Pan-Cancer Analysis of Whole Genomes

• p. 45 Extended Data Table 1, Myeloid-AML and Myeloid-MPN rows

  Acute myeloid leukaemia 10 3 7

• p. 8 Fig. 5a, number of samples for Myeloid−AML / Myeloid−MPN

  13

• p. 45 Extended Data Table 1, Myeloid rows

  Acute myeloid leukaemia 10

Only the authors can say what is right here.

Judge's note: ED Table 1 (p.45): AML 10, MDS 2, MPN 26, total 2,658. Fig. 5a (p.8, image plus layout text lines 944-988): AML 13, MDS 2, MPN 23. The Fig. 5a counts sum to 2,658. Every other type matches: Fig. 5a splits Kidney-RCC (111+33 = 144) and Skin-Melanoma (20+86+1 = 107) and merges Bone-Benign (7+9 = 16), all consistent with the table. Only the AML/MPN split differs, and no statement in the paper explains a reclassification. Only the authors can say which split is right.

Second check: another model agreed

• p. 3 Fig. 1 legend, panel a

  assessed in the validation exercise across n = 63 PCAWG samples

• p. 2 Benchmarking of genetic variant calls

  For 50 of these cases, we per- formed validation

• p. 25 Extended Data Fig. 2 legend

  across the n = 50 samples in the validation dataset

Only the authors can say what is right here.

Judge's note: p.2 says pipelines ran on 63 pilot pairs and validation was performed on 50 of them; the ED Fig. 2 legend (p.25) gives n = 50. The Fig. 1 legend gives n = 63 for the validation exercise. 63 may refer to the pilot set the callers were run on, but the label describes it as the validation set. Population label ambiguity.

Second check: another model agreed

• p. 3 Fig. 1b and legend

  Core algorithms included in the final PCAWG call set are shown in blue.

• p. 3 Extended Data Fig. 2b x-axis

  SMuFin

• p. 3 Fig. 1b, algorithms shown in blue

  MuTect2

Only the authors can say what is right here.

Judge's note: In the p.3 image, Fig. 1b plainly shows blue labels for Sanger, DKFZ and MuTect2 and a black SMuFin. The Fig. 1d legend lists DKFZ, SMuFin and Sanger, as does the ED Fig. 2b x-axis (p.25). The legend says 'core algorithms ... shown in blue', so the panels disagree about which indel caller is core. Only the authors can say which is right.

Second check: another model agreed

• p. 5 Fig. 3c panel titles

  Chromosome 5: 1,259,228

• p. 5 Fig. 3c panel titles

  Chromosome 5: 1,259,250

Only the authors can say what is right here.

Judge's note: Rests on outside knowledge: the TERT promoter hotspots (C228T/C250T) are at chr5:1,295,228 and 1,295,250 in GRCh37. The page image shows 1,259,228 and 1,259,250, which looks like a 95→59 transposition. The paper itself gives no coordinates to check against.

Second check: another model agreed

• p. 5 Fig. 3a/b x-axis

  Bone–Cart

• p. 5 Fig. 3 legend

  Abbreviations of the tumour types are defined in Extended Data Table 1

Judge's note: ED Table 1 (p.45) lists Bone-Benign, Bone-Epith, Bone-Osteosarc, SoftTissue-Leiomyo and SoftTissue-Liposarc, but no Bone-Cart. ED Fig. 4b also uses Bone-Cart, Bone-Leiomyo and Lymph-NOS, which are absent from the table, though that legend does not point to ED Table 1.

Second check: another model agreed

• p. 11 Replicative immortality section, left column

  evenly distributed across truncating SNVs, SVs and shallow dele-

• p. 44 Extended Data Fig. 13 legend

  c, Distribution of clonality of driver mutations in genes

• p. 11 Replicative immortality, paragraph on RB1 in C1

  truncating SNVs, SVs and shallow dele-tions (Extended Data Fig. 13c)

• p. 44 Extended Data Fig. 13 legend, panel c

  c, Distribution of clonality of driver mutations in genes relevant to telomere maintenance across clusters.

Only the authors can say what is right here.

