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Mouse Genomes Poster - Genetics 2010

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  • 1. The Mouse Genomes Project Whole genome sequencing and analysis of 17 laboratory and wild-derived mouse strains Thomas M. Keane1, Jim Stalker1, Binnaz Yalchin5, Martin Goodson5, Petr Danecek1, Sendu Bala1, Kim Wong1, Guy Slater1, Avigail Agam5, Ian Jackson2, Laura Reinholdt3, Leah Rae Donahue3, Steve Brown4, Andreas Heger5, Chris Ponting5, Ewan Birney6, Allan Bradley1, Richard Durbin1, Jonathan Flint5, David J. Adams1 1The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK. 2MRC-HGU, Edinburgh, UK. 3The Jackson Laboratory, Bar Harbor, Maine, USA. 4MRC-Harwell, Oxford, UK. 5Wellcome Trust Centre for Human Genetics, Oxford, UK. 6European Bioinformatics Institute, Hinxton, Cambridgeshire, UK. Inbred strains Introduction The Mouse Genomes Project is currently sequencing the genomes of 17 inbred mouse strains with the aim of generating a complete map of the nucleotide 129P2/OlaHsd and structural variation, and ultimately a de novo genome assembly, of each strain. The ability to manipulate the mouse genome, combined with the wealth of disease models and genetic studies available, makes the mouse the premier model Commonly used to make embryonic stem cell lines. organism for genetic approaches to mammalian biology. The clonal nature of inbred mouse strains means that sequence information for a strain can be directly applied to all experiments: past, present and future. Access to complete sequence of multiple inbred strains can therefore provide a permanent 129S1/SvImJ foundation for a systems biology approach to phenotypic variation in the mouse. Commonly used to make embryonic stem cell lines. Progenitor strain of the collaborative cross. Sequencing and Alignment (!" Sequencing Alignment 129S5/SvEvBrd '!" The sequencing for the project was The reads were aligned to the mm9 reference carried out at the Wellcome Trust Sanger &!" using MAQ. The alignments are stored in the Institute in 2009. All of the sequencing BAM alignment format. Each lane is aligned Commonly used to make embryonic stem cell lines. %!" was done on the Illumina GAII platform ?I?JK.FI:2>JL2" <J==2M.FI:2>JL2" individually, merged to the sequencing library ><M@=.FI:2>JL2" with 54, 76, and 108bp reads with an $!" <J==2M.><M@=.FI:2>JL2" level, PCR duplicates removed, and then insert size of 200-600bp. All of the strains A/J have been sequenced to >20x coverage #!" merged to produce a single BAM file per strain. The BAM files are available from the (fig. 1). project ftp site. An asthma model. Progenitor strain of the collaborative cross !" $" /" /" " /" /" " " " /" " " C" '" 8" " C" 6 ./ BC *E $/ H7 ./ .B .B -. +. < 12 +. )* )9 7 ( A. 5* +. 3F ,. and of the heterogeneous stock (HS) cross. ; 6 5. 9G 93 6 +, 9: 03 1. #$ #$ ?@ 5 83 *D 43 0+ 3+ D #. >2 0% 0' )9 9= #$ Fig 1: Sequencing and mapped coverage over the 17 strains AKR/J SNPs High leukemia incidence. Hyporesponsive to diets containing SNP Calling !########" high levels of fat and cholesterol, and resistant to aortic lesion !#######" formation. Progenitor strain of the HS cross. We called SNPs from the BAM files using multiple SNP callers: Samtools, GATK, QCALL, and our local realignment based approach. To create the final list of SNPs, we !######" merged the 4 callsets in various ways (fig. 2) and then compared the SNPs against !#####" BALB/cJ 10Mbp of manually finished sequence in the NOD/ShiLtJ strain. !####" -;<" &=>?;@A" !###" Prone to develop mammary and kidney cancer. Progenitor The Mouse Genomes !##" strain of the collaborative cross and HS cross. Project has generated 65M !#" SNPs (currently dbSNP has !" C3H/HeJ Fig 2: False positive/negative rates in the SNP calls based on 10Mbp of NOD/ShiLtJ 10M mouse SNPs) !$%&$"!