Towards a Complete Mouse Haplotype Map Mathew Pletcher Genomics Institute of the Novartis Research Foundation

Selected 2800 loci based on RH map positions Sequenced loci from 8 inbred strains ( A/J, BALBc/ByJ, CAST/Ei, C3H/HeJ, C57BL/6J, DBA/2J, SPRET/Ei, 129SvIm/J ) Identified approximately 15,500 SNPs – all publicly available at dbSNP and the Jax Phenome Database SNPview – a viewer to display SNP distributions and patterns ( SNP Discovery

SNPview ( chromosome view assembly position SSLPs strains

Representative SNPview Window

SNPview Data is Internally and Externally Linked

211 loci C57BL/6J SPRET/Ei CAST/Ei 129/SvImJ C3H/HeJ DBA/2J A/J BALB/cByJ 129/SvImJ C57BL/6J C3H/HeJ DBA/2J A/J BALB/cByJ 129/SvImJ C57BL/6J C3H/HeJ DBA/2J A/J BALB/cByJ Pos, Mbp SNP Distribution and Analysis for Chr. 4 SNPs can be viewed as: SNP alleles Major and minor alleles Haplotypes

DBA/2J A/J C57BL/6J A/J SNPs/500 kbp Chromosome Length Mbp DBA/2J/A/J C57BL/6J/A/J SNP Density on Chromosome 16 Celera data

129/SvImJ C57BL/6J C3H/HeJ DBA/2J A/J BALB/cByJ Pos, Mbp Chr. 10 haplotypes C57BL/6J/DBA/2J A/J/DBA/2J %bins/<100 SNPs Chr.1 Chr.2Chr.3 Chr.4 Chr.5 Chr.6 Chr.7 Chr.8 Chr.9 Chr.10 Chr.11 Chr.12 Chr.13 Chr.14 Chr.15 Chr.16 Chr.17 Chr.18 Chr.19 Chr.X C57BL/6J/A/J C57BL/6J/129X1/SvJ A/J/129X1/SvJ DBA/2J/129X1/SvJ Celera data Genome-wide SNP Density

Distribution of SNPs and SSLPs For two strains (A/J/BALB/cByJ), with 1112 randomly distributed SNPs the mean expected block length is 2.3Mb. Probability of the largest block 40Mb (2.8e-5), 60Mb (4.2e-9), 80Mb (6.4e-13),100Mb (9.6e-17) A/J BALB/cByJ A/J BALB/cByJ 227 loci 436 SSLPs 25 SSLPs(2) 73 SSLPs(4+) A/J BALB/cByJ A/J BALB/cByJ 165 loci 290 SSLPs 15 SSLPs(2) 39 SSLPs(4+) Chr Chr. 5 Pos, Mbp Co-distribution of SNPs and SSLPs Chr. 5 contains many short blocks of common and disparate haplotypes also shows a co-distribution of SSLPs and SNPs. In 5, 2, and 0.5 Mb bins co-distribution of bins was evaluated (1-P=10 -27, and 7.4x )

Chr. 10 haplotypes Utility of Mouse Haplotype Map Mapped mutant to 20MB region on MMU10 Shared haplotype made identifying new markers difficult Used haplotype map to identify most compatible mapping partner for narrowing region

A/J LP/J AKR/J MA/MyJ BALB/cByJ MAI/Pas BTBR MOLF/Ei BUB/BnJ MSM/Ms C3H/HeJ NOD/LtJ C57BL/10J NON/LtJ C57BL6J NZB/BlNJ C57BLKS/J NZW/LacJ C57BR/cdJ PERA/Ei C57L/J PL/J C58/J PWD/Ph CAST/Ei RIIIS/J CBA/J SEA/GnJ CE/J SEG/Pas CZECHII/Ei SJL/J DBA/1J SM/J DBA/2J SPRET/Ei DDK/Pas ST/bJ FVB/NJ SWR/J I/LnJ WSB/Ei JF1/Ms ZALENDE/Ei KK/HlJ 129S1/SvImJ LG/J 129X1/SvJ Beck et al., Nature Genetics (2000) vol. 1, 23–25 Extending the Haplotype Map to the Phenome Project

Initial Set Selection Goal – To pick an evenly spaced SNP set from the Celera collection that are from unique haplotypes and not recent strain specific mutations Preference was given to SNPs where each allele was found in two strains (DBA, 129X1, A/J, B6) Worked on assumption that selection criteria would favor older SNPs – musculus vs. domesticus

Initial Set Make-up Initial design produced nearly 5000 assays 941 SNPs represent cSNPs (splice site, mis-sense, or nonsense mutations) 1 gap bigger than 5MB Biggest Gap – 7.4MB on MMUX

Preliminary Data from SNP Assays Over 2300 SNP assays contain data for 90% of DNAs – Over 4500 assays contain data for at least 24 of the strains Average of 1200 SNPs found between any 2 strain pair combinations Average SNP frequency of roughly 40% in pairwise comparisons

C57BL/10 C57BL/6 C57BLKS MA/MyJ C57BR C58/JC57L/J Beck et al., Nature Genetics (2000) vol. 1, 23–25 C57 Breeding History

C57BL/10C57BL/6 C57BLKS MA/MyJ C57BR C58/J C57L/J Beck et al., Nature Genetics (2000) vol. 1, 23–25 Comparison of SNP-based Clustering to Breeding History MA/MyJ C58/J C57L/J C57BR C57BLKS C57BL/6 C57BL/10

SNP Data Detects Common Heritage Beck et al., Nature Genetics (2000) vol. 1, 23–25

Relationship of Wild-derived Mouse Strains M.m. musculus M.m. molossinus M.m. domesticus M.m. castaneus M. spretus CZECHII/Ei JF1 PERA/Ei CAST/Ei SPRET/Ei MAI/Pas MSM/Ms WSB/Ei SEG/Pas PWD/PH MOLF/Ei ZALENDE/Ei Prager et al. (1998) Mouse Genetics and Phylogeography

Silver (1995) Mouse Genetics: Concepts and Applications SNP Frequency M.m. musculus M.m. molossinus Lack of Diversity Between M.m. musculus and M.m. molossinus Wade et al. (2003) Nature 420, Ogura et al. (2003) Genomics 81,

A Domesticus Haplotype M.m. domesticusM.m. musculusM.m. domesticus SNP Frequency ? M.m. domesticus US Switz. Peru

Future Steps Do survey sequencing of wild-derived strains to assess true diversity Continue to fill in gaps in data set and continue to expand SNP collection Attempt to use data set to map phenotypic variants

Tim Wiltshire Whitney Barnes Patrick Merritt Candace Motta Franzmarie Lippincott Deborah Stradley Niusha Ziaee Serge Batalov Steve Kay Acknowledgements