Judge's note: The ED Fig. 13 image (p43) shows panel B with an Alterations legend that includes Truncating, Shallow deletion and Structural Variant. Panel C shows clonal [early/late/NA], subclonal and NA rows, with markers for Nonsense, Missense, Indel, Splice_Site, SV and Promoter only. The legend (p44) describes c as clonality. Panel c partly supports the sentence (SNVs, SVs) but not the shallow deletions, so the pointer probably should be 13b, or b and c.

Second check: another model agreed

• p. 47 Extended Data Table 3, 'Mutation distribution across genome' row

  11,12,15

• p. 11 Reference 11

  The landscape of viral associations in human cancers

Only the authors can say what is right here.

Judge's note: Checked ED Table 3 (p.47) and the reference list (p.11 crop). The row's findings (epigenetic state, cell of origin, TADs; tumour-type identification) match refs 15 (Akdemir, chromatin folding domains) and 12 (Jiao, deep-learning classification). Ref. 11 is about viral associations, and the table has no virus row even though its footnote says the key findings come from associated papers 4–18. The citation looks misplaced, but only the authors can say what was intended.

Second check: another model agreed

• p. 5 PCAWG tumours with no apparent drivers, left column

  power in the 70–90% range (Fig. 3b and Extended Data Fig. 4b)

• p. 5 Fig. 3b, Bone–Osteosarc

  Average detection sensitivity

Only the authors can say what is right here.

Judge's note: In the Fig. 3b image (p.5), the Bone–Osteosarc violin extends to 0 and has a dot at about 0.2. The other low points (Liver-HCC, Stomach, Biliary) are about 0.7–0.85. The sentence does not mention the outlier far below 70%, so the summary understates the range shown.

Second check: another model agreed

• p. 7 Timing clustered mutations in evolution

  affected 66 melanomas (61%)

• p. 7 Timing clustered mutations, right column

  thripsis events that affected 66 melanomas (61%)

• p. 45 Extended Data Table 1, Skin-Melanoma

  107

Only the authors can say what is right here.

Judge's note: The page 7 crop shows 66 (61%). ED Table 1 (p45 image) lists Skin-Melanoma as 107, and the same paragraph gives 10/86 cutaneous and 11/21 acral or mucosal, which also totals 107. No other melanoma denominator is stated nearby. The 61% looks truncated rather than rounded, or the authors used a different analysis set. This is a one-point discrepancy, so it is minor; the authors should confirm which denominator they used.

Second check: another model agreed

• p. 9 Germline effects on somatic mutations

  βrs12628403 = 0.57, Prs12628403 = 4.2 × 10−12

• p. 9 same paragraph

  protective against APOBEC3B-like mutagenesis (β = −0.43, P = 5.6 × 10−9

Only the authors can say what is right here.

Judge's note: Both crops confirm the signs as printed: −0.43 in Europeans and 0.57 in East Asians, with no minus sign visible in the image. For rs2142833 the sign agrees across populations (0.23 and 0.58), so the rs12628403 reversal stands out in a sentence describing an independent validation. The ED Fig. 10 legend (p38) gives no allele coding. A different effect-allele coding in the East Asian GWAS could explain the reversal, but nothing in the files states this. Only the authors can say whether the sign or the coding is intended.

Second check: another model agreed

• p. 10 Main text, L1 paragraph

  38% (1,075 out of 2,814) of PCAWG donors

• p. 41 Extended Data Fig. 12d axis labels

  All (2813)

Judge's note: The page 10 crop shows 2,814 and the ED Fig. 12d image (p41) shows 2813. The difference is one donor, and the percentage is 38% with either denominator. ED Fig. 12f counts MEIs by continental ancestry, a different analysis, so I did not use its total.

Second check: another model agreed

• p. 10 Main text, L1 paragraph

  all Plinian elements were infrequent (MAF ≤ 2%)

• p. 41 Extended Data Fig. 12c, Plinian column

  Plinian (8)

Only the authors can say what is right here.

Judge's note: In the ED Fig. 12c image (p41), the Plinian (8) column has most points near 0–2% and one red point clearly higher, at about 18% on the 0–100 allele frequency axis. The value is read from the plot, so the claim of 'all ≤ 2%' does not match the figure as drawn. The authors should clarify.

