Evaluating historical candidate genes for schizophrenia.
- Authors
- Farrell, M S; Werge, T; Sklar, P; Owen, M J; Ophoff, R A; O'Donovan, M C; Corvin, A; Cichon, S; Sullivan, P F
- Year
- 2015
- Journal
- Molecular psychiatry
- PMID
- 25754081
- DOI
- 10.1038/mp.2015.16
- PMCID
- PMC4414705
Prior to the genome-wide association era, candidate gene studies were a major approach in schizophrenia genetics. In this invited review, we consider the current status of 25 historical candidate genes for schizophrenia (for example, COMT, DISC1, DTNBP1 and NRG1). The initial study for 24 of these genes explicitly evaluated common variant hypotheses about schizophrenia. Our evaluation included a meta-analysis of the candidate gene literature, incorporation of the results of the largest genomic study yet published for schizophrenia, ratings from informed researchers who have published on these genes, and ratings from 24 schizophrenia geneticists. On the basis of current empirical evidence and mostly consensual assessments of informed opinion, it appears that the historical candidate gene literature did not yield clear insights into the genetic basis of schizophrenia. A likely reason why historical candidate gene studies did not achieve their primary aims is inadequate statistical power. However, the considerable efforts embodied in these early studies unquestionably set the stage for current successes in genomic approaches to schizophrenia.
Candidate gene publications per gene and per year. For each gene, the number of publications is indicated on the Y-axis, and the year is the X-axis. The data shown are from a PubMed query: (gene [All Fields] OR βprotein nameβ[All Fields]) AND (βschizophreniaβ[MeSH Terms] OR βschizophreniaβ[All Fields]). The goal of this PubMed query was to provide a rough gauge of the impact of a candidate gene on the field (which differs from the βpre-GWASβ column in Table 1).
LLM interpretation
This figure consists of a grid of 25 line plots showing the number of PubMed publications per year for various candidate genes associated with schizophrenia. The X-axis represents the year (from 1990 to 2010) and the Y-axis represents the number of papers (ranging from 0 to 100). While most genes show low or stable publication counts, genes such as BDNF, DISC1, DRD2, and NRG1 exhibit a clear upward trend in publication volume over time.
How many biologically interesting human genes are there?This bioinformatic analysis addressed the question: how many human genes are of legitimate interest to an integrative neuroscientist or psychiatric geneticist? (A) We intersected 19,304 gene models from GENCODE (v17, βKNOWNβ or βprotein_codingβ) with multiple data sources. Some genes can be in multiple categories. (B) Summary statistics (1=in set, 0=not in set): 35.6% of all genes are in classes A or B (=6869/19304), and 61.4% of all genes are in classes A, B, or C (=11849/19304). These numbers are conservative as adding βexpression in brain at any developmental stageβ would increase the numbers further. Thus, sizable proportions of all genes are of potential interest to a biologist. Biological interest is an imprecise criterion for the salience of a finding.
LLM interpretation
Figure (A) is a table categorizing 19,304 human genes into three classes (A, B, and C) based on various bioinformatic criteria, such as GWAS implications, differential expression in the brain, and disease associations, with gene counts provided for each type. Figure (B) consists of three bar charts showing the frequency of genes in each class and a summary table detailing the overlap between these classes. The summary table indicates that 38.62% of genes do not fall into any of the three categories, while various percentages represent genes belonging to one or more combinations of classes A, B, and C.
| Name | Type |
|---|---|
| 108 genome-wide significant loci local | variant |
| AKT1 | gene |
| alcohol | phenotype |
| alcohol dependence | phenotype |
| alcohol metabolic genes local | gene |
| Alzheimerβs disease | phenotype |
| antipsychotics | drug |
| apoE | gene |
| APOE Ξ΅4 allele | gene |
| APP | gene |
| autism | phenotype |
| Bdnf | gene |
| bipolar disorder | phenotype |
| candidate genes | cohort |
| candidate gene studies local | cohort |
| candidate gene study | cohort |
| Chrna7 | gene |
| common variants | cohort |
| common variation | variant |
| COMT | gene |
| DAO | gene |
| DAOA | gene |
| DISC1 | gene |
| disease gene local | gene |
| DRD2 | gene |
| DRD3 | gene |
| DRD4 | gene |
| DTNBP1 | gene |
| Early-onset Alzheimerβs disease | phenotype |
| endophenotype | phenotype |
| genetic marker | variant |
| GRM3 | gene |
| historical candidate genes local | gene |
| Htr2a | gene |
| human genes | gene |
| independent families local | cohort |
| informed investigators local | cohort |
| KCNN3 | gene |
| major depressive disorder | phenotype |
| MTHFR | gene |
| NOTCH4 local | gene |
| NRG1 | gene |
| particular gene local | gene |
| PGC | cohort |
| PGC mega-analysis local | cohort |
| PGC schizophrenia mega-analysis local | cohort |
| PGC schizophrenia working group local | cohort |
| population | cohort |
| PPP3CC | gene |
| PRODH local | gene |
| PSEN1 | gene |
| PSEN2 | gene |
| psychiatric disorders | phenotype |
| Psychiatric Genomics Consortium | cohort |
| rare CNVs | variant |
| Rare exonic variants local | variant |
| rare variant | cohort |
| RGS4 | gene |
| schizophrenia | phenotype |
| schizophrenia geneticists local | cohort |
| Schizophrenia geneticists local | cohort |
| Scottish pedigree local | cohort |
| SLC6A3 | gene |
| SLC6A4 | gene |
| SNP | cohort |
| SZGene local | cohort |
| SZGene meta-analyses local | cohort |
| t(1;11) translocation | variant |
| TNF | gene |
| ZDHHC8 | gene |
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