120 results found
Schafer V, White HE, Gerrard G, et al., 2021, Assessment of individual molecular response in chronic myeloid leukemia patients with atypical BCR-ABL1 fusion transcripts: recommendations by the EUTOS cooperative network, JOURNAL OF CANCER RESEARCH AND CLINICAL ONCOLOGY, ISSN: 0171-5216
Grant J, Stanley A, Balbi K, et al., 2021, Performance evaluation of the Biocartis Idylla EGFR Mutation Test using pre-extracted DNA from a cohort of highly characterised mutation positive samples., J Clin Pathol
AIMS: Targeted therapies for non-small cell lung carcinoma (NSCLC) rely on the detection of specific genomic lesions, such as mutations within the epidermal growth factor receptor (EGFR) gene. The Biocartis Idylla platform and single-use EGFR mutation test cartridge is CE-IVD for use with formalin-fixed paraffin embedded (FFPE) tumour material, but can also function off-scope using extracted DNA as input material. This can expand the utility of the platform and potentially conserve valuable tissue. METHODS: We sought to evaluate the performance of this system to detect known EGFR mutations using extracted DNA at different input levels. 130 next generation sequencing-characterised NSCLC cases possessing EGFR mutations that were theoretically detectable by the Idylla system were selected. Replicate analyses were performed using the Idylla EGFR test with up to three different DNA input levels (20 ng, 50 ng and 250 ng). RESULTS: Considering only variants within the test manufacturer's specified scope, the Idylla EGFR test generated concordant findings for 90.77% of cases at 20 ng DNA input, 98.46% at 50 ng input and 100% at 250 ng input. Analyses with discordant findings all generated control quantification cycle (CQ) values greater than 23. Very low CQ values were associated with EGFR gene amplification. CONCLUSIONS: The Idylla EGFR Mutation Test can be used at least as well with pre-extracted DNA than with direct FFPE input. In cases with control CQ >23, reanalysis with an increased DNA input should ideally be undertaken. If this is not possible, the risk of false negative calls may be mitigated by manual review of the quantitative PCR data and/or by reflexing to alternative analysis options.
Pfeifer H, Cazzaniga G, van der Velden VHJ, et al., 2020, Correction: Standardisation and consensus guidelines for minimal residual disease assessment in Philadelphia-positive acute lymphoblastic leukemia (Ph+ALL) by real-time quantitative reverse transcriptase PCR of e1a2 BCR-ABL1., Leukemia, Vol: 34
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Nteliopoulos G, Bazeos A, Claudiani S, et al., 2019, Somatic variants in epigenetic modifiers can predict failure of response to imatinib but not to second-generation tyrosine kinase inhibitors, Haematologica, Vol: 104, Pages: 2400-2409, ISSN: 0390-6078
There are no validated molecular biomarkers to identify newly-diagnosed individuals with chronic-phase chronic myeloid leukaemia likely to respond poorly to imatinib and who might benefit from first-line treatment with a more potent second-generation tyrosine kinase-inhibitor. Our inability to predict these 'high-risk' individuals reflects the poorly understood heterogeneity of the disease. To investigate the potential of genetic variants in epigenetic modifiers as biomarkers at diagnosis, we used Ion Torrent next-generation sequencing of 71 candidate genes for predicting response to tyrosine kinase-inhibitors and probability of disease progression. 124 subjects with newly-diagnosed chronic-phase chronic myeloid leukaemia began with imatinib (n=62) or second-generation tyrosine kinase-inhibitors (n=62) and were classified as responders or non-responders based on the BCRABL1 transcript levels within the first year and the European LeukemiaNet criteria for failure. Somatic variants affecting 21 genes (e.g. ASXL1, IKZF1, DNMT3A, CREBBP) were detected in 30% of subjects, most of whom were non-responders (41% non-responders, 18% responders to imatinib, 38% non-responders, 25% responders to second-generation tyrosine kinase-inhibitors). The presence of variants predicted the rate of achieving a major molecular response, event-free survival, progression-free survival and chronic-myeloid-leukaemia-related survival in the imatinib but not the second-generation tyrosine kinase-inhibitors cohort. Rare germline variants had no prognostic significance irrespective of treatment while some pre-leukaemia variants suggest a multi-step development of chronic myeloid leukaemia. Our data suggest that identification of somatic variants at diagnosis facilitates stratification into imatinib responders/non-responders, thereby allowing earlier use of second-generation tyrosine kinase-inhibitors, which, in turn, may overcome the negative impact of such variants on disease progression.
