Dataset Information

Genome-wide association study of suicide attempt in a Mexican population: a study protocol.

ABSTRACT:

Introduction

Suicidality is a complex behaviour and a major health problem; the speci?c features that could predispose to suicidal behaviour have been extensively investigated, most frequently in European and Asian populations. Therefore, our aim is to present a protocol that will explore suicide attempt in Mexican individuals diagnosed with psychiatric disorders, through a genome-wide association study (GWAS).

Method and analysis

We will perform a GWAS by comparing 700 individuals who have suicide attempt history, with control subjects without suicide attempt history (n=500). The genotyping will be conducted using the Infinium PsychArray BeadChip and quality controls will be applied to single nucleotides (SNPs) genotyped. After that, we will perform the imputation using reference panels provided by the Haplotype Reference Consortium. We will perform two different workflows: (A) the classic GWAS analysis applying the same weight to all the variants and (B) an algorithm with prediction of deleteriousness of variants.

Ethics and dissemination

This study was approved by the ethics and investigation committees of the National Institute of Genomic Medicine on 22 July 2015, No CEI 215/13. We plan to disseminate research findings in scientific conferences and as a manuscript in peer-reviewed journals.

Trial registration number

CEI 215/13.

SUBMITTER: Gonzalez-Castro TB

PROVIDER: S-EPMC6500275 | biostudies-literature | 2019 Apr

REPOSITORIES: biostudies-literature

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Publications

Genome-wide association study of suicide attempt in a Mexican population: a study protocol.

González-Castro Thelma Beatriz TB Genis-Mendoza Alma Delia AD Tovilla-Zárate Carlos Alfonso CA Martínez-Magaña José Jaime JJ Juárez-Rojop Isela Esther IE Sarmiento Emmanuel E Nicolini Humberto H

BMJ open 20190411 4

<h4>Introduction</h4>Suicidality is a complex behaviour and a major health problem; the speciﬁc features that could predispose to suicidal behaviour have been extensively investigated, most frequently in European and Asian populations. Therefore, our aim is to present a protocol that will explore suicide attempt in Mexican individuals diagnosed with psychiatric disorders, through a genome-wide association study (GWAS).<h4>Method and analysis</h4>We will perform a GWAS by comparing 700 individual ...[more]

PMID: 30975676

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Project description:BackgroundSuicide remains the 10th-ranked most frequent cause of death in the United States, accounting for over 40,000 deaths per year. Nonfatal suicide attempts lead to over 200,000 hospitalizations and 600,000 emergency department visits annually. Recent evidence indicates that responses to the commonly used Patient Health Questionnaire (PHQ9) can identify outpatients who are at risk of suicide attempt and suicide death and that specific psychotherapy or Care Management programs can prevent suicide attempts in high-risk patients. Motivated by these developments, the NIMH-funded Mental Health Research Network has undertaken a multisite trial of two outreach programs to prevent suicide attempts among outpatients identified by routinely administered PHQ9 questionnaires.Methods/designOutpatients who are at risk of suicide attempt are automatically identified using data from electronic health records (EHRs). Following a modified Zelen design, all those identified are assigned to continued usual care (i.e., no contact) or to be offered one of two population-based outreach programs. A Care Management intervention includes systematic outreach to assess suicide risk, EHR-based tools to implement risk-based care pathways, and care management to facilitate recommended follow-up. A Skills Training intervention includes interactive online training in Dialectical Behavior Therapy skills, supported by reminder and reinforcement messages from a skills coach. Each intervention supplements, rather than replaces, usual care; participants may receive any other services normally available. Interventions are delivered primarily by secure messaging through EHR patient portals. Suicide attempts and deaths following randomization are identified using state vital statistics data and health system EHR and insurance claim data. Primary evaluation will compare risk of suicide attempt or death over 18 months according to the initial assignment, regardless of intervention participation. Recruitment is underway in three health systems (Group Health Cooperative, HealthPartners, and Kaiser Permanente Colorado). Over 2500 participants have been randomized as of 1 March 2016, with enrollment averaging approximately 100 per week.DiscussionAssessing the effectiveness of population-based suicide prevention requires adherence to the principles of pragmatic trials: population-based enrollment, accepting variable treatment participation, assessing outcomes using health record data, and analyses based on intent-to-treat.Trial registrationClinicalTrials.gov registration # NCT02326883 , registered on 23 December 2014.

Project description:Suicidal behavior (SB) has a complex etiology of genes, environment or both. One of the genetic components in SB could be copy number variations (CNVs), since CNVs are implicated in a range of neurodevelopmental disorders. However, a recently published genome-wide and case-control study failed to observe a significant role of CNVs in SB (see E-MTAB-3519). Here we complement those initial observations by conducting a brief CNV-association study, for the first time in a family-based trio-sample with severe suicide attempt (SA) outcome in offspring (n=660 trios; the \GISS\ sample, see http://www.ncbi.nlm.nih.gov/pubmed/23422793 and refs therein). For association testing, we here used the FBAT-CNV methodology (http://www.ncbi.nlm.nih.gov/pubmed/18228561), which allows for CNV association testing directly on the raw intensity values (Illumina \log R ratio\), evaluating any type of CNVs (e.g. de novo or inherited) without reliance on CNV calling algorithms and robust to control selection biases. Here we have deposited these raw logR-values for 88,450 on-chip CNV-loci of the HumanOmni1-Quad_v1 chip, arranged in a standard pedigree format used as input for FBAT-CNV analysis in SVS software (goldenhelix.com): column 1 is the family ID, column 2 is the Subject type (1 = offspring, 2 = mother, 3 = father), column 3 is the father ID (? for missing), column 4 is the mother ID (? for missing), column 5 is the sex (1 = female, 0 = male), column 6 is the affection status (1 = suicide attempt, 0 = not affected) and columns 7 and onward are the logR-values for each CNV-loci as is listed in the header row. We observed experiment-wide significant association (P ≤ 5.6 x 10-7) of two proximal CNVs at chromosome 14 (Illumina markers cnvi0108946 and cnvi0118308, with NCBI 36.3 start positions 22794779 and 22582820). However, these CNV-associations mapped to T-cell receptor regions, and therefore most likely reflect inter-individual variation in somatic rearrangements occurring in white blood cells (as our source of DNA was blood), rather than association with SA. In conclusion, our results did not suggest any major role of CNVs in SA etiology, in line with the results of the recent case-control study (see E-MTAB-3519).

Dataset Information

Genome-wide association study of suicide attempt in a Mexican population: a study protocol.

Introduction

Method and analysis

Ethics and dissemination

Trial registration number

Publications

Genome-wide association study of suicide attempt in a Mexican population: a study protocol.

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