Supplementary Table 1. PIK3CA mutation in colorectal cancer

Transcription

1 Liao X et al. PIK3CA Mutation in Colorectal Cancer. Page 1 Supplementary Table 1. PIK3CA mutation in colorectal cancer Exon Domain Nucleotide change* Amino acid change* cases 9 Helical c.1621t>a p.e541t 1 9 Helical c.1624g>a p.e542k 40 # 9 Helical c.1631c>a p.t544n 3 # 9 Helical c.1631c>t p.t544i 1 9 Helical c.1633g>a p.e545k 57 9 Helical c.1634a>c p.e545a 1 9 Helical c.1634a>g p.e545g 1 9 Helical c.1636c>a p.q546k 14 # 20 Kinase c.3129g>t p.m1043i Kinase c.3133g>a p.d1045n 1 20 Kinase c.3136g>a p.a1046t 2 20 Kinase c.3137c>a p.a1046e 1 20 Kinase c.3139c>t p.h1047y 5 20 Kinase c.3140a>c p.h1047p 1 20 Kinase c.3140a>g p.h1047r Kinase c.3140a>t p.h1047l 11 # 20 Kinase c.3142c>t p.h1048y 1 # *Nomenclature of mutation follows the recommendations by the Human Genome Variation Society ( # One case had both c.1636c>a and c.1631c>a mutations, another had c.3140a>t and c.3142c>t mutations and another had c.1624g>a and c.1631c>a mutations.

2 Liao X et al. PIK3CA Mutation in Colorectal Cancer. Page 2 Supplementary Table 2. Clinical, pathological and molecular features of colorectal cancer according to PIK3CA mutation status in the Nurses Health Study PIK3CA wildtype Only in exon 9 PIK3CA mutation present P (exon 9 Only in exon vs. 20 exon 20) Feature No. No. No. No. No. No In both exon 9 and exon 20 P (across all categories) Mean age at diagnosis (years) ± SD 66.7 ± ± ± ± ± Year of diagnosis Prior to % % 19 36% 12 32% 1 50% 1997 or after % % 34 64% 25 68% 1 50% Family history of colorectal cancer in first degree relatives Absent % % 44 83% 28 76% 1 50% Present % % 9 17% 9 24% 1 50% Tumor location Rectum % % 10 19% 5 14% 0 0 Distal colon % % 15 28% 13 35% 1 50% Proximal colon % % 28 53% 19 51% 1 50% Disease stage I % % 17 32% 6 16% 0 0 II % % 16 30% 14 38% 1 50% III % % 13 25% 11 30% 1 50% IV 85 13% 72 13% 7 13% 6 16% 0 0 Unknown 31 5% 31 6% % 0 0

3 Liao X et al. PIK3CA Mutation in Colorectal Cancer. Page 3 Tumor grade Low % % 50 94% 31 84% 2 100% High 73 12% 64 12% 3 6% 6 16% 0 0 MSI status MSI-low/MSS % % 46 87% 28 76% 2 100% MSI-high % % 7 13% 9 24% 0 0 CIMP status CIMP-low/ % % 45 88% 27 73% 1 50% CIMP-high % % 6 12% 10 27% 1 50% BRAF status Wild-type % % 47 89% 27 75% 2 100% Mutant % % 6 11% 9 25% 0 0 KRAS status Wild-type % % 25 47% % 1 50% Mutant % % 28 53% 15 42% 1 50% Mean LINE-1 methylation level (%) ± SD 63.1 ± ± ± ± ± TP53 expression Negative % % 32 74% 21 70% 1 50% Positive % % 11 26% 9 30% 1 50%

