Nature Genetics: doi: /ng Supplementary Figure 1
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1 Supplementary Figure 1 Multiple samples from five patients (P4, P8, P14, P15 and P17) with Barrett s esophagus and adjacent EAC show that the poor overlap is not a result of sampling bias. Bar graphs showing the number of SNVs for samples of Barrett s esophagus (BE) and cancer (C) that are either present in all samples (teal), present in all BE samples and absent in all cancer samples (pink), or present in all cancer samples and absent in all BE samples (gray) for each particular patient. Purple bars show the number of remaining variants not accounted for in the other groups (for example, present in a proportion of samples).
2 Supplementary Figure 2 EAC samples display multiple copy number aberrations compared to paired Barrett s samples. (a) Copy number plots showing two examples of Barrett s esophagus genomes that are majority copy number 2, compared to the matched EAC samples, which contain multiple gains and losses. (b) Similar plots but for patients where copy number events can be seen in the Barrett s esophagus sample as well as in the EAC sample (but are not significant enough to make a call). (c) Examples of copy number events in the Barrett s esophagus sample that are not seen in the matching EAC sample. The top track shows the depth ratio in a 20-kb window, and the bottom track shows the B-allele ratio.
3 Supplementary Figure 3 Principal-component analysis of mutational context. The counts of each different mutational context in each of the three sets of SNVs (common, Barrett s esophagus (BE) unique, EAC unique) were used as input for a principal-component analysis. There is some separation between the common SNVs and the unique SNVs in the second component, but the differences between the groups are not striking (6.9% variance in the second component). (b) Plot showing the weights of the 96 different mutational contexts. Four mutational contexts C(A>C)C, G(C>G)G and C(A>T)C (all at the top right-hand side of the plot) as well as T(C>G)A (bottom right) seem to be the main cause for the separation in the second component.
4 Supplementary Figure 4 Copy number plot for one of the Barrett s esophagus samples with low-grade dysplasia. Copy number plot for one of the Barrett s esophagus samples with low-grade dysplasia that was sent for whole-genome sequencing. Large deletions on multiple chromosomes, including chromosomes 5, 11, 13, 18 and 21, can be seen.
5 Supplementary Table 1: Patient demographics and tumor characteristics for the esophageal adenocarcinoma patient cohort Patient characteristics n = 23 Sex, n (%) Male 19 (82.6) Female 4 (17.4) Age, years (%) < Median Range Tumor stage, n (%) IA IB IIA IIB IIIA IIIB IIIC IV Missing information Differentiation, n (%) Well/Moderate Moderate Moderate/poor Poor Barrett s esophagus pathology No dysplasia Indefinite for dysplasia Low grade dysplasia High grade dysplasia Maximum Length of Barrett s esophagus (cm) Median Range Length of tumor (mm) Median Range 3 (13.0) 13 (56.5) 7 (30.4) (13.0) 4 (17.4) 6 (26.1) 0 (0.0) 12 (52.2) 5 (21.7) 4 (17.4) 17 (73.9) 1 (4.3) 3 (13.0)
6 Supplementary Table 2: Esophageal adenocarcinoma patient information. Patient Centre Gender Age* TNM7 Stage Germline tissue BE maximal length (cm) Tumor length (mm) 1 Addenbrookes Hospital, Cambridge M 62 T2N0M0 IB Blood NA 40 2 St Thomas Hospital, London F 55 T2N1M0 IIB Blood Addenbrookes Hospital, Cambridge M 61 T3N2M1 IV Blood NA 80 4 Royal Surrey County Hospital, Guildford M 58 T3N1M0 IIIA Blood Gloucestershire Royal Hospital, Gloucester M 64 T1N0M0 IA Blood NA 22 6 Gloucestershire Royal Hospital, Gloucester M 73 T3N1Mx NA Blood NA 31 7 Addenbrookes Hospital, Cambridge M 75 T3N0M0 IIA Blood NA 20 8 Salford Royal Infirmary, Manchester M 65 T2N0M0 IB Blood Addenbrookes Hospital, Cambridge M 67 T1N0M0 IA Blood Addenbrookes Hospital, Cambridge F 79 T2N0M0 IB Blood Addenbrookes Hospital, Cambridge M 67 T4N2M0 IIIC Normal esophagus Addenbrookes Hospital, Cambridge M 65 T2N1M0 IIB Blood NA Royal Surrey County Hospital, Guildford F 61 T2N0M0 IB Blood 15 NA 14 St Thomas Hospital, London M 68 T3N1M0 IIIA Blood Royal Surrey County Hospital, Guildford M 75 T3N3M1 IV Blood Addenbrookes Hospital, Cambridge M 65 T3N1M0 IIIA Blood NA Royal Surrey County Hospital, Guildford M 82 T3N1M0 IIIA Blood St Thomas Hospital, London M 61 T3N1M0 IIIA Blood Addenbrookes Hospital, Cambridge M 75 T3N0M0 IIA Blood NA Edinburgh Royal Infirmary, Edinburgh F 79 T3N1M0 IIIA Blood NA NA 21 Royal Surrey County Hospital, Guildford M 61 T1N0M0 IA Blood Royal Surrey County Hospital, Guildford M 50 T3N3M0 IIIC Blood Addenbrookes Hospital, Cambridge M 64 TxNxMx NA Blood 2 NA *Age at time of diagnosis. NA = not available.
