Deprecated: Implicit conversion from float 233.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534
Deprecated: Implicit conversion from float 233.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534
Deprecated: Implicit conversion from float 233.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534
Deprecated: Implicit conversion from float 233.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534
Deprecated: Implicit conversion from float 233.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534
Deprecated: Implicit conversion from float 233.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534
Deprecated: Implicit conversion from float 233.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534
Deprecated: Implicit conversion from float 233.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534
Deprecated: Implicit conversion from float 233.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534
Warning: imagejpeg(C:\Inetpub\vhosts\kidney.de\httpdocs\phplern\28344990
.jpg): Failed to open stream: No such file or directory in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 117 Mol+Ther+Methods+Clin+Dev
2017 ; 4
(ä): 39-49
Nephropedia Template TP
gab.com Text
Twit Text FOAVip
Twit Text #
English Wikipedia
INSPIIRED: A Pipeline for Quantitative Analysis of Sites of New DNA Integration
in Cellular Genomes
#MMPMID28344990
Sherman E
; Nobles C
; Berry CC
; Six E
; Wu Y
; Dryga A
; Malani N
; Male F
; Reddy S
; Bailey A
; Bittinger K
; Everett JK
; Caccavelli L
; Drake MJ
; Bates P
; Hacein-Bey-Abina S
; Cavazzana M
; Bushman FD
Mol Ther Methods Clin Dev
2017[Mar]; 4
(ä): 39-49
PMID28344990
show ga
Integration of new DNA into cellular genomes mediates replication of retroviruses
and transposons; integration reactions have also been adapted for use in human
gene therapy. Tracking the distributions of integration sites is important to
characterize populations of transduced cells and to monitor potential outgrow of
pathogenic cell clones. Here, we describe a pipeline for quantitative analysis of
integration site distributions named INSPIIRED (integration site pipeline for
paired-end reads). We describe optimized biochemical steps for site isolation
using Illumina paired-end sequencing, including new technology for suppressing
recovery of unwanted contaminants, then software for alignment, quality control,
and management of integration site sequences. During library preparation, DNAs
are broken by sonication, so that after ligation-mediated PCR the number of
ligation junction sites can be used to infer abundance of gene-modified cells. We
generated integration sites of known positions in silico, and we describe
optimization of sample processing parameters refined by comparison to truth. We
also present a novel graph-theory-based method for quantifying integration sites
in repeated sequences, and we characterize the consequences using synthetic and
experimental data. In an accompanying paper, we describe an additional set of
statistical tools for data analysis and visualization. Software is available at
https://github.com/BushmanLab/INSPIIRED.