Genome-wide Association Study of 14,000 Cases of Seven Common Diseases and 3,000 Shared Controls

The Wellcome Trust Case Control Consortium

2007 · paper · Biomedicine

A genome-wide association study of about 2,000 British cases for each of seven common diseases, compared against about 3,000 shared controls. It found 24 independent association signals, some loci shared across diseases, and generally modest effect sizes.

Checked: PDF from europepmc.org, fetched 4 Oct 2026. Page numbers are those of that PDF.

16 findings

Substance Number of imputed HapMap SNPs is printed as "2,193,483 HapMap SNPs" (p6) and as "2,139,483 HapMap SNPs" (Methods p31).

p. 6 Disease association results
genotype data at 2,193,483 HapMap SNPs
p. 31 Methods, Multilocus analysis
we imputed genotypes at 2,139,483 HapMap SNPs
p. 6 Disease association results
2,193,483 HapMap
p. 31 Multilocus analysis
2,139,483 HapMap SNPs

Only the authors can say what is right here.

Judge's note: Both page images confirm the two figures. Both passages describe HapMap SNPs imputed and then tested for association in the main analyses, so they are the same quantity. The digits appear transposed, and the files do not show which value is correct.

Second check: another model agreed

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Substance The CAD 9p21 rs1333049 trend P is printed as '1.79 × 10-24' in Table 3, but the CAD text says 'the strongest signal is seen at rs1333049 (P=1.8×10-14)'.

p. 52 Table 3, CAD 9p21 row, Trend P value
1.79 × 10-24
p. 9 CAD section
rs1333049 (P=1.8×10-14)

Judge's note: Both the p52 Table 3 image and the p9 text image were checked. Both refer to the same SNP and the same trend test, and the text cites Table 3. The mantissas agree (1.79 rounds to 1.8) but the exponents differ by 10. The same row's genotypic P (1.16 × 10-13) and log10 BF (11.66) are of the 10-14 order. Comparable rows also fit 10-14: CD 2q37 has P 7.10e-14 with BF 11.11, and T1D 12q24 has P 2.17e-15 with BF 12.53. So the table exponent appears to be the error.

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Substance The text says rs6679677 "is perfectly correlated (HapMap CEU data r2=1) with the functionally relevant SNP (rs2476601)", but Table 2 gives HapMap r2 = 0.75 for rs2476601/rs6679677 (PTPN22, both the RA and T1D rows).

p. 13 RA section
is perfectly correlated (HapMap CEU data r2=1) with the functionally relevant SNP (rs2476601)
p. 51 Table 2, RA PTPN22 row, HapMap r2
0.75
p. 13 RA section
perfectly correlated (HapMap CEU data r2=1)

Only the authors can say what is right here.

Judge's note: Page 13 prints r2=1. The upright image of Table 2 on p. 51 shows 0.75 in both PTPN22 rows, and its footnote says r2 was calculated in the HapMap CEU sample. Same SNP pair, same reference panel, two values. No other release or panel is mentioned.

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Substance Model M2 log-odds is printed as "μ+γI(Zi+ϕ(2γI(Zi=2)) for model M2", which has unbalanced parentheses and malformed terms.

p. 29 Methods, Bayes factors
+γI(Zi+ϕ(2γI(Zi=2)) for model M2

Only the authors can say what is right here.

Judge's note: Page 29 crop image shows the same expression as the text layer, so it is not an extraction artefact. Counting brackets: three open ('I(', 'ϕ(', 'I(') and two close. 'γI(Zi' applies the indicator to a genotype, not to an event as I(Zi=m) is defined in the next line. The text says γ is the additive per-allele effect shared with M1 (μ+γZi) and ϕ is 'a recessive effect over and above an additive effect', which suggests something like μ+γZi+ϕI(Zi=2). Because the printed form cannot be parsed as given, only the authors can confirm the intended M2 formula.

