Topic: Genetics and APOE
It is estimated that the impact of related genes on the risk of Alzheimer's disease (AD) is nearly 70%. Identifying candidate causal genes can help treatment and diagnosis. The maturity of sequencing technology and the reduction of cost make genome-wide association study (GWAS) become an important means to find disease-related mutation sites. Because of linkage disequilibrium (LD), neither the gene regulated by SNP nor the specific SNP can be determined. Because GWAS is affected by sample size and interaction, we introduced empirical Bayes (EB) to make a meta-analysis of GWAS to greatly eliminate the bias caused by sample and the interaction of SNP. In addition, most SNPs are in the noncoding region, so it is not clear how they relate to phenotype. In this paper, expression quantitative trait locus (eQTL) studies and methylation quantitative trait locus (mQTL) studies are combined with GWAS to find the genes associated with Alzheimer disease in expression levels by pleiotropy. Summary data-based Mendelian randomization (SMR) is introduced to integrate GWAS and eQTL/mQTL data. Finally, we prioritized 274 significant SNPs, which belong to 20 genes by eQTL analysis and 379 significant SNPs, which belong to seven known genes by mQTL. Among them, 93 SNPs and 2 genes are overlapped. Finally, we did 10 case studies to prove the effectiveness of our method.
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APA 7th
Zhao, T., Hu, Y., Zang, T., & Wang, Y. (2019). Integrate GWAS, eQTL, and mQTL Data to Identify Alzheimer's Disease-Related Genes. Frontiers in genetics. https://doi.org/10.3389/fgene.2019.01021
Vancouver
Zhao T, Hu Y, Zang T, Wang Y. Integrate GWAS, eQTL, and mQTL Data to Identify Alzheimer's Disease-Related Genes. Frontiers in genetics. 2019. doi:10.3389/fgene.2019.01021. PMID: 31708967.
BibTeX
@article{zhao2019-31708967,
author = {Zhao, Tianyi and Hu, Yang and Zang, Tianyi and Wang, Yadong},
title = {{Integrate GWAS, eQTL, and mQTL Data to Identify Alzheimer's Disease-Related Genes}},
journal = {Frontiers in genetics},
year = {2019},
doi = {10.3389/fgene.2019.01021},
pmid = {31708967},
url = {https://doi.org/10.3389/fgene.2019.01021}
}
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Key findings
- In this paper, expression quantitative trait locus (eQTL) studies and methylation quantitative trait locus (mQTL) studies are combined with GWAS to find the genes associated with Alzheimer disease in expression levels by pleiotropy.
- Finally, we prioritized 274 significant SNPs, which belong to 20 genes by eQTL analysis and 379 significant SNPs, which belong to seven known genes by mQTL.
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Study details
- Study designmeta-analysis
- Evidence strengthHigh
How this study scored 68/100
Published in a peer-reviewed journal, and it is a meta-analysis pooling many studies. Scored zero for sample size, effect reported and studied in people because the record does not state it. We have no data on journal's citation record, times cited, citations per year, impact for its field and year, cited by studies here, still being cited, senior author's track record, institution's track record, multicenter collaboration and free to read, so those were left out: it earned 38 of the 56 points we could judge it on, which is 68 out of 100.
| Component | Points | Why |
|---|---|---|
| Journal tier | 7 / 10 | Tier 3 — peer-reviewed journal (Frontiers in genetics) |
| Journal's citation record | — / 4 | No journal record from OpenAlex — left out of this score |
| Study design | 12 / 12 | A meta-analysis pooling many studies |
| Strength of evidence | 5 / 5 | Rated “high” in our summary |
| Peer-review validation | 10 / 10 | Peer-reviewed. Published as an article in a named peer-reviewed journal. |
| How recent | 2 / 5 | 2019 — within 10 year(s) of the newest study here |
| Sample size | 0 / 4 | Participant count not stated — scores zero (not stated in the record — scored 0) |
| Effect reported | 0 / 3 | No effect size reported — scores zero (not stated in the record — scored 0) |
| Studied in people | 0 / 3 | Not stated whether this was studied in people — scores zero (not stated in the record — scored 0) |
| Randomized / blinded | 0 / 2 | A review of other studies — randomization is not credited here |
| Times cited | — / 7 | No citation count (not found in OpenAlex) — left out of this score |
| Citations per year | — / 5 | No citation count or no year — left out of this score |
| Impact for its field and year | — / 6 | No field-weighted citation impact (OpenAlex has none yet) — left out of this score |
| Cited by studies here | — / 6 | Not yet checked against this library's citation graph — left out of this score |
| Still being cited | — / 4 | No yearly citation counts — left out of this score |
| Senior author's track record | — / 4 | Senior author's record not available — left out of this score |
| Institution's track record | — / 3 | No institution listed in OpenAlex — left out of this score |
| Multicenter collaboration | — / 3 | Institutions not listed — left out of this score |
| Indexed in PubMed | 2 / 2 | Indexed in PubMed (PMID 31708967) |
| Free to read | — / 2 | Access not recorded — left out of this score |
| Points | 38 / 56 | Scored on 10 of 20 parts. We have no data for the rest, so they are left out: 38 of the 56 points we could judge it on is 68 out of 100. |
| Total | 68 / 100 | — |
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