Pelka D, Grant J, Hansel S, et al., 2019, Methylation Sensitive High Resolution Melting (MS-HRM) Assay for the Detection of BRCA1 and BRCA2 Promoter Hypermethylation, Cancer Conference of the National-Cancer-Research-Institute (NCRI), Publisher: NATURE PUBLISHING GROUP, Pages: 14-14, ISSN: 0007-0920
Pfeifer H, Cazzaniga G, van der Velden VHJ, et al., 2019, Standardisation and consensus guidelines for minimal residual disease assessment in Philadelphia-positive acute lymphoblastic leukemia (Ph plus ALL) by real-time quantitative reverse transcriptase PCR of e1a2 BCR-ABL1, LEUKEMIA, Vol: 33, Pages: 1910-1922, ISSN: 0887-6924
Wang J, Gerrard G, Poskitt B, et al., 2019, Targeted next generation sequencing of pancreatic solid pseudopapillary neoplasms show mutations in Wnt signaling pathway genes, Pathology International, Vol: 69, Pages: 193-201, ISSN: 1320-5463
Solid pseudopapillary neoplasms of the pancreas are rare neoplasms that have been shown to harbor recurrent somatic pathogenic variants in the beta-catenin gene, CTNNB1. Here, we used targeted next generation sequencing to analyze these tumors for other associated mutations. Six cases of solid pseudopapillary neoplasms were studied. DNA extracted from formalin-fixed paraffin embedded tissue blocks was analyzed using the Ion Torrent platform, with the 50-gene Ampliseq Cancer Hotspot Panel v2 (CHPv2), with further variant validation performed by Sanger sequencing. Four tumors (67%) were confirmed to harbor mutations within CTNNB1, two with c.109T > G p.(Ser37Ala) and two with c.94G > A p.(Asp32Asn). One case showed a frameshift deletion in the Adenomatous Polyposis Coli gene, APC c.3964delG p.(Glu1322Lysfs*93) with a variant allele frequency of 42.6%. Sanger sequencing on non-tumoral tissue confirmed the variant was somatic. The patient with the APC mutation developed metastasis and died. In addition to the four cases harboring CTNNB1 variants, we found a case characterized by poor outcome, showing a rare frameshift deletion in the APC gene. Since the APC product interacts with beta-catenin, APC variants may, in addition to CTNNB1, contribute to the pathogenesis of solid pseudopapillary neoplasms via the Wnt signaling pathway.
Gall TMH, Gerrard G, Frampton AE, et al., 2019, Can we predict long-term survival in resectable pancreatic ductal adenocarcinoma?, Oncotarget, Vol: 10, Pages: 696-706, ISSN: 1949-2553
Objective: Pancreatic ductal adenocarcinoma (PDAC) is an aggressive tumour associated with poor 5-year survival. We aimed to determine factors which differentiate short and long-term survivors and identify a prognostic biomarker. Methods: Over a ten-year period, patients with resected PDAC who developed disease recurrence within 12 months (Group I) and those who had no disease recurrence for 24 months (Group II) were identified. Clinicopathological data was analysed. Ion Torrent high-throughput sequencing on DNA extracted from FFPE tumour samples was used to identify mutations. Additionally, peripheral blood samples were analysed for variants in cell-free DNA, circulating tumour cells (CTCs), and microRNAs. Results: Multivariable analysis of clinicopathological factors showed that a positive medial resection margin was significantly associated with short disease-free survival (p = 0.007). Group I patients (n = 21) had a higher frequency of the KRAS mutant mean variant allele (16.93% ± 11.04) compared to those in Group II (n = 13; 7.55% ± 5.76, p = 0.0078). Group I patients also trended towards having a KRAS c.35G>A p.Gly12Asp mutation in addition to variants in other genes, such as TP53, CDKN2A, and SMAD4. Mutational status of cell-free DNA, and number of CTCs, was not found to be useful in this study. A circulating miRNA (hsa-miR-548ah-5p) was found to be significantly differentially expressed. Conclusions: Medial resection margin status and the frequency of KRAS mutation in the tumour tissue are independent prognostic indicators for resectable PDAC. Circulating miRNA hsa-miR-548ah-5p has the potential to be used as a prognostic biomarker.
