Depressive disorders account for a large and increasing global burden of disease. Although the condition of many patients improves with medication, only a minority experience full remission, and patients whose condition responds to one medication may not have a response to others. Individual variation in antidepressant treatment outcome is, at present, unpredictable but may have a partial genetic basis. We searched for genetic predictors of treatment outcome in 1,953 patients with major depressive disorder who were treated with the antidepressant citalopram in the Sequenced Treatment Alternatives for Depression (STAR*D) study and were prospectively assessed. In a split-sample design, a selection of 68 candidate genes was genotyped, with 768 single-nucleotide–polymorphism markers chosen to detect common genetic variation. We detected significant and reproducible association between treatment outcome and a marker in HTR2A (P range 1×10−6 to 3.7×10−5 in the total sample). Other markers in HTR2A also showed evidence of association with treatment outcome in the total sample. HTR2A encodes the serotonin 2A receptor, which is downregulated by citalopram. Participants who were homozygous for the A allele had an 18% reduction in absolute risk of having no response to treatment, compared with those homozygous for the other allele. The A allele was over six times more frequent in white than in black participants, and treatment was less effective among black participants. The A allele may contribute to racial differences in outcomes of antidepressant treatment. Taken together with prior neurobiological findings, these new genetic data make a compelling case for a key role of HTR2A in the mechanism of antidepressant action. Depressive disorders account for a large and increasing global burden of disease. Although the condition of many patients improves with medication, only a minority experience full remission, and patients whose condition responds to one medication may not have a response to others. Individual variation in antidepressant treatment outcome is, at present, unpredictable but may have a partial genetic basis. We searched for genetic predictors of treatment outcome in 1,953 patients with major depressive disorder who were treated with the antidepressant citalopram in the Sequenced Treatment Alternatives for Depression (STAR*D) study and were prospectively assessed. In a split-sample design, a selection of 68 candidate genes was genotyped, with 768 single-nucleotide–polymorphism markers chosen to detect common genetic variation. We detected significant and reproducible association between treatment outcome and a marker in HTR2A (P range 1×10−6 to 3.7×10−5 in the total sample). Other markers in HTR2A also showed evidence of association with treatment outcome in the total sample. HTR2A encodes the serotonin 2A receptor, which is downregulated by citalopram. Participants who were homozygous for the A allele had an 18% reduction in absolute risk of having no response to treatment, compared with those homozygous for the other allele. The A allele was over six times more frequent in white than in black participants, and treatment was less effective among black participants. The A allele may contribute to racial differences in outcomes of antidepressant treatment. Taken together with prior neurobiological findings, these new genetic data make a compelling case for a key role of HTR2A in the mechanism of antidepressant action. Major depressive disorder (MDD) is a major public health problem and a frequent reason why patients visit internists, family practitioners, psychiatrists, and other physicians.1Cassano P Fava M Depression and public health: an overview.J Psychosom Res. 2002; 53: 849-857Abstract Full Text Full Text PDF PubMed Scopus (353) Google Scholar MDD constitutes the fourth greatest disease burden worldwide, measured in disability-adjusted life years, which express years of healthy life lost to death and disability.2Ustun TB Ayuso-Mateos JL Chatterji S Mathers C Murray CJ Global burden of depressive disorders in the year 2000.Br J Psychiatry. 2004; 184: 386-392Crossref PubMed Scopus (1256) Google Scholar MDD is predicted to account for the second greatest global disease burden by 2020.3Murray CJ Lopez AD Evidence-based health policy—lessons from the Global Burden of Disease Study.Science. 