References and other resources#
Main resources including knowledge base and databases necessary for pipeline development
MSK-Impact pipeline: https://www.mskcc.org/msk-impact
dbSNP: Database of single nucleotide polymorphisms (SNPs) and multiple small-scale variations that include insertions/deletions, microsatellites, and non-polymorphic variants. https://www.ncbi.nlm.nih.gov/snp/ Download link: ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b150_GRCh38p7/VCF/All_20170710.vcf.gz
ClinVar: ClinVar aggregates information about genomic variation and its relationship to human health. https://www.ncbi.nlm.nih.gov/clinvar/ Download link: ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar_20171029.vcf.gz
SweGen: This dataset contains whole-genome variant frequencies for 1000 Swedish individuals generated within the SweGen project. Download link: https://swefreq.nbis.se/
ExAC: The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a wide variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. http://exac.broadinstitute.org/ Download link: ftp://ftp.broadinstitute.org/pub/ExAC_release/release1/ExAC.r1.sites.vep.vcf.gz
GTEx: The Genotype-Tissue Expression (GTEx) project aims to provide to the scientific community a resource with which to study human gene expression and regulation and its relationship to genetic variation. https://www.gtexportal.org/home/ Download URL by applying through: https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000424.v6.p1
OMIM: OMIM®, Online Mendelian Inheritance in Man®, An Online Catalog of Human Genes and Genetic Disorders. https://www.omim.org/ Download link: https://omim.org/downloads/ (registration required)
Drug resistance: An effort by Cosmic to annotate mutations identified in the literature as resistance mutations, including those conferring acquired resistance (after treatment) and intrinsic resistance (before treatment). Available through Cosmic: http://cancer.sanger.ac.uk/cosmic/drug_resistance
Mutational signatures: Signatures of Mutational Processes in Human Cancer. Available through Cosmic: http://cancer.sanger.ac.uk/cosmic/signatures
DGVa: The Database of Genomic Variants archive (DGVa) is a repository that provides archiving, accessioning and distribution of publicly available genomic structural variants, in all species. https://www.ebi.ac.uk/dgva
Cancer genomics workflow: MGI’s CWL Cancer Pipelines. https://github.com/genome/cancer-genomics-workflow/wiki
GIAB: The priority of GIAB is authoritative characterization of human genomes for use in analytical validation and technology development, optimization, and demonstration. https://github.com/genome-in-a-bottle
dbNSFP: dbNSFP is a database developed for functional prediction and annotation of all potential non-synonymous single-nucleotide variants (nsSNVs) in the human genome. https://sites.google.com/site/jpopgen/dbNSFP
1000Genomes: The goal of the 1000 Genomes Project was to find most genetic variants with frequencies of at least 1% in the populations studied. http://www.internationalgenome.org/ Download link: ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/
HapMap3: The International HapMap Project was an organization that aimed to develop a haplotype map (HapMap) of the human genome, to describe the common patterns of human genetic variation. HapMap 3 is the third phase of the International HapMap project. http://www.sanger.ac.uk/resources/downloads/human/hapmap3.html Download link: ftp://ftp.ncbi.nlm.nih.gov/hapmap/
GRCh38.p11: GRCh38.p11 is the eleventh patch release for the GRCh38 (human) reference assembly. https://www.ncbi.nlm.nih.gov/grc/human Download link: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/
dbVar: dbVar is NCBI’s database of genomic structural variation – insertions, deletions, duplications, inversions, mobile element insertions, translocations, and complex chromosomal rearrangements https://www.ncbi.nlm.nih.gov/dbvar Download link: https://www.ncbi.nlm.nih.gov/dbvar/content/ftp_manifest/
Drug sensitivity in cancer: Identifying molecular features of cancers that predict response to anti-cancer drugs. http://www.cancerrxgene.org/ Download link: ftp://ftp.sanger.ac.uk/pub4/cancerrxgene/releases
VarSome: VarSome is a knowledge base and aggregator for human genomic variants. https://varsome.com/about/
CADD: CADD is a tool for scoring the deleteriousness of single nucleotide variants as well as insertion/deletions variants in the human genome. CADD can quantitatively prioritize functional, deleterious, and disease causal variants across a wide range of functional categories, effect sizes and genetic architectures and can be used prioritize causal variation in both research and clinical settings.
