Transcript Approximate genealogical inference

The tangled genome
Gil McVean
The real heroes
PanMap – Genome sequencing of 10 Western Chimpanzees
• Patterns of small insertion and deletion are quite different
and reveal details of DNA repair pathways
• Patterns of recombination in humans and chimpanzees are
highly diverged at the fine-scale, but largely conserved at
broad scales
• There are a surprising number (6+ now ‘confirmed)’) of transspecific polymorphisms, probably maintained through hostpathogen interactions
A tangle of sequence
Difficulties of working with an incomplete reference
Using de novo assembly to find variants
EntireEntire
population
population
Sample 1
Sample 2
Chromosome 1
Prop. sites MIC
Pat
Marlon
Dylan
Marlies
Ruud
Dennis
Using Cortex leads to a high quality set of variants
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Mendel consistency
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Diversity in Western Chimpanzees
• Similar diversity as humans of European origin (0.06%-0.08%)
• Excess of common variants
• 1% variants shared with humans
Non-slippage indels are strongly biased to deletions
13:1 bias toward deletions.
Unexpected peak at 4bp
Indels as indicators of DNA repair processes
Insertions
deletions
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Longest
15 word
agreement
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Indel size
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Indel size
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TGACGAACTTAT
ACTGCTTGAATA
TGACGA
AT
AC
TGAATA
TGACTTAT
TGAC--AT
ACTGAATA
Losing GAAC
A tangle of trees
Myers et al. 2005
The zinc-finger protein PRDM9 determines hotspot location
Myers et al. 2010
PRDM9 Zinc fingers are radically different between humans
and chimps
Perhaps the most diverged gene between humans and chimpanzees
Repeatedly hit by adaptive evolution across mammals
Only known ‘speciation gene’ in mammals
Polymorphic in humans – leads to variation in hotspots and genome instability
Questions
• We know from previous work in a few regions that hotspot
locations tend not to be shared between humans and
chimpanzees
• Calculations suggested that only 40% of human hotspots were
driven by PRDM9 binding
• But..
– Is there any hotspot sharing?
– Do we conservation of recombination rates at any scale?
– What features determine hotspot location in chimpanzees?
The first genome-wide fine-scale map of recombination for a
non-reference organism
Auton et al. 2012
Chimpanzee recombination is dominated by hotspots in a
manner similar to humans
But the hotspots are not in the same locations
Fine-scale profiles around genes are similar
As is rate variation around CpG islands
Substantial PRDM9 diversity, but overlap in predicted binding
sequences
No signal for predicted binding sequences
Similarities at 1Mb scale
Human and chimp recombination rates are correlated at the
chromosomal scale
Human and chimp recombination rates are only correlated at
broad scales
Lower correlation in structural rearrangements
• All, bar one, of the inverted regions are pericentric so change in
position wrt to centromere does not contribute
• Change in proximity to telomere is important
A natural experiment: chromosomal fusion
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human
chimp
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Fusion region shows 3-fold decrease in recombination rate
Fusion region shows 3-fold decrease in recombination rate
A tangle of histories
Distribution of sickle allele
Of malaria
How many variants are shared through descent?
Human polymorphism
Chimpanzee polymorphism
9.4 million autosomal and
261,000 X chromosome
SNPs from 1000 genomes
Pilot 1 YRI (59 individuals)
3.8 million autosomal and 102,000
X chromosome SNPs from PanMap
Pan troglogdytes verus (10
individuals)
SNPs shared by humans and chimpanzees
(33,906 autosomal and 527 X chromosome)
reduce recurrent
mutation
identify potentially
functional coding
variants
Human-chimpanzee
shared coding SNPs
Human-chimpanzee shared haplotypes
At least two shared SNPs in 4kb with the same
LD
reduce artifactual sharing due to known or
cryptic paralogs by filtering out SNPs with
low 50 bp mappability, with high read depth,
or not found in 1000 Genomes Phase 1
135 shared non-synonymous SNPs
1 shared premature stop SNP
200 shared synonymous SNPs
130 regions with
shared haplotypes
outside the MHC
outside the MHC
7 resequenced using
Sanger sequencing
8 with more than two
pairs in LD
Outside of the MHC, six clear-cut cases of trans-species
polymorphisms
FREM3/GYPE
MTRR
All non-coding and putatively regulatory
IGFBP7
In intron of IGFBP7
20kb
IGFBP7 gene structure
4kb
Human-Chimpanzee shared SNPs
Regulatory region in HUVEC
Chromatin state segmentation
by HMM
DNaseI hypersensitive sites
Weak
enhancer
Strong
enhancer
Regulatory region in NHEK and HMEC
Strong
enhancer
Weak
enhancer
Weak
enhancer
Open chromatin by FAIRE
TFBS conserved in human/mouse/rat
TFBS identified by ChIP-seq
SRF
ISGF-3
GATA-2
Average pairwise differences
Primate phastCons score
CUTL1
RelA
Bach1
STAT3
• In total, 130 regions with shared human-chimpanzee
haplotypes. Six clear-cut cases of ancient balanced
polymorphisms.
• None are protein-coding. Eleven occur in non-coding genes
(e.g., 7 in lincRNAs). Eleven compelling cases of regulatory
regions.
• What do these regions have in common?
SNPs shared by humans
and chimpanzees
Shared haplotypes
Glycoproteins
Closest gene within 20 kb of a
human-chimp shared
haplotype (n=26, p=2x10-5,
FDR=0.03)
Shared coding
SNPs
Glycoproteins
Genes human-chimp
coding shared SNP (n=99,
p=0.017, FDR=0.20)
Enrichment of membrane glycoproteins
-> host-pathogen interactions
Project Participants
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University of Oxford
Adam Auton
Rory Bowden
Peter Humburg
Zam Iqbal
Gerton Lunter
Julian Maller
Simon Myers
Susanne Pfeifer
Isaac Turner
Oliver Venn
Peter Donnelly (PI)
Gil McVean (PI)
Biomedical Primate Research Centre
Ronald Bontrop
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University of Chicago
Adi Fledel-Alon
Ryan Hernandez (UCSF)
Ellen Leffler
Cord Melton
Laure Segurel
Molly Przeworski (PI)
•
Funders
Howard Hughes Medical Institute
National Institute of Health
Royal Society
Wellcome Trust
Where next?
Remarkable structural and sequence diversity in chimp
PRDM9
Variation greater than in human populations
Little correlation in fine-scale structure around DNA repeat elements
No activating motif discovered in chimp
CCTCCCT