1996; 274: 740-743Crossref PubMed Scopus (1629) Google Scholar Many patients can expect their condition to improve with antidepressant treatment, but only a minority experience full remission, and individual outcomes differ across medications. The largest study to date demonstrated that up to 63% of patients have improvement and that 47% of patients achieve complete remission of symptoms after an adequate trial with a single antidepressant.4Thase ME Haight BR Richard N Rockett CB Mitton M Modell JG VanMeter S Harriett AE Wang Y Remission rates following antidepressant therapy with bupropion or selective serotonin reuptake inhibitors: a meta-analysis of original data from 7 randomized controlled trials.J Clin Psychiatry. 2005; 66: 974-981Crossref PubMed Scopus (243) Google Scholar Patients whose treatment is unsuccessful with one antidepressant medication often have a response when treated with an antidepressant of a different chemical class (reviewed by Marangell5Marangell LB Switching antidepressants for treatment-resistant major depression.J Clin Psychiatry. 2001; 62: 12-17PubMed Google Scholar). Little is known about the basis for such marked individual variation in treatment outcome. Indirect evidence suggests that at least some of this variation has a genetic basis.6Serretti A Artioli P Quartesan R Pharmacogenetics in the treatment of depression: pharmacodynamic studies.Pharmacogenet Genomics. 2005; 15: 61-67Crossref PubMed Scopus (78) Google Scholar Outcome and side-effect patterns vary less between illness episodes than between individuals in some studies7Fava M Schmidt ME Zhang S Gonzales J Raute NJ Judge R Treatment approaches to major depressive disorder relapse. Part 2. Reinitiation of antidepressant treatment.Psychother Psychosom. 2002; 71: 195-199Crossref PubMed Scopus (40) Google Scholar, 8Franchini L Serretti A Gasperini M Smeraldi E Familial concordance of fluvoxamine response as a tool for differentiating mood disorder pedigrees.J Psychiatr Res. 1998; 32: 255-259Abstract Full Text PDF PubMed Scopus (138) Google Scholar but not all.9Remillard AJ Blackshaw SL Dangor A Differential responses to a single antidepressant in recurrent episodes of major depression.Hosp Community Psychiatry. 1994; 45: 359-361PubMed Google Scholar Other studies have shown that outcome of antidepressant treatment runs in families.8Franchini L Serretti A Gasperini M Smeraldi E Familial concordance of fluvoxamine response as a tool for differentiating mood disorder pedigrees.J Psychiatr Res. 1998; 32: 255-259Abstract Full Text PDF PubMed Scopus (138) Google Scholar, 10Stern SL Rush AJ Mendels J Toward a rational pharmacotherapy of depression.Am J Psychiatry. 1980; 137: 545-552Crossref PubMed Scopus (28) Google Scholar It has been suggested that a number of genetic variants influence outcome and/or side effects in comparatively small, naturalistic samples of patients treated for major depression, but these findings have often not been replicated (reviewed by Franchini et al.8Franchini L Serretti A Gasperini M Smeraldi E Familial concordance of fluvoxamine response as a tool for differentiating mood disorder pedigrees.J Psychiatr Res. 1998; 32: 255-259Abstract Full Text PDF PubMed Scopus (138) Google Scholar and Malhotra et al.11Malhotra AK Murphy Jr, GM Kennedy JL Pharmacogenetics of psychotropic drug response.Am J Psychiatry. 2004; 161: 780-796Crossref PubMed Scopus (277) Google Scholar). Since the effects of individual genes may be small, the definitive identification of alleles involved in antidepressant-treatment outcome may require large, well-characterized samples. The Sequenced Treatment Alternatives for Depression (STAR*D) study collected DNA from 1,953 subjects with MDD. At the first treatment step, participants received the selective serotonin reuptake inhibitor (SSRI) citalopram, with regular assessment of outcome and side effects.12Trivedi MH Rush AJ Wisniewski SR Nierenberg AA Warden D Ritz L Norquist G Howland RH Lebowitz B McGrath PJ Shores-Wilson K Biggs MM Balasubramani GK Fava M STAR*D Study Team Evaluation of outcomes with citalopram for depression using measurement-based care in STAR*D: implications for clinical practice.Am J Psychiatry. 