Fast and sensitive detection of indels induced by precise gene targeting

Zhang Yang; Catharina Steentoft; Camilla Hauge; Lars Hansen; Allan Lind Thomsen; Francesco Niola; Malene B Vester-Christensen; Morten Frödin; Henrik Clausen; Hans H Wandall; Eric P Bennett

doi:10.1093/nar/gkv126

Fast and sensitive detection of indels induced by precise gene targeting

Zhang Yang, Catharina Steentoft, Camilla Hauge, Lars Hansen, Allan Lind Thomsen, Francesco Niola, Malene B Vester-Christensen, Morten Frödin, Henrik Clausen, Hans H Wandall, Eric P Bennett

83 Citationer (Scopus)

Abstract

The nuclease-based gene editing tools are rapidly transforming capabilities for altering the genome of cells and organisms with great precision and in high throughput studies. A major limitation in application of precise gene editing lies in lack of sensitive and fast methods to detect and characterize the induced DNA changes. Precise gene editing induces double-stranded DNA breaks that are repaired by error-prone non-homologous end joining leading to introduction of insertions and deletions (indels) at the target site. These indels are often small and difficult and laborious to detect by traditional methods. Here we present a method for fast, sensitive and simple indel detection that accurately defines indel sizes down to ±1 bp. The method coined IDAA for Indel Detection by Amplicon Analysis is based on tri-primer amplicon labelling and DNA capillary electrophoresis detection, and IDAA is amenable for high throughput analysis.

Originalsprog	Engelsk
Artikelnummer	e59
Tidsskrift	Nucleic Acids Research
Vol/bind	43
Udgave nummer	9
Sider (fra-til)	1-8
Antal sider	8
ISSN	0305-1048
DOI	https://doi.org/10.1093/nar/gkv126
Status	Udgivet - 19 maj 2015

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10.1093/nar/gkv126Licens: CC BY

Citationsformater

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abstract = "The nuclease-based gene editing tools are rapidly transforming capabilities for altering the genome of cells and organisms with great precision and in high throughput studies. A major limitation in application of precise gene editing lies in lack of sensitive and fast methods to detect and characterize the induced DNA changes. Precise gene editing induces double-stranded DNA breaks that are repaired by error-prone non-homologous end joining leading to introduction of insertions and deletions (indels) at the target site. These indels are often small and difficult and laborious to detect by traditional methods. Here we present a method for fast, sensitive and simple indel detection that accurately defines indel sizes down to ±1 bp. The method coined IDAA for Indel Detection by Amplicon Analysis is based on tri-primer amplicon labelling and DNA capillary electrophoresis detection, and IDAA is amenable for high throughput analysis.",

author = "Zhang Yang and Catharina Steentoft and Camilla Hauge and Lars Hansen and Thomsen, {Allan Lind} and Francesco Niola and Vester-Christensen, {Malene B} and Morten Fr{\"o}din and Henrik Clausen and Wandall, {Hans H} and Bennett, {Eric P}",

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AU - Yang, Zhang

AU - Steentoft, Catharina

AU - Hauge, Camilla

AU - Hansen, Lars

AU - Thomsen, Allan Lind

AU - Niola, Francesco

AU - Vester-Christensen, Malene B

AU - Frödin, Morten

AU - Clausen, Henrik

AU - Wandall, Hans H

AU - Bennett, Eric P

PY - 2015/5/19

Y1 - 2015/5/19

N2 - The nuclease-based gene editing tools are rapidly transforming capabilities for altering the genome of cells and organisms with great precision and in high throughput studies. A major limitation in application of precise gene editing lies in lack of sensitive and fast methods to detect and characterize the induced DNA changes. Precise gene editing induces double-stranded DNA breaks that are repaired by error-prone non-homologous end joining leading to introduction of insertions and deletions (indels) at the target site. These indels are often small and difficult and laborious to detect by traditional methods. Here we present a method for fast, sensitive and simple indel detection that accurately defines indel sizes down to ±1 bp. The method coined IDAA for Indel Detection by Amplicon Analysis is based on tri-primer amplicon labelling and DNA capillary electrophoresis detection, and IDAA is amenable for high throughput analysis.

AB - The nuclease-based gene editing tools are rapidly transforming capabilities for altering the genome of cells and organisms with great precision and in high throughput studies. A major limitation in application of precise gene editing lies in lack of sensitive and fast methods to detect and characterize the induced DNA changes. Precise gene editing induces double-stranded DNA breaks that are repaired by error-prone non-homologous end joining leading to introduction of insertions and deletions (indels) at the target site. These indels are often small and difficult and laborious to detect by traditional methods. Here we present a method for fast, sensitive and simple indel detection that accurately defines indel sizes down to ±1 bp. The method coined IDAA for Indel Detection by Amplicon Analysis is based on tri-primer amplicon labelling and DNA capillary electrophoresis detection, and IDAA is amenable for high throughput analysis.

U2 - 10.1093/nar/gkv126

DO - 10.1093/nar/gkv126

M3 - Journal article

C2 - 25753669

SN - 0305-1048

VL - 43

SP - 1

EP - 8

JO - Nucleic Acids Research

JF - Nucleic Acids Research

IS - 9

M1 - e59

ER -

Fast and sensitive detection of indels induced by precise gene targeting

Abstract

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