Lecture 3b : Structural variants
Modern Genomic Technologies  (LF:DSMGT01 )
Vojta Bystry
vojtech.bystry@ceitec.muni.cz

NGS data analysis
2
2
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
•RC = Read count
‒Copy number variants (CNV)
•RP = Read pair
‒Pair-end sequencing
•SR = Split reads
•AS = Assembled read
‒
‒

Structural variants calling
5
•RC = Read count
‒Copy number variants (CNV)
•RP = Read pair
‒Pair-end sequencing
•SR = Split reads
•AS = Assembled read
‒
•A = DELETION
•B = INSERTION
•C = INVERSION
•D = DUPLICATION

Structural variants calling
6


Structural variants calling
7
•Copy number variants (CNV)
‒Copy number analysis (CNA)
•Structural variants (SV)
‒Discordant reads analysis
•Fusion genes analysis
‒SV in coding sequence
‒From RNA-seq
‒Medical application

Copy number variants
8
•Not-PCR amplified (WGS)
•PCR amplified (WES,targeted)
•
•

WGS copy number variants
9
•Running window
•Normalization to the absolute coverage
•
•

PCR amplified CNV
10
•Individual analysis problematic
•Somatic tumor-normal pairs
•Panel of (normal) samples
•

Structural variants calling
11


Fusion genes
12


13
www.ceitec.eu
CEITEC
@CEITEC_Brno
Vojta Bystry
vojtech.bystry@ceitec.muni.cz
Thank you for your attention!

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