Sample datasets#
TCRB: The Texas Cancer Research Biobank (TCRB) was created to bridge the gap between doctors and scientific researchers to improve the prevention, diagnosis and treatment of cancer. This work occurred with funding from the Cancer Prevention & Research Institute of Texas (CPRIT) from 2010-2014. http://txcrb.org/data.html Article: https://www.nature.com/articles/sdata201610
Relevant publications#
Including methodological benchmarking
MSK-IMPACT:
Original pipeline: Cheng, D. T., Mitchell, T. N., Zehir, A., Shah, R. H., Benayed, R., Syed, A., … Berger, M. F. (2015). Memorial sloan kettering-integrated mutation profiling of actionable cancer targets (MSK-IMPACT): A hybridization capture-based next-generation sequencing clinical assay for solid tumor molecular oncology. Journal of Molecular Diagnostics, 17(3), 251–264. https://doi.org/10.1016/j.jmoldx.2014.12.006
Case study: Cheng, D. T., Prasad, M., Chekaluk, Y., Benayed, R., Sadowska, J., Zehir, A., … Zhang, L. (2017). Comprehensive detection of germline variants by MSK-IMPACT, a clinical diagnostic platform for solid tumor molecular oncology and concurrent cancer predisposition testing. BMC Medical Genomics, 10(1), 33. https://doi.org/10.1186/s12920-017-0271-4
Case study: Zehir, A., Benayed, R., Shah, R. H., Syed, A., Middha, S., Kim, H. R., … Berger, M. F. (2017). Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients. Nature Medicine, 23(6), 703–713. https://doi.org/10.1038/nm.4333
Application of MSK-IMPACT: Zehir, A., Benayed, R., Shah, R. H., Syed, A., Middha, S., Kim, H. R., … Berger, M. F. (2017). Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients. Nature Medicine, 23(6), 703–713. https://doi.org/10.1038/nm.4333
Review on bioinformatic pipelins: Leipzig, J. (2017). A review of bioinformatic pipeline frameworks. Briefings in Bioinformatics, 18(3), 530–536. https://doi.org/10.1093/bib/bbw020
Mutational signature reviews:
Helleday, T., Eshtad, S., & Nik-Zainal, S. (2014). Mechanisms underlying mutational signatures in human cancers. Nature Reviews Genetics, 15(9), 585–598. https://doi.org/10.1038/nrg3729
Alexandrov, L. B., & Stratton, M. R. (2014). Mutational signatures: The patterns of somatic mutations hidden in cancer genomes. Current Opinion in Genetics and Development, 24(1), 52–60. https://doi.org/10.1016/j.gde.2013.11.014
Review on structural variation detection tools:
Lin, K., Bonnema, G., Sanchez-Perez, G., & De Ridder, D. (2014). Making the difference: Integrating structural variation detection tools. Briefings in Bioinformatics, 16(5), 852–864. https://doi.org/10.1093/bib/bbu047
Tattini, L., D’Aurizio, R., & Magi, A. (2015). Detection of Genomic Structural Variants from Next-Generation Sequencing Data. Frontiers in Bioengineering and Biotechnology, 3(June), 1–8. https://doi.org/10.3389/fbioe.2015.00092
Two case studies and a pipeline (unpublished): Noll, A. C., Miller, N. A., Smith, L. D., Yoo, B., Fiedler, S., Cooley, L. D., … Kingsmore, S. F. (2016). Clinical detection of deletion structural variants in whole-genome sequences. Npj Genomic Medicine, 1(1), 16026. https://doi.org/10.1038/npjgenmed.2016.26
Review on driver gene methods: Tokheim, C. J., Papadopoulos, N., Kinzler, K. W., Vogelstein, B., & Karchin, R. (2016). Evaluating the evaluation of cancer driver genes. Proceedings of the National Academy of Sciences, 113(50), 14330–14335. https://doi.org/10.1073/pnas.1616440113
Detection of IGH::DUX4 rearrangement: Rezayee, F., Eisfeldt, J., Skaftason, A., Öfverholm, I., Sayyab, S., Syvänen, A. C., … & Barbany, G. (2023). Feasibility to use whole-genome sequencing as a sole diagnostic method to detect genomic aberrations in pediatric B-cell acute lymphoblastic leukemia. Frontiers in Oncology, 13, 1217712. https://doi.org/10.3389/fonc.2023.1217712
Resource, or general notable papers including resource and KB papers related to cancer genomics