2006; 163: 28-40Crossref PubMed Scopus (2645) Google Scholar A genetic association study of phenotypes measuring outcome of citalopram treatment was undertaken in the STAR*D sample, with use of 768 markers selected to detect common sequence variation within each of 68 candidate genes. The rationale, methods, and design of the STAR*D study have been detailed elsewhere.13Rush AJ Fava M Wisniewski SR Lavori PW Trivedi MH Sackeim HA Thase ME Nierenberg AA Quitkin FM Kashner TM Kupfer DJ Rosenbaum JF Alpert J Stewart JW McGrath PJ Biggs MM Shores-Wilson K Lebowitz BD Ritz L Niederehe G Sequenced treatment alternatives to relieve depression (STAR*D): rationale and design.Control Clin Trials. 2004; 25: 119-142Abstract Full Text Full Text PDF PubMed Scopus (737) Google Scholar In brief, investigators at 14 regional centers across the United States implemented a standard study protocol at 41 clinical sites. Subjects provided separate written informed consent for study participation and for the collection of blood samples for genetic studies. Outpatients aged 18–75 years with a baseline Hamilton Depression Rating Scale score14Hamilton M A rating scale for depression.J Neurol Neurosurg Psychiatry. 1960; 23: 56-62Crossref PubMed Scopus (24271) Google Scholar, 15Hamilton M Development of a rating scale for primary depressive illness.Br J Soc Clin Psychol. 1967; 6: 278-296Crossref PubMed Scopus (6872) Google Scholar of ≥14 who met DSM-IV16American Psychiatric Association Diagnostic and statistical manual of mental disorders. 4th ed. American Psychiatric Association, Washington, DC1994Google Scholar criteria for nonpsychotic MDD were eligible. Patients with bipolar, psychotic, or obsessive-compulsive disorders were excluded, as were those with primary eating disorders, general medical conditions that contraindicated study medications, substance dependence requiring inpatient detoxification, and clear nonresponse or intolerance to any protocol antidepressant during current episode or those who were pregnant or breast-feeding. The 16-item Quick Inventory of Depressive Symptomatology–Clinician-rated (QIDS-C16)12Trivedi MH Rush AJ Wisniewski SR Nierenberg AA Warden D Ritz L Norquist G Howland RH Lebowitz B McGrath PJ Shores-Wilson K Biggs MM Balasubramani GK Fava M STAR*D Study Team Evaluation of outcomes with citalopram for depression using measurement-based care in STAR*D: implications for clinical practice.Am J Psychiatry. 2006; 163: 28-40Crossref PubMed Scopus (2645) Google Scholar, 13Rush AJ Fava M Wisniewski SR Lavori PW Trivedi MH Sackeim HA Thase ME Nierenberg AA Quitkin FM Kashner TM Kupfer DJ Rosenbaum JF Alpert J Stewart JW McGrath PJ Biggs MM Shores-Wilson K Lebowitz BD Ritz L Niederehe G Sequenced treatment alternatives to relieve depression (STAR*D): rationale and design.Control Clin Trials. 2004; 25: 119-142Abstract Full Text Full Text PDF PubMed Scopus (737) Google Scholar, 17Rush AJ Trivedi MH Ibrahim HM Carmody TJ Arnow B Klein DN Markowitz JC Ninan PT Kornstein S Manber R Thase ME Kocsis JH Keller MB The 16-item Quick Inventory of Depressive Symptomatology (QIDS), Clinician Rating (QIDS-C), and Self-Report (QIDS-SR): a psychometric evaluation in patients with chronic major depression.Biol Psychiatry. 2003; 54: 573-583Abstract Full Text Full Text PDF PubMed Scopus (2176) Google Scholar, 18Trivedi MH Rush AJ Ibrahim HM Carmody TJ Biggs MM Suppes T Crismon ML Shores-Wilson K Toprac MG Dennehy EB Witte B Kashner TM The Inventory of Depressive Symptomatology, Clinician Rating (IDS-C) and Self-Report (IDS-SR), and the Quick Inventory of Depressive Symptomatology, Clinician Rating (QIDS-C) and Self-Report (QIDS-SR) in public sector patients with mood disorders: a psychometric evaluation.Psychol Med. 2004; 34: 73-82Crossref PubMed Scopus (719) Google Scholar was obtained at baseline and at each treatment visit, to measure symptom severity. The intraclass correlation coefficient for the QIDS-C16, repeated across raters over 4 years, was 0.96 (A.J.R.'s unpublished data). Patients with a baseline QIDS-C16 >10 were eligible if the treating clinician determined that outpatient treatment with an antidepressant medication was indicated and safe. At level 1, the protocol required an adequate dose of citalopram for a sufficient time to maximize the likelihood of treatment success, to ensure that those who did not improve were most likely unresponsive to the medication, not just underdosed.12Trivedi MH Rush AJ Wisniewski SR Nierenberg AA Warden D Ritz L Norquist G Howland RH Lebowitz B McGrath PJ Shores-Wilson K Biggs MM Balasubramani GK Fava M STAR*D Study Team Evaluation of outcomes with citalopram for depression using measurement-based care in STAR*D: implications for clinical practice.Am J Psychiatry. 