Titel: Optical Mapping – Comprehensive Detection of structural genomic variants
ID: W8-005
Art: Invited talk
Redezeit: 15 min
Session: Workshop 8
(Epi-)Genomics and Cancer

Referent: Udo Koehler (München/DE)

Abstract - Text


Optical Genome Mapping (OGM) is a whole genome approach used to identify structural genomic variants (SVs). It can be applied for evaluation of individuals with constitutional disorders such as developmental delay/intellectual disability/congenital anomalies, and any other structural variation of the genome and detects structural variants which may be missed by Next-Generation Sequencing or cytogenetic methods. Variants include unbalanced (copy number gains and losses) as well as balanced genomic structural aberrations (e.g. inversions, insertions, translocations). Interstitial deletions can be detect at a resolution as precise as 500 base pairs.Further, OMG can be applied to detect repeat expansion (e.g. FMR1), and repeat contraction, such as D4Z4 in FSHD. To investigate these structural variations, very high molecular weight DNA (250 kb on average) is extracted from EDTA blood or tissue samples stored at -80°C. After direct fluorophore labelling and staining of specific sequence motifs of single DNA molecules, sample is loaded on flow cells containing nanochannels in which labelled DNA molecules are uncoiled and scanned with a laser (Saphyr, Bionano). Molecules are aligned de novo to a reference genome for constructing consensus genome maps, which are then visualised through software Access (Bionano). Since June 2021, MGZ applied Optical Mapping for the detection of a plurality of genomic variants in up-to-date (Dec., 1st.2021) 51 patients. Indications include: copy number loss (9 patients), copy number gains (8), complex insertion (1), balanced translocation (5), hereditary cancer genes (5), FSHD (3), miscellaneous genes (10), balanced microarray results (10). OMG not only depicts chromosome and genomic position of copy number gains, but also its orientation (direct or inverted). In cases of apparently balanced translocations it uncovers the exact breakpoints and involvement of breakpoint genes. In a patient with an insertion (18;13) it precised breakpoints of the inserted segment, further it depicts an inversion of the inserted segment and a small deletion in one of the breakpoints. In a case of Familial Adenomatous Polyposis (FAP) it uncovers highly complex genomic structural variants (insertion/deletion/inversion), thus solving a long time open case of genetic cause of FAP. For FSHD cases, Optical Mapping, demonstrates the number of D4Z4 repeats, whereas hypomethylation detection of D4Z4 is currently not available. To conclude, Optical Mapping is an excellent tool for the detection of structural genomic variants thus closing the gap between karyotyping, Fluorescence-in situ hybridisation, chromosomal microarray analysis, short read Next-Generation sequencing, and targeted long read sequencing.