New insights into the pharmacogenomics of antidepressant response from the GENDEP and STAR∗D studies: Rare variant analysis and high-density imputation

C. Fabbri, K. E. Tansey, R. H. Perlis, J. Hauser, N. Henigsberg, W. Maier, O. Mors, A. Placentino, M. Rietschel, D. Souery, G. Breen, C. Curtis, L. Sang-Hyuk, S. Newhouse, H. Patel, M. Guipponi, N. Perroud, G. Bondolfi, M. O'Donovan, G. LewisJoanna M Biernacka, Richard M Weinshilboum, A. Farmer, K. J. Aitchison, I. Craig, P. McGuffin, R. Uher, C. M. Lewis

Research output: Contribution to journalArticle

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Abstract

Genome-wide association studies have generally failed to identify polymorphisms associated with antidepressant response. Possible reasons include limited coverage of genetic variants that this study tried to address by exome genotyping and dense imputation. A meta-analysis of Genome-Based Therapeutic Drugs for Depression (GENDEP) and Sequenced Treatment Alternatives to Relieve Depression (STARD) studies was performed at the single-nucleotide polymorphism (SNP), gene and pathway levels. Coverage of genetic variants was increased compared with previous studies by adding exome genotypes to previously available genome-wide data and using the Haplotype Reference Consortium panel for imputation. Standard quality control was applied. Phenotypes were symptom improvement and remission after 12 weeks of antidepressant treatment. Significant findings were investigated in NEWMEDS consortium samples and Pharmacogenomic Research Network Antidepressant Medication Pharmacogenomic Study (PGRN-AMPS) for replication. A total of 7062 950 SNPs were analyzed in GENDEP (n = 738) and STARD (n = 1409). rs116692768 (P = 1.80e ? 08, ITGA9 (integrin ?9)) and rs76191705 (P = 2.59e ? 08, NRXN3 (neurexin 3)) were significantly associated with symptom improvement during citalopram/escitalopram treatment. At the gene level, no consistent effect was found. At the pathway level, the Gene Ontology (GO) terms GO: 0005694 (chromosome) and GO: 0044427 (chromosomal part) were associated with improvement (corrected P = 0.007 and 0.045, respectively). The association between rs116692768 and symptom improvement was replicated in PGRN-AMPS (P = 0.047), whereas rs76191705 was not. The two SNPs did not replicate in NEWMEDS. ITGA9 codes for a membrane receptor for neurotrophins and NRXN3 is a transmembrane neuronal adhesion receptor involved in synaptic differentiation. Despite their meaningful biological rationale for being involved in antidepressant effect, replication was partial. Further studies may help in clarifying their role.

Original languageEnglish (US)
Pages (from-to)413-421
Number of pages9
JournalPharmacogenomics Journal
Volume18
Issue number3
DOIs
StatePublished - May 22 2018

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Pharmacogenetics
Antidepressive Agents
Gene Ontology
Exome
Single Nucleotide Polymorphism
Citalopram
trkC Receptor
Genome
Genome-Wide Association Study
Research
Integrins
Quality Control
Haplotypes
Genes
Meta-Analysis
Chromosomes
Genotype
Phenotype
Membranes
Pharmaceutical Preparations

ASJC Scopus subject areas

  • Molecular Medicine
  • Genetics
  • Pharmacology

Cite this

New insights into the pharmacogenomics of antidepressant response from the GENDEP and STAR∗D studies : Rare variant analysis and high-density imputation. / Fabbri, C.; Tansey, K. E.; Perlis, R. H.; Hauser, J.; Henigsberg, N.; Maier, W.; Mors, O.; Placentino, A.; Rietschel, M.; Souery, D.; Breen, G.; Curtis, C.; Sang-Hyuk, L.; Newhouse, S.; Patel, H.; Guipponi, M.; Perroud, N.; Bondolfi, G.; O'Donovan, M.; Lewis, G.; Biernacka, Joanna M; Weinshilboum, Richard M; Farmer, A.; Aitchison, K. J.; Craig, I.; McGuffin, P.; Uher, R.; Lewis, C. M.

In: Pharmacogenomics Journal, Vol. 18, No. 3, 22.05.2018, p. 413-421.

