The mapping results were compared to the known aberrations from karyotyping, FISH (Fluorescence in situ hybridization) analysis, array-CGH and RNA-panel sequencing (methods are described in [23 (link)]). Whole transcriptome sequencing (RNAseq) of diagnostic samples (in 5/12 patients, #1–5) was performed as a service at the Sequencing Core Facility of the Max Planck Institute for Molecular Genetics (Berlin, Germany) (Table 1 ). Sequencing libraries were prepared from DNA and total RNA using TruSeq kits (Illumina, San Diego, CA, USA) and sequenced on HiSeq2000 platform (Illumina, San Diego, CA, USA). The read pairs were aligned to the human genome reference hg19 using STAR (RNAseq) aligners and further processed by Picard tools (http://broadinstitute.github.io/picard/releases/tag/1.113 accessed on 29 August 2021).
We focus here on called SVs and CNVs, which are known to be clinically relevant or which may be clinically relevant based on their frequency in reference genomes but we will not address polymorphic regions according to DGV (http://dgv.tcag.ca/dgv/app/home , release date 25 February 2021). A selected number of SVs called in Bionano, but undetected by standard methods were validated by breakpoint-spanning PCR or FISH.
We focus here on called SVs and CNVs, which are known to be clinically relevant or which may be clinically relevant based on their frequency in reference genomes but we will not address polymorphic regions according to DGV (
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