Back

Widespread methylation quantitative trait loci and their role in schizophrenia risk

Perzel Mandell, K. A.; Eagles, N. J.; Wilton, R.; Price, A. J.; Semick, S. A.; Collado-Torres, L.; Tao, R.; Han, S.; Szalay, A. S.; Hyde, T. M.; Kleinman, J. E.; Weinberger, D. R.; Jaffe, A. E.

2020-09-24 genomics
10.1101/2020.09.24.311878 bioRxiv
Show abstract

DNA methylation (DNAm) regulates gene expression and may represent gene-environment interactions. Using whole genome bisulfite sequencing, we surveyed DNAm in a large sample (n=344) of human brain tissues. We identify widespread genetic influence on local methylation levels throughout the genome, with 76% of SNPs and 38% of CpGs being part of methylation quantitative trait loci (meQTLs). These associations can further be clustered into regions that are differentially methylated by a given SNP, highlighting putative functional regions that explain much of the heritability associated with risk loci. Furthermore, some CpH sites associated with genetic variation. We have established a comprehensive, single base resolution view of association between genetic variation and genomic methylation, and implicate schizophrenia GWAS-associated variants as influencing the epigenetic plasticity of the brain. One-sentence summaryMost genetic variants associated with DNA methylation levels, and implicated schizophrenia GWAS variants in the human brain.

Matching journals

The top 7 journals account for 50% of the predicted probability mass.

1
Biological Psychiatry
○ 137 papers in training set
Top 0.1%
14.6%
Similar papers in this journal
2
Proceedings of the National Academy of Sciences
● 2444 papers in training set
Top 4%
9.4%
Similar papers in this journal
3
Science Advances
● 1243 papers in training set
Top 3%
6.5%
Similar papers in this journal
4
Science
● 477 papers in training set
Top 1%
6.0%
Similar papers in this journal
5
Cell Genomics
○ 172 papers in training set
Top 0.8%
5.3%
Similar papers in this journal
6
Genome Biology
○ 637 papers in training set
Top 2%
5.3%
7
Human Molecular Genetics
◐ 141 papers in training set
Top 0.5%
4.7%
50% of probability mass above
8
Nature Communications
○ 5641 papers in training set
Top 31%
4.2%
9
Nature Neuroscience
○ 252 papers in training set
Top 2%
3.3%
10
Neuropsychopharmacology
○ 153 papers in training set
Top 1%
3.1%
11
PLOS Genetics
● 862 papers in training set
Top 4%
3.0%
12
Genome Research
● 468 papers in training set
Top 3%
2.6%
13
eLife
● 5828 papers in training set
Top 43%
2.4%
14
Genome Medicine
○ 183 papers in training set
Top 2%
2.3%
15
Scientific Reports
○ 3612 papers in training set
Top 50%
1.8%
16
Nucleic Acids Research
◐ 1281 papers in training set
Top 9%
1.7%
17
Molecular Psychiatry
○ 282 papers in training set
Top 4%
1.7%
18
Nature Genetics
○ 286 papers in training set
Top 3%
1.6%
19
Clinical Epigenetics
○ 60 papers in training set
Top 0.3%
1.4%
20
Translational Psychiatry
○ 260 papers in training set
Top 3%
1.1%
21
Communications Biology
○ 993 papers in training set
Top 24%
1.1%
22
Science Translational Medicine
● 127 papers in training set
Top 3%
1.1%
23
The American Journal of Human Genetics
○ 234 papers in training set
Top 2%
1.1%
24
American Journal of Medical Genetics Part B: Neuropsychiatric Genetics
○ 26 papers in training set
Top 0.4%
1.0%
25
Nature
○ 645 papers in training set
Top 11%
0.8%
26
BMC Genomics
○ 406 papers in training set
Top 9%
0.6%
27
Human Genetics and Genomics Advances
○ 84 papers in training set
Top 2%
0.6%
28
Journal of Biological Chemistry
○ 690 papers in training set
Top 11%
0.6%
29
PLOS ONE
● 5266 papers in training set
Top 64%
0.6%

"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.