Copy the folderFaculty/Sarah/Tues_merlinto the C Drive

C:/Tues_merlin

MERLIN (and other Abecasis products)Sarah Medland & Kate MorleyBoulder 2009

MERLIN softwarePrograms:GRRMERLINMinXMERLIN-regressPedstatsPedwipePedmerge

We will be using CygwinUnix emulator for windowsOpen by double clickingMigrate to this sessions working directorycd C:/tues_merlinCheck to see the files in the directoryls

Data Input FilesGetting your data into Merlin

Input File TypesPedigree FileFamily relationshipsPhenotype dataGenotype dataData FileDescribes contents of pedigree fileMap FileRecords location of genetic markers

Example Pedigree File

Data File Field Codes

CodeDescriptionMMarker Genotype.AAffection Status.TQuantitative Trait.CCovariate.ZZygosity.S[n]Skip n columns.

First step check relationshipsGRR

GRR - www.sph.umich.edu/csg/abecasis/GRRGraphs mean IBS against sd IBSEither within families or across everyone in the sampleIdeally 200+ markers genotyped in common for each pairIf you want to try this laterSample.ped1300 individuals from 200 familiesGenotyped on 320 markers across the genome

Load grr.pedTick all pairs

GRR is good for findingMZ pairs labeled as sib-pairsDuplicatesDads that arent dadsFull sibs who are half-sibs

Manipulating Data FilesPedmerge

Manipulating Data FilesPedmergeCombine multiple data files Remove columns from a ped fileRecode the dat file so unwanted columns are skippedAssumes ped and dat files have the same prefix example.ped example.dat

Type pedmerge

Checking for genotype errorPedstats

Usagepedstats.exe p pedstats.ped d pedstats.dat

Summarizes pedigree

Trait summary

Pedstats will crash if there are Medelian errors

Draw a diagram for this familyfamiddadmumsexA1A21100m321200f211312m231412f331512f33

3/22/12/33/33/3

Mendelian errorsTry to localize the errorShort term solution delete the bad genotypesLong term solution retype the family at this marker

After fixing the problems

Merlin

MERLINAutomates simple linkage tests (black box)Uses fast multipoint calculations to generate IBD and kinship matricesKey options are vc (variance components analysis) useCovariates (user-specified covariates)Means modelCan incorporate user-specified covariatesVariance components model

Merlin's Standard Variance Components Model - AQEEnvironmental component Non shared, uses identity matrixAdditive Polygenic component Shared among relatives, according to kinship matrixQTL componentShared when individuals are IBD, kinship matrix at marker

What is a Kinship Coefficient?Kinship coefficient (): probability that two alleles sampled at random, one from each individual, are identical by descent

2 x ij = expected proportion of alleles IBD across genome for individuals i and j ( )But will vary at each locus

1 / 21 / 2For MZ twins = .5For Full sibs = .25

General covariance model

Practical overviewUsing the LDL data from chromosome 19 (yesterday afternoons practical)Data cleaningMerging phenotype and genotype dataChecking you data with pedstatsVC analysis in MERLINMERLIN-regress analysisComparison of MERLIN vs Mx

Step #1: combining phenotypes and genotypesStart with four files:pheno.ped + pheno.dat (phenotype data)geno.ped + geno.dat (genotype data)

Combine .ped files and combine .dat files using pedmerge to create 1 pedigree file and 1 .dat file

Practical #1: commandsHave a look at your fileshead Combine your pedigree files and dat files pedmerge pheno geno linkage

Check your file using the head commandCalls up the programmeNames of the two sets of files to be combined (N.B. the matching .ped and .dat files must have the same name)Name of the newly created .ped and .dat files

linkage.ped

Step #2: checking your data with pedstatsPedstats provides preliminary data checksInitial check of input filesPedigree consistencyInformation on genetic marker dataMarker heterozygosityProportion of individuals genotypedTests of Hardy Weinberg equilibrium

Prac #2: commands./pedstats -x-9999.000 -d linkage.dat -p linkage.ped > prac2.out

pedstats -x-9999.000

d linkage.dat p linkage.ped

> prac2.out

Calls up the programmeSpecifies the missing valueIdentify the .dat fileIdentify the .ped fileSend the output to a text file

Step #3: running VC linkage./merlin --vc -x -9999.000 -p linkage.ped -d linkage.dat -m linkage.map > linkage.out

merlin --vc -x -9999.000

-p linkage.ped -d linkage.dat -m linkage.map

> linkage.outCalls up the programmeSpecifies VC linkage and the missing valueIdentify the .ped, .dat, and .map filesSend the output to a text file

