Introduction to the Data Set

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Figure 1

Image 1 of 1: ‘Figure showing Type 2 diabetes & insulin.’

Created in BioRender.com

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Figure 2

Image 1 of 1: ‘Figure showing intercross breeding design.’

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Input File Format

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Figure 1

Image 1 of 1: ‘Table showing the mouse genotypes as BB, BR, and RR.’

Attie Sample Genotypes

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Figure 2

Image 1 of 1: ‘Figure showing the colors and letter codes of the CC/DO founders.’

CC and DO Founder Alleles

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Figure 3

Image 1 of 1: ‘Figure showing CC and DO genomes’

Example Collaborative Cross and Diversity Outbred genomes

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Figure 4

Image 1 of 1: ‘Table showing the marker, chromosome, and centimorgan position for five markers’

Attie Genetic Map

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Figure 5

Image 1 of 1: ‘Table showing top five rows of physical marker map.’

Attie Physical Map

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Figure 6

Image 1 of 1: ‘Table showing top five rows of phenotype table, including insulin’

Attie Phenotypes

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Figure 7

Image 1 of 1: ‘Table showing the top five rows of covariates table’

Attie Covariates

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Figure 8

Image 1 of 1: ‘Attie Control File’

{alt=‘Figure showing the qtl2 control file’, width=75%}

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Calculating Genotype Probabilities

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Figure 1

Image 1 of 1: ‘Genotype probabilities must be calculated between typed markers; adapted from Broman & Sen, 2009’

{‘a chromosome with two typed markers labeled BR and RR with a locus of unknown genotype between them’}

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Figure 2

Image 1 of 1: ‘Figure showing three-dimensional array of genotype probabilities (genoprobs)’

Three-dimensional genotype probabilities array

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Figure 3

Image 1 of 1: ‘See this page for a graphical review of data structures in R’

{‘a web page showing R data structures including one-dimensional vectors and lists, two dimensional dataframes and matrices, and n-dimensional arrays’}.

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Figure 4

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Figure 5

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Figure 6

Image 1 of 1: ‘Genotype and allele probabilities’

{‘a table showing the probabilities for each of 36 genotypes in the Diversity Outbred followed by a second table showing probabilities for each of the 8 founder alleles’}

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Performing a genome scan

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Figure 1

Image 1 of 1: ‘adapted from Broman & Sen, 2009’

adapted from Broman & Sen, 2009

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Figure 2

Image 1 of 2: ‘Squared error for a single data point’

Image 2 of 2: ‘The line of best fit minimizes the sum of squared errors’

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Figure 3

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Figure 4

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Figure 5

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Figure 6

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Figure 7

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Calculating A Kinship Matrix

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Figure 1

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Performing a genome scan with a linear mixed model

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Figure 1

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Figure 2

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Figure 3

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Performing a genome scan with binary traits

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Figure 1

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Figure 2

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Figure 3

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Performing a permutation test

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Figure 1

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Figure 2

Image 1 of 1: ‘Significance Thresholds with/without Kinship’

{alt=“Comparison of significane threholds”,width=“50%”}

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Figure 3

Image 1 of 1: ‘Significance Threshold Variance’

{alt=“Figure showing decreasing variance of significance threshold estimates with increasing permutations”,width=75%}

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Finding QTL peaks

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Figure 1

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Estimating QTL effects

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Figure 1

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Figure 2

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Figure 3

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Figure 4

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Figure 5

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Figure 6

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Figure 7

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Figure 8

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Figure 9

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Figure 10

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Figure 11

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Integrating Gene Expression Data

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Figure 1

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Figure 2

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Figure 3

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Figure 4

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QTL Mapping in Diversity Outbred Mice

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Figure 1

Image 1 of 1: ‘Benzene study dosing showing 6 hours per day, 5 days per week of inhalation.’

Benzene Study Dosing

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Figure 2

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Figure 3

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Figure 4

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Figure 5

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Figure 6

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Figure 7

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Figure 8

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Figure 9

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Figure 10

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Figure 11

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Figure 12

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Figure 13

Image 1 of 1: ‘SNP Imputation’

{alt=“Figure showing haplotypes being used to impute founder SNPs onto DO genomes.”,width=75%}

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Figure 14

Image 1 of 1: ‘Bone Marrow MN-RET Association Mapping’

{alt=“Plot showing LOD of each SNP in QTL interval”,width=100%}

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Figure 15

Image 1 of 1: ‘Bone Marrow MN-RET Association Mapping’

{alt=“Plot showing LOD of each SNP in QTL interval with genes below”,width=100%}

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Figure 16

Image 1 of 1: ‘Bone Marrow MN-RET Association Mapping’

{alt=“Plot showing LOD of each SNP in QTL interval with genes below and strain distribution pattern above”,width=100%}

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Figure 17

Image 1 of 1: ‘Sult3a1/Sult3a2 Liver eQTL’

{Figure showing LOD plots of Sult3a1 & 2 and CAST-specific haplotype effects}

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Figure 18

Image 1 of 1: ‘Ensembl gene tree of Sult3a1 & Sult3a2’

{Figure showing that Sult3a1 & 2 are paralogs}

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Figure 19

Image 1 of 1: ‘Ensembl Structural Variants’

{alt=“Ensembl viewer showing genes and structural variants under that chromosome 10 QTL peak”,width=100%}

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Figure 20

Image 1 of 1: ‘Ensembl Structural Variants’

{alt=“Ensembl viewer showing genes and structural variants under that chromosome 10 QTL peak”,width=100%}

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Figure 21

Image 1 of 1: ‘DO Founder BAM file pileups’

{alt=“Figure showing CAST with a duplication at the Sult3a1/2 locus.”,width=100%}

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Figure 22

Image 1 of 1: ‘Benezene metabolism pathways’

{alt=“Figure showing benezene metabolism pathways”,width=100%}

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Figure 23

Image 1 of 1: ‘Benzene metabolism hypothesis’

{alt=“Figure showing mice carrying the CAST allele being protected from benezene toxicity”,width=100%}

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Figure 24

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Figure 25

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Figure 26

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