SLALOM suggests caution with meta-analysis fine-mapping interpretation
SLALOM suggests caution with meta-analysis fine-mapping interpretation
After researchers combine multiple genome-wide association studies into a meta-analysis, they often seek causal variants using methods built for single-cohort studies. CGM PI’s Hilary Finucane, Mark Daly, and colleagues showed that this fine-mapping approach is often miscalibrated due to heterogeneous characteristics of the individual cohorts, such as different genotyping arrays or imputation panels. They built a quality control method, SLALOM, and applied it to 14 disease endpoints from the Global Biobank Meta-analysis Initiative (GBMI), finding that 68 percent of fine-mapped loci showed signs of potential inaccuracy. The findings suggest caution when interpreting meta-analysis fine-mapping results until improved methods are available.
Read more in Cell Genomics and Masa Kanai’s tweetorial.
Distinct patterns of emotional and behavioral change in child psychiatry outpatients during the COVID-19 pandemic
Distinct patterns of emotional and behavioral change in child psychiatry outpatients during the COVID-19 pandemic
This was the first publication on pandemic-related mental health changes in child psychiatric outpatients in the United States. Empirically-derived multivariate models showed that child psychiatric outpatients had highly variable emotional and behavioral reactions to the pandemic, with some showing stability, others even showing improvement, and two groups manifesting distinctive patterns of worsening symptoms predicted by their prior psychopathology. Results have implications for clinical care as well as ongoing research on genetic contributions to youth mental health.
Read more in Child and Adolescent Psychiatry and Mental Health
December 14, 2022
Publication
CGM Primary Investigator
Improving polygenic prediction in ancestrally diverse populations
Improving polygenic prediction in ancestrally diverse populations
Polygenic risk scores (PRS) have attenuated cross-population predictive performance, which reduces their clinical value in non-European populations and exacerbates healthcare disparities. This study, conducted by CGM Investigators Tian Ge, Hailiang Huang, Alicia Martin and colleagues, developed a computational framework, termed PRS-CSx, that can integrate genomic data from multiple populations to improve polygenic prediction in diverse populations. Leveraging large-scale global biobanks and disease-focused cohorts, the investigators showed that PRS-CSx substantially improved the prediction accuracy of biomarkers and disease risk in non-European populations. This work represents an important step towards the implementation of PRS into routine healthcare.
Read more in Nature Genetics
December 13, 2022
Publication Name
CGM Primary Investigators
Identification of Genetic Variation Influencing Metformin Response in a Multi-Ancestry Genome-Wide Association Study in the Diabetes Prevention Program (DPP)
Identification of Genetic Variation Influencing Metformin Response in a Multi-Ancestry Genome-Wide Association Study in the Diabetes Prevention Program (DPP)
Genome-wide significant loci for metformin response in type 2 diabetes reported elsewhere have not replicated in the Diabetes Prevention Program (DPP). To assess pharmacogenetic interactions in pre-diabetes, CGM investigator Jose Florez and colleagues conducted a GWAS in the DPP. Cox proportional hazards models tested associations with diabetes incidence in the metformin (n=876) and placebo (n=887) arms. Multiple linear regression assessed association with one-year change in metformin-related quantitative traits, adjusted for baseline trait, age, sex, and 10 ancestry principal components. The investigators identified four genome-wide significant variants after correcting for correlated traits (p<9×10-9). These novel ethnic-specific associations require further investigation but may have implications for tailored therapy.
Read more in Diabetes
Sensitive periods in development and risk for psychiatric disorders and related endpoints: A systematic review of child maltreatment findings
Sensitive periods in development and risk for psychiatric disorders and related endpoints: A systematic review of child maltreatment findings
Childhood maltreatment increases the likelihood of mental health problems, but outcomes vary widely. The timing of maltreatment may help explain these outcome differences. Specifically, impacts might be stronger during sensitive periods in development when the brain is maximally sensitive to particular types of environmental input. Is there consensus about peak periods of sensitivity to childhood maltreatment? This review led by CGM investigator Erin Dunn, analysis of observational studies in humans found that most studies (75%, or 89 of 118 studies) reported timing effects, but did not identify consistent sensitive periods across studies. The investigators also examined study characteristics to inform a discussion of practices to support future research.
Read more in The Lancet Psychiatry
December 11, 2022
Publication Name
CGM Primary Investigator
‘Holy moly, that is a slow burn’: Research center in Boston aims to jump-start precision psychiatry
‘Holy moly, that is a slow burn’: Research center in Boston aims to jump-start precision psychiatry
CGM PI and Director of the PNGU, Jordan Smoller, was featured in GBH to discuss the inception and research bing conducted in the Center for Precision Psychiatry.
Learn more at WGBH.
Down Syndrome Program: new research paper on COVID-19 in group homes
Down Syndrome Program: new research paper on COVID-19 in group homes
For the past 2 years, during the pandemic, CGM PI, Brian Skotko, and his multidisciplinary team set up and implemented a randomized control trial to see if they could design a multimodal behavioral intervention that could reduce COVID-19 infection, hospitalization, and death for those persons living in group homes in MA. They focused on people with serious mental illness (SMI) and people with intellectual and/or developmental disabilities (ID/DD)—and the staff who work with them in group homes. This “protocol paper” describes our unique design: a hybrid type 1 effective-implementation cluster randomized trial, which means that half of the 400 participating group homes got our tailored intervention (and the other half continued to receive the statewide recommendations). For the past 2 years, they have been implementing this trial, which has now come to a close.
Read more in Contemporary Clinical Trials
December 9, 2022
Publication
CGM Primary Investigator
Brian Skotko
Nucleosides Associated With Incident Ischemic Stroke in the REGARDS and JHS Cohorts
Nucleosides Associated With Incident Ischemic Stroke in the REGARDS and JHS Cohorts
This manuscript is the first to show a link between specific nucleoside metabolites and the risk of future stroke, independent of traditional stroke risk factors. In this study, CGM Investigator Taylor Kimberly and colleagues also sought to determine whether these candidates were a reflection of genes or environment through GWA studies. Their findings suggest that the top metabolites were related to environmental or behavioral patterns, ultimately leading our group to focus on potential links between diet, the gut microbiome, and stroke risk.
Read more in Neurology.
Polygenic risk scores for diverse cohorts
Polygenic risk scores for diverse cohorts
Even though the application of polygenic risk scores (PRSs) in precision medicine has been widely explored, there is limited evidence of its clinical utility across disease areas. To facilitate the development of best practices for PRS calculation, Alicia Martin, and colleagues used data from Global Biobank Meta-analysis Initiative. The researchers explored methods for PRS calculation and prediction accuracy in nine different biobanks for 14 disease endpoints. They outline a framework for PRS analyses of multi-ancestry genome-wide association studies across multiple biobanks and highlight the importance of best practices for PRS in the biobank-scale genomics era.
Read more in Cell Genomics