Warford A, Rahman M, Hughes JA, et al., 2019, Pushing the boundaries of in situ hybridisation for mRNA demonstration: demonstration of kappa and lambda light chain restriction in follicular lymphoma, BRITISH JOURNAL OF BIOMEDICAL SCIENCE, Vol: 76, Pages: 143-146, ISSN: 0967-4845
Banerjee SM, Acedo P, El Sheikh S, et al., 2019, Verteporfin Photodynamic therapy with 5 aza-deoxy-cytidine for neo-adjuvant treatment of primary breast cancer: Results of pre-clinical investigations, 17th World Congress of the International-Photodynamic-Association (IPA), Publisher: SPIE-INT SOC OPTICAL ENGINEERING, ISSN: 0277-786X
Alikian M, Ellwood R, Tatarinova O, et al., 2018, DNA-Based Digital PCR for the Quantification of Residual Disease in CML - Sensitivity or Specificity?, 60th Annual Meeting of the American-Society-of-Hematology (ASH), Publisher: AMER SOC HEMATOLOGY, ISSN: 0006-4971
Meecham AJ, Gerrard G, Costa H, et al., 2017, Evaluation of Nucleic Acid Performance and Preservation in Formalin-Free PAXGene Tissue Fixative: A Comparison to Formalin, 10th Joint Meeting of the British-Division of the International-Academy-of-Pathology and the Pathological-Society-of-Great-Britain-and-Ireland, Publisher: WILEY, Pages: S25-S25, ISSN: 0022-3417
Meecham AJ, Gerrard G, Costa H, et al., 2017, Implementation of Formalin-Free PAXGene Tissue Fixative into Routine Use: Evaluation of H&E Morphology, IHC and FISH, 10th Joint Meeting of the British-Division of the International-Academy-of-Pathology and the Pathological-Society-of-Great-Britain-and-Ireland, Publisher: WILEY, Pages: S26-S26, ISSN: 0022-3417
Schaefer V, Ernst T, Saussele S, et al., 2017, Assessment of molecular response in CML patients with atypical BCR-ABL1 transcripts. Recommendations by the EUTOS collaboration, Publisher: KARGER, Pages: 221-221, ISSN: 2296-5270
Nteliopoulos G, Bazeos A, Gerrard G, et al., 2016, Somatic Mutations in Epigenetic Modifiers Identified Using Next Generation Sequencing (NGS) in Diagnostic Samples of CML-CP Can Predict Poor Outcome on Imatinib Which Is Abrogated By Frontline 2G-TKI Therapy, 58th Annual Meeting and Exposition of the American-Society-of-Hematology (ASH), Publisher: AMER SOC HEMATOLOGY, ISSN: 0006-4971
Ernst T, Schafer V, White HE, et al., 2016, Assessment of Molecular Response in CML Patients with Atypical BCR-ABL Tanscripts. Recommendations By the EUTOS Collaboration, 58th Annual Meeting and Exposition of the American-Society-of-Hematology, Publisher: AMER SOC HEMATOLOGY, ISSN: 0006-4971
Wong CL, Innes AJ, Ma B, et al., 2016, Differential Expression of Genes Associated with Oncogene-Induced Senescence and Senescence Associated Secretory Phenotype in the Absence of Differential Expression of High Molecular Risk Genes and Genes Associated with JAK-STAT Pathway in Sorted Cells of Patients with Polycythemia Vera and Primary Myelofibrosis, 59th Annual Meeting and Exposition of the American-Society-of-Hematology (ASH)/Symposium on the Basic Science of Hemostasis and Thrombosis, Publisher: American Society of Hematology, Pages: 4283-4283, ISSN: 0006-4971
Schaefer V, Ernst T, Saussele S, et al., 2016, Assessment of molecular response in CML patients with atypical BCR-ABL1 transcripts. Recommendations by the EUTOS collaboration, Publisher: KARGER, Pages: 221-221, ISSN: 2296-5270
