Lecture 4 : Structural variants
Modern methods for genome analysis
(PřF:Bi7420)
Vojta Bystry
vojtech.bystry@ceitec.muni.cz
NGS data analysis
22
Raw data
.fastq
Genome/Transcriptome
Reference Mapping
.bam
Interaction
analysis
CHIP-seq
Expression
analysis
RNAseq
Variant
analysis
WES
de-multiplexing
Not known
reference
QC
QC
Experiment
design
Not ”classic”
reference
Metagenomics
Reference
assembly
Immunogenetic
VDJ-genes
CRISPR
sgRNA
Methylation
Bisulfide-seq…
Structural variants calling
3
Structural variants calling
4
• Copy number variants (CNV)
‒ Copy number analysis (CNA)
• Structural variants (SV)
‒ Discordant reads analysis
‒ Mainly from WGS
• Fusion genes analysis
‒ From RNA-seq
‒ SV in genes
‒ Medical application
Copy number variants
5
• Not-PCR amplified (WGS)
• PCR amplified (WES,targeted)
WGS copy number variants
6
• Running window
• Normalization to the absolute coverage
• Low-coverage WGS CNV
‒ Over large regions
‒ Good for somatic low tumor purity
‒ Minimal variant size vs. coverage trade-off
PCR amplified CNV
7
• Individual analysis problematic
• Panel of (normal) samples
• BAF frequency
‒ Help CNA
‒ Can call “loss of heterozygosity” LOH
Structural variants calling
8
• RP = Read pair
‒ Pair-end sequencing
• SR = Split reads
Structural variants calling
9
• RP = Read pair
‒ Pair-end sequencing
• SR = Split reads
Structural variants calling
10
• RP = Read pair
‒ Pair-end sequencing
• SR = Split reads
• Tools:
‒ Delly, Manta,
GRIDSS
Fusion genes
11
Fusion genes
12
Fusion genes
13
Fusion genes
14
Long reads
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• Short reads
‒ 1kb
• Long reads
‒ 100 – 1000kb
• Hot topic
Long reads
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• Short reads
‒ 1kb
• Long reads
‒ 100 – 1000kb
• Hot topic
Long reads
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• Short reads
‒ 1kb
• Long reads
‒ 100 – 1000kb
• Hot topic
Complex variants
18
19www.ceitec.eu
CEITEC
@CEITEC_Brno
Vojta Bystry
vojtech.bystry@ceitec.muni.cz
Thank you for your attention!