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Lavrichenko K, Helgeland Ø, Njølstad PR, et al. SeeCiTe: a method to assess CNV calls from SNP arrays using trio data. Bioinformatics. 2021;doi: 10.1093/bioinformatics/btab028.
Lavrichenko, K., Helgeland, �. �., Njølstad, P. R., Jonassen, I., & Johansson, S. (2021). SeeCiTe: a method to assess CNV calls from SNP arrays using trio data. Bioinformatics (Oxford, England), . https://doi.org/10.1093/bioinformatics/btab028
Lavrichenko, Ksenia, et al. "SeeCiTe: a method to assess CNV calls from SNP arrays using trio data." Bioinformatics (Oxford, England) vol. (2021). doi: https://doi.org/10.1093/bioinformatics/btab028
Lavrichenko K, Helgeland Ø, Njølstad PR, Jonassen I, Johansson S. SeeCiTe: a method to assess CNV calls from SNP arrays using trio data. Bioinformatics. 2021 Jan 18; doi: 10.1093/bioinformatics/btab028. Epub 2021 Jan 18. PMID: 33459766; PMCID: PMC8317106.
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Bioinformatics. 2021 Jan 18; doi: 10.1093/bioinformatics/btab028. Epub 2021 Jan 18.

SeeCiTe: a method to assess CNV calls from SNP arrays using trio data.

Bioinformatics (Oxford, England)

Ksenia Lavrichenko, Øyvind Helgeland, Pål R Njølstad, Inge Jonassen, Stefan Johansson

Affiliations

  1. Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway.
  2. Department of Clinical Science, University of Bergen, Bergen, Norway.
  3. Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway.
  4. Department of Pediatrics and Adolescents, Haukeland University Hospital, Bergen, Norway.
  5. Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway.

PMID: 33459766 PMCID: PMC8317106 DOI: 10.1093/bioinformatics/btab028

Abstract

MOTIVATION: Single nucleotide polymorphism (SNP) genotyping arrays remain an attractive platform for assaying copy number variants (CNVs) in large population-wide cohorts. However current tools for calling CNVs are still prone to extensive false positive calls when applied to biobank scale arrays. Moreover, there is a lack of methods exploiting cohorts with trios available (e.g. nuclear family) to assist in quality control and downstream analyses following the calling.

RESULTS: We developed SeeCiTe (Seeing Cnvs in Trios), a novel CNV quality control tool that post-processes output from current CNV calling tools exploiting child-parent trio data to classify calls in quality categories and provide a set of visualizations for each putative CNV call in the offspring. We apply it to the Norwegian Mother, Father, and Child Cohort Study (MoBa) and show that SeeCiTe improves the specificity and sensitivity compared to the common empiric filtering strategies. To our knowledge it is the first tool that utilizes probe-level CNV data in trios (and singletons) to systematically highlight potential artefacts and visualize signal intensities in a streamlined fashion suitable for biobank scale studies.

AVAILABILITY AND IMPLEMENTATION: The software is implemented in R with the source code freely available at https://github.com/aksenia/SeeCiTe.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

© The Author(s) 2021. Published by Oxford University Press.

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