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Correcting reference bias from the Illumina Isaac aligner enables analysis of cancer genomes

https://doi.org/10.1101/836171
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1016/j.cell.2012.04.023openalex-snapshot
The Life History of 21 Breast Cancers
inferredcites →https://doi.org/10.1016/j.cell.2018.02.020openalex-snapshot
Timing the Landmark Events in the Evolution of Clear Cell Renal Cell Cancer: TRACERx Renal
inferredcites →https://doi.org/10.1016/j.cell.2018.06.039openalex-snapshot
Genomic Hallmarks and Structural Variation in Metastatic Prostate Cancer
inferredcites →https://doi.org/10.1016/j.cell.2018.10.019openalex-snapshot
Genomic Hallmarks and Structural Variation in Metastatic Prostate Cancer
inferredcites →https://doi.org/10.1016/j.fertnstert.2014.01.051openalex-snapshot
Development and validation of a next-generation sequencing–based protocol for 24-chromosome aneuploidy screening of embryos
inferredcites →https://doi.org/10.1016/s0889-8553(21)00590-2openalex-snapshot
Barrett's Esophagus and Esophageal Adenocarcinoma
inferredcites →https://doi.org/10.1016/s1470-2045(18)30687-9openalex-snapshot
Lenalidomide maintenance versus observation for patients with newly diagnosed multiple myeloma (Myeloma XI): a multicentre, open-label, randomised, phase 3 trial
inferredcites →https://doi.org/10.1038/leu.2017.177openalex-snapshot
Whole-genome sequencing of chronic lymphocytic leukaemia reveals distinct differences in the mutational landscape between IgHVmut and IgHVunmut subgroups
inferredcites →https://doi.org/10.1038/nature23305openalex-snapshot
Correction of a pathogenic gene mutation in human embryos
inferredcites →https://doi.org/10.1038/ncomms14500openalex-snapshot
In vivo genome editing with a small Cas9 orthologue derived from Campylobacter jejuni
inferredcites →https://doi.org/10.1038/ng.2354openalex-snapshot
Fast and accurate genotype imputation in genome-wide association studies through pre-phasing
inferredcites →https://doi.org/10.1038/ng.3357openalex-snapshot
Whole-genome sequencing provides new insights into the clonal architecture of Barrett's esophagus and esophageal adenocarcinoma
inferredcites →https://doi.org/10.1038/nmeth.3284openalex-snapshot
Digenome-seq: genome-wide profiling of CRISPR-Cas9 off-target effects in human cells
inferredcites →https://doi.org/10.1038/s41436-019-0618-7openalex-snapshot
The complete costs of genome sequencing: a microcosting study in cancer and rare diseases from a single center in the United Kingdom
inferredcites →https://doi.org/10.1038/s41576-019-0114-6openalex-snapshot
Resolving genetic heterogeneity in cancer
inferredcites →https://doi.org/10.1038/s41588-018-0128-6openalex-snapshot
Quantification of subclonal selection in cancer from bulk sequencing data
inferredcites →https://doi.org/10.1038/s41592-018-0051-xopenalex-snapshot
Strelka2: fast and accurate calling of germline and somatic variants
inferredcites →https://doi.org/10.1056/nejmoa1616288openalex-snapshot
Tracking the Evolution of Non–Small-Cell Lung Cancer
inferredcites →https://doi.org/10.1073/pnas.1009843107openalex-snapshot
Allele-specific copy number analysis of tumors
inferredcites →https://doi.org/10.1093/bioinformatics/btp324openalex-snapshot
Fast and accurate short read alignment with Burrows–Wheeler transform
inferredcites →https://doi.org/10.1093/bioinformatics/bts271openalex-snapshot
Strelka: accurate somatic small-variant calling from sequenced tumor–normal sample pairs
inferredcites →https://doi.org/10.1093/bioinformatics/btt314openalex-snapshot
Isaac: ultra-fast whole-genome secondary analysis on Illumina sequencing platforms
inferredcites →https://doi.org/10.1101/031021openalex-snapshot
Validation of Illumina’s Isaac variant calling workflow
inferredcites →https://doi.org/10.1101/161562openalex-snapshot
The evolutionary history of 2,658 cancers
inferredcites →https://doi.org/10.1101/484402openalex-snapshot
Ccube: A fast and robust method for estimating cancer cell fractions
inferredcites →https://doi.org/10.1101/cshperspect.a026625openalex-snapshot
Principles of Reconstructing the Subclonal Architecture of Cancers
inferredcites →https://doi.org/10.1101/gr.107524.110openalex-snapshot
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
inferredcites →https://doi.org/10.1111/bjh.15406openalex-snapshot
Clinical‐grade validation of whole genome sequencing reveals robust detection of low‐frequency variants and copy number alterations in CLL
inferredcites →https://doi.org/10.1126/scitranslmed.aaa1408openalex-snapshot
Clonal status of actionable driver events and the timing of mutational processes in cancer evolution
inferredcites →https://doi.org/10.1136/bmj.k1687openalex-snapshot
The 100 000 Genomes Project: bringing whole genome sequencing to the NHS
inferredcites →https://doi.org/10.1158/1538-7445.am2018-3000openalex-snapshot
Abstract 3000: Pervasive intra-tumour heterogeneity and subclonal selection across cancer types
inferredcites →https://doi.org/10.1182/blood-2010-04-279596openalex-snapshot
A compendium of myeloma-associated chromosomal copy number abnormalities and their prognostic value
inferredcites →https://doi.org/10.1186/s13059-018-1476-3openalex-snapshot
Timing somatic events in the evolution of cancer

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1038/s41467-024-50107-4openalex-snapshot
Replication timing alterations are associated with mutation acquisition during breast and lung cancer evolution
inferred← citeshttps://doi.org/10.1038/s41591-023-02682-0openalex-snapshot
Insights for precision oncology from the integration of genomic and clinical data of 13,880 tumors from the 100,000 Genomes Cancer Programme
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