Contributions
Abstract: PB1698
Type: Publication Only
Background
The 100,000 Genomes Project in England is an initiative to sequence 100,000 genomes from patients with rare disease and cancer. One of the goals of the Cancer Programme is transformation with the aim of creating and embedding clinical pathways into National Health Service (NHS) care allowing cancer patients in the future, equitable and rapid access to Whole Genome Sequencing (WGS) which has the potential to simultaneously detect all types of variant and new predicative biomarkers such as mutational signatures. During 2017 eligibility for the Project was widened to include patients with haematological malignancies. Although there is a long track record of genetic analysis of both liquid and solid haematological tumours to aid diagnosis and therapy choice, significant clinical pathway adaptions are required to provide appropriate material for WGS.
Aims
For solid haematological tumours adaptions have mainly focused around the need to provide tumour DNA of sufficient quantity and quality for WGS which has driven the collection of fresh frozen samples from tumour types which would normally be processed in formalin (e.g. lymphoma). For liquid haematological cancers where it is usually possible to obtain good quality (unfixed) tumour DNA from blood or bone marrow, the challenge lies with the collection of suitable samples for germline (GL) DNA. It is usual practice in cancer WGS to sequence tumour and GL DNA samples to allow GL variants to be subtracted from the tumour sequence aiding the interpretation of somatic variants. For most cancer types a blood sample can be used as the source of GL DNA. However, collecting an equivalent GL sample from patients with many subtypes of haematological malignancy is difficult: if malignant cells are present in the blood or bone marrow, leucocyte DNA is unsuitable as it may contain tumour-specific acquired genetic changes.
Methods
Alternative GL DNA sources used in research include salvia, cultured fibroblasts from skin biopsies or post treatment blood taken once malignant cells have been cleared. The main disadvantages of these are potential tumour contamination and/or the delay between obtaining the tumour sample and the GL sample which would be problematic if WGS is to be used in diagnostic pathways.
Results
Work has been carried out to optimise the source of GL DNA for each type of haematological malignancy and appropriate solutions have been adopted. These include DNA extracted from saliva which has been collected post chemotherapy (once myeloid cells have been cleared from the blood) and cultured fibroblasts, often considered the ‘gold standard’ GL source. Measures to mitigate the effect of delayed GL collection include a two-step WGS analysis approach where the sequence is initially analysed using a reference GL sequence to identify urgent prognostic and diagnostic markers with subsequent more comprehensive analysis performed when the patient GL DNA is available. Additional studies have explored the practicality of using DNA extracted from sorted T cells for GL DNA which can be obtained at the time of diagnosis without incurring delays. This includes ensuring that sufficient T cell DNA of suitable purity can be robustly obtained and if the potential presence of genomic variants associated with clonal haematopoiesis of indeterminate potential (CHIP) would be compatible with current WGS analysis pipelines.
Conclusion
Due to this work we are now seeing the development of viable clinical pathways which will ensure that NHS patients with haematological malignancies can benefit from the diagnostic and therapeutic potential of WGS.
Session topic: 3. Acute myeloid leukemia - Biology & Translational Research
Keyword(s): Diagnosis, Genomics, Molecular markers
Abstract: PB1698
Type: Publication Only
Background
The 100,000 Genomes Project in England is an initiative to sequence 100,000 genomes from patients with rare disease and cancer. One of the goals of the Cancer Programme is transformation with the aim of creating and embedding clinical pathways into National Health Service (NHS) care allowing cancer patients in the future, equitable and rapid access to Whole Genome Sequencing (WGS) which has the potential to simultaneously detect all types of variant and new predicative biomarkers such as mutational signatures. During 2017 eligibility for the Project was widened to include patients with haematological malignancies. Although there is a long track record of genetic analysis of both liquid and solid haematological tumours to aid diagnosis and therapy choice, significant clinical pathway adaptions are required to provide appropriate material for WGS.
Aims
For solid haematological tumours adaptions have mainly focused around the need to provide tumour DNA of sufficient quantity and quality for WGS which has driven the collection of fresh frozen samples from tumour types which would normally be processed in formalin (e.g. lymphoma). For liquid haematological cancers where it is usually possible to obtain good quality (unfixed) tumour DNA from blood or bone marrow, the challenge lies with the collection of suitable samples for germline (GL) DNA. It is usual practice in cancer WGS to sequence tumour and GL DNA samples to allow GL variants to be subtracted from the tumour sequence aiding the interpretation of somatic variants. For most cancer types a blood sample can be used as the source of GL DNA. However, collecting an equivalent GL sample from patients with many subtypes of haematological malignancy is difficult: if malignant cells are present in the blood or bone marrow, leucocyte DNA is unsuitable as it may contain tumour-specific acquired genetic changes.
Methods
Alternative GL DNA sources used in research include salvia, cultured fibroblasts from skin biopsies or post treatment blood taken once malignant cells have been cleared. The main disadvantages of these are potential tumour contamination and/or the delay between obtaining the tumour sample and the GL sample which would be problematic if WGS is to be used in diagnostic pathways.
Results
Work has been carried out to optimise the source of GL DNA for each type of haematological malignancy and appropriate solutions have been adopted. These include DNA extracted from saliva which has been collected post chemotherapy (once myeloid cells have been cleared from the blood) and cultured fibroblasts, often considered the ‘gold standard’ GL source. Measures to mitigate the effect of delayed GL collection include a two-step WGS analysis approach where the sequence is initially analysed using a reference GL sequence to identify urgent prognostic and diagnostic markers with subsequent more comprehensive analysis performed when the patient GL DNA is available. Additional studies have explored the practicality of using DNA extracted from sorted T cells for GL DNA which can be obtained at the time of diagnosis without incurring delays. This includes ensuring that sufficient T cell DNA of suitable purity can be robustly obtained and if the potential presence of genomic variants associated with clonal haematopoiesis of indeterminate potential (CHIP) would be compatible with current WGS analysis pipelines.
Conclusion
Due to this work we are now seeing the development of viable clinical pathways which will ensure that NHS patients with haematological malignancies can benefit from the diagnostic and therapeutic potential of WGS.
Session topic: 3. Acute myeloid leukemia - Biology & Translational Research
Keyword(s): Diagnosis, Genomics, Molecular markers