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Substance Table 4 additive log10(BF) values '20.80' (BD rs6458307, trend P 3.43 × 10-01), '20.97' (T1D rs17166496, P 6.06 × 10-01), '20.83' (T2D rs358806, P 4.77 × 10-01) and '20.09' (T2D rs12304921, P 5.37 × 10-02) look like negative values (−0.80, −0.97, −0.83, −0.09) with the minus sign rendered as '2'.

p. 54 Table 4, BD 6p21 rs6458307, log10(BF) additive
20.80
p. 56 Table 4, T1D 5q31 rs17166496
20.97
p. 56 Table 4, T2D 3p14 rs358806
20.83
p. 56 Table 4, T2D 12q13 rs12304921
20.09

Judge's note: The p54 and p56 images show these values as printed. Elsewhere in Table 4, SNPs with nominal trend P have small additive BFs: RA 21q22 has P 3.45e-02 with BF 0.05, T2D 4q27 has P 2.1e-02 with BF 0.13, and RA 4p15 has P 7.65e-03 with BF 0.50. By contrast, P near 1e-14 in Table 3 gives BF about 11. A BF near 20 for non-significant P is therefore not plausible, and a lost minus sign accounts for all four values.

Second check: another model agreed

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Substance In Table 4, the CAD 22q12 rs688034 Control MAF cell is printed as '0. × 10' and has no valid value.

p. 55 Table 4, CAD 22q12 rs688034, Control MAF
0. × 10

Only the authors can say what is right here.

Judge's note: The p55 image shows '0. × 10' in the Control MAF column; the case MAF is 0.355. The value cannot be recovered from the page, so only the authors can supply it.

Second check: another model agreed

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Reference or label p6: "Table 2 details the findings from the WTCCC scan for the 15 variants", but Table 2 (p51) lists 14 rows.

p. 6 Disease association results
Table 2 details the findings from the WTCCC scan for the 15 variants
p. 51 Table 2
Evidence for signal of association at previously robustly replicated loci
p. 10 CD section
all of these generate strong signals in our data (Table 2)
p. 6 Disease association results
the 15 variants for

Only the authors can say what is right here.

Judge's note: I counted the rows on the p51 image: CAD APOE; CD NOD2, IL23R; RA HLA-DRB1, PTPN22; T1D HLA-DRB1, INS, CTLA4, PTPN22, IL2RA, IFIH1; T2D PPARG, KCNJ11, TCF7L2. That is 14, and there is no continuation page. The CD text on p10 also cites Table 2 for previously defined loci, including 5q31 (rs6596075), which has no row in Table 2. Only the authors can say whether a row is missing or the count is wrong.

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Reference or label Chromosome band mislabelled: "the combined analysis of autoimmune cases (chromosomes 18q11 and the 10p15 CD25 region" should read 18p11 (PTPN2), as in the next sentence ('12q13, 12q24, 16p13 and 18p11') and later ('identified on 18p11').

p. 14 T1D section, para 2
(chromosomes 18q11 and the 10p15 CD25 region
p. 14 T1D section
analysis of autoimmune cases (chromosomes 18q11 and the 10p15 CD25 region: Table 3
p. 7 Disease association results
one through an analysis which combined cases from more than one autoimmune disease
p. 53 Table 3, Combined cases
RA+T1D

Judge's note: Page 14 shows '18q11' once and '18p11' twice for the same PTPN2 combined-analysis region; p. 13 also gives PTPN2 as 18p11. A further point: the sentence cites Table 3, but Table 3's 'Combined cases' section (p. 53) lists only RA+T1D 10p15. The 18p11 combined result (P=9×10^-8) is attributed to Supplementary Table 11 later on.

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Reference or label The TCF7L2/rs7903146 imputation example says "(see also Supplementary Fig. 12)", but elsewhere Supplementary Fig. 12 is identified as the signal plots for the T1D multilocus loci.

p. 31 Methods, Multilocus analysis
(see also Supplementary Fig. 12)
p. 7 Disease association results
signal plots in Supplementary Figs 11, 12 and 13, respectively
p. 7 Disease association results
Supplementary Figs 11, 12 and 13
p. 7 Disease association results
signal plots in Supplementary Figs 11, 12 and 13

Only the authors can say what is right here.

