Author Correction: Application of Mendelian randomization to explore the causal role of the human gut microbiome in colorectal cancer (Scientific Reports, (2023), 13, 1, (5968), 10.1038/s41598-023-31840-0)
Publikation: Spezielle Publikationen/Beiträge › Korrekturen (Errata und Widerrufe) › Begutachtung
Beitragende
Abstract
Correction to: Scientifc Reports, published online 12 April 2023 The original version of this Article contained errors. The colocalisation analysis parameters using the ‘coloc’ package detailing the outcome dataset type were incorrectly specified and default prior probability was erroneously changed from 1e−05 to 1e−06. As a result, in the Results section, under the subheading ‘Sensitivity analyses’, “Therefore, focusing on the difference between the tested hypotheses (see Methods), colocalisation results provided evidence that neither G. Bifidobacterium nor G. unclassified, O. Bacteroidales were likely to share a causal variant with overall or site-specific CRC (Table 2). Regional association plots confirmed findings from genetic colocalisation for G. unclassified, O. Bacteroidales (Fig. 3; Supplementary Fig. 1). However, despite little evidence for genetic colocalisation for G. Bifidobacterium with overall and site-specific CRC, regional association plots suggest the genomic region surrounding the rs4988235 SNP is important in both abundance of G. Bifidobacterium and CRC risk (Fig. 3; Supplementary Fig. 2).” now reads: “Therefore, focusing on the difference between the tested hypotheses (see Methods), colocalisation results provided little evidence that G. unclassified, O. Bacteroidales was likely to share a causal variant with overall or site-specific CRC (Table 2). Regional association plots confirmed findings from genetic colocalisation for G. unclassified, O. Bacteroidales (Fig. 3; Supplementary Fig. 1). Whilst there was evidence for genetic colocalisation for G. Bifidobacterium with overall (with a posterior probability of 0.87) CRC risk and, to a lower extent, with site-specific CRC risk (posterior probabilities ranged from 0.05–0.72), regional association plots suggest the wider genomic region surrounding the rs4988235 SNP is important in both abundance of G. Bifidobacterium and CRC risk (Fig. 3; Supplementary Fig. 2).” Also, in the Discussion section, “It is worth noting that, whilst limited by power, our colocalisation analyses provided little evidence to suggest that either of these microbial traits (i.e., G. Bifidobacterium and G. unclassified, O. Bacteroidales) shared causal variants with CRC, which is a necessary (but not a sufficient) criterion for causality. Therefore, further analyses with a much larger quantity of microbiome-related SNPs, larger GWASs from which these SNPs are discovered and importantly replicated, plus a better understanding of the relationships between host genetic variation and the gut microbiome are required to provide conclusive evidence in this context.” now reads: “It is worth noting that, whilst limited by power, our colocalisation analyses provided some evidence to suggest that G. Bifidobacterium (but not G. unclassified, O. Bacteroidales) shared causal variants with CRC, which is a necessary (but not a sufficient) criterion for causality. Therefore, further analyses with a much larger quantity of microbiome-related SNPs, larger GWASs from which these SNPs are discovered and importantly replicated, plus a better understanding of the relationships between host genetic variation and the gut microbiome and comprehensive sensitivity analyses that we present here are required to provide conclusive evidence in this context.” Further, in the Materials and methods section, under the subheading ‘Sensitivity analyses’, “Colocalisation analyses were conducted using the ‘coloc’ R package with default parameters 40.” now reads: “Colocalisation analyses were conducted using the ‘coloc’ R package with default parameters (i.e., with the prior probabilities of the SNP being associated with the exposure, the outcome or both traits being specified as 1 × 10 −04, 1 × 10 −04 and 1 × 10 −05, respectively 40), additionally specifying that the exposures (i.e., microbial traits) were continuous and that the outcome (i.e., CRC risk) was binary (with either the ‘quant’ or ‘cc’ option, respectively, specified as the type of data).” Moreover, in Table 2, all the values were incorrect. The original Table 2 appears below. (Table presented.) Posterior probabilities relating to associations between microbial traits and both overall and site-specific colorectal cancer. Microbial trait and CRC risk H0 H1 H2 H3 H4 G. Bifidobacterium (AB) and overall CRC 0.86 0.11 0.03 0.004 0.0001 G. Bifidobacterium (AB) and distal colon cancer risk 0.85 0.11 0.04 0.01 0.0001 G. Bifidobacterium (AB) and proximal colon cancer risk 0.85 0.11 0.04 0.01 0.0001 G. Bifidobacterium (AB) and colon cancer risk 0.86 0.11 0.03 0.004 0.0001 G. Bifidobacterium (AB) and rectal cancer risk 0.85 0.11 0.04 0.01 0.0001 G. unclassified, O. Bacteroidales (P/A) and overall CRC 0.78 0.16 0.05 0.01 0.0002 G. unclassified, O. Bacteroidales (P/A) and proximal colon cancer risk 0.79 0.14 0.06 0.01 0.0002 G. unclassified, O. Bacteroidales (P/A) and colon cancer risk 0.80 0.14 0.04 0.01 0.0001 G. unclassified, O. Bacteroidales (P/A) and rectal cancer risk 0.79 0.14 0.06 0.01 0.0002 AB = abundance; CRC = colorectal cancer; P/A = presence versus absence. Letters in the microbial trait name represent the taxon classification level from which that microbial trait was observed, with “G” and “O” representing “genus” and “order”, respectively. All microbial traits that were not confidently classified at the genus level were organised into unclassified groups within higher classification levels (represented by “unclassified”). H0: Neither trait has a genetic association in the region, H1: Only the first trait (i.e., the microbial trait) has a genetic association in the region, H2; Only the second trait (i.e., breast cancer risk) has a genetic association in the region, H3: Both traits are associated but have different causal variants and H4: Both traits are associated and have the same causal variant. Finally, the Supplementary Information 2 file contained an error, where the column headings ‘EA’ and ‘OA’ in Supplementary Table 2 were inadvertently reversed (except for G. Bifidobacterium). The original Article and its accompanying Supplementary Information 2 file have been corrected.
Details
Originalsprache | Englisch |
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Seiten | 12131 |
Band | 13 |
Ausgabenummer | 1 |
Fachzeitschrift | Scientific reports |
Publikationsstatus | Veröffentlicht - 26 Juli 2023 |
Peer-Review-Status | Ja |
Externe IDs
PubMedCentral | PMC10371981 |
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Scopus | 85165874986 |