Dr. Gordana Raca from Children’s Hospital Los Angeles Presents Findings That Show Saphyr Detects Druggable Gene Fusions in Pediatric Acute Leukemias that NGS and Cytogenetics Missed
Leukemia accounts for more than a quarter of cancer cases in children and remains the second leading cause of cancer death. Karyotyping and fluorescent in situ hybridization (FISH) do not efficiently detect genetic subtypes, so Children’s Hospital Los Angeles (CHLA) currently combines four different methods to characterize their patients’ leukemia genomes: karyotyping, extensive FISH panels, chromosomal microarray (CMA), and a custom-designed NGS gene panel for pediatric cancers called OncoKids. Still, 15% of pediatric Acute Lymphoblastic Leukemia (ALL) cases showed no main genetic driver after those four tests.
The study analyzed one Acute Myeloid Leukemia (AML) case and eight ALL cases which had normal karyotypes and tested negative for commonly known genetic drivers by the standard of care in leukemia testing. Among Dr. Raca’s findings was that Saphyr detected gene fusions that aided in patient stratification and prognosis, including one gene fusion that can be treated with drugs such as Gleevec. The gene fusions were missed by the traditional techniques because they either had not been reported in pediatric cancer before and were therefore not part of the OncoKids NGS panel, or because they were simply undetectable by standard methods. In seven out of eight cases, OGM detected SVs that CHLA’s four separate analysis methods missed. OGM was also able to identify the exact copy number, location and orientation of a repeat in the PAX5 gene that defines a novel ALL subtype, which other methods were unable to do.
A recording of the presentation by
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Source: Bionano Genomics