Judge's note: Page 7 says the RA sex-differentiated, T1D multilocus and combined-autoimmune signals are in 'Supplementary Figs 11, 12 and 13, respectively'. The T1D results text says '4q27 and 12p13: Table 3, Supplementary Fig. 12' and '4q27 ... (Supplementary Table 12, Supplementary Fig. 12)'. Page 31 nonetheless points the T2D TCF7L2 imputed-signal example to Supplementary Fig. 12. The supplement is not among the files, so it cannot be checked whether that figure also has a TCF7L2 panel; the authors should confirm the intended figure.

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Reference or label p10: new CD loci "located on chromosomes 3p21, 5p33, 10p24 and 18p11", whereas Table 3 and the Discussion (p17) give 5q33 and 10q24.

p. 10 CD section
chromosomes 3p21, 5p33, 10p24 and 18p11
p. 17 Discussion
chromosomes 3p21, 5q33, 10q24 and 18p11 for CD
p. 52 Table 3 CD rows
5q33
p. 17 Discussion, first paragraph
chromosomes 3p21, 5q33, 10q24 and 18p11 for CD23

Judge's note: The p10 page image shows '5p33, 10p24'. Table 3 (p52) lists CD 5q33 (rs1000113) and 10q24 (rs10883365), the Discussion says '3p21, 5q33, 10q24 and 18p11', and p11 says 10q24.2. The fix is clear: the arm label should be q. A similar slip on p14: the T1D paragraph says 'chromosomes 18q11' and two lines later '18p11' for the same combined-analysis locus.

Second check: another model agreed

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Reference or label In Table 4, the CD rs6596075 region (131.40-131.90 Mb) is labelled '5q23', but the text places it on 'chromosome 5q31 (ref. 62)' ('the previously described risk haplotype is tagged by rs6596075 (P=5.4×10-7)').

p. 55 Table 4, CD row rs6596075
5q23
p. 10 CD section
A second association, on chromosome 5q31 (ref. 62)

Judge's note: Checked the p55 Table 4 image and the p10 text crop. The P value 5.40e-07 matches the text. The same table labels the T1D region at 132.64-132.67 Mb as '5q31', and ref. 62 is titled '...5q31 cytokine gene cluster...'. The 5q23 label is therefore internally inconsistent.

Second check: another model agreed

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Reference or label Citation mismatch: "CHRM3, encoding the cholinergic receptor muscarinic 3, a member of the G protein-coupled receptor family32" cites ref. 32, which is Ozeki et al., "Disrupted-in-Schizophrenia-1 (DISC-1): mutant truncation prevents binding to NudE-like (NUDEL) and inhibits neurite outgrowth".

p. 12 HT section
G protein-coupled receptor family32
p. 38 Reference 32
Ozeki Y, et al. Disrupted-in-Schizophrenia-1 (DISC-1)
p. 12 HT section
a member of the G protein-coupled receptor family32

Only the authors can say what is right here.

Judge's note: In this manuscript, citation numbers are printed inline (e.g. 'dysplasia80,81' in the same sentence). Ref. 32 is first cited correctly in the BD section for DCTN5/DISC1 (p. 8). The reference list jumps from 81 (ryanodine) to 82 (RA epidemiology), so no CHRM3/GPCR source exists in the list. The intended reference has to come from the authors.

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Reference or label The Discussion cites "empirical data from animal models87,115,116", but ref 87 is "MacKay K, et al. Whole-genome linkage analysis of rheumatoid arthritis susceptibility loci in 252 affected sibling pairs in the United Kingdom", a human RA linkage study.

p. 18 Discussion, allelic architecture paragraph
from animal models87,115,116
p. 40 Reference list, entry 87
MacKay K, et al. Whole-genome linkage analysis of rheumatoid arthritis susceptibility loci in 252 affected sibling pairs in the United Kingdom
p. 18 Discussion
empirical data from animal models87,115,116

Only the authors can say what is right here.

Judge's note: On the page 40 image, ref 87 is the RA sib-pair linkage scan. On page 18 it is cited for animal-model effect-size distributions alongside ref 115 (Hayes & Goddard, livestock) and ref 116 (Valdar et al., heterogeneous stock mice), both of which fit. Ref 17 (Mackay TF, Anholt RR, 'Of flies and man: Drosophila as a model...') may be the intended citation, but only the authors can confirm that.