Research output: Contribution to journalArticle

Fabbri, C, Tansey, KE, Perlis, RH, Hauser, J, Henigsberg, N, Maier, W, Mors, O, Placentino, A, Rietschel, M, Souery, D, Breen, G, Curtis, C, Sang-Hyuk, L, Newhouse, S, Patel, H, Guipponi, M, Perroud, N, Bondolfi, G, O'Donovan, M, Lewis, G, Biernacka, JM, Weinshilboum, RM, Farmer, A, Aitchison, KJ, Craig, I, McGuffin, P, Uher, R & Lewis, CM 2018, 'New insights into the pharmacogenomics of antidepressant response from the GENDEP and STAR∗D studies: Rare variant analysis and high-density imputation', Pharmacogenomics Journal, vol. 18, no. 3, pp. 413-421. https://doi.org/10.1038/tpj.2017.44
Fabbri, C. ; Tansey, K. E. ; Perlis, R. H. ; Hauser, J. ; Henigsberg, N. ; Maier, W. ; Mors, O. ; Placentino, A. ; Rietschel, M. ; Souery, D. ; Breen, G. ; Curtis, C. ; Sang-Hyuk, L. ; Newhouse, S. ; Patel, H. ; Guipponi, M. ; Perroud, N. ; Bondolfi, G. ; O'Donovan, M. ; Lewis, G. ; Biernacka, Joanna M ; Weinshilboum, Richard M ; Farmer, A. ; Aitchison, K. J. ; Craig, I. ; McGuffin, P. ; Uher, R. ; Lewis, C. M. / New insights into the pharmacogenomics of antidepressant response from the GENDEP and STAR∗D studies : Rare variant analysis and high-density imputation. In: Pharmacogenomics Journal. 2018 ; Vol. 18, No. 3. pp. 413-421.
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T2 - Rare variant analysis and high-density imputation

AU - Fabbri, C.

AU - Tansey, K. E.

AU - Perlis, R. H.

AU - Hauser, J.

AU - Henigsberg, N.

AU - Maier, W.

AU - Mors, O.

AU - Placentino, A.

AU - Rietschel, M.

AU - Souery, D.

AU - Breen, G.

AU - Curtis, C.

AU - Sang-Hyuk, L.

AU - Newhouse, S.

AU - Patel, H.

AU - Guipponi, M.

AU - Perroud, N.

AU - Bondolfi, G.

AU - O'Donovan, M.

AU - Lewis, G.

AU - Biernacka, Joanna M

AU - Weinshilboum, Richard M

AU - Farmer, A.

AU - Aitchison, K. J.

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N2 - Genome-wide association studies have generally failed to identify polymorphisms associated with antidepressant response. Possible reasons include limited coverage of genetic variants that this study tried to address by exome genotyping and dense imputation. A meta-analysis of Genome-Based Therapeutic Drugs for Depression (GENDEP) and Sequenced Treatment Alternatives to Relieve Depression (STARD) studies was performed at the single-nucleotide polymorphism (SNP), gene and pathway levels. Coverage of genetic variants was increased compared with previous studies by adding exome genotypes to previously available genome-wide data and using the Haplotype Reference Consortium panel for imputation. Standard quality control was applied. Phenotypes were symptom improvement and remission after 12 weeks of antidepressant treatment. Significant findings were investigated in NEWMEDS consortium samples and Pharmacogenomic Research Network Antidepressant Medication Pharmacogenomic Study (PGRN-AMPS) for replication. A total of 7062 950 SNPs were analyzed in GENDEP (n = 738) and STARD (n = 1409). rs116692768 (P = 1.80e ? 08, ITGA9 (integrin ?9)) and rs76191705 (P = 2.59e ? 08, NRXN3 (neurexin 3)) were significantly associated with symptom improvement during citalopram/escitalopram treatment. At the gene level, no consistent effect was found. At the pathway level, the Gene Ontology (GO) terms GO: 0005694 (chromosome) and GO: 0044427 (chromosomal part) were associated with improvement (corrected P = 0.007 and 0.045, respectively). The association between rs116692768 and symptom improvement was replicated in PGRN-AMPS (P = 0.047), whereas rs76191705 was not. The two SNPs did not replicate in NEWMEDS. ITGA9 codes for a membrane receptor for neurotrophins and NRXN3 is a transmembrane neuronal adhesion receptor involved in synaptic differentiation. Despite their meaningful biological rationale for being involved in antidepressant effect, replication was partial. Further studies may help in clarifying their role.

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