The chordoma genome Peter Campbell, Wellcome Trust Sanger Institute
description
Transcript of The chordoma genome Peter Campbell, Wellcome Trust Sanger Institute
Chordoma• 1% of primary malignant bone
tumours. • 0.5-1/1000,000/year.• 0 - 90 yrs: 55, any age, • Male to female ratio 2:1
29%
33%
32%
• 37% metastasize
• 5% dedifferentiation
• Overall median survival ~7 years
Coding point mutations – 23 chordomas
1. Whole exome sequencing
2. Variant discovery
3. Validation and confirmation
Sample ascertainment
Sample QC
Whole exome library
preparation
Massively parallel sequencing (Illumina)
NGS data QC & filtering
Whole exome
mapping
Normal –Tumour sequence
comparison
Raw variant discovery
Variant annotation
Variant selection
Variant resequencing Roche 454
Somatic variant
confirmation
Define driver mutations
Targeted resequencing
studies
Calculate prevalence
Recurrently mutated genes
sam
ple
gene
gene
freq
(exc
l si
lent
)
gene
cds
(bp)
wt a
llele
mut
alle
le
cons
eque
nce
p. c.
PD3814a AUTS2 2 3780 C A missense p.T1047N c.3140C>APD7186a AUTS2 2 3780 T C essential splice p.? c.660+2T>CPD3820a DCC 2 4344 C T missense p.A455V c.1364C>TPD7186a DCC 2 4344 A G missense p.T1110A c.3328A>GPD3819a DNAH17 2 13458 G A missense p.R1515C c.4543C>TPD7185a DNAH17 2 13458 ag deletion D_ag 2PD4929a FLG 2 12186 T C missense p.H2505R c.7514A>GPD4929a FLG 2 12186 G A missense p.S3149F c.9446C>TPD4929a GPR110 2 2736 G C missense p.N437K c.1311C>GPD7184a GPR110 2 2736 C T missense p.G253R c.757G>APD4188a ITGA10 2 3504 tc deletion D_tc 2PD4188a ITGA10 2 3504 T insertion I_T 1PD4187a LYST 2 11406 ac deletion D_ac 2PD4927a LYST 2 11406 ataac deletion D_ataac 5PD3814a PIK3CA 2 3207 G A missense p.E545K c.1633G>APD7187a PIK3CA 2 3207 G T missense p.M1043I c.3129G>TPD3814a PRICKLE3 2 1885 C A missense p.V130L c.388G>TPD7185a PRICKLE3 2 1885 G T missense p.A301D c.902C>APD3804a PTPRZ1 2 6948 C A missense p.T957N c.2870C>APD6370a PTPRZ1 2 6948 C G missense p.A2267G c.6800C>GPD4187a RELN 2 10383 C G missense p.E2910Q c.8728G>CPD6370a RELN 2 10383 A T missense p.S594T c.1780T>APD3808a SCN2A 2 6018 C T missense p.S1974L c.5921C>TPD4929a SCN2A 2 6018 g deletion D_g 1PD4928a SLC9A10 2 3534 G A missense p.R721C c.2161C>TPD4929a SLC9A10 2 3534 T C missense p.I911V c.2731A>GPD3807a SLCO5A1 2 2547 G C missense p.P341A c.1021C>GPD4926a SLCO5A1 2 2547 C T missense p.R596Q c.1787G>APD4928a VCAN 2 10191 G A missense p.V132I c.394G>APD7185a VCAN 2 10191 T A missense p.D1366E c.4098T>APD3815a XIRP2 2 10650 C A missense p.N2480K c.7440C>APD3821a XIRP2 2 10650 G T missense p.Q1680H c.5040G>T
Summary of exome data• 10-30 coding mutations per patient
• No frequently mutated novel genes
• Recurrent mutations in genes regulating histone modification
• Recurrent mutations leading to activation of PI3K signalling
Hallmarks of chromothripsis• Massive genomic rearrangement in localised chromosomal regions
• Whole chromosomes, chromosome arms or chromosome bands
• Alternating copy number states• 2, 3 or occasionally 4 discrete states with many switches
• Retention of heterozygosity in higher copy number state
• Clustering of breakpoints
• Ends essentially randomly joined in random orientation• Approx equal numbers of rearrangements with ‘deletion-type’, ‘tandem-
duplication-type’ and ‘inverted’ orientation
Rearrangement screens in sarcoma
Histology Number Number with chromothripsis
Osteosarcoma 10 3
Chordoma 14 2
Myxofibrosarcoma 5 3
Pleomorphic sarcoma 2 2
MPNST 2 2
Liposarcoma 2 0
Leiomyosarcoma 2 2
Chondrosarcoma 2 0
Solitary fibrous tumour 1 0
Total 40 14 (35%)
Level of association – rs2305089
CASESA allele freq
CONTROLSA allele freq P value OR 95% CI
Discovery 0.88 0.53 4.4x10-9 6.1 3.1-12.1
Replication 0.83 0.53 2.8x10-4 4.1 1.8-9.5
Combined 4.6x10-12 5.3 3.1-8.9
Conclusions• Chordomas show 10-30 coding mutations per patient
• Frequent incidence of chromothripsis
• Germline predisposition with brachyury SNP
Acknowledgements
Cancer Genome Project• Jose Tubio & Susie Cooke• Patrick Tarpey• David McBride• John Marshall & Keiran Raine• Adam Butler & Jon Teague• Lucy Stebbings & Catherine Leroy• Sarah O’Meara, Laura Mudie• Mike Stratton & Andy Futreal
University College London• Adrienne Flanagan• Roberto Tibrabosco• Fernanda Amary • Nischalan Pillay
Chordoma Foundation• Josh Sommer