatory disorder with a complex genetic component.  Genes in the HLA complex on chromosome 6 play a major role in RA susceptibility, but several other regions also contribute significantly to overall genetic risk.

1st Genome Screen  A non-parametric analysis using SIBPAL in the first screen confirmed linkage of the HLA locus to RA (p < ). However, the analysis also revealed a number of non-HLA loci on chromosomes 1, 4, 12, 16, and 17 with evidence for linkage at a significance level of p< (Jawaheer D, et. al. Am J Hum Genet Apr; 68(4): )

2nd Genome Screen  The combined analysis of both data sets (512 families) showed evidence for linkage at the level of P < at chromosomes 1, 6, 10, 12, 16, 17 and 18. Linkage at HLA was also confirmed (P < 5 x 10(-12)). Inclusion of DRB1*04 as a covariate significantly increased the probability of linkage on chromosome 6. (Jawaheer et. al. Arthritis Rheum Apr;48(4):906-16).

Fine Mapping  High density mapping data on chromosomes 1, 6, 8, 10, 12, 16, 17 and 18  Mlink  GHP / asm  LODPAL  Merlin

Merlin  ?furl=/abecasis/Merlin/index.html ?furl=/abecasis/Merlin/index.html  Merlin can be used for linkage analysis, ibd and kinship estimation, haplotyping, error detection and simulation.linkage analysisibd and kinship estimation haplotypingerror detection simulation

Merlin npl Analysis on fine mapping data  For each chromosome, npl analysis alone, npl analysis with assumed error model, and npl analysis using error-wiped data are done.  npl analysis alone: –merlin -d *dat -p *.ped -m *.map -ff --npl  npl analysis with assumed error model: –merlin -d *dat -p *.ped -m *.map -ff --npl --fit  npl analysis using error-wiped data: –merlin -d *dat -p *.ped -m *.map -ff --error (generates merlin.err) pedwipe -d *.dat -p *.ped (generates wiped.ped, wiped.dat) merlin -d wiped.dat -p wiped.ped *.map -ff --npl

Results  Except for chr18 (in which npl analysis using wiped files gave slightly higher LOD score than in an assumed error model at 54 Mb), all other chromosomes gave best LOD scores in npl analysis using an assumed error model.  Results are consistent with former analyses in terms of the peaks.

Different Quantitative Trait Analysis Options in Merlin  Pedigree wide regression analysis (implemented in MERLIN-REGRESS) is suitable for traits that are approximately normally distributed in the population, even after selection. This method requires specification of the trait mean, variance and heritability in the population.  Variance components analyses (--vc option), can incorporate user-specified covariates (-- useCovariate option), and are designed for unselected, normally distributed traits.  Non-parametric analyses (--qtl and --deviates options) look for excess sharing among individuals in the same tail of the trait distribution. These analyses make no assumptions about the trait distribution, but have low power for normally distributed traits.

Results genome screen including quantitative traits  Using merlin treating RA as a discrete factor and performing an NPL type of analysis  Using merlin-regress to perform pedigree wide regression analysis on quantitative traits  Year2004/Mar04/MerlinRegress/ antiCCP_RFIgM.xl s antiCCP_RFIgM.xl s  Confirmed by Olga & Lei Lei’s software: – 04/Apr04/Alltraits/Ch6/SAS/sumSAS4traits.xls

Troubleshooting in Merlin 1. Program sitting there forever solution: trim the pedigree 2. Message for some families: "SKIPPED: Requires impossible recombination pattern” The most likely cause is that a recombination event was observed between two or more markers separated by a recombination fraction of zero.

Thank you!