4 Liao X et al. PIK3CA Mutation in Colorectal Cancer. Page 4 Supplementary Table 3. Clinical, pathological and molecular features of colorectal cancer according to PIK3CA mutation status in the Health Professionals Follow-Up Study PIK3CA mutation present PIK3CA wildtype exon 9 (exon 9 vs. exon 20 9 and exon 20 Only in P Only in In both exon Feature No. No. No. exon 20) No. No. No P (across all categories) Mean age at diagnosis (years) ± SD 71.1 ± ± ± ± ± Year of diagnosis Prior to % % 24 43% 19 53% 2 40% 1997 or after % % 32 57% 17 47% 3 60% Family history of colorectal cancer in first degree relatives Absent % % 46 82% 26 72% 2 40% Present 99 18% 76 17% 10 18% 10 28% 3 60% Tumor location Rectum % % 7 13% 5 14% 1 20% Distal colon % % 17 30% 12 33% 1 20% Proximal colon % % 32 57% 19 53% 3 60% Disease stage I % % 16 29% 9 25% 3 60% II % % 12 21% 14 39% 0 0 III % % 11 20% 8 22% 0 0 IV 66 12% 52 12% 8 14% 4 11% 2 40% Unknown 71 13% 61 14% 9 16% 1 3% 0 0

5 Liao X et al. PIK3CA Mutation in Colorectal Cancer. Page 5 Tumor grade Low % % 52 95% 32 89% 5 100% High 38 7% 31 7% 3 5% 4 11% 0 0 MSI status MSI-low/MSS % % 54 96% 24 69% 4 80% MSI-high 60 11% 46 11% 2 4% 11 31% 1 20% CIMP status CIMP-low/ % % 43 86% 25 74% 3 60% CIMP-high 58 12% 40 10% 7 14% 9 26% 2 40% BRAF status Wild-type % % 52 93% 30 83% 4 80% Mutant 43 8% 32 7% 4 7% 6 17% 1 20% KRAS status Wild-type % % 23 41% 17 47% 1 20% Mutant % % 33 59% 19 58% 4 80% Mean LINE-1 methylation level (%) ± SD 62.4 ± ± ± ± ± TP53 expression Negative % % 24 69% 18 67% 2 67% Positive % % 11 31% 9 33% 1 33%

6 Liao X et al. PIK3CA Mutation in Colorectal Cancer. Page 6 Supplementary Table 4. Clinical, pathological and molecular features of colorectal cancer according to overall PIK3CA mutation status PIK3CA wildtype mutant PIK3CA P Feature No. No. No. No Sex Male % % 97 51% Female % % 92 49% Mean age (years) ± SD 68.7 ± ± ± Year of diagnosis 0.53 Prior to % % 77 41% 1997 or after % % % Family history of colorectal cancer in first degree relatives 0.18 Absent % % % Present % % 42 22% Tumor location Rectum % % 28 15% Distal colon % % 59 31% Proximal colon % % % Disease stage 0.25 I % % 51 27% II % % 57 30% III % % 44 23% IV % % 27 14% Unknown 102 9% 92 9% 10 6% Tumor grade 0.60 Low % % % High 111 9% 95 10% 16 9% MSI status 0.77 MSI-low/MSS % % % MSI-high % % 30 16%

7 Liao X et al. PIK3CA Mutation in Colorectal Cancer. Page 7 CIMP status 0.34 CIMP-low/ % % % CIMP-high % % 35 20% BRAF status 0.72 Wild-type % % % Mutant % % 26 14% KRAS status < Wild-type % % 88 47% Mutant % % % Mean LINE-1 methylation level (%) ± SD 62.8 ± ± ± TP53 expression Negative % % 98 70% Positive % % 42 30%

8 Liao X et al. PIK3CA Mutation in Colorectal Cancer. Page 8 Supplementary Table 5. analysis of the relations between KRAS mutation and PIK3CA mutation in colorectal cancers Variable independently associated with PIK3CA OR P KRAS mutation vs wild-type 2.65 ( ) < Other variables in the model CIMP high vs low/ ( ) The multivariate logistic regression model initially included age, sex, year of diagnosis, tumor location, microsatellite instability, CpG island methylator phenotype, KRAS, BRAF and LINE-1 methylation. A backward elimination with threshold of p=0.05 was used to select variables in the final models. CI, confidence interval; OR, odds ratio.

