Modeling Linkage Disequilibrium Increases Accuracy of Polygenic Risk Scores

Polygenic risk scores have shown great promise in predicting complex disease risk and will become more accurate as training sample sizes increase. The standard approach for calculating risk scores involves linkage disequilibrium (LD)-based marker pruning and applying a p value threshold to association statistics, but this discards information and can reduce predictive accuracy. We introduce LDpred, a method that infers the posterior mean effect size of each marker by using a prior on effect sizes and LD information from an external reference panel. Theory and simulations show that LDpred outperforms the approach of pruning followed by thresholding, particularly at large sample sizes. Accordingly, predicted R(2) increased from 20.1% to 25.3% in a large schizophrenia dataset and from 9.8% to 12.0% in a large multiple sclerosis dataset. A similar relative improvement in accuracy was observed for three additional large disease datasets and for non-European schizophrenia samples. The advantage of LDpred over existing methods will grow as sample sizes increase.

LD Score regression distinguishes confounding from polygenicity in genome-wide association studies

Both polygenicity (many small genetic effects) and confounding biases, such as cryptic relatedness and population stratification, can yield an inflated distribution of test statistics in genome-wide association studies (GWAS). However, current methods cannot distinguish between inflation from a true polygenic signal and bias. We have developed an approach, LD Score regression, that quantifies the contribution of each by examining the relationship between test statistics and linkage disequilibrium (LD). The LD Score regression intercept can be used to estimate a more powerful and accurate correction factor than genomic control. We find strong evidence that polygenicity accounts for the majority of the inflation in test statistics in many GWAS of large sample size.

Cuidar da pessoa com esquizofrenia em processo de reabilitação psicossocial

Este ensino clínico permitiu-nos prestar cuidados de enfermagem especializados a 16 homens com esquizofrenia em processo de reabilitação psicossocial. Na sua maioria são: adultos, solteiros, da região sul de Portugal, com uma média de 9 anos de escolaridade, com história de consumo de substâncias (álcool, tabaco, haxixe, cocaína, heroína e anfetaminas), institucionalizados na Casa de Saúde do Telhal (CST) há mais de 11 anos. Todos apresentam diagnósticos de enfermagem das várias dimensões do adoecer, com exceção da dimensão comportamental excitatória, sendo os de maior prevalência: “Conhecimento sobre Processo de doença/Cuidados na doença/Tratamento, Não Demonstrado”; Cognição, Comprometida”; “Processo Social, Alterado”; “Autoestima, Diminuída”. Foram desenvolvidos 4 programas de intervenção: consulta de enfermagem de saúde mental e psiquiatria (CESMP); atelier de estimulação cognitiva (AEC); programa de desenvolvimento de competência intrapessoais, interpessoais e profissionais (PDCIIP); programa de psicoeducação (SABER+). A satisfação global com os programas foi superior a 7 (numa escala de 1 a 10) e os resultados que foram percebidos pela maioria dos reabilitandos situaram-se acima das suas expectativas iniciais. De uma forma geral, todos registaram ganhos: no desempenho cognitivo (em particular os que beneficiaram do AEC); na adaptação psicossocial – nomeadamente ao nível do insight; os reabilitandos que beneficiaram do programa SABER+ melhoraram ainda os comportamentos demonstrados de aceitação do estado de saúde; no bem-estar psicológico – nomeadamente ao nível da autoestima (sobretudo os que beneficiaram da CESMP e/ou do PDCIIP), dos afetos positivos e dos comportamentos de motivação; nos vários domínios da qualidade de vida (QdV) medidos pelo WHOQOL-Bref em particular o domínio ambiental; todos elevaram o seu nível de conhecimentos nos 3 eixos em que que se estruturou o programa de psicoeducação (processo da doença, cuidados na doença, tratamento da doença); na adesão à medicação, sobretudo os que integraram o programa de psicoeducação, contudo todos tendem a necessitar de ajuda parcial para conseguir demonstrar conhecimento no cumprimento do esquema terapêutico e estão envolvidos em treinos supervisionados de preparação e autoadministração; ABSTRACT: This clinical training allowed us to provide skilled nursing care to 16 men with schizophrenia in a psychosocial rehabilitation setting. Most of these individuals are: adults, singles, from the southern region of Portugal, with an average of 9 years of schooling, with a history of substance abuse (alcohol, tobacco, cannabis, cocaine, heroin and amphetamines), institutionalized in Casa de Saúde do Telhal (CST) for over 11 years. We find nursing diagnoses from all of the disease dimensions with the exception of excitatory behavioral dimension, being the most prevalent: "knowledge about disease process / care / treatment, not stated"; cognition, impaired", "social process, impaired”, “self-esteem, decreased". We developed 4 intervention programs: psychiatry and mental health nursing consultation (CESMP); atelier of cognitive stimulation (AEC); intrapersonal, interpersonal and professional competences training (PDCIIP); psychoeducation (SABER+). The overall satisfaction with the programs was above 7 (on a scale of 1 to 10) and the results noticed by most patients were above their initial expectations. All registered nursing results were: in cognitive performance (particularly those who benefited from the AEC); in psychosocial adaptation - especially in terms of insight; patients who benefited from the SABER+ program demonstrated improved further acceptance of their health condition, psychological well-being, particularly in terms of self-esteem (especially those who benefited from the CESMP and/or the PDCIIP), positive affects and motivation; in the different domains of quality of life (QoL) measured by WHOQOL-Bref in particular the environmental domain; every patients raised their level of knowledge in the 3 axes in which the psychoeducational program (SABER+) was structured (disease process, care and treatment); in medication adherence, especially those who benefited of the psychoeducational program, however all the patients tend to need partial help to demonstrate knowledge in meeting the therapeutic regimen and are involved in supervised training programs for preparation and self administration.