Annotation Query (AnnoQ): an integrated and interactive platform for large-scale genetic variant annotation

Abstract

The Annotation Query (AnnoQ) (http://annoq.org/) is designed to provide comprehensive and up-to-date functional annotations for human genetic variants. The system is supported by an annotation database with ∼39 million human variants from the Haplotype Reference Consortium (HRC) pre-annotated with sequence feature annotations by WGSA and functional annotations to Gene Ontology (GO) and pathways in PANTHER. The database operates on an optimized Elasticsearch framework to support real-time complex searches. This implementation enables users to annotate data with the most up-to-date functional annotations via simple queries instead of setting up individual tools. A web interface allows users to interactively browse the annotations, annotate variants and search variant data. Its easy-to-use interface and search capabilities are well-suited for scientists with fewer bioinformatics skills such as bench scientists and statisticians. AnnoQ also has an API for users to access and annotate the data programmatically. Packages for programming languages, such as the R package, are available for users to embed the annotation queries in their scripts. AnnoQ serves researchers with a wide range of backgrounds and research interests as an integrated annotation platform.

MOLGENIS VIP: an open-source and modular pipeline for high-throughput and integrated DNA variant analysis

“…Worldwide, around 350 million people are affected by one of 4440 RDs with a known genetic cause 4 . Pinpointing the causal RD variants among all the variants detected in targeted-enrichment sequencing, such as adaptive sampling and whole exome sequencing (WES), or even in whole genome sequencing (WGS) data, is not a trivial task and cannot be performed using a single strategy 2,[5][6][7] . Several in silico pipelines have been created to combine published tools into a single solution 2,5 .…”

“…Pipelines are also required to adapt to the continuous emergence of new bioinformatic methods and knowledge bases. Ideally, they should also include tools to interpret variants according to the American College of Medical Genetics (ACMG) guidelines 5,6,18 , which helps to accommodate more advanced variant interpretation and prioritization methods 17,19 .…”

“…Pipelines are also required to adapt to the continuous emergence of new bioinformatic methods and knowledge bases. Ideally, they also include tools to interpret variants according to the American College of Medical Genetics (ACMG) guidelines 5,6,18 , which helps to accommodate more advanced variant interpretation and prioritization methods 17,19 . Finally, because variant interpretation pipelines involve different algorithms and resources, their installation and operation can require bioinformatic expertise.…”

“…Following this step, we created one sample sheet with the patients from the routine diagnostic cohort and one sample sheet containing the patients from the Solve-RD research cohort. Both sample sheets specified the used HPO terms, affected status, reference genomes, sequencing types, and the proband, maternal and paternal WES data (supplementary table5,6).…”