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Comment
. 2023 Dec 21;6(1):1296.
doi: 10.1038/s42003-023-05646-9.

Reply to: Genetic differentiation at probe SNPs leads to spurious results in meQTL discovery

Youshu Cheng  1   2 , Boyang Li  1   2 , Xinyu Zhang  2   3 , Bradley E Aouizerat  4   5 , Hongyu Zhao  6   7 , Ke Xu  8   9
Affiliations
Comment

Reply to: Genetic differentiation at probe SNPs leads to spurious results in meQTL discovery

Youshu Cheng et al. Commun Biol. .
No abstract available

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Conflict of interest statement

The authors declare no competing interests.

Figures

Fig. 1
Fig. 1. Comparing the replication rate between CpGs with probe-SNPs and CpGs without probe-SNPs.
The Methyl-seq data (N = 211) were used to replicate the meQTLs identified by Li et al. CpG sites with common probe-SNP within 50bp were defined using the SNPs in a the 1000 Genomes and b the study sample population, respectively. The p-values were derived from χ2 test.
See this image and copyright information in PMC

Comment on

References

    1. Li B, et al. Incorporating local ancestry improves identification of ancestry-associated methylation signatures and meQTLs in African Americans. Commun. Biol. 2022;5:401. doi: 10.1038/s42003-022-03353-5. - DOI - PMC - PubMed
    1. Price ME, et al. Additional annotation enhances potential for biologically-relevant analysis of the Illumina Infinium HumanMethylation450 BeadChip array. Epigenetics Chromatin. 2013;6:4. doi: 10.1186/1756-8935-6-4. - DOI - PMC - PubMed
    1. Naeem H, et al. Reducing the risk of false discovery enabling identification of biologically significant genome-wide methylation status using the HumanMethylation450 array. BMC Genomics. 2014;15:51. doi: 10.1186/1471-2164-15-51. - DOI - PMC - PubMed
    1. Huan T, et al. Genome-wide identification of DNA methylation QTLs in whole blood highlights pathways for cardiovascular disease. Nat. Commun. 2019;10:4267. doi: 10.1038/s41467-019-12228-z. - DOI - PMC - PubMed
    1. Hannon E, et al. An integrated genetic-epigenetic analysis of schizophrenia: evidence for co-localization of genetic associations and differential DNA methylation. Genome Biol. 2016;17:176. doi: 10.1186/s13059-016-1041-x. - DOI - PMC - PubMed