GIAB: Zook, J. M., Catoe, D., McDaniel, J., Vang, L., Spies, N., Sidow, A., … Salit, M. (2016). Extensive sequencing of seven human genomes to characterize benchmark reference materials. Scientific Data, 3, 160025. https://doi.org/10.1038/sdata.2016.25
Methods and tools#
Excluding multiple method comparison or benchmarking tools
BreakDancer: Chen, K., Wallis, J. W., Mclellan, M. D., Larson, D. E., Kalicki, J. M., Pohl, C. S., … Elaine, R. (2013). BreakDancer - An algorithm for high resolution mapping of genomic structure variation. Nature Methods, 6(9), 677–681. https://doi.org/10.1038/nmeth.1363
Pindel: Ye, K., Schulz, M. H., Long, Q., Apweiler, R., & Ning, Z. (2009). Pindel: A pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics, 25(21), 2865–2871. https://doi.org/10.1093/bioinformatics/btp394
SVDetect: Zeitouni, B., Boeva, V., Janoueix-Lerosey, I., Loeillet, S., Legoix-né, P., Nicolas, A., … Barillot, E. (2010). SVDetect: A tool to identify genomic structural variations from paired-end and mate-pair sequencing data. Bioinformatics, 26(15), 1895–1896. https://doi.org/10.1093/bioinformatics/btq293
Purityest: Su, X., Zhang, L., Zhang, J., Meric-bernstam, F., & Weinstein, J. N. (2012). Purityest: Estimating purity of human tumor samples using next-generation sequencing data. Bioinformatics, 28(17), 2265–2266. https://doi.org/10.1093/bioinformatics/bts365
PurBayes: Larson, N. B., & Fridley, B. L. (2013). PurBayes: Estimating tumor cellularity and subclonality in next-generation sequencing data. Bioinformatics, 29(15), 1888–1889. https://doi.org/10.1093/bioinformatics/btt293
ANNOVAR: Wang, K., Li, M., & Hakonarson, H. (2010). ANNOVAR: Functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Research, 38(16), 1–7. https://doi.org/10.1093/nar/gkq603
ASCAT: Van Loo, P., Nordgard, S. H., Lingjaerde, O. C., Russnes, H. G., Rye, I. H., Sun, W., … Kristensen, V. N. (2010). Allele-specific copy number analysis of tumors. Proceedings of the National Academy of Sciences, 107(39), 16910–16915. https://doi.org/10.1073/pnas.1009843107
Treeomics: Reiter, J. G., Makohon-Moore, A. P., Gerold, J. M., Bozic, I., Chatterjee, K., Iacobuzio-Donahue, C. A., … Nowak, M. A. (2017). Reconstructing metastatic seeding patterns of human cancers. Nature Communications, 8, 14114. https://doi.org/10.1038/ncomms14114
deconstructSigs: Rosenthal, R., McGranahan, N., Herrero, J., Taylor, B. S., & Swanton, C. (2016). deconstructSigs: delineating mutational processes in single tumors distinguishes DNA repair deficiencies and patterns of carcinoma evolution. Genome Biology, 17(1), 31. https://doi.org/10.1186/s13059-016-0893-4
MutationalPatterns: Blokzijl, F., Janssen, R., van Boxtel, R., & Cuppen, E. (2017). MutationalPatterns: comprehensive genome-wide analysis of mutational processes. bioRxiv, 1–20. https://doi.org/https://doi.org/10.1101/071761
MaSuRCA: Zimin, A. V., Marçais, G., Puiu, D., Roberts, M., Salzberg, S. L., & Yorke, J. A. (2013). The MaSuRCA genome assembler. Bioinformatics, 29(21), 2669–2677. https://doi.org/10.1093/bioinformatics/btt476
VarDict: Lai, Z., Markovets, A., Ahdesmaki, M., Chapman, B., Hofmann, O., Mcewen, R., … Dry, J. R. (2016). VarDict: A novel and versatile variant caller for next-generation sequencing in cancer research. Nucleic Acids Research, 44(11), 1–11. https://doi.org/10.1093/nar/gkw227
vt: Tan, A., Abecasis, G. R., & Kang, H. M. (2015). Unified representation of genetic variants. Bioinformatics, 31(13), 2202–2204. https://doi.org/10.1093/bioinformatics/btv112
peddy: Pedersen, B. S., & Quinlan, A. R. (2017). Who’s Who? Detecting and Resolving Sample Anomalies in Human DNA Sequencing Studies with Peddy. American Journal of Human Genetics, 100(3), 406–413. https://doi.org/10.1016/j.ajhg.2017.01.017
GQT: Layer, R. M., Kindlon, N., Karczewski, K. J., & Quinlan, A. R. (2015). Efficient genotype compression and analysis of large genetic-variation data sets. Nature Methods, 13(1). https://doi.org/10.1038/nmeth.3654
Tool sets and softwares required at various steps of pipeline development
