The Current State of Mutation Detection and Prospects for Long Read Sequencing
summary
Consortium processes 2,800 tumor‑normal pairs (≈500 TB) across ~16,000 cloud cores and validates mutations by NimbleGen capture of ~130,000 sites with ~1,000× resequencing. SNV callers reach up to ~98% sensitivity but indel sensitivity tops ~55–60% and SV callers show poor recall. Nanopore work uses the MinION event‑level HMM to call SNPs and CpG methylation (nanopore methylation correlates with bisulfite), assemblies reach ~0.3% consensus error but homopolymers and scaling raw‑signal alignment remain unsolved.
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chapters (16)
- 0:00Overview
- 0:28PCAWG . Goal Comprehensive analysis of a large collection of cancer genomes with a focus on the non-coding genome
- 1:42Seven Cloud Data Centers Twelve Cloud Compute Sites
- 2:42PCAWG Mutation Calling Process SOIR
- 4:06PCAWG Validation
- 5:00SNV Precision-Recall
- 6:49SV Precision-Recall
- 8:26Nanopore Sequencing
- 11:45Event Detection
- 13:28Base Calling
- 15:22Haplotype-based SNP calling
- 16:33Nanopore HMM
- 20:12Human CpG Island Methylation
- 21:36Some open analysis problems OICR
- 26:53Acknowledgements
- 27:35Indel Precision-Recall without simple repeats SOIR
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