Download Themes of large scale SNP association studies in melanoma

Genetic Variants and Melanoma Risk
Simon N. Stacey
SNPs and Association Studies:
Freq SNP-A in Cases / Freq SNP-A in Controls
AAGGTTA
to
~
Risk of Disease with SNP-A / Risk of Disease
without SNP-A
~
Relative Risk (RR) or Odds Ratio (OR)
ATGGTTA
Marker of Predisposition
Location, Location, Location
Themes of large scale SNP association studies in melanoma :
Searching for melanoma variants among:
•
Genes affecting variation in pigmentation in Europeans
•
Genes affecting nevus counts
•
Genes affecting related cancers: Basal Cell Carcinoma (BCC)
•
Genes directly associated with melanoma risk
•
Rare variants detected by large scale sequencing
Multiple Testing in Genome Wide Association Studies
•
Bonferroni adjusted threshold for genome-wide significance:
•
300,000 SNPs is 1.7 x 10-7
•
1M SNPs is 5 x 10-8
•
5M SNPs is 1 x 10-8
Genetic variants that affect pigmentation traits in Europeans
Using pigmentation to detect cancer loci: chr20 ASIP locus:
Melanoma risk variants in MC1R pathway:
ASIP
Pigmentation-associated variants in
MC1R, ASIP and Tyrosinase loci confer risk
of both Melanoma and BCC
Variants affecting nevus count confer risk of melanoma:
Loci near CDKN2A and PLA2G6 (22p13) implicated
Do variants that confer risk of BCC also confer risk of melanoma?
BCC variant in TERT-CLPTM1L associated with lung,
bladder, prostate cancer
Variants in CDKN2A/B are also associated with melanoma,
breast cancer, NPC and glioma
BCC and multi-cancer TERT variant is protective against melanoma:
Association of TERT-CLPTM1L rs401681 with BCC and CM
Number
Frequency
Sample Group
Risk Allele
Cases
Controls
Cases
Controls
OR
95% CI
P
Iceland BCCa
C
1,850
34,998b
0.60
0.55
1.23
(1.14, 1.33)
6.0 x 10-8
Eastern Europe BCCa
C
525
525
0.62
0.57
1.19
(1.00, 1.42)
4.5 x 10-2
U.S. BCC
C
908
826
0.59
0.56
1.12
(0.98, 1.28)
0.10
Spain BCC
C
185
1,758
0.55
0.54
1.08
(0.86, 1.35)
0.50
All Non-Icelandic BCC
C
1,618
3,109
NA
NA
1.13
(1.03, 1.25)
1.1 x 10-2
All BCC Combined
C
3,468
38,107
NA
NA
1.20
(1.13, 1.27)
4.8 x 10-9
Iceland CMa
C
591
34,998b
0.52
0.55
0.90
(0.80, 1.01)
7.9 x 10—2
Sweden CMa
C
1,056
2,631
0.49
0.54
0.85
(0.77, 0.94)
1.2 x 10—3
Spain CMa
C
748
1,758
0.51
0.54
0.90
(0.80, 1.02)
9.4 x 10—2
Holland CM
C
736
1,832
0.53
0.57
0.83
(0.73,0.94)
3.9 x 10—3
Austria CM
C
152
376
0.53
0.53
0.98
(0.75,1.27)
0.88
Italy CM
C
560
368
0.49
0.56
0.74
(0.62, 0.89)
1.2 x 10—3
All CM Combined
C
3,843
41,963
NA
NA
0.86
(0.81, 0.91)
5.0 x 10—8
•
Related to the different roles of senescence and genome stability in melanocyte
and keratinocyte transformation?