7 Supplementary Table 3: Paired Barrett s esophagus, esophageal adenocarcinoma (EAC) and normal sample sequencing statistics. mapq = mapping quality, HiQ = high quality bases. The error rate HiQ gives the percentage of high quality bases that have mismatches to the reference genome. The sample purity for the EAC and Barrett s esophagus samples are also given. Patient Sample type purity-filtered pairs % aligned pairs median insert size % mapq=0 error rate HiQ genome coverage mapq>3 Callable genome totalnumbersnps Sample purity 1 EAC 1,244,932, Normal 590,520, Barrett's 1,195,274, EAC 1,482,353, Normal 557,666, Barrett's 931,330, EAC 1,009,393, Normal 1,161,403, Barrett's 986,130, EAC 1,229,915, Normal 702,258, Barrett's 921,904, EAC 980,497, Normal 659,466, Barrett's 880,868, EAC 1,115,303, Normal 748,774, Barrett's 953,373, EAC 1,249,130, Normal 620,715,
8 7 Barrett's 1,199,786, EAC 1,357,442, Normal 762,452, Barrett's 946,965, EAC 1,092,099, Normal 577,280, Barrett's 1,038,034, EAC 950,588, Normal 807,792, Barrett's 935,820, EAC 995,657, Normal 639,793, Barrett's 1,135,954, EAC 1,068,844, Normal 559,984, Barrett's 955,544, EAC 1,338,170, Normal 715,607, Barrett's 916,018, EAC 1,024,602, Normal 752,798, Barrett's 1,015,964, EAC 1,428,413, Normal 791,855, Barrett's 1,130,452, EAC 1,066,283, Normal 770,574, Barrett's 944,468, EAC 1,039,100, Normal 716,508,
9 17 Barrett's 1,168,839, EAC 1,258,875, Normal 696,954, Barrett's 1,011,091, EAC 1,295,238, Normal 623,088, Barrett's 1,195,290, EAC 1,299,881, Normal 622,692, Barrett's 1,039,910, EAC 1,070,994, Normal 642,977, Barrett's 1,034,752, EAC 1,027,607, Normal 510,088, Barrett's 913,440, EAC 1,363,277, Normal 579,686, Barrett's 1,408,290,
10 Supplementary Table 4: Information linking the EGA identifier found in EGAD to the patients presented in this manuscript. EGA Identifier Sample type Patient LP Barrett's 1 LP Tumor 1 LP DNA_H01 Barrett's 2 LP DNA_C03 Barrett's 2 LP DNA_D03 Barrett's 2 LP DNA_H01 Tumor 2 LP DNA_D01 Barrett's 3 LP DNA_D01 Tumor 3 LP DNA_E01 Barrett's 4 LP DNA_E02 Barrett's 4 LP DNA_F02 Barrett's 4 LP DNA_D01 Tumor 4 LP DNA_G02 Tumor 4 LP DNA_C01 Barrett's 5 LP DNA_A02 Tumor 5 LP DNA_C01 Barrett's 6 LP DNA_C01 Tumor 6 LP Barrett's 7 LP Tumor 7 LP DNA_G01 Barrett's 8 LP DNA_H02 Barrett's 8 LP DNA_G01 Tumor 8 LP DNA_A03 Tumor 8 LP DNA_B03 Tumor 8 LP DNA_A01 Barrett's 9
11 LP DNA_A01 Tumor 9 LP DNA_A01 Barrett's 10 LP DNA_A01 Tumor 10 LP DNA_A01 Barrett's 11 LP DNA_A03 Tumor 11 LP DNA_A01 Barrett's 12 LP DNA_A01 Tumor 12 LP DNA_F01 Barrett's 13 LP DNA_F01 Tumor 13 LP DNA_E01 Barrett's 14 LP DNA_A01 Barrett's 14 LP DNA_E01 Tumor 14 LP DNA_C01 Tumor 14 LP DNA_D01 Tumor 14 LP DNA_A01 Barrett's 15 LP DNA_E01 Barrett's 15 LP DNA_F01 Barrett's 15 LP DNA_C01 Tumor 15 LP DNA_G01 Tumor 15 LP DNA_H01 Tumor 15 LP DNA_A02 Barrett's 16 LP DNA_F03 Tumor 16 LP DNA_D01 Barrett's 17 LP DNA_A02 Barrett's 17 LP DNA_B02 Barrett's 17 LP DNA_C02 Barrett's 17 LP DNA_D02 Barrett's 17 LP DNA_B02 Tumor 17 LP DNA_F01 Barrett's 18
12 LP DNA_F01 Tumor 18 LP DNA_A01 Barrett's 19 LP DNA_A01 Tumor 19 LP DNA_A01 Barrett's 20 LP DNA_A01 Tumor 20 LP DNA_B01 Barrett's 21 LP DNA_B01 Tumor 21 LP DNA_B01 Barrett's 22 LP DNA_E01 Tumor 22 LP Barrett's 23 LP Tumor 23 barretts_1c Barrett's with gastric metaplasia AHM1051 barretts_1a Barrett's with intestinal metaplasia AHM1051 barretts_1d Barrett's with low grade dysplasia AHM1051 barretts_1e Early cancer AHM1051 SS CSS.casava18 FFPE Barrett's with dysplasia AHM1051 SS CSS.casava18 FFPE Barrett's with gastric metaplasia AHM1051 SS CSS.casava18 FFPE Barrett's with high grade dysplasia AHM1051 SS CSS.casava18 FFPE Barrett's with intestinal metaplasia AHM1051 SS CSS.casava18 FFPE Barrett's with intestinal metaplasia AHM1051 SS CSS.casava18 FFPE Barrett's with low grade dysplasia AHM1051 SS CSS.casava18 FFPE germline AHM1051 barretts_1b germline AHM1051
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