Contributions
Abstract: PB1369
Type: Publication Only
Session title: Acute lymphoblastic leukemia - Clinical
Background
Cytogenetics has led to the discovery of multiple chromosomal anomalies associated with hemato-oncologic diseases in children and adolescents. From its beginning till now, and with the contribution of the molecular biology, there has been an improvement of the classic cytogenetic that allow cytogenetists to perform a more precise diagnosis. The introduction of next generation sequencing (NGS) has dramatically changed the way clinical molecular laboratories analyze their samples over the past 10 years, but for most clinical cytogenetic analyses a combination of karyotyping (KT), fluorescence in situ hybridization (FISH) and CNV-microarrays are still performed to detect genetic biomarkers of disease. Each of these tests has its own limitations such as maximum banding resolution (KT), knowledge of which loci to test and is limited in throughput (FISH) and lacking the ability to identify balanced chromosomal aberrations, to map gained material or nor are able to detect mosaicism lower than 5-20% (CNV-microarrays). These conventional cytogenetic techniques allow the detection of Structural variants (SV) significantly contributing to the discovery of disease causing genes are part of the routine diagnostic workflow in any tertiary hospital in the national health system. This is especially important in a center such as Hospital Infantil Universitario Niño Jesús, which cares for children and adolescents, populations in which rare genetic-based diseases are added to hemato-oncological pathology, for which genetic diagnosis is essential during the diagnostic phase. Recently, genome-imaging of extremely long linear molecules by optical genome mapping (OGM) to detect SVs and copy number variants (CNVs) has emerged as an efficient technology to replace the conventional cytogenetic diagnostic techniques improving the limitations mentioned above.
Aims
Our main objective was performed a clinical validation study of Acute lymphoblastic and myeloid leukaemia samples by (OGM) using Bionano Saphyr platform previously analysed using karyotyping, FISH and/or CNV-microarrays. Moreover, we proposed to identify new cytogenetic alterations related to paediatric diseases not previously detected by current methodologies.
Methods
Bone marrow aspirates and frozen cell samples at diagnosis of patients with leukaemia were processed for OGM with the Bionano Genomics Saphyr System. In brief, the ultra-high molecular weight (UHMW) gDNA from children and adolescent samples was extracted, labelled and loaded onto Bionano chip to perform a run in Saphyr platform. Then, the data collection was analysed and the results were validated and statistically analysed. Finally, novel findings by OGM were examined.
Results
We obtained not only a full concordance with previously diagnostic results obtained by conventional cytogenetic techniques but also we described novel structural variants missed by the other methods which could play an important role for the outcome of the leukaemia disease.
Conclusion
The analysis of SV and CNV by OGM emerge as a powerful tool in cytogenetic laboratories improving the pediatric routine diagnosis of Acute Leukemia both in children and adolescents.
Keyword(s): Acute leukemia, Cytogenetics, Diagnosis, Pediatric
Abstract: PB1369
Type: Publication Only
Session title: Acute lymphoblastic leukemia - Clinical
Background
Cytogenetics has led to the discovery of multiple chromosomal anomalies associated with hemato-oncologic diseases in children and adolescents. From its beginning till now, and with the contribution of the molecular biology, there has been an improvement of the classic cytogenetic that allow cytogenetists to perform a more precise diagnosis. The introduction of next generation sequencing (NGS) has dramatically changed the way clinical molecular laboratories analyze their samples over the past 10 years, but for most clinical cytogenetic analyses a combination of karyotyping (KT), fluorescence in situ hybridization (FISH) and CNV-microarrays are still performed to detect genetic biomarkers of disease. Each of these tests has its own limitations such as maximum banding resolution (KT), knowledge of which loci to test and is limited in throughput (FISH) and lacking the ability to identify balanced chromosomal aberrations, to map gained material or nor are able to detect mosaicism lower than 5-20% (CNV-microarrays). These conventional cytogenetic techniques allow the detection of Structural variants (SV) significantly contributing to the discovery of disease causing genes are part of the routine diagnostic workflow in any tertiary hospital in the national health system. This is especially important in a center such as Hospital Infantil Universitario Niño Jesús, which cares for children and adolescents, populations in which rare genetic-based diseases are added to hemato-oncological pathology, for which genetic diagnosis is essential during the diagnostic phase. Recently, genome-imaging of extremely long linear molecules by optical genome mapping (OGM) to detect SVs and copy number variants (CNVs) has emerged as an efficient technology to replace the conventional cytogenetic diagnostic techniques improving the limitations mentioned above.
Aims
Our main objective was performed a clinical validation study of Acute lymphoblastic and myeloid leukaemia samples by (OGM) using Bionano Saphyr platform previously analysed using karyotyping, FISH and/or CNV-microarrays. Moreover, we proposed to identify new cytogenetic alterations related to paediatric diseases not previously detected by current methodologies.
Methods
Bone marrow aspirates and frozen cell samples at diagnosis of patients with leukaemia were processed for OGM with the Bionano Genomics Saphyr System. In brief, the ultra-high molecular weight (UHMW) gDNA from children and adolescent samples was extracted, labelled and loaded onto Bionano chip to perform a run in Saphyr platform. Then, the data collection was analysed and the results were validated and statistically analysed. Finally, novel findings by OGM were examined.
Results
We obtained not only a full concordance with previously diagnostic results obtained by conventional cytogenetic techniques but also we described novel structural variants missed by the other methods which could play an important role for the outcome of the leukaemia disease.
Conclusion
The analysis of SV and CNV by OGM emerge as a powerful tool in cytogenetic laboratories improving the pediatric routine diagnosis of Acute Leukemia both in children and adolescents.
Keyword(s): Acute leukemia, Cytogenetics, Diagnosis, Pediatric