2006; 163: 28-40Crossref PubMed Scopus (2645) Google Scholar No concomitant medications were allowed, aside from benzodiazepines and hypnotics if needed. A CONSORT (Consolidated Standards of Reporting Trials) diagram of the current study sample is shown in figure 1. DNA samples were collected from 1,953 participants. A sample of 20 ml of whole blood was collected in citrate-treated vacuum tubes and was shipped overnight to the Rutgers Cell Repository, where lymphocytes were extracted and cryopreserved using standard methods. DNA was extracted using GenePure chemistry (Qiagen) and was shipped on dry ice to the NIH laboratories. Samples were arrayed using a Tecan Genesis robot (Lipsky Lab), then sex-verified with a set of three X-linked and two Y-linked markers (McMahon Lab). Four sex discrepancies were identified and were excluded before samples were genotyped further. A summary of the sample characteristics is shown in table 1. Those who consented to have blood drawn were similar to those in the full study sample but showed slight differences in several variables that reached statistical significance because of the large sample size. Subjects who consented to have blood drawn were older and better educated, with higher household income, and were more likely to be married, to be retired, and to describe themselves as white. These subjects were also more likely to come from a primary-care setting and to report more time elapsed since their first major depressive episode (MDE), more episodes, and greater comorbidity. These differences cannot affect the genetic association results, which derive from comparisons among the genotyped subjects. However, these differences may limit the generalizability of our findings, and clinical outcomes in the genotyped sample may differ somewhat from those in the full STAR*D sample.12Trivedi MH Rush AJ Wisniewski SR Nierenberg AA Warden D Ritz L Norquist G Howland RH Lebowitz B McGrath PJ Shores-Wilson K Biggs MM Balasubramani GK Fava M STAR*D Study Team Evaluation of outcomes with citalopram for depression using measurement-based care in STAR*D: implications for clinical practice.Am J Psychiatry. 2006; 163: 28-40Crossref PubMed Scopus (2645) Google ScholarTable 1Selected Demographic and Clinical Characteristics of the STAR*D SamplePatients with Blood DrawnComparisonCharacteristicComplete Sample (N=4,041)Yes (n=1,953)No (n=2,088)Test Statisticat = Absolute value of Student's t test; χ2 = χ2 test or Kruskal-Wallis results when variables are continuous.dfPbNS = nonsignificant at the P<.05 level.Sociodemographic: Mean (±SD) age (years)40.5 ± 13.342.7 ± 13.438.4 ± 12.9t = 10.314,037<.0001 Sex:χ2 = 1.481NS Male1,509 (37.3)748 (38.3)761 (36.4) Female2,532 (62.7)1,205 (61.7)1,327 (63.6) Race:χ2 = 13.202.0014 White3,055 (75.7)1,526 (78.2)1,529 (73.4) Black709 (17.6)313 (16.0)396 (19.0) Other/mixed272 (6.7)113 (5.8)159 (7.6) Mean (±SD) no. of years of education13.4 ± 3.213.6 ± 3.213.3 ± 3.2χ2 = 13.011.0003 Employment:χ2 = 19.652<.0001 Employed2,311 (57.3)1,092 (55.9)1,219 (58.6) Unemployed1,489 (36.9)715 (36.6)774 (37.2) Retired234 (5.8)146 (7.5)88 (4.2) Mean (±SD) monthly household income (U.S. $)2,419 ± 3,1432,521 ± 3,2022,318 ± 3,082χ2 = 6.231.0125 Medical insurance:χ2 = .682NS Private2,022 (51.8)998 (52.4)1,024 (51.2) Public553 (14.2)270 (14.2)283 (14.1) None1,332 (34.1)638 (33.5)694 (34.7) Marital status:χ2 = 15.123.0017 Single1,207 (29.9)545 (27.9)662 (31.8) Married/cohabiting1,663 (41.2)838 (42.9)825 (39.6) Divorced/separated1,037 (25.7)493 (25.2)544 (26.1) Widowed128 (3.2)77 (3.9)51 (2.4)Clinical: Mean (±SD) age at first MDE (years)25.5 ± 14.426.1 ± 14.924.9 ± 13.9χ2 = 3.401NS Mean (±SD) time