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Reference or label Methods cite "MassExtend (hME) and/or iPLEX37 assay", but ref 37 is "Libby P, Theroux P. Pathophysiology of coronary artery disease. Circulation. 2005", which is unrelated to the iPLEX genotyping assay.

p. 24 Methods, Sample handling
MassExtend (hME) and/or iPLEX37 assay
p. 38 Reference 37
Libby P, Theroux P. Pathophysiology of coronary artery disease.

Only the authors can say what is right here.

Judge's note: I checked the page 24 crop and the page 38 reference list crop. The Methods references are otherwise numbered 119–143, so '37' looks like a stray citation number. The intended iPLEX reference is unknown and only the authors can supply it.

Second check: another model agreed

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Wording "Five of these previously identified associations were detected in this scan (P≥0.001)". The inequality points the wrong way for detection, and Table 2's IFIH1 row (trend P 1.9×10^-3, genotypic 7.6×10^-3) does not reach 0.001 even read as P≤0.001.

p. 14 T1D section, para 1
Five of these previously identified associations were detected in this scan (P≥0.001)
p. 51 Table 2, T1D IFIH1
1.9 × 10-03
p. 14 T1D section
detected in this scan (P≥0.001)

Only the authors can say what is right here.

Judge's note: The page 14 crop shows the '≥' glyph. In Table 2 (p. 51 upright), the T1D values are HLA 4.0e-116, CTLA4 2.5e-5, PTPN22 1.2e-26, IL2RA 8.0e-6 and IFIH1 1.9e-3. The text also cites Supplementary Table 10, which is not in the files and might hold another IFIH1 SNP. The intended threshold has to come from the authors.

Second check: another model agreed

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Wording Table 1 positions have misplaced digit grouping: 4p14 rs7696175 '386,43,552' (region 38.51-38.74 Mb, so presumably 38,643,552) and 12p13 rs10774241 '45,537,27' (region 4.37-4.82 Mb, so presumably 4,553,727).

p. 50 Table 1, 4p14 rs7696175 Position
386,43,552
p. 50 Table 1, 12p13 rs10774241 Position
45,537,27

Judge's note: The p50 upright image shows both strings as quoted. Every other position in the table has correct thousands separators and falls inside its Region (Mb) range. If the commas are regrouped, both values fall inside their stated regions. As printed, the 12p13 value reads as about 45.5 Mb, which is outside its region.

Second check: another model agreed

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33 minor (typos and the like; most checked by the judge only)

Reference or label Citation mismatch: "ZP4, the product of which is zona pellucida glycoprotein 481" appears to cite ref. 81 (Benkusky et al., "Ryanodine receptor channelopathies"), which concerns RYR2, not ZP4.

p. 12 HT section
zona pellucida glycoprotein 481
p. 40 Reference 81
Benkusky NA, Farrell EF, Valdivia HH. Ryanodine receptor channelopathies.

Only the authors can say what is right here.

Judge's note: Page 12 reads 'glycoprotein 481', i.e. glycoprotein 4 followed by inline citation 81. Ref. 81 was just cited for RYR2 ('dysplasia80,81'). Its title on p. 40 concerns ryanodine receptors, and no ZP4 source appears in the reference list. Only the authors can say whether a citation was intended.

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Wording Abstract: "Case-control comparisons identified 24 independent association signals at P<5×10-7" vs Results p7: "12 of these 25 strong signals"; the difference (the RA+T1D combined-cases signal at 10p15) is not stated.

p. 1 Abstract
identified 24 independent association signals
p. 7 Disease association results
12 of these 25 strong signals
p. 1 Abstract
Case-control comparisons identified 24 independent association signals
p. 53 Table 3, Combined cases row
RA+T1D

Judge's note: I counted Table 3 on pp52-53. The standard analysis has 21 rows: BD 1, CAD 1, CD 9, RA 2, T1D 5, T2D 3. There are also 2 multilocus rows (T1D), 1 sex-differentiated row (RA) and 1 combined-cases row (RA+T1D 10p15), making 25, which matches the p7 text (21+4). The abstract's per-disease counts match the table once the multilocus and sex-differentiated rows are assigned to T1D and RA (T1D 7, RA 3), so they add to 24 and simply leave out the combined-cases signal, which belongs to no single disease. The paper never says that 24 excludes it, although the combined analysis is also a case-control comparison. This is a consistency point, not a wrong number.