9 Liao X et al. PIK3CA Mutation in Colorectal Cancer. Page 9 Supplementary Table 6. PIK3CA exon 9 or exon 20 mutation in colorectal cancer and patient mortality PIK3CA status No. Colorectal cancer-specific mortality Overall mortality Stagestratified (95% Stagestratified (95% Wild-type (referent) 1 (referent) 1 (referent) (referent) 1 (referent) 1 (referent) Exon 9 mutant (regardless of exon 20 status) Exon 20 mutant (regardless of exon 9 status) ( ) 0.96 ( ) 1.15 ( ) 1.01 ( ) 1.15 ( ) 1.11 ( ) ( ) 0.90 ( ) 1.09 ( ) 0.94 ( ) 0.98 ( ) 0.92 ( ) The multivariate, stage-stratified Cox regression model initially included age, sex, year of diagnosis, tumor location, tumor grade, microsatellite instability, CpG island methylator phenotype, KRAS mutation, BRAF mutation, LINE-1 methylation and PIK3CA mutation status in the other exon. A backward elimination with a threshold of P = 0.05 was used to select variables in the final models. CI, confidence interval;, hazard ratio.

10 Liao X et al. PIK3CA Mutation in Colorectal Cancer. Page 10 Supplementary Table 7. PIK3CA mutation in colorectal cancer and patient mortality according to cohort (gender) Colorectal cancer-specific mortality Overall mortality PIK3CA status No. Stagestratified (95% Stagestratified (95% Men (HPFS) Women (NHS) Wild-type (referent) 1 (referent) 1 (referent) (referent) 1 (referent) 1 (referent) Mutant ( ) 1.07 ( ) 1.01 ( ) ( ) 1.03 ( ) 0.93 ( ) Wild-type (referent) 1 (referent) 1 (referent) (referent) 1 (referent) 1 (referent) Mutant ( ) 1.00 ( ) 1.11 ( ) ( ) 0.85 ( ) 0.88 ( ) The multivariate, stage-stratified Cox regression model initially included age, sex, year of diagnosis, tumor location, tumor grade, microsatellite instability, CpG island methylator phenotype, KRAS mutation, BRAF mutation and LINE-1 methylation. A backward elimination with a threshold of P = 0.05 was used to select variables in the final models. CI, confidence interval; HPFS, Health Professionals Follow-Up Study;, hazard ratio; NHS, Nurses Health Study.

11 Liao X et al. PIK3CA Mutation in Colorectal Cancer. Page 11 Supplementary Table 8. Combined PIK3CA and BRAF mutation status in colorectal cancer and patient mortality PIK3CA BRAF No. Colorectal cancer-specific mortality Overall mortality Stagestratified stratified Stage- (95% (95% Wild-type Wild-type (referent) 1 (referent) 1 (referent) (referent) 1 (referent) 1 (referent) Mutant Wild-type Wild-type Mutant Mutant Mutant ( ) 1.09 ( ) 1.24 ( ) 0.82 ( ) 1.11 ( ) 1.19 ( ) 0.80 ( ) 1.37 ( ) 2.40 ( ) ( ) 1.17 ( ) 1.06 ( ) 0.88 ( ) 1.21 ( ) 1.07 ( ) 0.80 ( ) 1.34 ( ) 1.48 ( ) PIK3CA KRAS Wild-type Wild-type (referent) 1 (referent) 1 (referent) (referent) 1 (referent) 1 (referent) Mutant Wild-type Wild-type Mutant Mutant Mutant ( ) 1.42 ( ) 1.18 ( ) 0.97 ( ) 1.19 ( ) 0.87 ( ) 1.0 ( ) 1.17 ( ) 0.85 ( ) ( ) 1.27 ( ) 1.11 ( ) 0.91 ( ) 1.15 ( ) 0.93 ( ) 0.89 ( ) 1.09 ( ) 0.84 ( ) The multivariate, stage-stratified Cox regression model initially included age, sex, year of diagnosis, tumor location, tumor grade, microsatellite instability, CpG island methylator phenotype, KRAS mutation and LINE-1 methylation. A backward elimination with a threshold of P = 0.05 was used to select variables in the final models. CI, confidence interval;, hazard ratio.