Oncotarget

Research Papers:

MTTE: an innovative strategy for the evaluation of targeted/exome enrichment efficiency

Katarzyna Klonowska, Luiza Handschuh, Aleksandra Swiercz, Marek Figlerowicz and Piotr Kozlowski _

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Oncotarget. 2016; 7:67266-67276. https://doi.org/10.18632/oncotarget.11646

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Abstract

Katarzyna Klonowska1, Luiza Handschuh1,2, Aleksandra Swiercz1,3, Marek Figlerowicz1,3, Piotr Kozlowski1,4

1European Centre for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland

2Department of Hematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, 60-569 Poznan, Poland

3Institute of Computing Science, Poznan University of Technology, 60-965 Poznan, Poland

4Institute of Technology and Chemical Engineering, Poznan University of Technology, 60-965 Poznan, Poland

Correspondence to:

Piotr Kozlowski, email: kozlowp@yahoo.com

Keywords: MTTE, exome enrichment, next generation sequencing, MLPA, capillary electrophoresis

Received: May 15, 2016     Accepted: July 28, 2016     Published: August 27, 2016

ABSTRACT

Although currently available strategies for the preparation of exome-enriched libraries are well established, a final validation of the libraries in terms of exome enrichment efficiency prior to the sequencing step is of considerable importance. Here, we present a strategy for the evaluation of exome enrichment, i.e., the Multipoint Test for Targeted-enrichment Efficiency (MTTE), PCR-based approach utilizing multiplex ligation-dependent probe amplification with capillary electrophoresis separation. We used MTTE for the analysis of subsequent steps of the Illumina TruSeq Exome Enrichment procedure. The calculated values of enrichment-associated parameters (i.e., relative enrichment, relative clearance, overall clearance, and fold enrichment) and the comparison of MTTE results with the actual enrichment revealed the high reliability of our assay. Additionally, the MTTE assay enabled the determination of the sequence-associated features that may confer bias in the enrichment of different targets. Importantly, the MTTE is low cost method that can be easily adapted to the region of interest important for a particular project. Thus, the MTTE strategy is attractive for post-capture validation in a variety of targeted/exome enrichment NGS projects.


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