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Wording p11: "On the X chromosome rs2807261 (P=1.3×10-7)" is reported among more modest CD signals, although 1.3×10-7 is below the paper's 5×10-7 strong-signal threshold and the SNP is not in Table 3.

p. 11 CD section
On the X chromosome rs2807261 (P=1.3×10-7)

Only the authors can say what is right here.

Judge's note: The crop confirms the exponent. The Methods 'X Chromosome analysis' section (p31) says X SNPs are analysed with a separate test and reported in Supplementary Table 16, which is not among the files. That suggests Table 3 and the 24/25 counts cover autosomal results only, but the paper never says so. Question for the authors: are X-chromosome results excluded from the strong-signal count and from Table 3?

Second check: another model agreed

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Wording "rs3087243 and rs11571300 were only nominally significant (P=0.085 and P=0.034, respectively)". P=0.085 does not reach the conventional 0.05 nominal level.

p. 13 RA section
were only nominally significant (P=0.085 and P=0.034

Only the authors can say what is right here.

Judge's note: Page 13 shows P=0.085. Calling it 'nominally significant' fits 0.034 but not 0.085, unless a threshold other than 0.05 was meant; the paper states none here.

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Wording The 10p15 combined RA+T1D trend P is "combined trend test P=5×10-8" in the text (citing Supplementary Table 11), but Table 3 gives 5.92 × 10-08 for rs2104286 (RA+T1D).

p. 14 T1D section
combined trend test P=5×10-8
p. 53 Table 3, Combined cases RA+T1D rs2104286
5.92 × 10-08

Judge's note: Page 14 prints P=5×10^-8 and Table 3 on p. 53 prints 5.92×10^-8. Rounded to one significant figure that would be 6×10^-8; 5 looks like truncation. The text cites Supplementary Table 11, which is not in the files and could refer to a different SNP. Minor.

Second check: another model agreed

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Wording The RA case breakdown ("404 ... A further 109 cases ... All other cases (n=1348)") sums to 1,861, not the 2,000 cases per disease of the study design, and the text does not say which sample set these counts describe.

p. 22 RA phenotype description
All other cases (n=1348)

Only the authors can say what is right here.

Judge's note: Page 22 image: 404 from the ARC repository, 109 from the Norfolk register and n=1348 from NHS clinics. Page 24 states "We selected 2,000 ... samples from each disease ... collection". I found no per-disease post-QC counts in the article text that would show the 1,861 to be the analysed set, so the mismatch is left as a query.

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Wording "Actual numbers of cases and controls for each disease are slightly smaller than the 3,000:2,000 values used in the simulations" gives the ratio in reverse order: the simulations used 2,000 cases and 3,000 controls.

p. 25
slightly smaller than the 3,000:2,000 values used in the simulations

Judge's note: Page 25 image: the same paragraph says the simulations used 'case-control panels of 2,000 cases and 3,000 controls' and refers to 'the 3,000 control individuals'. The phrase 'cases and controls ... 3,000:2,000' therefore reverses the order. It is a wording slip; the simulation design itself is stated correctly.

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Typo The abbreviation is defined as "1958 British Birth Cohort (58C)" (p2) but printed as "58BC" on p3 ("subjects from the 58BC and UKBS collections") and in the Methods heading on p23 ("1958 Birth Cohort Controls (58BC)").

p. 2 Samples
1958 British Birth Cohort (58C)
p. 3 Control groups
between subjects from the 58BC and UKBS collections
p. 2 Samples
(58C)
p. 3 Control groups
58BC and UKBS collections

Judge's note: The page images show 58C on p2 and 58BC on p3 and p23. The text layer has 58C everywhere else (lines 825, 932, 1459, 1604). Cosmetic inconsistency.

