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Conventional and Single-Molecule Targeted Sequencing Method for Specific Variant Detection in IKBKG while Bypassing the IKBKGP1 Pseudogene  Glynis Frans,

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Presentation on theme: "Conventional and Single-Molecule Targeted Sequencing Method for Specific Variant Detection in IKBKG while Bypassing the IKBKGP1 Pseudogene  Glynis Frans,"— Presentation transcript:

1 Conventional and Single-Molecule Targeted Sequencing Method for Specific Variant Detection in IKBKG while Bypassing the IKBKGP1 Pseudogene  Glynis Frans, Wim Meert, Jutte Van der Werff Ten Bosch, Isabelle Meyts, Xavier Bossuyt, Joris R. Vermeesch, Matthew S. Hestand  The Journal of Molecular Diagnostics  Volume 20, Issue 2, Pages (March 2018) DOI: /j.jmoldx Copyright © 2018 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

2 Figure 1 IKBKG (alias NEMO) locus on the X chromosome. Large arrows illustrate exons 1 and 2, as well as the duplicated exons 3 to 10. Smaller arrows F and R indicate the long-range primers used to target IKBKG and bypass IKBKGP1. Low copy repeats (LCR) 1 and 2 regions are indicated. Chr, chromosome. Reprinted with permission from Glynis Frans.2 The Journal of Molecular Diagnostics  , DOI: ( /j.jmoldx ) Copyright © 2018 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

3 Figure 2 Mapping results in the Integrative genomics viewer ( from reads aligned to the forced IKBKG reference and the hg38 reference IKBKG and IKBKGP1 loci. Because the pseudogene (hg38 IKBKGP1) is in the opposite orientation, its display has been mirrored for display purposes. Red arrows and green arrows illustrate two different examples of corresponding dips and peaks (with underlying single-nucleotide polymorphisms) owing to mis-mappings. White Illumina reads indicate poor mapping quality. Ill-mem, Illumina aligned with BWA-mem; PB-mem, PacBio aligned with BWA-mem; PB-sw, PacBio aligned with BWA-sw. The Journal of Molecular Diagnostics  , DOI: ( /j.jmoldx ) Copyright © 2018 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

4 Figure 3 Sensitivity and 1 − specificity plots from all single-nucleotide polymorphism results. Wrong zygosity calls were treated as false negatives. Either Sanger sequencing (Sanger) or the consensus standard (consensus) was used as the gold standard. FB, FreeBayes (circles); Hap, GATK HaplotypeCaller (triangles); Ill-mem (black), Illumina aligned with BWA-mem; PB-mem (red), PacBio aligned with BWA-mem; PB-sw (blue), PacBio aligned with BWA-sw; Uni, GATK Unified Genotyper (diamonds); Var, Varscan (squares). The Journal of Molecular Diagnostics  , DOI: ( /j.jmoldx ) Copyright © 2018 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

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