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References from Applications and analysis of targeted genomic sequencing in cancer studies. Local targets link to admitted publications; unresolved targets remain external evidence.
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Routine multiplex mutational profiling of melanomas enables enrollment in genotype-driven therapeutic trials
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Genome-wide detection of structural variants and indels by local assembly
2017 · External reference
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Prevalence and detection of low-allele-fraction variants in clinical cancer samples
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Disease evolution and outcomes in familial AML with germline CEBPA mutations
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Intratumor heterogeneity inferred from targeted deep sequencing as a prognostic indicator
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Targeted massively parallel sequencing of a panel of putative breast cancer susceptibility genes in a large cohort of multiple-case breast and ovarian cancer families
10.1136/jmedgenet-2015-103452 · 2016 · External reference
Whole-exome and targeted sequencing identify ROBO1 and ROBO2 mutations as progression-related drivers in myelodysplastic syndromes
2015 · External reference
Implications of mutational spectrum in myelodysplastic syndromes based on targeted next-generation sequencing
10.18632/oncotarget.19628 · 2017 · External reference
Genetics and prognostication in splenic marginal zone lymphoma: Revelations from deep sequencing
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Whole-genome sequencing identifies ADGRG6 enhancer mutations and FRS2 duplications as angiogenesis-related drivers in bladder cancer
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Evaluation of hybridization capture versus amplicon-based methods for whole-exome sequencing
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Targeted enrichment of genomic DNA regions for next-generation sequencing
10.1093/bfgp/elr033 · 2011 · External reference
Assessment of capture and amplicon-based approaches for the development of a targeted next-generation sequencing pipeline to personalize lymphoma management
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Amplification of overlapping DNA amplicons in a single-tube multiplex PCR for targeted next-generation sequencing of BRCA1 and BRCA2
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Targeted next-generation sequencing at copy-number breakpoints for personalized analysis of rearranged ends in solid tumors
2014 · External reference
Spectrum and functional validation of PSMB5 mutations in multiple myeloma
2018 · External reference
A multiple myeloma-specific capture sequencing platform discovers novel translocations and frequent, risk-associated point mutations in IGLL5
10.1038/s41408-018-0062-y · 2018 · External reference
Performance of a multigene genomic classifier in thyroid nodules with indeterminate cytology
2018 · External reference
Analytical performance of the ThyroSeq v3 genomic classifier for cancer diagnosis in thyroid nodules
10.1002/cncr.31245 · 2018 · External reference
Clinical actionability enhanced through deep targeted sequencing of solid tumors
10.1373/clinchem.2014.231100 · 2015 · External reference
Targeted sequencing using a 47 gene multiple myeloma mutation panel (M3P) in -17p high risk disease
10.1111/bjh.13171 · 2015 · External reference
Targeted next-generation sequencing panel (ThyroSeq) for detection of mutations in thyroid cancer
10.1210/jc.2013-2292 · 2013 · External reference
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Cancer Genome Atlas Pan-cancer analysis project
2015 · External reference
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Universal patterns of selection in cancer and somatic tissues
10.1016/j.cell.2017.09.042 · 2017 · External reference
Functional impact bias reveals cancer drivers
10.1093/nar/gks743 · 2012 · External reference
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Genomic profiling reveals spatial intra-tumor heterogeneity in follicular lymphoma
10.1038/s41375-018-0043-y · 2018 · External reference
Assessment of minimal residual disease in standard-risk AML
10.1056/nejmoa1507471 · 2016 · External reference
Clinical implications of genomic alterations in the tumour and circulation of pancreatic cancer patients
10.1038/ncomms8686 · 2015 · External reference
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10.1093/bioinformatics/btp698 · External reference
10.1038/nmeth.1923
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10.1093/bioinformatics/btp352
10.1093/bioinformatics/btp352 · External reference
The genome analysis toolkit: a mapreduce framework for analyzing next-generation DNA sequencing data Aaron
2010 · External reference
Strelka2: fast and accurate calling of germline and somatic variants
2018 · External reference
VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing
10.1101/gr.129684.111 · 2012 · External reference
10.1093/bioinformatics/btp394
10.1093/bioinformatics/btp394 · External reference
ANNOVAR: Functional annotation of genetic variants from high-throughput sequencing data
10.1093/nar/gkq603 · 2010 · External reference
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The ensembl variant effect predictor
10.1186/s13059-016-0974-4 · 2016 · External reference
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10.1093/bioinformatics/btu356
10.1093/bioinformatics/btu356 · External reference
JointSNVMix: a probabilistic model for accurate detection of somatic mutations in normal/tumour paired next-generation sequencing data
10.1093/bioinformatics/bts053 · 2012 · External reference
Comparing the performance of selected variant callers using synthetic data and genome segmentation
10.1186/s12859-018-2440-7 · 2018 · External reference
Evaluation of nine somatic variant callers for detection of somatic mutations in exome and targeted deep sequencing data
10.1371/journal.pone.0151664 · 2016 · External reference
Intersect-then-combine approach: improving the performance of somatic variant calling in whole exome sequencing data using multiple aligners and callers
2017 · External reference
High-resolution clonal mapping of multi-organ metastasis in triple negative breast cancer
10.1038/s41467-018-07406-4 · 2018 · External reference
Evaluating somatic tumor mutation detection without matched normal samples
2017 · External reference
10.1093/bioinformatics/btu067
10.1093/bioinformatics/btu067 · External reference
Effect of next-generation exome sequencing depth for discovery of diagnostic variants
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10.1101/gr.123638.111 · External reference
Using VarScan 2 for germline variant calling and somatic mutation detection
10.1002/0471250953.bi1504s44 · 2013 · External reference
Deep sequencing reveals clonal evolution patterns and mutation events associated with relapse in B-cell lymphomas
2014 · External reference
Sequence artefacts in a prospective series of formalin-fixed tumours tested for mutations in hotspot regions by massively parallel sequencing
2014 · External reference
10.1002/humu.22771
10.1002/humu.22771 · External reference
Variation across 141,456 human exomes and genomes reveals the spectrum of loss-of-function intolerance across human protein-coding genes
2019 · External reference
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10.1038/nature19057 · External reference
10.1038/nmeth.2890
10.1038/nmeth.2890 · External reference
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10.1016/j.jmoldx.2017.01.011 · 2017 · External reference
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10.1038/nbt.3520 · External reference
CONTRA: Copy number analysis for targeted resequencing
10.1093/bioinformatics/bts146 · 2012 · External reference
SeqCNV: A novel method for identification of copy number variations in targeted next-generation sequencing data
10.1186/s12859-017-1566-3 · 2017 · External reference
Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection
10.1038/nmeth.3407 · 2016 · External reference