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Pooled CRISPR Inverse PCR sequencing (PCIP-seq): simultaneous sequencing of retroviral insertion points and the associated provirus in thousands of cells with long reads 558130
Artesi, Maria; Hahaut, Vincent; Ashrafi, Fereshteh et al.
2019
 

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Abstract :
[en] Retroviral infections create a large population of cells, each defined by a unique proviral insertion site. Methods based on short-read high throughput sequencing can identify thousands of insertion sites, but the proviruses within remain unobserved. We have developed Pooled CRISPR Inverse PCR sequencing (PCIP-seq), a method that leverages long reads on the Oxford Nanopore MinION platform to sequence the insertion site and its associated provirus. We have applied the technique to three exogenous retroviruses, HTLV-1, HIV-1 and BLV, as well as endogenous retroviruses in both cattle and sheep. The long reads of PCIP-seq improved the accuracy of insertion site identification in repetitive regions of the genome. The high efficiency of the method facilitated the identification of tens of thousands of insertion sites in a single sample. We observed thousands of SNPs and dozens of structural variants within proviruses and uncovered evidence of viral hypermutation, recombination and recurrent selection.
Disciplines :
Genetics & genetic processes
Author, co-author :
Artesi, Maria ;  Université de Liège - ULiège > Medical Genomics-Unit of Animal Genomics
Hahaut, Vincent ;  Université de Liège - ULiège > Dpt. de gestion vétérinaire des Ressources Animales (DRA) > GIGA-R : Génomique animale
Ashrafi, Fereshteh
Marcais, Ambroise
Hermine, Olivier
Griebel, Philip
Arsic, Natasa
van der Meer, Frank
Burny, Arsène ;  Université de Liège - ULiège > Agro Biotech Gembloux
Bron, Dominique
Charlier, Carole  ;  Université de Liège - ULiège > Medical Genomics-Unit of Animal Genomics
Georges, Michel  ;  Université de Liège - ULiège > Dpt. de gestion vétérinaire des Ressources Animales (DRA) > Génomique animale
Van den Broeke, Anne
Durkin, Keith  ;  Université de Liège - ULiège > Medical Genomics-Unit of Animal Genomics
More authors (4 more) Less
Language :
English
Title :
Pooled CRISPR Inverse PCR sequencing (PCIP-seq): simultaneous sequencing of retroviral insertion points and the associated provirus in thousands of cells with long reads 558130
Publication date :
2019
Available on ORBi :
since 27 June 2019

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