So why would we run Mx Merlin can not analyse ordinal dataLimited correction for ascertainmentLimited multivariate linkage repeated measures using the mean and TRT correlationOnly runs an AE model no C or D

A 86% E 14%

Chart1

9.599.593

10.1210.118

12.4612.46

5.565.562

3.243.242

4.754.752

1.791.789

1.461.46

1.981.975

1.341.339

1.31.3

MERLIN

Mx

cM

Chi-square

AE

Change in -2LL

cMAE

MERLINMXmerlin lodmx lodregress lod

09.599.592.052.051.537

510.1210.122.172.171.199

1012.4612.462.672.670.725

155.565.561.191.190.387

203.243.240.690.690.097

254.754.751.021.020.177

301.791.790.380.380.279

351.461.460.310.310.439

401.981.980.420.420.44

451.341.340.290.290.488

501.31.300.280.280.441

cMACE

MERLINMXmerlin lodmx lodregress lod

020.2022.914.334.91

516.6020.953.554.49

1010.7214.212.303.04

156.147.951.311.70

202.444.060.520.87

252.333.300.500.71

302.663.240.570.69

353.454.050.740.87

403.363.460.720.74

453.443.430.740.73

503.163.230.680.69

Change in -2LL

MERLIN

Mx

cM

Chi-square

AE

Sheet2

MERLIN

Mx

cM

Chi-square

ACE

Sheet3

A 60%C 30%E 10%

Chart2

20.222.913

16.620.948

10.7214.212

6.147.951

2.444.055

2.333.302

2.663.239

3.454.046

3.363.464

3.443.428

3.163.228

MERLIN

Mx

cM

Chi-square

ACE

Change in -2LL

cMAE

MERLINMXmerlin lodmx lodregress lod

09.599.592.052.051.537

510.1210.122.172.171.199

1012.4612.462.672.670.725

155.565.561.191.190.387

203.243.240.690.690.097

254.754.751.021.020.177

301.791.790.380.380.279

351.461.460.310.310.439

401.981.980.420.420.44

451.341.340.290.290.488

501.31.300.280.280.441

cMACE

MERLINMXmerlin lodmx lodregress lod

020.2022.914.334.91

516.6020.953.554.49

1010.7214.212.303.04

156.147.951.311.70

202.444.060.520.87

252.333.300.500.71

302.663.240.570.69

353.454.050.740.87

403.363.460.720.74

453.443.430.740.73

503.163.230.680.69

Change in -2LL

MERLIN

Mx

cM

Chi-square

AE

Sheet2

MERLIN

Mx

cM

Chi-square

ACE

Sheet3

Merlin Regress

AimTo develop a regression-based method thatHas same power as maximum likelihood variance components, for sib pair dataWill generalise to general pedigreesIs computationally efficient

Multivariate Regression ModelWeighted Least Squares EstimationWeight matrix based on IBD informationDependent variables = IBDIndependent variables = Trait

General approachStandard regression based methods model trait (D2, S2) in terms of estimated IBD statusY = + + Instead IBD estimate is regressed on trait value = + Y +

Extend to general pedigrees = + Y +

Dependent VariablesEstimated IBD sharing of all pairs of relativesExample:

Independent VariablesSquares and cross-products(equivalent to non-redundant squared sums and differences)Example

EstimationFor a family, regression model is

Estimate Q by weighted least squares, and obtain sampling variance, family by familyCombine estimates across families, inversely weighted by their variance, to give overall estimate, and its sampling variance

Why is that better?Regression methods assume that the dependant variable (left hand side) is normally distributed

Distribution of pi-hat

Why is that better?But central limit theorem works well when data a symmetric with mode in the centreIn a general pedigree, sib-pairs provide the most information on linkageIBD under null hypothesis (with complete inheritance information)0 25%0.5 50%1 25%

Selected SamplesMerlin-regress is particularly suited to the analysis of selected samples

Ordinary variance component analysis (e.g. using Merlin) gives biased QTL estimatesMerlin-regress is designed to be robust to data selection

Example Data BMI 10000 pairs

Selected Sample 500 pairs

Results VC

Results Merlin-Regress

Practical #4: running regress./merlin-regress -x -9999.000 -p linkage.ped -d linkage.dat -m linkage.map --mean ? --variance ? --heritability ? > linkage2.out merlin-regress --vc -x -9999.000

-p linkage.ped -d linkage.dat -m linkage.map

--mean ? --variance ? --heritability ?

> linkage.outCalls up the programmeSpecifies VC linkage and the missing valueIdentify the .ped, .dat, and .map filesSend the output to a text fileSpecify the mean, variance, and heritability from the whole population (Pedstats)

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