since first MDE (years)15.0 ± 13.116.6 ± 13.913.5 ± 12.1χ2 = 42.071<.0001 Mean (±SD) no. of MDEs5.9 ± 11.46.4 ± 12.55.4 ± 10.2χ2 = 11.091.0009 Suicide ever attempted:χ2 = 6.261.0123 Yes667 (16.5)293 (15.0)374 (17.9) No3,370 (83.5)1,659 (85.0)1,711 (82.1) No. of psychiatric comorbidities:χ2 = 24.394<.0001 01,510 (38.2)781 (40.9)729 (35.7) 11,028 (26.0)510 (26.7)518 (25.4) 2607 (15.4)282 (14.8)325 (15.9) 3342 (8.7)133 (7.0)209 (10.2) ≥4465 (11.8)204 (10.7)261 (12.8)Current episode: Clinical setting:χ2 = 29.971<.0001 Primary1,575 (39)846 (43.3)729 (34.9) Specialty2,466 (61)1,107 (56.7)1,359 (65.1) Mean (±SD) duration of current episode (mo)24.5 ± 52.024.8 ± 53.124.3 ± 51.0χ2 = .781.3764 HDRS-17c17-item Hamilton Depression Rating Scale.14,1518.8 ± 6.518.4 ± 6.219.6 ± 6.9t = 1.65330.099 QID-S1613.8 ± 4.213.4 ± 4.114.5 ± 4.5t = 2.20373.0283Note.—All data are no. (%) of patients, unless otherwise indicated.a t = Absolute value of Student's t test; χ2 = χ2 test or Kruskal-Wallis results when variables are continuous.b NS = nonsignificant at the P<.05 level.c 17-item Hamilton Depression Rating Scale.14Hamilton M A rating scale for depression.J Neurol Neurosurg Psychiatry. 1960; 23: 56-62Crossref PubMed Scopus (24271) Google Scholar, 15Hamilton M Development of a rating scale for primary depressive illness.Br J Soc Clin Psychol. 1967; 6: 278-296Crossref PubMed Scopus (6872) Google Scholar Open table in a new tab Note.— All data are no. (%) of patients, unless otherwise indicated. All phenotype definitions and assignments were settled in advance and were assigned before genotyping. Patients were scored for treatment outcome in two ways: designated remission and response (fig. 2). In the absence of external validators, our choice of categorical phenotypes was guided (1) by careful work with the STAR*D clinicians—in advance of the genotyping—to develop distinctions that had face validity and took advantage of the large body of data available from the STAR*D trial; (2) by ensuring maximal contrast between the outcome groups, to improve power, and creating “probable” groups that approximated the more narrowly defined categories, to test their robustness; (3) and by paying special attention to full remission of symptoms, since this was the primary target outcome of treatment. Remitters achieved a QIDS-C16 score of ≤5 at the last treatment visit; probable remitters achieved a score of 6 or 7. Nonremitters had a QIDS-C16 score of ≥10 at the last visit. Those with a final QIDS-C16 score in the borderline range of 8 and 9 were excluded from analysis. Responders achieved at least a 50% reduction in baseline QIDS-C16 at the last treatment visit; probable responders achieved a 45%–50% reduction. Nonresponders did not achieve even a 40% reduction in baseline QIDS-C16 score at the last treatment visit. Those with a reduction in QIDS-C16 in the borderline range of 40%–45% were excluded from analysis. Only patients who completed at least 6 wk of treatment were included in the primary analysis. Patients who achieved the required QIDS-C16 scores after <6 wk of treatment but who received at least 3 wk of treatment were assigned to the appropriate outcome group but were classified as “probable.” Those who did not complete at least 3 wk of treatment were excluded from analysis. Similarly, subjects who were classified as “intolerant” or “probably intolerant” were removed from the nonremitter and nonresponder groups but were retained in the remitter and responder groups, since intolerant subjects were probably not able to take the full effective dose of citalopram but might have responded if they had. Assessment of tolerability is discussed below. Subjects who did not adhere to the treatment regimen were excluded from analysis. As a secondary test, relative change in QIDS-C16 score at the last visit (expressed as percentage change from initial score) was tested as a quantitative trait, after removal of intolerant and nonadherent subjects. Medication tolerability comprises an individual's objective and perceived side-effect burden and typically increases over time and with response to treatment.19Cassano P Fava M Tolerability issues during long-term treatment with antidepressants.Ann Clin Psychiatry. 