Schizophrenia Polygenic Risk Score as a Predictor of Antipsychotic Efficacy in First-Episode Psychosis

Am J Psychiatry. 2019 Jan 1;176(1):21-28. doi: 10.1176/appi.ajp.2018.17121363. Epub 2018 Nov 5.


Objective: Pharmacogenomic studies of antipsychotics have typically examined effects of individual polymorphisms. By contrast, polygenic risk scores (PRSs) derived from genome-wide association studies (GWAS) can quantify the influence of thousands of common alleles of small effect in a single measure. The authors examined whether PRSs for schizophrenia were predictive of antipsychotic efficacy in four independent cohorts of patients with first-episode psychosis (total N=510).

Method: All study subjects received initial treatment with antipsychotic medication for first-episode psychosis, and all were genotyped on standard single-nucleotide polymorphism (SNP) arrays imputed to the 1000 Genomes Project reference panel. PRS was computed based on the results of the large-scale schizophrenia GWAS reported by the Psychiatric Genomics Consortium. Symptoms were measured by using total symptom rating scales at baseline and at week 12 or at the last follow-up visit before dropout.

Results: In the discovery cohort, higher PRS significantly predicted higher symptom scores at the 12-week follow-up (controlling for baseline symptoms, sex, age, and ethnicity). The PRS threshold set at a p value <0.01 gave the strongest result in the discovery cohort and was used to replicate the findings in the other three cohorts. Higher PRS significantly predicted greater posttreatment symptoms in the combined replication analysis and was individually significant in two of the three replication cohorts. Across the four cohorts, PRS was significantly predictive of adjusted 12-week symptom scores (pooled partial r=0.18; 3.24% of variance explained). Patients with low PRS were more likely to be treatment responders than patients with high PRS (odds ratio=1.91 in the two Caucasian samples).

Conclusions: Patients with higher PRS for schizophrenia tended to have less improvement with antipsychotic drug treatment. PRS burden may have potential utility as a prognostic biomarker.

Keywords: Antipsychotics; First Episode Psychosis; Polygenic Risk Score; Schizophrenia.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adult
  • Antipsychotic Agents / therapeutic use*
  • Episode of Care
  • Female
  • Genome-Wide Association Study
  • Humans
  • Male
  • Multifactorial Inheritance
  • Predictive Value of Tests
  • Prognosis
  • Psychopathology
  • Psychotic Disorders* / diagnosis
  • Psychotic Disorders* / drug therapy
  • Psychotic Disorders* / etiology
  • Psychotic Disorders* / psychology
  • Risk Assessment / methods*
  • Schizophrenia* / diagnosis
  • Schizophrenia* / drug therapy
  • Schizophrenic Psychology
  • Treatment Outcome


  • Antipsychotic Agents