Molecular Inversion Probes for targeted resequencing in non-model organisms

Applications that require resequencing of hundreds or thousands of predefined genomic regions in numerous samples are common in studies of non-model organisms. However few approaches at the scale intermediate between multiplex PCR and sequence capture methods are available. Here we explored the util...

Full description

Saved in:
Bibliographic Details
Published in:Scientific reports 2016-04, Vol.6 (1), p.24051-24051, Article 24051
Main Authors: Niedzicka, M., Fijarczyk, A., Dudek, K., Stuglik, M., Babik, W.
Format: Article
Language:English
Subjects:
631/158/2452
631/181/457
Algorithms
Animals
Binding sites
Crosses, Genetic
DNA probes
Exons
Experiments
Gene expression
Genes
Genetic Markers - genetics
Genomes
Genomics
Genotype
Genotyping
Humanities and Social Sciences
Hybridization
multidisciplinary
Organisms
Performance assessment
Polymerase Chain Reaction
Polymorphism, Single Nucleotide
Probes
Salamandridae - genetics
Science
Science (multidisciplinary)
Sensitivity and Specificity
Sequence Analysis, DNA - methods
Software
Temperature
Transcriptome
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary:Applications that require resequencing of hundreds or thousands of predefined genomic regions in numerous samples are common in studies of non-model organisms. However few approaches at the scale intermediate between multiplex PCR and sequence capture methods are available. Here we explored the utility of Molecular Inversion Probes (MIPs) for the medium-scale targeted resequencing in a non-model system. Markers targeting 112 bp of exonic sequence were designed from transcriptome of Lissotriton newts. We assessed performance of 248 MIP markers in a sample of 85 individuals. Among the 234 (94.4%) successfully amplified markers 80% had median coverage within one order of magnitude, indicating relatively uniform performance; coverage uniformity across individuals was also high. In the analysis of polymorphism and segregation within family, 77% of 248 tested MIPs were confirmed as single copy Mendelian markers. Genotyping concordance assessed using replicate samples exceeded 99%. MIP markers for targeted resequencing have a number of advantages: high specificity, high multiplexing level, low sample requirement, straightforward laboratory protocol, no need for preparation of genomic libraries and no ascertainment bias. We conclude that MIP markers provide an effective solution for resequencing targets of tens or hundreds of kb in any organism and in a large number of samples.
ISSN:2045-2322
2045-2322
DOI:10.1038/srep24051