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
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"
individually, merged to the sequencing library
with 54, 76, and 108bp reads with an $!"
level, PCR duplicates removed, and then
insert size of 200-600bp. All of the strains
A/J have been sequenced to >20x coverage #!"
merged to produce a single BAM ﬁle per
strain. The BAM ﬁles are available from the
(ﬁg. 1). project ftp site.
An asthma model. Progenitor strain of the collaborative cross !"
and of the heterogeneous stock (HS) cross.
Fig 1: Sequencing and mapped coverage over the 17 strains
High leukemia incidence. Hyporesponsive to diets containing SNP Calling
high levels of fat and cholesterol, and resistant to aortic lesion !#######"
formation. Progenitor strain of the HS cross. We called SNPs from the BAM ﬁles using multiple SNP callers: Samtools, GATK,
QCALL, and our local realignment based approach. To create the ﬁnal list of SNPs, we !######"
merged the 4 callsets in various ways (ﬁg. 2) and then compared the SNPs against !#####"
BALB/cJ 10Mbp of manually ﬁnished sequence in the NOD/ShiLtJ strain. !####" -;<"
Prone to develop mammary and kidney cancer. Progenitor The Mouse Genomes !##"
strain of the collaborative cross and HS cross. Project has generated 65M
SNPs (currently dbSNP has
C3H/HeJ Fig 2: False positive/negative rates in the SNP calls based on 10Mbp of NOD/ShiLtJ
10M mouse SNPs) !$%&$"!$%'!" !$%'(" )*+" ),-" .)/." 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, <=>?@"
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.
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.
This strain is a polygenic model for type 1 (non-obese)
diabetes. Progenitor strain of the collaborative cross.
New Zealand Obese.
Susceptible to type II diabetes.
Progenitor strain of the collaborative cross.
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/
EUCOMM in order to determine potential
250000 functional consequences.
Resistant to cancer and infections.
Displays extremely long life-span. Progenitor strain of the 0
Fig 7: Corresponding knockout of genes completely deleted Fig. 8: Number of genes disrupted by a large deletion