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Samenvatting DT2 genoombiologie
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samenvatting van de stof voor deeltoets 2 van het vak genoombiologie aan de UU. samenvatting bevat aantekeningen van alle hoorcolleges die relevant zijn voor dit tentamen.
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DT2 genoombiologieInhoud
W5.......................................................................................................................... 2
Genomic variation and pangenomes...................................................................2
W6.......................................................................................................................... 6
Structural Variants in Cancer Biology..................................................................6
W7........................................................................................................................ 10
Comparative Genomics & Synteny (of animals) & Recent Human evolution.....10
Synteny/Colinearity:....................................................................................... 10
Selectie:......................................................................................................... 11
Orthologie-inferentie...................................................................................... 12
Incomplete lineage sorting:............................................................................12
W8........................................................................................................................ 14
Gene and Genome Duplications........................................................................14
,W5
Genomic variation and pangenomes
Typen genomische variatie:
- Single nucleotide variaties – SNP/ SNV
- Indels – inserties/ deleties (1 bp - 1000 bp)
- Structural variants (SV) – grotere variaties
o Detecteren met paired end sequencing
- Mobiele elementen – SINE, LINE Transpositie (300bp - 6 kb)
- Genomische structurele variatie (1 kb - 5 Mb)
o Grootschalige inserties/deleties (Copy Number Variation: CNV)
o Segmentale duplicaties (> 1kb, > 90% sequentieovereenkomst)
o Chromosomale inversies, translocaties, fusies
Elk individu heeft 1% variabel tov referentie
, Hoe varianten detecteren:
Pangenoom:
- Waarom hebben we pangenomen nodig?
o Alignments vatten de relaties tussen
sequenties samen, waardoor
vermoedelijke evolutionaire en
functionele informatie zichtbaar wordt
o Pangenomen kunnen de volledige set
genomische elementen in een bepaalde
soort of clade modelleren, waardoor de
referentie-bias wordt verminderd.
- Wat is een pangenoom
o Verder gaan dan een enkel referentiegenoom
Vertekening
Ontbrekende gebieden/onvolledig
o Term pangenoom gepopulariseerd in microbiologie in 2005 (Tettelin
et al., 2005)
o Pan betekent alles,
Core genen/ genomische regio’s
Vervangbare/accessory genen/
genomische regio’s
Unieke genen/ genomische regio’s
Pangenomes can be open and closed
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