Second check: another model agreed

• p. 25 Extended Data Fig. 2 legend

  union, calls made by all variant- calling algorithms

Judge's note: Checked p.25. In both panels the union boxes have the highest sensitivity and among the lowest precision, which is how a union behaves. intersect3 ('any three') shows the opposite pattern and, with three core callers, is effectively 'all'. So 'all' misdescribes the union; 'any' was presumably meant. This is a wording slip in the legend, and the data are unaffected.

Second check: another model agreed

• p. 6 Main text, right column, end of paragraph on aneuploidy

  mutations or fusion genes of focal CNAs

• p. 6 Missing-driver cases paragraph

  point mutations or fusion genes of focal CNAs

• p. 6

  such as point mutations or fusion genes of focal CNAs

Judge's note: The p.6 text reads 'of'. The sentence is a list of alternative driver event types, so 'or' is meant.

Second check: none (judge only)

• p. 9 Fig. 6b, x-axis label of long-read panel

  Chr. 5: 14,8202,017–148,202,805

Judge's note: The crop of the Fig. 6b long-read panel shows the misplaced comma. The end coordinate 148,202,805 shows the intended format. This is a cosmetic digit-grouping typo.

Second check: none (judge only)

• p. 9 Fig. 6b legend

  inserted inbetween the tandem duplication

Judge's note: Visible in the Fig. 6 legend crop on page 9. Cosmetic spelling error.

Second check: none (judge only)

• p. 14

  Fei-Fei Fei Liu141,469

Judge's note: The page 14 crop shows 'Fei-Fei Fei Liu' in the image itself, so it is not an extraction artefact. The intended form is likely 'Fei-Fei Liu'.

Second check: none (judge only)

• p. 18

  51932Program in Computational Biology and

Judge's note: The page 18 crop shows superscript 519 followed by '32Program' in normal-size type, so the stray digits are in the PDF itself.

Second check: none (judge only)

• p. 20 Methods, Uniform processing and somatic variant calling

  and choses the optimal method for each variant type

Judge's note: Visible in the page 20 crop. Grammatical typo.

Second check: none (judge only)

• p. 24 Extended Data Fig. 1 legend

  Europen Molecular Biology

Judge's note: Seen in crop C033-a (p.24) as printed.

Second check: none (judge only)

• p. 27 Extended Data Fig. 4 legend, panel b

  the width proportional is to density

• p. 27 Extended Data Fig. 4 legend, panel b

  (the width proportional is to density)

Judge's note: Seen in crop C035-a (p.27) as printed.

Second check: none (judge only)

• p. 30 Extended Data Fig. 6 legend

  Mann– Whittney U-test

• p. 30 Extended Data Fig. 6 legend

  two-sided Mann–Whittney U-test

Judge's note: Seen in crop C036-a (p.30). The Extended Data Fig. 12 legend (p.42) spells it 'Mann–Whitney'.

Second check: none (judge only)

• p. 39 Extended Data Fig. 11a,c panel titles

  SV tandem dupliation

Judge's note: Page image p.39: the misspelling appears in the panel A title and in all four panel C titles.

Second check: none (judge only)

• p. 43 Extended Data Fig. 13b tumour-type legend

  Bone-Leiomyo

• p. 43 Extended Data Table 1

  SoftTissue-Leiomyo

Judge's note: Seen on p.43 (ED Fig. 13b tumour-type legend: 'Bone-Leiomyo'; ED Fig. 13a legend uses 'SoftTissue-Leiomyo') and on p.39 (ED Fig. 11k axis: 'Bone-Leiomyo'). ED Table 1 (p.45) lists only 'SoftTissue-Leiomyo'. This is a label inconsistency, and the intended type can be inferred.

Second check: none (judge only)

• p. 45 Extended Data Table 1, second Bone-Benign row

  Chrondromyxoid fibroma

Judge's note: Seen in page image p.45 as printed.

Second check: none (judge only)

• p. 48 Reporting Summary, Software and code – Data analysis

  BWA-MEM v0.78.8-r455

Only the authors can say what is right here.

Judge's note: Rests on outside knowledge: BWA releases are numbered 0.7.x, and r455 corresponds to 0.7.8. Crop C043-a (p.48) confirms the printed string 'v0.78.8-r455'. The main text (Methods) names BWA-MEM without a version, so there is nothing to cross-check against.

Second check: none (judge only)