Transcript Talk

Efficient Computation of
Minimum Recombination With
Genotypes (Not Haplotypes)
Yufeng Wu and Dan Gusfield
University of California, Davis
CSB 2006
1
Haplotypes/Genotypes
• Diploid organisms have two copies of (not
identical) chromosomes. A single copy is a
haplotype, vector of 0,1. The mixed
description is a genotype, vector of 0,1,2. At
each site,
– If both haplotypes are 0, genotype is 0
– If both haplotypes are 1, genotype is 1
– If one is 0 and the other is 1, genotype is 2
• Key fact: easier to collect genotypes, but
many downstream applications work better
with haplotypes
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Haplotyping
Sites: 1 2 3 4 5 6 7 8 9
Haplotype
Genotype
Phasing the 2s
0 1 1 1 0 0 1 1 0
0 1 0
1
1 1 0 1 0 0 1 0 0
1 1 1
0
2 1 2 1 0 0 1 2 0
2 1 2 1 0 0 1 2 0
Haplotype Inference (HI) Problem: given a set of n
genotypes, infer the real n haplotype pairs that form the
given genotypes
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Two-stage Approach
• Given a set of genotypes G, we are interested
in downstream problems
• Many HI solutions for G
• Two stage: first infer the “correct” HI solution
from the genotypes, then do the downstream
analysis with the inferred haplotypes
• Haplotype inference: extensively studied and
believed to be accurate to certain extent
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One-stage Approach
• What effect does the haplotyping
inaccuracy has on downstream
questions?
• Our work: directly use genotype data for
downstream problems
– Without fixing a choice for the HI solution
– Minimum recombination problem
5
Recombination: Single
Crossover
• Recombination is one of the principle genetic
force shaping variation within species
• Two equal length sequences generate a third
equal length sequence
110001111111001
11000 0000001111
Prefix
000110000001111
Suffix
breakpoint
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Kreitman’s Data (1983)
0000000011000000001101110111100000000000000
0010000000000000001101110111100000000000000
0000000000000000000000000000000000010000101
0000000000000000110000000000000000010011000
0001100010110011110000000000000000001000000
0010000000000001000000000000001010111000010
0010000000000001000000000000011111101000000
1111100010111001000000000000011111101100000
1111100010111001000000000000011111101100000
1111100010111001000000000000011111101100000
1111111110000101000010001000011111101000000
Question: what is the minimum number of
recombinations needed to derive these sequences?
Assume at most 1 mutation per site
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Minimizing Recombination
• Compute the minimum number of
recombinations (Rmin) for deriving
a set of haplotypes, assuming at
most 1 mutation per site
– NP-hard in general
– Heuristics
– Lower bounds on Rmin
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Lower Bounds on Genotypes
• For a particular recombination lower bound
method L, what is the range of possible
bounds for L over all possible HI solutions?
– MinL(G): minimum L over all HI solutions for G.
– MaxL(G): maximum L over all HI solutions for G.
• This paper: HK bound, connected component
bound and relaxed haplotype bound.
– Polynomial-time algorithms for MaxHK, MinCC.
– Heuristic method for relaxed haplotype bound.
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Lower Bound: Incompatibility
12345
Incompatibility Graph (IG):
a 00010
A node each site, edge
b10010
between incompatible pair
c 00100
M
d10100
e 01100
f 01101
g00101
1 2 3 4 5
• Two sites (columns) p, q are incompatible if columns
p,q contains all four ordered pairs (gametes): 00, 01,
10, 11
• Sites p,q are incompatible  A recombination must
occur between p,q
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HK Bound (1985)
• Arrange the nodes of the
incompatibility graph on the
line in order that the sites
appear in the sequence.
• HK bound = maximum number
of non-overlapping edges in
incompatibility graph (IG).
• Easy to compute for haplotype
data.
1
2
3
4
5
HK Lower Bound = 1
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IG for HI Solutions
HI1
01010
10101
00202
22200
HI2
01010
01010
10101
10101
00000
00101
01000
10100
01010
01010
10101
10101
00001
00100
00000
11100
HK = 1
1
2
3
4
5
HK = 3
1
2
3
4
5
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HK Bounds on Genotypes
• Known efficient algorithm for MinHK(G)
(Wiuf, 2004).
• This paper: polynomial-time algorithm
for MaxHK(G)
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Maximal Incompatibility Graph
G
01010
10101
00202
22200
MIG(G)
1
2
3
4
5
E(G) = {12, 23,
35}
• An edge between sites p and q if there is a
phasing of p, q so p and q are incompatible
– Each pair of sites is considered independently
• E(G): a maximum-sized set of nonoverlapping edges in MIG(G)
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MaxHK(G)
• Claim: MaxHK(G) = |E(G)|
• MaxHK(G)  |E(G)|
– MIG(G): supergraph of IG(H) for any HI solution H
• If we can find an HI solution H, whose every
pair of sites in E(G) is incompatible, then
HK(H)  |E(G)|
• Together, MaxHK(G) = |E(G)|
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Finding such an H
MIG(G)
• Phase sites from left to right.
• Each component in E(G) is a simple path
• Each site only constrained by at most one site to the left
Phasing G for Incompatibility
01010
01010
10101
10101
00?0?
00?0?
0??00
1??00
01010
01010
10101
10101
00?0?
00?0?
00?00
11?00
01010
01010
10101
10101
0010?
0000?
00000
11100
• No matter how a previous site p is phased, can always
phase this site q to make p, q incompatible
Haplotyping With Minimum
Number of Recombinations
•
Compute Rmin(G)
– Haplotyping on a network with fewest
recombinations
•
•
•
NP-hard
This paper: A branch and bound method
computing exact Rmin(G) for data with small
number of sites
APOE data: 47 non-trivial genotypes, 9 sites
– Our method: 2 minutes, Rmin(G) = 5
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Application: Recombination
Hotspot
•
•
•
Recombination hotspot: regions where
recombination rate is much higher than
neighboring regions
Previous study (Bafna and Bansal, 2005): a
recombination lower bound with inferred
haplotypes were used to identify
recombination hotspots
Our work: compute the exact Rmin(G) with
genotypes for a sliding window of a small
number of SNPs to detect recombination
hotspots
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MS32 data (Jeffreys, et al.
2001)
Result from haplotypes
(Bafna and Bansal, 2005)
Result from original
genotypes (this paper)
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Other Applications
• Finding true Rmin from genotypes G
– Two stage approach: run PHAS to get an HI
solution H, and compute Rmin(H)
– One stage approach: directly compute
Rmin(G)
• Accuracy of haplotype inference on a
minimum network
• Simulation results: comparable, slightly
weaker and non-conclusive
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Summary
• Main goal of this paper: develop
computational tools for the minimum
recombination problem with genotypes
– Polynomial-time algorithm for MaxHK and MinCC
problems
– Practical heuristics for other problems
– Simulation results to several application questions
are not conclusive
– Our tools facilitate the study of these problems
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Thank You
• Software: available upon request
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