FastQC: Quality control tool. https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Cutadapt: Adapter removal tool. https://cutadapt.readthedocs.io/en/stable/
Trim Galore!: FastQC and Cutadapt wrapper. https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
Picardtools: BAM/SAM/VCF/CRAM manipulator. http://broadinstitute.github.io/picard/
MarkDuplicate: Mark duplicate reads and potentially remove them
LiftoverVcf: liftover VCF between builds
CollectHsMetric: Collects hybrid-selection (HS) metrics for a SAM or BAM file
CollectAlignmentSummaryMetrics: Produces a summary of alignment metrics from a SAM or BAM file
CollectGcBiasMetrics: Collect metrics regarding GC bias
CollectWgsMetrics: Collect metrics about coverage and performance of whole genome sequencing (WGS) experiments
GATK: A variant discovery tool: https://gatk.broadinstitute.org/hc/en-us
BaseRecalibrator: Detect systematic error in base quality score
Somatic Indel Realigner: Local Realignment around Indels
ContEst: Estimate cross sample contamination
DepthOfCoverage: Assess sequence coverage by sample, read group, or libraries
DuplicateReadFilter: remove duplicated from flag set by MarkDuplicates
Samtools: Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format http://www.htslib.org/
Sambamba: Tools for working with SAM/BAM/CRAM data http://lomereiter.github.io/sambamba/
bcftools: Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants http://www.htslib.org/doc/bcftools.html
vcftools: VCFtools is a program package designed for working with VCF files, such as those generated by the 1000 Genomes Project. https://vcftools.github.io/index.html
Delly2: An integrated structural variant prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations https://github.com/dellytools/delly
PLINK: PLINK: Whole genome data analysis toolset https://www.cog-genomics.org/plink2
freebayes: a haplotype-based variant detector. https://github.com/ekg/freebayes
AscatNGS: Allele-Specific Copy Number Analysis of Tumors, tumor purity and ploidy https://github.com/cancerit/ascatNgs
MutationalPatterns: R package for extracting and visualizing mutational patterns in base substitution catalogues https://github.com/UMCUGenetics/MutationalPatterns
desconstructSigs: identification of mutational signatures within a single tumor sample https://github.com/raerose01/deconstructSigs
treeOmics: Decrypting somatic mutation patterns to reveal the evolution of cancer https://github.com/johannesreiter/treeomics
controlFreeC: Copy number and allelic content caller http://boevalab.com/FREEC/
MuTect2: Call somatic SNPs and indels via local re-assembly of haplotypes https://gatk.broadinstitute.org/hc/en-us/articles/360037593851-Mutect2
Annovar: annotation of detected genetic variation http://annovar.openbioinformatics.org/en/latest/
Strelka: Small variant caller https://github.com/Illumina/strelka
Manta: Structural variant caller https://github.com/Illumina/manta
PurBayes: estimate tumor purity and clonality
VarDict: variant caller for both single and paired sample variant calling from BAM files https://github.com/AstraZeneca-NGS/VarDict
SNPeff/SNPSift: Genomic variant annotations and functional effect prediction toolbox. http://snpeff.sourceforge.net/ and http://snpeff.sourceforge.net/SnpSift.html
IGV: visualization tool for interactive exploration http://software.broadinstitute.org/software/igv/
SVDetect: a tool to detect genomic structural variations http://svdetect.sourceforge.net/Site/Home.html
GenomeSTRiP: A suite of tools for discovering and genotyping structural variations using sequencing data http://software.broadinstitute.org/software/genomestrip/
BreakDancer: SV detection from paired end reads mapping https://github.com/genome/breakdancer
pIndel: Detect breakpoints of large deletions, medium sized insertions, inversions, and tandem duplications https://github.com/genome/pindel
VarScan: Variant calling and somatic mutation/CNV detection https://github.com/dkoboldt/varscan
