The Bionano Genome Imaging workflow starts with mega-base size DNA isolation. A single enzymatic reaction labels the genome at a specific sequence motif occurring approximately 15 times per 100 kbp in the human genome. The long, labeled DNA molecules are linearized in nanochannel arrays on a Saphyr chip® and imaged in an extremely high throughput, automated manner by the Saphyr® Genome Imaging Instrument. Using pairwise alignments, the molecules are assembled into local maps or whole genome de novo assemblies. Changes in patterning or spacing of the labels are detected automatically, genome wide, to call all structural variants.

Identification of complex rearrangements in cancer often requires a combination of approaches and are typically performed sequentially. This sequential approach manages costs but increases the turn-around time and complicates understanding the genetic makeup of the sample. A leukemia sample presented a challenging karyogram, necessitating aCGH as a complement to validate t(1;2). Suspicion of a previously missed t(5;14) called for a FISH analysis. Results from karyotyping and FISH were inconclusive since the acceptor chromosome couldn’t be clearly identified. The two events were captured by Bionano in a single experiment and benign structural variants were automatically filtered out without complex pipelines.¹

1. Neveling K et al. bioRxiv 2020.02.06.935742

A team led by Dr. Alex Hoischen from Radboud University Medical Center (RUMC) in the Netherlands reported the results of a successful validation study comparing the performance of Bionano’s Saphyr to traditional cytogenetic methods for the clinical analysis of 48 leukemia genomes, with a combination of myeloid and lymphoid leukemias. Saphyr was 100% concordant with the standard of care for the detection of somatic chromosomal abnormalities. All previously reported aberrations were identified, and in the complex cases, Bionano allowed for a better resolution and a more complete picture of complex aberrations. A complex chromothripsis structure was resolved unambiguously and in other cases, additional fusions were identified, or marker chromosomes of unknown origin were resolved. Generally, Bionano results were more complete than all three individual previous tests and most likely delivered the true underlying genomic architecture.

A consortium led by Dr. Brynn Levy at Columbia, who validated chromosomal microarray for cytogenetic use, is leading an AML clinical benchmark study. The consortium includes Penn State University, Harvard University, The Pathgroup, Mayo Clinic, University of Washington, and others.

Dr. Alex Hoischen (RUMC), a pioneer in bringing new technologies to the clinic, and Dr. Laila El Khattabi (Cochin Hospital Paris) are leading a group of European labs performing a clinical validation on constitutional disorder testing.

Dr. Guillermo Garcia-Manero, head of MD Anderson’s AML & MDS Moon Shot Program and Dr. Rashmi Kanagal-Shamanna, director of the hematopathology microarray facility, are performing a clinical benchmark study on patients with Myelodysplastic Syndrome.

Dr. Ravi Kolhe from Augusta University who clinically validated several diagnostic assays is developing a Lab Developed Test for cancer based on leukemia and glioblastoma samples.

Dr. Eddy Maher from NHS Lothian in Edinburgh, who introduced chromosomal microarray in the UK clinics, is running a clinical validation for cytogenetic testing and NHS certification.