File formats (cont.)
GFF/GTF/BED formats, 89
GTF/GFF file, 87, 88
mate I, 80
mate II, 80
read, 80
SAM (see SAM (Sequence Alignment/Map)
format)
sequencing coverage, 80, 81
sequencing depth, 80
SRA file, 92
VCF file format, 91, 92
Fragmentation methods, 41
Fragments Per Kilobase Million (FPKM), 163
Functional analysis, 168
Functional annotation, de novo transcripts, 160
G
Gain-of-function alterations, 19
Galaxy, 137
GATK package, 66
GenBank, 113
Gene, 4, 33
Gene expression analysis, 157
Gene expression quantification
counting reads per exons, 164
counting reads per genes, 162, 163
counting reads per transcripts, 163
de novo assemblies, 161
reference-based alignments, 161
Gene fusions, 20
Gene ontology (GO-term), 160, 168
Gene ontology-based annotation, 160
Gene Set Enrichment Analysis (GSEA), 168
Gene silencing, 20
Genes, 178
Genetic codons, 6, 7
Genetic regulatory networks (GRNs), 178
Genetic resistance, 30
Genetic variants
base calling, 124
Bayesian variant calling, 126–128
in CARD3 gene, 135
classes, 130
de novo, 133, 134
filtering and post-processing, 134
germline analyses, 125
heuristic variant calling, 128, 130
naive variant calling, 125, 126
Phred-based variant quality score, 132
variant annotation, 135
whole exome/genome sequencing, 125
Genome Analysis Toolkit, 63
Genome and transcriptome sequencing
cellular processes, 25
gene expression patterns, 25
in vitro tumor models, 25, 26
in vivo tumor models, 26
intra-tumor heterogeneity, 27–28
single-cell DNA/RNA, 27
TCGA, 25
Genome assembly, 138
Genome sequence, 34, 155
Genome sequence and annotation files, 106
Genomes Project, 32
Genomic annotations, 152, 153
Genomic DNA, 181
Genomic feature association analysis, 190
Genomic region-based annotations, 135
Genomic subtypes, 28
GFF (General Feature Format), 87
GFF/GTF/BED formats, 89
Graphical user interphase (GUI), 72
GTF (General Feature Format), 87
H
Heterozygous single nucleotide substitution, 56
HISAT2 (alignment tool), 120
Histones, 179
Histopathology, 33
HOMER software tool, 183
HTSeq, 162, 166
Human genome, 4
base pairs, 6
components, 9, 10
non-coding DNA, 6
regulatory mechanisms
enhancer, 9
promoter, 9
silencer, 9
terminator, 9
regulatory sequences, 8
I
ICGC for Accelerating Research in Genomic
Oncology (ICGC-ARGO), 31
Illumina adaptor sequences, 147
Illumina NGS workflows
cluster generation, 49
data analysis, 49
library preparation, 49
sequencing, 49
Illumina sequencing technologies
BeadArray Microarray Technology, 48
cycles, 56
214
Index
GFF/GTF/BED formats, 89
GTF/GFF file, 87, 88
mate I, 80
mate II, 80
read, 80
SAM (see SAM (Sequence Alignment/Map)
format)
sequencing coverage, 80, 81
sequencing depth, 80
SRA file, 92
VCF file format, 91, 92
Fragmentation methods, 41
Fragments Per Kilobase Million (FPKM), 163
Functional analysis, 168
Functional annotation, de novo transcripts, 160
G
Gain-of-function alterations, 19
Galaxy, 137
GATK package, 66
GenBank, 113
Gene, 4, 33
Gene expression analysis, 157
Gene expression quantification
counting reads per exons, 164
counting reads per genes, 162, 163
counting reads per transcripts, 163
de novo assemblies, 161
reference-based alignments, 161
Gene fusions, 20
Gene ontology (GO-term), 160, 168
Gene ontology-based annotation, 160
Gene Set Enrichment Analysis (GSEA), 168
Gene silencing, 20
Genes, 178
Genetic codons, 6, 7
Genetic regulatory networks (GRNs), 178
Genetic resistance, 30
Genetic variants
base calling, 124
Bayesian variant calling, 126–128
in CARD3 gene, 135
classes, 130
de novo, 133, 134
filtering and post-processing, 134
germline analyses, 125
heuristic variant calling, 128, 130
naive variant calling, 125, 126
Phred-based variant quality score, 132
variant annotation, 135
whole exome/genome sequencing, 125
Genome Analysis Toolkit, 63
Genome and transcriptome sequencing
cellular processes, 25
gene expression patterns, 25
in vitro tumor models, 25, 26
in vivo tumor models, 26
intra-tumor heterogeneity, 27–28
single-cell DNA/RNA, 27
TCGA, 25
Genome assembly, 138
Genome sequence, 34, 155
Genome sequence and annotation files, 106
Genomes Project, 32
Genomic annotations, 152, 153
Genomic DNA, 181
Genomic feature association analysis, 190
Genomic region-based annotations, 135
Genomic subtypes, 28
GFF (General Feature Format), 87
GFF/GTF/BED formats, 89
Graphical user interphase (GUI), 72
GTF (General Feature Format), 87
H
Heterozygous single nucleotide substitution, 56
HISAT2 (alignment tool), 120
Histones, 179
Histopathology, 33
HOMER software tool, 183
HTSeq, 162, 166
Human genome, 4
base pairs, 6
components, 9, 10
non-coding DNA, 6
regulatory mechanisms
enhancer, 9
promoter, 9
silencer, 9
terminator, 9
regulatory sequences, 8
I
ICGC for Accelerating Research in Genomic
Oncology (ICGC-ARGO), 31
Illumina adaptor sequences, 147
Illumina NGS workflows
cluster generation, 49
data analysis, 49
library preparation, 49
sequencing, 49
Illumina sequencing technologies
BeadArray Microarray Technology, 48
cycles, 56
214
Index