Absence/presence calling in microarray-based CGH experiments with non-model organisms.
Structural variations in genomes are commonly studied by (micro)array-based comparative genomic hybridization. The data analysis methods to infer copy number variation in model organisms (human, mouse) are established. In principle, the procedures are based on signal ratios between test and reference samples and the order of the probe targets in the genome. These procedures are less applicable to experiments with non-model organisms, which frequently comprise non-sequenced genomes with an unknown order of probe targets. We therefore present an additional analysis approach, which does not depend on the structural information of a reference genome, and quantifies the presence or absence of a probe target in an unknown genome. The principle is that intensity values of target probes are compared with the intensities of negative-control probes and positive-control probes from a control hybridization, to determine if a probe target is absent or present. In a test, analyzing the genome content of a known bacterial strain: Staphylococcus aureus MRSA252, this approach proved to be successful, demonstrated by receiver operating characteristic area under the curve values larger than 0.9995. We show its usability in various applications, such as comparing genome content and validating next-generation sequencing reads from eukaryotic non-model organisms.
MicroArray Department & Integrative Bioinformatics Unit (MAD-IBU), Swammerdam Institute for Life Sciences (SILS), Faculty of Science (FNWI), University of Amsterdam (UvA), 1098 XH, Amsterdam, the Netherlands Netherlands Bioinformatics Centre (NBIC), 6525 GA, Nijmegen, the Netherlands.
Martijs J
MJ
Jonker
MicroArray Department & Integrative Bioinformatics Unit (MAD-IBU), Swammerdam Institute for Life Sciences (SILS), Faculty of Science (FNWI), University of Amsterdam (UvA), 1098 XH, Amsterdam, the Netherlands Netherlands Bioinformatics Centre (NBIC), 6525 GA, Nijmegen, the Netherlands.
Wim C
WC
de Leeuw
MicroArray Department & Integrative Bioinformatics Unit (MAD-IBU), Swammerdam Institute for Life Sciences (SILS), Faculty of Science (FNWI), University of Amsterdam (UvA), 1098 XH, Amsterdam, the Netherlands Department of Aquatic Ecology and Ecotoxicology, Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, the Netherlands.
Marino
M
Marinković
MicroArray Department & Integrative Bioinformatics Unit (MAD-IBU), Swammerdam Institute for Life Sciences (SILS), Faculty of Science (FNWI), University of Amsterdam (UvA), 1098 XH, Amsterdam, the Netherlands.
Floyd R A
FR
Wittink
MicroArray Department & Integrative Bioinformatics Unit (MAD-IBU), Swammerdam Institute for Life Sciences (SILS), Faculty of Science (FNWI), University of Amsterdam (UvA), 1098 XH, Amsterdam, the Netherlands Netherlands Bioinformatics Centre (NBIC), 6525 GA, Nijmegen, the Netherlands.
Han
H
Rauwerda
MicroArray Department & Integrative Bioinformatics Unit (MAD-IBU), Swammerdam Institute for Life Sciences (SILS), Faculty of Science (FNWI), University of Amsterdam (UvA), 1098 XH, Amsterdam, the Netherlands Netherlands Bioinformatics Centre (NBIC), 6525 GA, Nijmegen, the Netherlands.
Oskar
O
Bruning
MicroArray Department & Integrative Bioinformatics Unit (MAD-IBU), Swammerdam Institute for Life Sciences (SILS), Faculty of Science (FNWI), University of Amsterdam (UvA), 1098 XH, Amsterdam, the Netherlands.
Wim A
WA
Ensink
Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands.
Ad C
AC
Fluit
Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands.
C H
CH
Boel
MicroArray Department & Integrative Bioinformatics Unit (MAD-IBU), Swammerdam Institute for Life Sciences (SILS), Faculty of Science (FNWI), University of Amsterdam (UvA), 1098 XH, Amsterdam, the Netherlands.
Mark de
Md
Jong
MicroArray Department & Integrative Bioinformatics Unit (MAD-IBU), Swammerdam Institute for Life Sciences (SILS), Faculty of Science (FNWI), University of Amsterdam (UvA), 1098 XH, Amsterdam, the Netherlands Netherlands Bioinformatics Centre (NBIC), 6525 GA, Nijmegen, the Netherlands t.m.breit@uva.nl.
Timo M
TM
Breit
D000818:Animals; D055028:Comparative Genomic Hybridization / Q000379:methods*; D003627:Data Interpretation, Statistical; D056914:Genomic Structural Variation; D023281:Genomics; D059014:High-Throughput Nucleotide Sequencing; D008957:Models, Genetic; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D015345:Oligonucleotide Probes; D013211:Staphylococcus aureus / Q000235:genetics
D015345:Oligonucleotide Probes