Cancer (cont.)
types, 20
Cancer diagnosis
bioinformatic analysis, 21
ctDNA, 22
gene sequencing, 21
genetic tests, 21
high-throughput sequencing, 21
liquid biopsies, 22
loci, 22
RAS-/TP53-cancer associated mutations, 22
tumors shed cells and DNA, 22
VUS, 21
Cancer sequencing and mutation classification
ClinVar, 32
COSMIC, 31
ICGC, 31
PCAWG, 31
TCGA, 30, 31
Cancer treatment, sequencing
BET and MEK inhibitors, 29
BRAF inhibitors, 28
challenges, 32
ctDNA mutations identification, 30
ERBB2 amplification, 29
gene panel testing, 33
genetic resistance, 30
genomic subtypes, 28
liquid biopsies, 30
opportunities and perspectives, 32
PARP inhibitors, 29
precision and personalized design, 28
RNA expression analysis, 29
T-cell therapy, 29
therapeutical targets, 29
TILs, 29
TMB, 29
transcriptomic characterization, 29
tumor mutational landscape, 30
Cancer-associated genes, 26
Candidate variant, 135
Carcinogenic agents, 22
Catalog of Somatic Mutations in Cancer
(COSMIC), 31
Cataloging non-coding driver mutations, 31
cDNA library, 145
Cell-free DNA (cfDNA), 22
Cell type deconvolution, 28
Chemotherapy, 29
ChIP-DNA, 179
ChIP-fragment density, 183
ChIP-Seq data analysis
annotatePeaks.pl program, 188
BedTools, 187
CNV, input sample, 184
DNA–protein interaction, 178
DNA quality, 178–180
GRNs, 178
heatmaps, 188, 189
histone modifications, 178
motif discovery, 189
peaks/regions, 184–186, 189
QC, 180–184
R packages, 186
RNA Polymerase II, 178
R script, 189
sequencing pre-process, 180–184
TFBS, 178, 189
TSS, 187, 189
venn diagram, 186, 187
workflow, 178
Chromatin, 178
Chromatin-immunoprecipitation (ChIP-Seq), 9
Chronological sequence, 2
CIBERSORT, 28
CIGAR (Concise Idiosyncratic Gapped Alignment
Report), 84–86
Circular consensus sequencing (CCS), 52
Circulating tumor cells (CTCs), 22
Circulating tumor DNA (ctDNA), 22
ClinVar, 32
Clustering analysis, 168
Clusterprofiler package, 168
Colorectal cancer (CRC), 26
Command line analysis tools, 60
Command line interfaces (CLI)
Bash, 72
GUI, 72
shell, 72
Command line interpreter Bash, 73
Command line tool, 73
file system manipulation, 72
Command Line tools package, 61
Complementary DNA (cDNA), 145, 146
Complex illnesses, 2
Computer setup
CPU power, 60
hard drive space, 60
Linux/Unix-based operating system, 60
RAM, 60
software tools, 60
Computer setup installation
.bash_profile, 61
Bioconda, 62, 63
descriptive folder- and filenames, 67
GATK package, 66
Genome Analysis Toolkit, 63
GNU compilers, 61
212
Index
types, 20
Cancer diagnosis
bioinformatic analysis, 21
ctDNA, 22
gene sequencing, 21
genetic tests, 21
high-throughput sequencing, 21
liquid biopsies, 22
loci, 22
RAS-/TP53-cancer associated mutations, 22
tumors shed cells and DNA, 22
VUS, 21
Cancer sequencing and mutation classification
ClinVar, 32
COSMIC, 31
ICGC, 31
PCAWG, 31
TCGA, 30, 31
Cancer treatment, sequencing
BET and MEK inhibitors, 29
BRAF inhibitors, 28
challenges, 32
ctDNA mutations identification, 30
ERBB2 amplification, 29
gene panel testing, 33
genetic resistance, 30
genomic subtypes, 28
liquid biopsies, 30
opportunities and perspectives, 32
PARP inhibitors, 29
precision and personalized design, 28
RNA expression analysis, 29
T-cell therapy, 29
therapeutical targets, 29
TILs, 29
TMB, 29
transcriptomic characterization, 29
tumor mutational landscape, 30
Cancer-associated genes, 26
Candidate variant, 135
Carcinogenic agents, 22
Catalog of Somatic Mutations in Cancer
(COSMIC), 31
Cataloging non-coding driver mutations, 31
cDNA library, 145
Cell-free DNA (cfDNA), 22
Cell type deconvolution, 28
Chemotherapy, 29
ChIP-DNA, 179
ChIP-fragment density, 183
ChIP-Seq data analysis
annotatePeaks.pl program, 188
BedTools, 187
CNV, input sample, 184
DNA–protein interaction, 178
DNA quality, 178–180
GRNs, 178
heatmaps, 188, 189
histone modifications, 178
motif discovery, 189
peaks/regions, 184–186, 189
QC, 180–184
R packages, 186
RNA Polymerase II, 178
R script, 189
sequencing pre-process, 180–184
TFBS, 178, 189
TSS, 187, 189
venn diagram, 186, 187
workflow, 178
Chromatin, 178
Chromatin-immunoprecipitation (ChIP-Seq), 9
Chronological sequence, 2
CIBERSORT, 28
CIGAR (Concise Idiosyncratic Gapped Alignment
Report), 84–86
Circular consensus sequencing (CCS), 52
Circulating tumor cells (CTCs), 22
Circulating tumor DNA (ctDNA), 22
ClinVar, 32
Clustering analysis, 168
Clusterprofiler package, 168
Colorectal cancer (CRC), 26
Command line analysis tools, 60
Command line interfaces (CLI)
Bash, 72
GUI, 72
shell, 72
Command line interpreter Bash, 73
Command line tool, 73
file system manipulation, 72
Command Line tools package, 61
Complementary DNA (cDNA), 145, 146
Complex illnesses, 2
Computer setup
CPU power, 60
hard drive space, 60
Linux/Unix-based operating system, 60
RAM, 60
software tools, 60
Computer setup installation
.bash_profile, 61
Bioconda, 62, 63
descriptive folder- and filenames, 67
GATK package, 66
Genome Analysis Toolkit, 63
GNU compilers, 61
212
Index