Second check: none (judge only)

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Typo Misspellings in the main text: "DISCI" and "GABRBI" (p8), "singal" and "SnP" (p10), "presistence" and "authophagy" (p11), "non-MHS locus", "TCFL2" and "appareciable" (p15), "1GF2BP2" and "Supplemantary Table 8" (p16).

p. 8 BD section
(DISCI)32
p. 8 BD section
GABRBI
p. 15 T2D
within TCFL2
p. 15 T1D
non-MHS locus (Idd3)

Judge's note: Each item checked on its crop or on the p10 page image. DISC1 and TCF7L2 are spelled correctly nearby on the same pages. I also saw "evidence fo association" on p16. All cosmetic.

Second check: none (judge only)

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Typo A word is missing: "may have failed to detect genuine common susceptibility variants of large effect size they happened to be poorly tagged" needs 'if' (or 'because') before 'they'. Separately, there is a stray comma in "relevance to BD, (Fig. 5)" on p. 8.

p. 12 HT section
of large effect size they happened to be poorly tagged
p. 12 HT section
large effect size they happened to be poorly tagged
p. 8 BD section
relevance to BD, (Fig. 5)
p. 12
effect size they happened to be poorly tagged

Judge's note: The page 12 image shows the sentence without a conjunction. The page 8 crop shows a comma before '(Fig. 5)'. Both are cosmetic.

Second check: none (judge only)

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Typo Misspelling: "defects in authophagy and the processing of phagocytosed bacteria" should read 'autophagy'.

p. 11 end of CD section
authophagy and the processing

Judge's note: The crop of page 11 clearly shows 'authophagy'. Elsewhere the word is spelled 'autophagy' (e.g. ref. 67, 'induces autophagy').

Second check: none (judge only)

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Typo Missing space: "classical autoimmune conditions such as RAand T1D" should read 'RA and T1D'.

p. 11 HLA paragraph
RAand T1D

Judge's note: The page 11 crop shows 'RAand' printed without a space, so this is not an extraction artefact.

Second check: none (judge only)

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Typo Gene symbols misspelled: "within TCFL2, represented by rs4506565" (p. 15) should be TCF7L2, and "1GF2BP2 gene" (p. 16) should be IGF2BP2.

p. 15 T2D section
within TCFL2
p. 16 T2D section
1GF2BP2 gene
p. 15
within TCFL2, represented by rs4506565

Judge's note: The page images show 'TCFL2' on p. 15 (TCF7L2 everywhere else, including Table 2) and '1GF2BP2', with the digit one, on p. 16.

Second check: none (judge only)

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Typo Typo: "a major non-MHS locus (Idd3)" should be non-MHC.

p. 15 T1D section
a major non-MHS locus (Idd3)
p. 15 T1D paragraph
non-MHS locus
p. 15
non-MHS locus (Idd3)

Judge's note: Page 15 shows 'non-MHS'. MHC is the abbreviation defined and used throughout (e.g. the p. 14 T1D section), and 'MHS' is never defined.

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Typo Misspelling in the 12p13 paragraph: "the effect of impuation is to tip an already-strong signal" should read "imputation". The other misspellings bundled in this cluster are judged separately under C032, C033, C035 and C036.

p. 15 T1D/T2D sections
the effect of impuation
p. 15 T2D section
The appareciable familial aggregation
p. 16 T2D section
Supplemantary Table 8
p. 16 T2D section
evidence fo association

Judge's note: On the page 15 image, the 12p13 paragraph reads "where the effect of impuation is to tip an already-strong signal". Crops a and e show this same instance. This cluster also bundles 'appareciable', 'perallele', 'Supplemantary' and 'fo association'. Each of those has its own cluster (C032, C033, C035, C036), where it is confirmed, so this verdict covers 'impuation' only.

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Typo Misspelling in the T2D introduction: "The appareciable familial aggregation of T2D" should read "appreciable".

p. 15 T2D intro
appareciable familial aggregation

Judge's note: Seen on the page 15 image, in the first paragraph of the Type 2 diabetes section.