Cross NCP, White HE, Ernst T, et al., 2016, Development and evaluation of a secondary reference panel for BCR-ABL1 quantification on the International Scale, LEUKEMIA, Vol: 30, Pages: 1844-1852, ISSN: 0887-6924
Bond J, Domaschenz R, Roman-Trufero M, et al., 2016, Direct interaction of Ikaros and Foxp1 modulates expression of the G protein-coupled receptor G2A in B-lymphocytes and acute lymphoblastic leukemia, Oncotarget, Vol: 7, Pages: 65923-65936, ISSN: 1949-2553
Ikaros and Foxp1 are transcription factors that play key roles in normal lymphopoiesis and lymphoid malignancies. We describe a novel physical and functional interaction between the proteins, which requires the central zinc finger domain of Ikaros. The Ikaros-Foxp1 interaction is abolished by deletion of this region, which corresponds to the IK6 isoform that is commonly associated with high-risk acute lymphoblastic leukemia (ALL). We also identify the Gpr132 gene, which encodes the orphan G protein-coupled receptor G2A, as a novel target for Foxp1. Increased expression of Foxp1 enhanced Gpr132 transcription and caused cell cycle changes, including G2 arrest. Co-expression of wild-type Ikaros, but not IK6, displaced Foxp1 binding from the Gpr132 gene, reversed the increase in Gpr132 expression and inhibited G2 arrest. Analysis of primary ALL samples revealed a significant increase in GPR132 expression in IKZF1-deleted BCR-ABL negative patients, suggesting that levels of wild-type Ikaros may influence the regulation of G2A in B-ALL. Our results reveal a novel effect of Ikaros haploinsufficiency on Foxp1 functioning, and identify G2A as a potential modulator of the cell cycle in Ikaros-deleted B-ALL.
Gerrard G, Foong HE, Mudge K, et al., 2016, Cepheid xpert monitor platform for the confirmation of BCR-ABL1 IS conversion factors for the molecular monitoring of chronic myeloid leukaemia., Leukemia Research, Vol: 49, Pages: 47-50, ISSN: 1873-5835
Molecular monitoring of BCR-ABL1 expression in chronic myeloid leukaemia (CML) is well established. As the International Scale (IS) normalised BCR-ABL1/ABL1 ratio at 3 months post-treatment is now an important milestone in patients' treatment schedule, the reliable and reproducible measurement of BCR-ABL1 levels is therefore paramount. IS conversion factors (CF) are established via sample exchange and yearly ratification with an external reference laboratory. Since any change to an established IS CF could lead to discontinuity in longitudinal results, we wished to add an internal verification step as an additional safeguard. We used the Cepheid GeneXpert qPCR and IS calibrated Xpert BCR-ABL Monitor cartridge system, parallel to our in-house pipeline on 50 CML samples, over the period of one week to verify the CF for those samples and compare it to the externally provided CF. The median non-IS in-house BCR-ABL1/ABL1 values were significantly different than that from the IS GeneXpert, but they became non-significant when adjusted to CF provided by the CXM and by the current external CF, validating it. These metrics can help decide to accept or reject an updated CF value, especially where a significant change in CF might lead to a discontinuity in ongoing patient monitoring.
