David
Aylor
Fernando
Pardo‐Manuel
de
Villena
Rich
–
captures
diversity
of
8
founder
strains
Random
–
novel
allele
combinations
Robust
–
appropriate
power
for
mapping
Reproducible
–
inbred
A/J
C57BL6/J
129S1/SvImJ
NOD/Lt
NZO/HlLt
PWK/PhJ
CAST/EiJ
WSB/EiJ
17
29
22
Funnels
• 
• 
• 
• 
• 
• 
• 
97
Males
68
Funnels
Generations
F5‐F12
Affymetrix
390K
SNP
array
165K
Fully
Informative
SNPs
Phased
Heterozygous
Loci
Assigned
Founder
Identity
University
of
North
Carolina
•  Array
Performance
Estimates
•  Funnel
Constraints
 
 
 
 
Mitochondria
Y
Chromosome
Heterozygous
Allele
Combinations
Sibling
Genotype
Combinations
•  Founder
Contributions
•  Genome‐wide
Heterozygosity
Impossible
Allele
Combinations
in
Subsequent
Generations
Mitochondria
129S1/vImJ
Y
Chromosome
NZO/HILtJ
NOD/LtJ
NZO/H1LtJ
Chr 1
Chr 7
Chr 9
•  High
quality
SNP
data
•  High
con]idence
haplotype
reconstruction
•  Uniform
distributions
of
founder
alleles
•  New
allele
combinations
between
loci
•  Progress
toward
genome‐wide
homozygosity
Breeding
Genotyping
Lisa
Branstetter
Samie
Ahmed
Darla
Miller
Tim
Bell
Elissa
Chessler
Ryan
Buus
John
Calloway
Biological
Samples
Brittany
Hill
Francis
Collins
Mike
Vernon
Samir
Kelada
Computation
Array
Design
Andrew
Hulbert
Yueming
Ding
Catie
Welsh
Hyuna
Yang
Wei
Wang
Gary
Churchill
Leonard
McMillan
Funding
NCI
(1U01
CA134240)
Systems
Genetics
Resource
Consortium
NIGMS
(1P50
GM076468)
Genome
Dynamics:
Evolution,
Organization
and
Function
UNC
University
Cancer
Research
Fund
Lineberger
Comprehensive
Cancer
Center