The Cancer Genome Atlas Pan-Cancer Analysis Project
Nature Genetics, 2013 · paper · Biomedicine
Describes the Pan-Cancer initiative, which compares molecular changes in DNA, RNA, protein and epigenetics across the first 12 tumor types profiled by The Cancer Genome Atlas. It aims to show how therapies effective in one cancer might extend to others with similar profiles.
Checked: PDF from nature.com, fetched 4 Oct 2026. Page numbers are those of that PDF.
2 findings
Reference or label Figure 1 legend expands UCEC as 'uterine cervical and endometrial carcinoma', while the figure panel labels it 'Endometrial (UCEC)' and cervical cancer is not among the 12 tumor types.
- p. 3 Figure 1 legend
uterine cervical and endometrial carcinoma (UCEC)
- p. 3 Figure 1 legend
lymphoblastic acute myeloid leukemia (LAML)
Judge's note: Rests on outside knowledge: UCEC stands for uterine corpus endometrial carcinoma. Page 3 image: the legend reads 'uterine cervical and endometrial carcinoma (UCEC)', and the panel reads 'Endometrial (UCEC)'. The text (p3) treats cervical cancer as a separate site. The legend's expansion introduces a tumor type that is not in the data set.
Second check: another model agreed
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Reference or label Figure 1 legend defines LAML as 'lymphoblastic acute myeloid leukemia', a self-contradictory term; the panel says 'Leukemia (LAML)'.
- p. 3 Figure 1 legend
lymphoblastic acute myeloid leukemia (LAML)
Judge's note: Page 3 image: the legend reads 'lymphoblastic acute myeloid leukemia (LAML)'. 'Lymphoblastic' (lymphoid lineage) contradicts 'myeloid'. LAML is acute myeloid leukemia. The fix is to delete 'lymphoblastic'.
Second check: another model agreed
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9 minor (typos and the like; most checked by the judge only)
Reference or label Box 1: "Eight 'marker papers' ... have been published so far8–12,14,27" cites only seven references (8, 9, 10, 11, 12, 14, 27).
- p. 2 Box 1, last sentence
Eight ‘marker papers’ (comprehensive initial publications on each of the tumor types) have been published so far8–12,14,27
- p. 2 Box 1, last sentence
Eight ‘marker papers’ (comprehensive initial publications on each of the tumor types) have been published so far8–12,14,27.
- p. 2 Box 1, last sentence
Eight
- p. 2 Box 1, last sentence
published so far8–12,14,27
Only the authors can say what is right here.
Judge's note: Page 2 image confirms the superscript reads 8–12,14,27. In the reference list, refs 8–12 and 14 are TCGA network papers, ref 27 is Kandoth et al., and ref 13 (Perou 2000) is excluded from the range. That gives seven cited papers for a stated count of eight. Either one marker paper (possibly LAML) is uncited or the count is wrong; only the authors can say which.
Second check: another model agreed
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Wording Text says the freeze covered 'the first 12 TCGA tumor types, each pro-filed using 6 different genomic, epigenomic, transcriptional and proteomic platforms', but Table 1 lists LAML RPPA as 'NA' (not available).
- p. 2 The Pan-Cancer project, para 1
each pro-filed using 6 different genomic, epigenomic, transcriptional and proteomic platforms
- p. 5 Table 1, LAML row
LAML NA 194 198 197 187 179
- p. 2 The Pan-Cancer project, para 1
on the first 12 TCGA tumor types, each pro-filed using 6 different genomic, epigenomic, transcriptional and proteomic platforms
- p. 5 Table 1, LAML row
NA
Only the authors can say what is right here.
Judge's note: Page 2 image: the sentence attaches 'each' to the 12 tumor types. Page 5 Table 1 crop: the LAML row reads NA for RPPA, and the table footnote defines NA as not available. Box 2 (p4) also says only that 93% of samples were assessed on at least one platform. So the per-type claim does not hold for LAML. This is a wording overstatement; the data themselves are not affected.
Second check: another model agreed
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Wording Box 2 states "a total of 5,074 tumor samples, of which 93% had been assessed for genomic, epigenomic, and gene and protein expression data on at least one platform each (Table 1)", but the Table 1 totals for RPPA (2,674) and expression (4,080) are below 93% of 5,074.
- p. 4 Box 2, paragraph 1
12 data set includes a total of 5,074 tumor samples, of which 93% had been assessed
- p. 5 Table 1, Total row
3,247
Only the authors can say what is right here.
Judge's note: 93% of 5,074 is about 4,719 samples. Read literally (each data category), this cannot hold for protein (2,674) or gene expression (4,080) data. The intended meaning, for example pooling microRNA with expression, is not stated. The authors should clarify which platforms the 93% refers to.
Second check: another model agreed
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Typo The Fig. 1 legend misspells "glioblastoma multiformae (GBM)"; the term is 'glioblastoma multiforme'.
- p. 3 Figure 1 legend
glioblastoma multiformae (GBM)
Judge's note: The misspelling is visible in the legend crop.
Second check: none (judge only)
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Typo ICGC is expanded as "International Cancer Genomics Consortium".
- p. 3 Main text col 1
International Cancer Genomics Consortium
Only the authors can say what is right here.
Judge's note: Rests on outside knowledge: the consortium's official name is International Cancer Genome Consortium. The page prints 'Genomics', as quoted.
Second check: none (judge only)
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Typo BCR is expanded as 'Biospecimen Core Resource' in the Box 2 text but as 'Biospecimen Collection Resource (BCR)' in the Figure 2 legend.
- p. 4 Box 2 text
by the Biospecimen Core Resource
- p. 4 Figure 2 legend
Biospecimen Collection Resource (BCR)
- p. 4 Box 2 text
Biospecimen Core Resource
- p. 4 Box 2 text
processed by the Biospecimen Core Resource
Judge's note: Page 4 image: Box 2 reads 'processed by the Biospecimen Core Resource'; the Figure 2 legend reads 'Biospecimen Collection Resource (BCR)'. One abbreviation has two expansions. The GSC/DCC variants raised in some notes are handled in C009.
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Typo Box 2 says 'Genome Sequencing Centers (GSCs)' and 'TCGA Data Coordinating Center (DCC)', but the Figure 2 legend says 'Genomic Sequencing Centers' and 'TCGA Data Coordination Center (DCC)'.
- p. 4 Box 2 text
Genome Sequencing Centers (GSCs)
- p. 4 Figure 2 legend
Genomic Sequencing Centers (GCCs and GSCs). Data sets were deposited in the TCGA Data Coordination Center (DCC)
- p. 4 Figure 2 legend
Genomic Sequencing Centers (GCCs and GSCs)
- p. 4 Box 2 text
Genome Sequencing Centers
Judge's note: Page 4 image confirms both variants. These are inconsistent expansions of the same abbreviations within one box and its figure.
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Typo RPPA is expanded as "reverse-phase proteomic arrays (RPPAs)" on p4 but as "Reverse-phase protein arrays" in Table 1 footnote a.
- p. 4 Main text col 1
reverse-phase proteomic arrays (RPPAs)
- p. 5 Table 1 footnote a
Reverse-phase protein arrays measuring protein
- p. 5 Table 1 footnote a
Reverse-phase protein arrays
Judge's note: Both expansions are confirmed in the crops.
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Typo Author list prints 'Melisssa Cline8,9' with a triple 's'.
- p. 7 Genome Data Analysis Center author list
Melisssa Cline8,9
- p. 7 Genome Data Analysis Center list
Melisssa Cline
Judge's note: The page 7 crop shows 'Melisssa Cline' printed. This is a misspelling of Melissa.
Second check: none (judge only)