1. A multi-strain, high-resolution mouse haplotype map reveals three distinctive genetic signatures
Laboratory of Population Genetics

2. Motivations
An accurate high-resolution haplotype map of the mouse genome enables prioritization of QTL candidate genes
Different haplotype block structures have been reported in different studies
>10MB block size in GNF study (Wiltshire et al, PNAS 2003)
Mb block size in WI study (Wade et al, Nature 2002)
kb block size in a 8MB region chr 19 (Park et al, Genome Research 2003)
Analysis of a 10Mb region on chromosome 7 using the Celera mouse SNPs reveals a different genetic variation pattern
Celera mouse chromosome 16 SNP data are publicly available
Laboratory of Population Genetics

3. Objectives
Develop an integrated, high resolution, multi-strain mouse haplotype map
Compare the haplotype structure derived from high-density SNPs with those derived from low density markers
Perform experimental validation in regions of conflict and in regions of interest across 20 inbred strains
Analyze biological factors that have contributed to the formation mouse genetic variation patterns
Laboratory of Population Genetics

4. Data Sources Chromosome 16 reference sequence
MGSCv3 (NCBI build 30, Feb. 2003)
SNP Data
Laboratory of Population Genetics

5. Construction of Multi-Strain Haplotype Blocks with High Density SNP Markers
Method
Greedy algorithm that starts with two-haplotype per block
Seed: a minimum of two adjacent SNPs with no-ambiguity in haplotype assignment
Singleton SNP that breaks the two-haplotype configuration does not affect block extension
Results
2,083 blocks
65,068 (95% ) Celera SNPs in 5 laboratory inbred strains.
Laboratory of Population Genetics

6. Distribution of Haplotype Block Size
Laboratory of Population Genetics

7. Blocks with Different Size Have Similar SNP Density Distribution
Laboratory of Population Genetics

8. A 2.4-Mb Haplotype Block with Varying SNP Density
DBA/2J
A/J
129X1/SvJ
129S1/SvImJ
C57BL/6J
#SNP/10kb
400000
800000
>20
11-20
6-10
2-5 1
#SNP/10kb
SNP
Experimental
Validation
B6 Allele
Non-B6 Allele
374 SNPs over 2.4Mb. Avg Density=0.156/kb. 153 of which were in hotspots (red and orange)

9. A 2.4-Mb Region with High SNP Density but Heterogeneous Variation Pattern (Erosion)
Antaxin 2 binding protein 1 (nucleic acid binding, RNA binding)
129S1
DBA/2J
A/J
129X1 B6
>20
11-20
6-10
2-5 1
#SNP/10kb
B6 Allele
Non-B6 Allele
Missing Data
Laboratory of Population Genetics

10. Details of Haplotype Erosion Across 160KB
Location
5,721,639-5,878,633bp on chr16
Blocks
179SNPs in 14 blocks with the major pattern
116 SNPs in 19 blocks with the other patterns
49 Singleton SNPs
129S1/SvImJ
DBA/2J
A/J
129X1/SvJ
C57BL/6J
SNP Density
Laboratory of Population Genetics

11. Other Heterogeneous Haplotype Patterns
2) Segmentation
129S1
DBA/2J
A/J
129X1
C57BL/6J
SNP Density
Laboratory of Population Genetics

12. Other Heterogeneous Haplotype Patterns
3) Segmentation with Erosion
4) Random
Laboratory of Population Genetics

13. Three Major Variation Patterns
SNP Deserts: >1Mb with <0.5SNP per 10kb
Large Blocks: >300kb “melded” haplotype blocks with consistent variation patterns
Block Breakers: regions with heterogeneous variation patterns

14. Predictive Power of Haplotype Structures
Test the ability to use the haplotype structure in one study to predict allelic variations in another study
Our Haploytpe Blocks
98% accuracy on WI B6/129S1 SNPs that do not overlap with Celera SNPs
92% accuracy on GNF B6/129S1/AJ/DBA haplotypes
WI B6/129S1 Haplotype Blocks
74% accuracy on Celera B6/129S1 genotypes
85% accuracy on GNF B6/129S1 genotypes
80% GNF markers are non-polymorphic across inbred strains used in Celera and WI shotgun sequencing
Laboratory of Population Genetics

15. SNP Deserts in Chromosome 16
6 >1Mb SNP deserts in the five inbred strains used for Celera shotgun sequencing
All 6 SNP deserts overlap with WI SNP deserts conserved across all WI strains
0.21% WI B6/SvJ SNPs in our SNP deserts
0.97% WI all SNPs in our SNP deserts
5 out of the 6 deserts have at least one end as part of large haplotype blocks
SNP deserts are not genetically homogeneous
There are STRP polymorphisms
There are indel polymorphisms
Laboratory of Population Genetics

16. Validation of a SNP Desert N
NNNNNN NN011111N
Other Lab inbred
B6,AKRJ
Skive
Czech
5 STRPs and 1 SNP in a 15kb SNP desert in all laboratory inbred strains
The STRPs and the 1 SNP have the same variation pattern as the neighboring regions with high SNP density among the laboratory inbred strains
Additional 120 SNPs discovered between the laboratory inbred strains and feral inbred strains
Laboratory of Population Genetics

17. A Gene-Coding Region with Varying SNP Density
WI SNPs
Celera SNPs
Mis-sense??
silent e3
e12
down
UTR3 e4
mRNA sequence is MGC clone: from mammary tissues metastasized to lung
The 10kb region is included in a 77kb haplotype block with 44 SNPs
Variations in the mRNA sequence do not overlap with WI and Celera SNPs
>=2 haplotypes in the regions??
Laboratory of Population Genetics

18. Results of Experimental Validation
>down
hap s1;129x1;AJ;BALB;C3HHe;DBA
hap AKRJ;C57BL
hap Czech;Skive
>UTR3 /num_SNP=25 /num_strain=10 /num_hap=4
hap s1;129x1;AJ;BALB;C3HHe;DBA2J;
hap N AKRJ;
hap Czech;Skive;
hap C57BL;
>NM_145481_e12 /num_SNP=7 /num_strain=10 /num_hap=4
hap s1;129x1;AJ;BALB;
hap AKRJ;
hap C3HHe;C57BL;DBA2J;
hap Czech;Skive;
>e4
hap1 0 Others
hap2 1 Czech;Skive
Mis-sense SNP does not validate
Silent SNP validates

19. Laboratory of Population Genetics
Mouse cSNPs
Synonymous: 185
Non-synonymous: 100
Laboratory of Population Genetics

20. Haplotype Diversity in 43 Target Regions Assayed by 94 Amplicons
Laboratory of Population Genetics

21. Conclusions
We have compiled an accurate, multi-strain, high-resolution haplotype map for mouse chromosome 16
We have discovered three distinctive genetic variation patterns for laboratory inbred mouse: SNP deserts, large blocks and block breakers
Large haplotype blocks may consist regions with varying SNP density
Selection in inbreeding may have an effect on SNP distribution in protein coding regions as well as SNP rate in gene coding regions
Our method is scalable for whole-genome analysis
Laboratory of Population Genetics

22. Acknowledgement Laboratory of Population Genetics
Ken Buetow
Kent Hunter
Michael Gandolph
Bill Rowe
Michael Edmonson
Jenny Kelly
University of Wisconsin
Rob Williams
Laboratory of Population Genetics