The Translational Bioinformatics Conference (TBC) was established in 2011 as a partnership between Asian and US investigators with the goal of bringing together scientists with the diverse expertise that contribute to the new and growing field of translational bioinformatics. The first conference, led by Dr. Ju Han Kim, Professor and Chair of the Division of […]
From the Crawford Lab: We have developed a set of text-mining algorithms to extract education and occupation, both important variables that describe socioeconomic status (SES), from electronic health records. The development and evaluation of the algorithm is described in PMC5147499, and the exclusion, jobs, and prefix lists developed for this algorithm can be found here. Detailed […]
The leaves are falling and there’s a crispness to the morning air. I suppose that means it’s time for a Crawford lab summer update! After looking back at my summer calendar, I am left wondering what I did. To be sure, it was filled with regular stuff. You know, grants, papers, and the occasional study […]
Body mass index (BMI) is an important outcome and covariate adjustment for many clinical association studies. Accurate assessment of BMI, therefore, is a critical part of many study designs. Electronic health records (EHRs) are a growing source of clinical data for research purposes, and have proven useful for identifying and replicating genetic associations. EHR-based data […]
As I stare at my calendar, I am realizing that classes start in two and a half weeks. Geez, where did the summer go? Wait—what happened to spring??? Well, technically I did post about the 2017 Pacific Symposium on Biocomputing (PSB) and the 2017 Joint Summits on Translational Science before 2018 rolled around, so I […]
From the Crawford Lab: The Hi-MC package provides high-level mitochondrial haplogroups given standard PLINK .map and.ped files. Hi-MC is a cost-effective approach to characterize major haplogroups in large sample sizes similar to those described in PMC4113317. Detailed usage of the package can be found on the github, the preprint, and the final publication in PeerJ.
From the Bush Lab and Haines Lab, Mariusz Butkiewicz has developed COCOS, a plugin for the Ensembl Variant Effect Predictor (VEP) plugin for annotating reading frame changes. The plugin captures Amino Acid sequence alterations stemming from variants that produce an altered reading frame, e.g. stop-lost variants and small genetic Insertion and Deletions (InDels). The GitHub repository for COCOS can be found here.
From the Bush Lab: This archive contains scripts and data for performing an analysis looking for cis-interacting variants that influence gene expression. Our publication can be found here: http://www.cell.com/ajhg/fulltext/S0002-9297(16)30323-8 Analysis workflow Tarball archive of analysis scripts Tarball archive of data files
Mutations in APP, PSEN1, and PSEN2 lead to early-onset Alzheimer disease (EOAD) but account for only approximately 11% of EOAD overall, leaving most of the genetic risk for the most severe form of Alzheimer disease unexplained. This extreme phenotype likely harbors highly penetrant risk variants, making it primed for discovery of novel risk genes and pathways for […]
Molecular and clinical heterogeneity critically hinders better treatment outcome for glioblastomas (GBMs); integrative analysis of genomic and epigenomic data may provide useful information for improving personalized medicine. By applying training-validation approach, we identified a novel hypomethylation signature comprising of three CpGs at non-CpG island (CGI) open sea regions for GBMs. The hypomethylation signature consistently predicted […]
Genotype imputation is a powerful strategy for achieving the large sample sizes required for identification of variants underlying complex phenotypes, but imputation of rare variants remains problematic. Genetically isolated populations offer one solution, however population-specific reference panels are needed to assure optimal imputation accuracy and allele frequency estimation. Here we report the Anabaptist Genome Reference […]