$%'!" !$%'(" )*+" ),-" .)/." 012" 0(3./" 0)'4" 0.)" 5.)" /&*+" 675" 687" &9," '&-:4" 9'." Fig 3: Total and private SNP numbers across the strains Spontaneously develops mammary tumours. Highly susceptible to Gram-negative bacterial infections. Progenitor Short Indels Endogeneous Retroviral Elements strain of the HS cross. !####" Calling Strategy It has been estimated that Endogenous Retroviral We used a few different approaches for calling short elements (ERVs) are a significant source (~10%) C57BL/6NJ indels. We called indels from the BAM files using of spontaneous germ line mutations among !###" Samtools, by local realignment around potential indels laboratory mouse strains. Two high-copy families Used in the KOMP and EUCOMM programmes to knockout !##" every gene in the mouse genome. using Dindel, and by aligning de novo assembled of ERVs in particular, IAP and ETns, <=>?@" 7ABC?>D" contigs to call indels. We are currently finalising the have been found to be responsible for the vast !#" short indel callset. majority of these mutations. We have catalogued CAST/EiJ the full repertoire of ERVs insertions across the !" set of 17 strains. 0" " )" " '" " " " " :" 3" 1" " " " 3" +" 8" 6' ,- % *) ! 4 '. ,< 6< 3* 56 56 57 . 1' 38 $' $9 /0 7; /2 .7 *+ '3 & $3 ; + !4 !4 $% !4 67 ) '( & $% Resistant to cancer and infections. Fig 4: Total and private number of IAP insertions CBA/J Structural Variation Renal tubulointerstitial lesions observed at a high frequency. Prone to exocrine pancreatic insufficiency syndrome. We call structural variations (SVs) from the data by observing various types Progenitor strain of the HS cross. of patterns in the alignment of the read pairs vs. the expected fragment size distribution. We use a combination of a few different SV programs such as DBA/2J Breakdancer, Pindel, CND, and single-end read clustering to call the full range of SVs. Develops agressive early hearing loss. Extreme intolerance to alcohol and morphine. Aging DBA/2J mice develop progressive eye abnormalities The automated caller runs a local assembly step in order to do an initial computational validation of the SV calls. LP/J In order to validate our calls, we have manually annotated chr19 for SVs High susceptibility to audiogenic seizures. This strain is also and the compared the calls against our automated caller. We have also Fig 5: Visualisation of a large deletion Fig 6: Visualisation of a large inversion reported to have a fairly high incidence of tumors that develop validated a subset of each type of SV by PCR later in life. Progenitor strain of the HS cross. NOD/ShiLtJ This strain is a polygenic model for type 1 (non-obese) diabetes. Progenitor strain of the collaborative cross. NZO/HILtJ New Zealand Obese. Susceptible to type II diabetes. Progenitor strain of the collaborative cross. PWK/PhJ Strain Distribution Patterns From Variation to Function Susceptibility to type I diabetes and various behavioral traits. The vast majority of SVs are shared between All of the variants called are being compared Progenitor strain of the collaborative cross. the strains owing to the common origins of the against the known QTLs and the ongoing classical laboratory strains. mouse knockout projects such as KOMP/ SPRET/EiJ 300000 EUCOMM in order to determine potential 250000 functional consequences. 200000 Resistant to cancer and infections. Total 150000 Shared WSB/EiJ 100000 50000 Displays extremely long life-span. Progenitor strain of the 0 129P2 129S1_SvImJ 129S5 A_J AKR_J BALBc_J C3H_HeJ C57BL_6N CBA_J DBA_2J LP_J NOD NZO CAST_Ei PWK_Ph Spretus_Ei WSB_Ei collaborative cross. Fig 7: Corresponding knockout of genes completely deleted Fig. 8: Number of genes disrupted by a large deletion Contact: mousegenomes@sanger.ac.uk http://www.sanger.ac.uk/mousegenomes

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