2004; 16: 15-25Crossref PubMed Scopus (123) Google Scholar Since failure to consider tolerability could lead to misclassification of intolerant patients as nonresponders, we scored all subjects as tolerant, probably tolerant, intolerant, or probably intolerant on the basis of an algorithm that considered study exit data and the Global Rating of Side Effect Burden (GRSEB).13Rush AJ Fava M Wisniewski SR Lavori PW Trivedi MH Sackeim HA Thase ME Nierenberg AA Quitkin FM Kashner TM Kupfer DJ Rosenbaum JF Alpert J Stewart JW McGrath PJ Biggs MM Shores-Wilson K Lebowitz BD Ritz L Niederehe G Sequenced treatment alternatives to relieve depression (STAR*D): rationale and design.Control Clin Trials. 2004; 25: 119-142Abstract Full Text Full Text PDF PubMed Scopus (737) Google Scholar In brief, all subjects who elected to continue citalopram at the end of the level 1 treatment period were considered tolerant, whereas subjects who refused to continue citalopram or who left the study because of side effects were considered intolerant. The remaining subjects were classified on the basis of GRSEB score into probably tolerant (no more than moderate side effects) or probably intolerant (more than moderate side effects). A small number of subjects with missing GRSEB scores were classified according to whether they took citalopram for <4 wk (probably intolerant) or ≥4 wk (probably tolerant). Sixty-eight genes were chosen for study from among a larger list of plausible candidates. Genes primarily involved in drug metabolism were excluded, by prior agreement, since these will be studied by another group using the same set of DNA samples. Genes were scored by an expert panel (D.C., W. Drevets, H.M., and F.J.M.) on the basis of (1) prior evidence of association with antidepressant outcome (1–3 points), (2) prior evidence of association with major mood disorders (1–3 points), and (3) known functional variant(s) (0–1 points). Under this scoring system, candidate genes could receive 0–7 points; higher scores conferred higher priority for study. Genes with a score of ≥4 were used to seed sets of related genes broadly encompassing five main pathways: serotonin related (n=20), glutamate related (n=16), dopamine related (n=3), adrenergic (n=4), and neurotrophic (n=4), along with selected genes in other pathways (n=21). The complete list of genes studied is shown in table 2.Table 2List of Genes ScreenedHypothesis and Gene SymbolGene NameDopamine hypothesis: THTyrosine hydroxylase COMTCatechol-O-methyltransferase MAOAMonoamine-oxidase AAdrenergic hypothesis: ADRA2Aalpha-2a adrenergic receptor ADRA2Calpha-2c adrenergic receptor DBHDopamine beta-hydroxylase SLC6A2Norepinephrin transporterSerotonin hypothesis: SLC6A4Serotonin transporter TPH1Tryptophane hydroxylase-1 TPH2Tryptophane hydroxylase-2 HTR1ASerotonin receptors HTR1BSerotonin receptors HTR1DSerotonin receptors HTR1ESerotonin receptors HTR1FSerotonin receptors HTR2ASerotonin receptors HTR2B/PSMD1Serotonin receptors HTR2CSerotonin receptors HTR3ASerotonin receptors HTR3BSerotonin receptors HTR3CSerotonin receptors HTR3DSerotonin receptors HTR3ESerotonin receptors HTR4Serotonin receptors HTR5ASerotonin receptors HTR6Serotonin receptors HTR7Serotonin receptorsGlutamate hypothesis: GRIA1AMPA receptors GRIA2AMPA receptors GRIA3AMPA receptors GRIA4AMPA receptors GRIN1NMDA receptors GRIN2ANMDA receptors GRIN2BNMDA receptors GRIN2CNMDA receptors GRIN2DNMDA receptors GRIN3ANMDA receptors GRIK1Kainate receptors GRIK2Kainate receptors GRIK3Kainate receptors GRIK4Kainate receptors GRIK5Kainate receptors SLC1A1Glutamate/aspartate transporterNeurotrophin hypothesis: BDNFBDNF NTRK2Trk-B BCL2B-cell CLL/lymphoma 2 BAG1BCL2-associated athanogeneOther signaling pathways: PPP1R1BDARP-32 NR3C2Mineralocorticoid receptor CREB1CREB MAPK1Mitogen-activated protein kinase 1 GSK3BGlycogen synthase kinase 3 beta CAMK1Calcium/calmodulin-dependent protein kinase I PPP3R2Calcineurin B (located within GRIN3A)Other genes: FKBP5FK506 binding protein 5 LAMA4Laminin alpha-4 GNB3Guanine nucleotide binding protein OGG18-Oxoguanine DNA glycosylase NET-5Tetraspan NET-5 NBL1Neuroblastoma, suppression of tumorigenicity 1 GRWD1Glutamate-rich WD repeat containing 1 RPP30Ribonuclease P (30 kDa) RNF20Hypothetical protein FLJ20690 FBXO38F-box only protein 38 ARHGAP10rho GTPase activating protein 21 NR1I2Orphan nuclear receptor PAR2 KDELR1KDELR1 protein ATP1A3ATPase, Na+/K+ transporting, alpha-3 polypeptide Open table in a new tab For each candidate gene, genotype data spanning the coding region and up to 2 kb of flanking sequence were downloaded from the International HapMap Project, accessed November 2004.20The International HapMap Consortium The International HapMap Project.Nature. 