Optical Mapping of Genomic DNA Using Saphyr

Optical mapping was performed on genomic DNA from the proband by running dual enzymes (BspQI, BssSI) on the Bionano Genomics (San Diego, CA, USA) Saphyr platform (https://bionanogenomics.com/support-page/saphyr-system). Analysis was performed as described previously (Eisfeldt et al. 2019 (link)). Briefly, the optical maps were analyzed using Bionano-solve (Bionano-solve">https://bionanogenomics.com/support-page/Bionano-solve), aligned to Hg19 reference genome using Bionano RefAligner (version 5649) and output files were converted into VCF files using a custom script (https://github.com/J35P312/smap2vcf). Variants of interest were visualized in Bionano access.

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Eisfeldt J., Pettersson M., Petri A., Nilsson D., Feuk L, & Lindstrand A. (2020). Hybrid sequencing resolves two germline ultra-complex chromosomal rearrangements consisting of 137 breakpoint junctions in a single carrier. Human Genetics, 140(5), 775-790.

Publication 2020

Saphyr platform Bionano-solve RefAligner

Enzymes Genome Maps Optical

Corresponding Organization :

Other organizations : Karolinska University Hospital, Karolinska Institutet, Science for Life Laboratory, Uppsala University

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Variable analysis

independent variables

Enzyme used for optical mapping (BspQI, BssSI)
Bionano Genomics Saphyr platform

dependent variables

Optical maps generated from genomic DNA
Variants identified from the optical maps

control variables

Hg19 reference genome used for alignment
Bionano RefAligner (version 5649) used for alignment

controls

No positive or negative controls were explicitly mentioned in the provided information.

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