GWAS directly for melanoma associated variants:
•
•
•
•
Bishop et al. 2009 Nature Genetics 41, 920-925
Amos et al. 2011 Human Molecular Genetics 20, 5012-5023
MacGregor 2011 Nature Genetics 43, 1114-1118
Barrett et al 2011 Nature Genetics 43, 1108-1113
Chromosomal region
1q21
1q42
2q33
5p15
5p13
6p25
9p23
9p21
11q13
11q14
11q22
16q24
15q13
20q11
21q22
22q13
•
•
•
•
•
Candidate Gene(s)
ARNT / SETDB1
PARP1
CASP8
TERT
SLC45A2
IRF4
TYRP1
MTAP-CDKN2A
CCND1
TYR
ATM
MC1R
OCA2
ASIP
MX2
PLA2G6
Pigmentation Effect
Cancer Phenotype
Eye Color, Hair Color, (Nevus Count?) Melanoma
Melanoma
Melanoma
Nevus Count
Melanoma Protective / BCC Risk
Hair Color, Eye Color
Melanoma, BCC
Freckling, Hair Color
Uncertain
Eye Color
Melanoma
Nevus Count
Melanoma (BCC, another SNP)
Melanoma
Eye Color, Freckling
Melanoma, BCC
Melanoma
Hair Color, Freckling
Melanoma, BCC
Eye Color
Uncertain
Hair Color, Freckling
Melanoma, BCC
Melanoma
Nevus Count
Melanoma
Majority of variants are associated with known risk factors
Effect on risk factors often does not fully account for effect of variant on melanoma
Some pigmentation variants do not appear to be associated with melanoma risk
Increasing number of variants have no discernable effect on pigmentation
Variants are common and with modest effects
Search for rare variants through genome sequencing:
TA Manolio et al. Nature 461, 747-753 (2009) doi:10.1038/nature08494
High power is required to detect association of rare variants:
•
Shows OR required to detect variants to P= 2x10-9
at 80% power
•
Bonferroni GWS for 30M variants
•
Rare variants need large effects and/or large
sample sizes to detect by association
•
Sequence data from large numbers of people are
required
•
Integrated approach using both statistical and
biological data is required
Icelandic Sequencing Project:
•
Whole genome sequencing of 1,800 Icelanders
•
Average coverage 18x
•
Identified 23 million SNPs and 8 million short indels and added functional annotation
•
Used as a training set to impute genotypes of 72,000 SNP phased, chip-typed Icelanders
•
Phasing and imputation allows us to carry out case:control associations studies based
on full-resolution genomic sequence data (i.e. 30 million variants)
Icelandic Sequencing Project discovers BCC variant in TP53:
Icelandic Sequencing Project results for MITF E318K:
•
Bertolotto et al 2011 Nature and Yokoyama et al 2011 Nature reported variant E318K in
MITF in familial and sporadic melanoma
•
Integrated association and biological data
•
Investigated in Icelandic sequencing project data and replication cohorts:
MITF E318K
GROUP
ICELAND
SWEDEN
VALENCIA
ZARAGOZA
VIENNA
MILAN
HOLLAND
P value
3.61E-04
7.92E-03
1.44E-03
0.05
1.00
1.00
0.05
OR
2.28
5.47
3.90
3.61
1.03
inf
2.68
Number Aff
COMBINED
P value
2.99E-08
OR
2.52
95%CI
1.82-3.49
1057
947
288
1211
552
1339
Freq Aff Number Ctr
0.0038
0.0079
0.0069
0.0029
0.0009
0.0045
2162
1958
1812
1065
368
1787
Freq Ctr
0.0057
0.0007
0.0020
0.0019
0.0028
0.0000
0.0017
Collaborators:
deCODE Genetics
•Patrick Sulem
• Gisli Masson
•Daniel F. Gudbjartsson
•Thorunn Rafnar
•Sigurjón Axel Guðjónsson
•Guðmar Þorleifsson
•Augustine Kong
•Unnur Thorsteinsdottir
•Kari Stefansson
Comprehensive Cancer Centre and Radboud University
Medical Centre Nijmegen
•Lambertus A. Kiemeney
•Katja Aben
National University Hospital Iceland
•Jon H. Olafsson
•Bardur Sigurgeirsson
•Kristrun R. Benediktsdottir
•Kristin Thorisdottir
•Rafn Ragnarsson
Instituto Valenciano de Oncologica, Valencia
•Eduardo Nagore
Karolinska Institutet
•Johan Hansson
•Annika Lindblom
Medical University of Vienna
• Ichiro Okamoto
• Hubert Pehamberger
• Judith Wendt
DKFZ Heidelberg Group
•Rajiv Kumar
University Hospital Zaragoza
•José I. Mayordomo
Fondazione IRCCS Istituto Nazionale Tumori, Milan
• Monica Roldolfo
• Licia Rivoltini