VEP: Variant Effect Predictor https://www.ensembl.org/info/docs/tools/vep/index.html
Probablistic2020: Simulates somatic mutations, and calls statistically significant oncogenes and tumor suppressor genes based on a randomization-based test https://github.com/KarchinLab/probabilistic2020
2020plus: Classifies genes as an oncogene, tumor suppressor gene, or as a non-driver gene by using Random Forests https://github.com/KarchinLab/2020plus
vtools: variant tools is a software tool for the manipulation, annotation, selection, simulation, and analysis of variants in the context of next-gen sequencing analysis. https://vatlab.github.io/vat-docs/
vt: A variant tool set that discovers short variants from Next Generation Sequencing data. https://genome.sph.umich.edu/wiki/Vt and https://github.com/atks/vt
CNVnator: a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads. https://github.com/abyzovlab/CNVnator
CNVpytor: a tool for copy number variation detection and analysis from read depth and allele imbalance in whole-genome sequencing. https://github.com/abyzovlab/CNVpytor
SvABA: Structural variation and indel detection by local assembly. https://github.com/walaj/svaba
indelope: find indels and SVs too small for structural variant callers and too large for GATK. https://github.com/brentp/indelope
peddy: peddy compares familial-relationships and sexes as reported in a PED/FAM file with those inferred from a VCF. https://github.com/brentp/peddy
cyvcf2: cyvcf2 is a cython wrapper around htslib built for fast parsing of Variant Call Format (VCF) files. https://github.com/brentp/cyvcf2
GQT: Genotype Query Tools (GQT) is command line software and a C API for indexing and querying large-scale genotype data sets. https://github.com/ryanlayer/gqt
LOFTEE: Loss-Of-Function Transcript Effect Estimator. A VEP plugin to identify LoF (loss-of-function) variation. Assesses variants that are: Stop-gained, Splice site disrupting, and Frameshift variants. https://github.com/konradjk/loftee
PureCN: copy number calling and SNV classification using targeted short read sequencing https://bioconductor.org/packages/release/bioc/html/PureCN.html
SVCaller: A structural variant caller. https://github.com/tomwhi/svcaller
SnakeMake: A workflow manager. http://snakemake.readthedocs.io/en/stable/index.html
BWA: BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. It consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM. http://bio-bwa.sourceforge.net/
wgsim: Wgsim is a small tool for simulating sequence reads from a reference genome. It is able to simulate diploid genomes with SNPs and insertion/deletion (INDEL) polymorphisms, and simulate reads with uniform substitution sequencing errors. https://github.com/lh3/wgsim
dwgsim: Whole genome simulation can be performed with dwgsim. dwgsim is based off of wgsim found in SAMtools. https://github.com/nh13/DWGSIM
THetA: Tumor Heterogeneity Analysis. This algorithm estimates tumor purity and clonal/subclonal copy number aberrations directly from high-throughput DNA sequencing data. https://github.com/raphael-group/THetA
Skewer: Adapter trimming, similar to cutadapt. https://github.com/relipmoc/skewer
Phylowgs: Application for inferring subclonal composition and evolution from whole-genome sequencing data. https://github.com/morrislab/phylowgs
superFreq: SuperFreq is an R package that analyses cancer exomes to track subclones. https://github.com/ChristofferFlensburg/superFreq
readVCF-r: Read VCFs into R and annotatte them. https://bioconductor.org/packages/release/bioc/html/VariantAnnotation.html
vcfr: Read VCFs into R. https://github.com/knausb/vcfR
msisensor: microsatellite instability detection using paired tumor-normal https://github.com/ding-lab/msisensor
MOSAIC: MicrOSAtellite Instability Classifier https://github.com/ronaldhause/mosaic
MANTIS: Microsatellite Analysis for Normal-Tumor InStability https://github.com/OSU-SRLab/MANTIS
SBDB: A toolkit for constricting and querying structural variant databases https://github.com/J35P312/SVDB