2003; 426: 789-796Crossref PubMed Scopus (4688) Google Scholar Since the STAR*D sample is mostly white, data from the CEPH sample (Utah residents with northern and western European ancestry) were used. The program LDSelect21Carlson CS Eberle MA Rieder MJ Yi Q Kruglyak L Nickerson DA Selecting a maximally informative set of single-nucleotide polymorphisms for association analyses using linkage disequilibrium.Am J Hum Genet. 2004; 74: 106-120Abstract Full Text Full Text PDF PubMed Scopus (1297) Google Scholar was used to select an optimal set of available SNPs to genotype, at an r2 threshold of ≥0.8. From the remaining SNPs, we further excluded those with a minor-allele frequency <7.5%, since we expected the alleles that contribute to treatment outcome in this data set to be common. Six nonsynonymous SNPs and four SNPs reported elsewhere22Binder EB Salyakina D Lichtner P Wochnik GM Ising M Putz B Papiol S et al.Polymorphisms in FKBP5 are associated with increased recurrence of depressive episodes and rapid response to antidepressant treatment.Nat Genet. 2004; 36: 1319-1325Crossref PubMed Scopus (704) Google Scholar, 23Hahn MK Mazei-Robison MS Blakely RD Single nucleotide polymorphisms in the human norepinephrine transporter gene affect expression, trafficking, antidepressant interaction, and protein kinase C regulation.Mol Pharmacol. 2005; 68: 457-466Crossref PubMed Scopus (71) Google Scholar to be associated with treatment outcome were added to the set, which brought the total to 768. Illumina then performed a bioinformatic screen that identified 12 markers that would likely fail in their BeadArray assay. Predicted failures were replaced by a nearby marker that was in strong linkage disequilibrium (LD) with the excluded SNP, if available. Absent this, a nearby marker with an allele frequency similar to that of the excluded marker was selected. The complete list of SNPs genotyped, along with flanking sequence and expected alleles, is available on request. Since all of the collected samples were not available at the start of the experiment, only the first 1,380 samples were shipped to Illumina, where they were genotyped on the Illumina BeadArray platform, a highly accurate, high-throughput assay.24Gunderson KL Kruglyak S Graige MS Garcia F Kermani BG Zhao C Che D Dickinson T Wickham E Bierle J Doucet D Milewski M Yang R Siegmund C Haas J Zhou L Oliphant A Fan JB Barnard S Chee MS Decoding randomly ordered DNA arrays.Genome Res. 2004; 14: 870-877Crossref PubMed Scopus (245) Google Scholar At Illumina, 99.78% of samples were successfully genotyped, and 97.92% of SNPs produced usable data, so that a total of 1,034,602 of a possible 1,035,504 genotypes were returned, including 11,280 blind duplicate genotypes, all of which matched exactly. On the basis of the results of the first 1,380 samples, five SNPs in the remaining samples were genotyped using Taqman chemistry, were scored on a fluorescent plate reader (Molecular Dynamics) without regard to phenotype. By design, 394 samples were genotyped at rs7997012 and rs1928040 both by Illumina and in-house (McMahon Lab). No discrepancies were detected. The primary experiment was based on comparison of allele and genotype frequencies between subjects who benefited or did not benefit from citalopram therapy. Because the number of tests in this experiment was large, a split sample design was employed. The 1,380 samples genotyped for all SNPs were divided, a priori, into a discovery sample and a replication sample. The discovery sample consisted of two-thirds of the total sample genotyped at Illumina; the replication sample consisted of the remaining one-third. The choice of asymmetric sample sizes for the discovery and test samples was based on the large overall sample size. Splitting the sample