Second check: none (judge only)

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Typo Fused words in the FTO paragraph: "characterized by a perallele OR for T2D of ~1.25" should read "per-allele".

p. 15 FTO paragraph
perallele OR

Judge's note: Seen on the page 15 image, last paragraph. Elsewhere the paper writes "per-allele" (for example "per-allele ORs" on page 18).

Second check: none (judge only)

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Typo Misspelling in the CDKAL1 paragraph: "(Supplemantary Table 8)" should read "Supplementary".

p. 16 CDKAL1 paragraph
Supplemantary Table 8
p. 16
(Supplemantary Table 8)

Judge's note: Seen on the page 16 image, at the end of the first paragraph. Both crops show the same single occurrence.

Second check: none (judge only)

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Typo Typo in the SLC30A8/LOC387761/EXT2 paragraph: "show evidence fo association with T2D" should read "of".

p. 16 SLC30A8 paragraph
evidence fo association
p. 16
show evidence fo association with T2D

Judge's note: Seen on the page 16 image and in crop C037-a.

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Typo The gene symbol is printed with the digit one: "mapping to the 1GF2BP2 gene", for IGF2BP2.

p. 16 T2D replicating signals
1GF2BP2 gene
p. 16
mapping to the 1GF2BP2 gene

Judge's note: In the zoomed crop of page 16 the first character of the italic gene symbol is a digit '1' with a flag, not a capital I, and the text layer agrees. This is a typesetting error in the PDF, not an extraction artefact.

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Typo Typos: Figure 5 legend 'Black points represent SNPs tyred in the study' (typed), 'taken from the USCS Genome Browser' (UCSC), and T2D section 'departures from additivity (Supplemantary Table 8)' (Supplementary).

p. 47 Figure 5 legend
SNPs tyred in the study
p. 48 Figure 5 legend
USCS Genome Browser
p. 16 T2D section
Supplemantary Table 8

Judge's note: All three misspellings can be seen on the page images: p47 Fig. 5 legend 'tyred', p48 legend continuation 'USCS Genome Browser', and p16 'Supplemantary Table 8'. These are cosmetic spelling errors.

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Typo Misspelling in the Acknowledgements: "(particulary R. Pettitt)" should read "particularly".

p. 21 Acknowledgements
(particulary R. Pettitt)

Judge's note: The text layer of page 21 contains 'particulary'. This is a simple spelling slip that the text layer is unlikely to have introduced, so it is confirmed on the quoted text and the crop reference.

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Typo The same number is formatted two ways in one paragraph: "3,622 consenting blood donors" and "from the 3622 samples recruited".

p. 23 UKBS controls
3622 samples recruited
p. 23 UKBS controls
3,622 consenting blood donors

Judge's note: Seen on the page 23 image, UKBS paragraph. This is a purely cosmetic inconsistency.

Second check: none (judge only)

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Typo DNA extraction protocol prints "centrifugation (2.000 r.p.m., 10 min, 20 °C)" with a decimal point as thousands separator, whereas the same paragraph uses "2,500 r.p.m." and "3,000 r.p.m."

p. 24 DNA extraction
2.000 r.p.m.
p. 24 DNA extraction
2,500 r.p.m.

Judge's note: Page 24 image: the first centrifugation step reads '2.000 r.p.m.', and later steps in the same paragraph read '2,500' and '3,000 r.p.m.'. Only the separator is inconsistent; the intended value (2,000) is clear.

Second check: none (judge only)

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Typo Sample handling reads "broad geographical region and age at requirement" (recruitment intended), and the Figure 2 legend reads "concentration band (see Method)" where the legend's previous sentence says 'Methods'.

p. 24 Sample handling
age at requirement
p. 44 Figure 2 legend
(see Method)

Judge's note: Page 24 image confirms 'age at requirement'. Page 44 (Figure 2 legend) image confirms '(see Method)', while the same legend says 'filters described in Methods'. Both are copy-editing slips. The 'age at requirement' item is also listed in C051.

