MTTE: an innovative strategy for the evaluation of targeted/exome enrichment efficiency
| Autor: | Katarzyna Klonowska, Piotr Kozlowski, Luiza Handschuh, Aleksandra Swiercz, Marek Figlerowicz |
|---|---|
| Rok vydání: | 2016 |
| Předmět: |
next generation sequencing
0301 basic medicine Genetics Gene Expression Profiling capillary electrophoresis Electrophoresis Capillary High-Throughput Nucleotide Sequencing Computational biology Biology MLPA 03 medical and health sciences 030104 developmental biology Oncology MTTE exome enrichment Humans Exome Multiplex Multiplex ligation-dependent probe amplification Multiplex Polymerase Chain Reaction Research Paper |
| Zdroj: | Oncotarget |
| ISSN: | 1949-2553 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|