Mauricio O. Carneiro

TL;DR: This unit describes how to use BWA and the Genome Analysis Toolkit to map genome sequencing data to a reference and produce high‐quality variant calls that can be used in downstream analyses.

TL;DR: A novel assembly-based approach to variant calling, the GATK HaplotypeCaller and Reference Confidence Model, that determines genotype likelihoods independently per-sample but performs joint calling across all samples within a project simultaneously, showing that the accuracy of indel variant calling is superior in comparison to other algorithms.

TL;DR: In this paper, the authors performed whole-genome sequencing in 2,657 European individuals with and without diabetes, and exome sequencing for 12,940 individuals from five ancestry groups.

TL;DR: Large-scale sequencing does not support the idea that lower-frequency variants have a major role in predisposition to type 2 diabetes, but most fell within regions previously identified by genome-wide association studies.

TL;DR: Together, this study reveals the alteration of WNT, hedgehog, histone methyltransferase and now N-CoR pathways across medulloblastomas and within specific subtypes of this disease, and nominates the RNA helicase DDX3X as a component of pathogenic β-catenin signalling in medullOBlastoma.