Second check: none (judge only)

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Typo Methods typos: "HampMap CEU individuals" (HapMap), "Estiamtes of λ" (Estimates), "can by analysed using snpMatrix" (be), "age at requirement" (recruitment).

p. 28 Comparing linkage disequilibrium
HampMap CEU individuals
p. 28 Over-dispersion
Estiamtes of
p. 32 Software
can by analysed using snpMatrix
p. 24 Sample handling
age at requirement

Judge's note: Page 28 image confirms 'HampMap CEU individuals and our 58C' and 'Estiamtes of λ were also calculated'. Page 32 image confirms 'can by analysed using snpMatrix'. Page 24 confirms 'age at requirement', which is also covered in C047. All are cosmetic.

Second check: none (judge only)

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Typo Power calculations: "simulated independently from theses calculated frequencies" should read 'these'.

p. 25 Power calculations
from theses calculated frequencies

Judge's note: Page 25 image confirms 'theses calculated frequencies'.

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Typo "We let G={G1,..., Gk} denote the genotype data on the K individuals": the last index is lowercase k, but the count is defined as uppercase K.

p. 31 Methods, Multilocus analysis
G={G1,..., Gk} denote the genotype data on the K individuals

Judge's note: Page 31 image shows 'G={G1,..., Gk}' with an italic lowercase k, followed by 'on the K individuals' with an uppercase K. This is a notation inconsistency that does not affect the method.

Second check: none (judge only)

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Typo The CHIAMO contact is given as "marchini@stas.ox.ac.uk", whereas the SNPTEST and IMPUTE contacts are "marchini@stats.ox.ac.uk".

p. 32 Methods, Software
marchini@stas.ox.ac.uk
p. 32 Methods, Software
marchini@stats.ox.ac.uk

Judge's note: Page 32 image: the CHIAMO paragraph has 'stas.ox.ac.uk', and the two later paragraphs have 'stats.ox.ac.uk'. The first appears to be a typo.

Second check: none (judge only)

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Typo Ref. 137 reads "Genotyping over 100,000 SNPs on a pair of oligonucleotide arrays. 1, 104-105. Nat Methods. 2004; 1:104–105."; the volume and pages appear twice.

p. 33 Reference 137
pair of oligonucleotide arrays. 1, 104-105. Nat Methods. 2004; 1:104–105.

Judge's note: Page 33 crop image confirms that the stray fragment '1, 104-105.' appears after the title and before the journal field.

Second check: none (judge only)

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Typo Reference-list typos: Ref. 48 "immunolocalization in Chinese hamster ovary calls" (cells); Ref. 72 "Taylor Franics Group" (Francis); Ref. 98 author "Brad OJ".

p. 39 Reference 48
immunolocalization in Chinese hamster ovary calls
p. 41 Ref 98
Brad OJ
p. 41 Ref 97
337–388
p. 39 Ref 48
ovary calls

Judge's note: Images confirm 'ovary calls' (page 39), 'Taylor Franics Group' (page 40) and 'Brad OJ' (page 41). 'calls' and 'Franics' are evident typos. Whether 'Brad OJ' should be 'Brand OJ' rests on outside knowledge of the cited author's name and is for the authors to confirm. The Ref. 97 page range is handled in C060.

Second check: none (judge only)

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Typo The Table 2 footnote says 'Positions are in NCBI build-35 coordinates.', but Table 2 has no position or region column.

p. 51 Table 2 footnote
Positions are in NCBI build-35 coordinates.

Judge's note: The p51 image shows that Table 2's columns are Collection, Gene, Chromosome (band), Reported SNP, WTCCC SNP, HapMap r2 and the two P values. No coordinates are tabulated, so this boilerplate sentence (also used under Tables 1 and 3) has nothing to refer to. It is harmless.

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Typo In Table 3, the T1D MHC rs9272346 homozygote odds ratio is printed as '18.52 (27.03-12.69)', with the interval bounds in reverse order.

p. 52 Table 3, T1D MHC rs9272346, Homozygote odds ratio
(27.03-12.69)
p. 52 Table 3, T1D MHC row
18.52 (27.03-12.69)

Judge's note: The p52 image shows the bounds upper-first. Every other interval in Tables 3 and 4 is printed lower-upper. 18.52 lies between 12.69 and 27.03, so only the order is wrong.

Second check: code check

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