genetic analysis research applications, 48
library, 49
NGS workflows, 49
SBS, 48, 49
sequence regions and homopolymers, 50
terminator-bound dNTPs, 50
Illumina
® Library Preparation workflow, 40
Immunohistochemistry, 33
In vitro tumor models, 25, 26
In vivo tumor models, 26
Indels, 129, 131, 133
Indexed DNA/cDNA libraries, 43
Informed consent, 33
Integrative Genomics Viewer (IGV), 137, 161
Interdisciplinary approach, 33
International Cancer Genome Consortium (ICGC),
31
Interspersed nuclear elements (SINEs), 10
Inter-tumor heterogeneity, 28
Intra-tumor heterogeneity
bioinformatics analyses, 27
clonal mutations, 28
deconvolution methods, 28
differential expression analysis, 28
dissect patterns, 28
immune infiltration signatures, 28
single-cell sequencing technologies, 28
Intron–exon structure, 4
Ion Torrent, 51
K
Kyoto Encyclopedia of Genes and Genomes
(KEGG), 160, 168
L
Library preparation, 40, 43
Linux/Unix commands, 73, 74
Linux/Unix file system, 72
Liquid biopsies, 22, 30
Long interspersed nuclear elements (LINEs), 10
Long-read sequencing, 40
M
MacOS, 61
Melanoma tumors, 29
Messenger RNA (mRNA), 146
alternative splicing, 4
genetic code, 12
poly-A-tail, 9
protein, 5, 6
sequence, 12, 13
translation, 6
Methylation sequencing, 11
MicroRNA (miRNA), 146
Minimal residual disease (MRD), 30
MinION, 54
Missense mutations, 20
Molecular biology, 144
Multi-nucleotide variants (MNVs), 131
Multiple contigs, 138
Multivariate statistical methods, 166
Mutagenic agents, 22
Mutational processes, 23
Mutational signature analysis, 23, 25
Mutational signatures, 23, 24, 33
Mutations
ambiguous signature assignment, 23
aristolochic acid, 23
classes, 23
driver mutations, 18
genome, 22
hybridization, 21
passenger mutations, 18
patterns, 22
somatic mutations, 18, 19
Mycobacterium smegmatis, 53
N
Naive variant calling, 125, 126
National Health Institutes, 32
National Health System, 32
Needleman–Wunsch Algorithm, 114
Neoepitopes, 29
Next-generation sequencing (NGS), 144, 168
de novo sequencing, 11
DNA and RNA sequencing, 9
DNA–protein interactions, 9
expression analysis, 9
methyl-Seq, 10
targeted sequencing, 11
WGS, 10
whole-exome sequencing, 10
NGS data
big data, 80
file formats (see File formats)
preprocessing, 100, 101
Quality Check procedure (see Quality Check
via FastQC program)
NGS data analysis
computer setup, 60, 61
programs, 60
R, 60
NGS libraries, 40
NGS library preparation workflow
Index
215
library, 49
NGS workflows, 49
SBS, 48, 49
sequence regions and homopolymers, 50
terminator-bound dNTPs, 50
Illumina
® Library Preparation workflow, 40
Immunohistochemistry, 33
In vitro tumor models, 25, 26
In vivo tumor models, 26
Indels, 129, 131, 133
Indexed DNA/cDNA libraries, 43
Informed consent, 33
Integrative Genomics Viewer (IGV), 137, 161
Interdisciplinary approach, 33
International Cancer Genome Consortium (ICGC),
31
Interspersed nuclear elements (SINEs), 10
Inter-tumor heterogeneity, 28
Intra-tumor heterogeneity
bioinformatics analyses, 27
clonal mutations, 28
deconvolution methods, 28
differential expression analysis, 28
dissect patterns, 28
immune infiltration signatures, 28
single-cell sequencing technologies, 28
Intron–exon structure, 4
Ion Torrent, 51
K
Kyoto Encyclopedia of Genes and Genomes
(KEGG), 160, 168
L
Library preparation, 40, 43
Linux/Unix commands, 73, 74
Linux/Unix file system, 72
Liquid biopsies, 22, 30
Long interspersed nuclear elements (LINEs), 10
Long-read sequencing, 40
M
MacOS, 61
Melanoma tumors, 29
Messenger RNA (mRNA), 146
alternative splicing, 4
genetic code, 12
poly-A-tail, 9
protein, 5, 6
sequence, 12, 13
translation, 6
Methylation sequencing, 11
MicroRNA (miRNA), 146
Minimal residual disease (MRD), 30
MinION, 54
Missense mutations, 20
Molecular biology, 144
Multi-nucleotide variants (MNVs), 131
Multiple contigs, 138
Multivariate statistical methods, 166
Mutagenic agents, 22
Mutational processes, 23
Mutational signature analysis, 23, 25
Mutational signatures, 23, 24, 33
Mutations
ambiguous signature assignment, 23
aristolochic acid, 23
classes, 23
driver mutations, 18
genome, 22
hybridization, 21
passenger mutations, 18
patterns, 22
somatic mutations, 18, 19
Mycobacterium smegmatis, 53
N
Naive variant calling, 125, 126
National Health Institutes, 32
National Health System, 32
Needleman–Wunsch Algorithm, 114
Neoepitopes, 29
Next-generation sequencing (NGS), 144, 168
de novo sequencing, 11
DNA and RNA sequencing, 9
DNA–protein interactions, 9
expression analysis, 9
methyl-Seq, 10
targeted sequencing, 11
WGS, 10
whole-exome sequencing, 10
NGS data
big data, 80
file formats (see File formats)
preprocessing, 100, 101
Quality Check procedure (see Quality Check
via FastQC program)
NGS data analysis
computer setup, 60, 61
programs, 60
R, 60
NGS libraries, 40
NGS library preparation workflow
Index
215