Nteliopoulos G, Bazeos A, Gerrard G, et al., 2016, PRESENCE OF SOMATIC AND GERMLINE MUTATIONS IN EPIGENETIC MODIFIERS IN CML-CP, 21st Congress of the European Hematology Association, Publisher: FERRATA STORTI FOUNDATION, Pages: 235-235, ISSN: 0390-6078
Wong CL, Gerrard G, Norziha ZA, et al., 2016, A prospective multicentre study of the demographic, molecular and clinical landscape of myeloproliferative neoplasm in a developing country, 36th World Congress of the International-Society-of-Hematology, Publisher: Wiley, Pages: 135-135, ISSN: 1365-2141
Gupta M, Costa H, Rathbone V, et al., 2016, How to Get the Most From FFPE, 205th Meeting of the Pathological-Society-of-Great-Britain-and-Ireland, Publisher: WILEY-BLACKWELL, Pages: S3-S3, ISSN: 0022-3417
Alikian MA, Peter Ellery PE, Martin Forbes MF, et al., 2016, Next-Generation Sequencing-Assisted DNA-Based Digital PCR for a Personalized Approach to the Detection and Quantification of Residual Disease in Chronic Myeloid Leukemia Patients, Journal of Molecular Diagnostics, Vol: 18, Pages: 176-189, ISSN: 1943-7811
Recent studies indicate that 40% of chronic myeloid leukemia patients who achieve sustained undetectable BCR-ABL1 transcripts on tyrosine kinase inhibitor therapy remain disease-free after drug discontinuation. In contrast, 60% experience return of detectable disease and have to restart treatment, thus highlighting the need for an improved method of identifying patients with the lowest likelihood of relapse. Here we describe the validation of a personalized DNA-based digital PCR (dPCR) approach for quantifying very low levels of residual disease, which involves the rapid identification of t(9;22) fusion junctions using targeted next-generation sequencing coupled with the use of a dPCR platform. t(9;22) genomic breakpoints were successfully mapped in samples from 32 of 32 patients with early stage disease. Disease quantification by DNA-based dPCR was performed using the Fluidigm BioMark platform on 46 follow-up samples from 6 of the 32 patients, including 36 samples that were in deep molecular remission. dPCR detected persistent disease in 81% of molecular-remission samples, outperforming both RT-dPCR (25%) and DNA-based quantitative PCR (19%). We conclude that dPCR for BCR-ABL1 DNA is the most sensitive available method of residual-disease detection in chronic myeloid leukemia and may prove useful in the management of tyrosine kinase inhibitor withdrawal.
Wong CL, Ma B, Adamowicz-Brice M, et al., 2015, DNA Methylation Profiling of Sorted Peripheral Blood Cells Using Microarray and Next Generation Sequencing Reveals Distinct Molecular Signatures in the Polymorphonuclear and Mononuclear Cells of Patients with Essential Thrombocythemia, Polycythemia Vera and Primary Myelofibrosis, 57th Annual Meeting of the American Society of Hematology, Publisher: American Society of Hematology, ISSN: 0006-4971
Wong CL, Ma B, Gerrard G, et al., 2015, Gene expression profiling of sorted peripheral blood cells using microarray and next generation sequencing reveals distinct molecular signatures in the polymorphonuclear and mononuclear cells of patients with polycythemia vera and primary myelofibrosis, 57th Annual Meeting of the American Society of Hematology, Publisher: American Society of Hematology, Pages: 5201-5201, ISSN: 0006-4971
Wong CL, Gerrard G, Adamowicz-Brice M, et al., 2015, Targeted sequencing of sorted peripheral blood cells reveals novel germline and somatic variants in the polymorphonuclear and mononuclear cells of patients with essential thrombocythemia, polycythemia vera and primary myelofibrosis, 57th Annual Meeting of the American Society of Hematology, Publisher: American Society of Hematology, Pages: 5213-5213, ISSN: 0006-4971
Claudiani S, Gupta N, Baik JS, et al., 2015, Excellent Outcome and Good Tolerability of Long-Term Imatinib in Patients with Chronic Myeloid Leukemia (CML), 57th Annual Meeting of the American-Society-of-Hematology, Publisher: AMER SOC HEMATOLOGY, ISSN: 0006-4971
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