Analysis Of Hematologic Malignancies Research Articles

Abstract 2931: Optical genome mapping workflow for identification and annotation of variants in hematological diseases

Abstract Guidelines from WHO, NCCN and others, for the genetic analysis of hematological malignancies included structural variation analysis. Traditionally, this has relied on a combination of three cytogenetic technologies for structural variation analysis: karyotyping, FISH, and microarray, are used to detect copy number variants, translocations, inversions. Next generation sequencing is also applied for mutation analysis but has not been successful for structural variation analysis. These traditional methods have many very manual aspects and require extensive expertise. Optical genome mapping (OGM) consolidates assays into a single laboratory assay in which the output provides the visualization of structural and copy number variants at one time. OGM is able to comprehensively detect structural variations genome wide down to 5% variant allele fraction for CNVs, inversions, and translocations from blood and bone marrow aspirates making it an attractive choice for hematologic malignancy genomic analysis. Preanalytical and analytical steps require approximately 4-5 days from sample to processed data with structural variation calls. Dynamic filtering in the user interface can be configured to remove most polymorphic variants and prioritize relevant variants. In addition, the OGM graphical user interface software, Bionano Access 1.7, allows for the user to assign classification/relevance to the variants for each case. For example, an ALL sample with t(9;22), deletion of CDKN2A, and whole chromosome gains of 4,6, and 10 can be easily visualized with the Circos plot and, then, can be further examined and annotated as needed. A second analyst can repeat the process blind to the first analysis and a supervisor can adjudicate the classifications. A variety of cases with hallmark abnormalities from various leukemias will be presented with the filtering and prioritization workflow used to derive them. This comprehensive technology allows for a quicker, more reliable output than traditional cytogenetic approaches. Citation Format: Jennifer Hauenstein, Andy Pang, Alka Chaubey, Alex Hastie. Optical genome mapping workflow for identification and annotation of variants in hematological diseases [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2931.

PO-52 Immunophenotypic analysis of haematological malignancies in a Pakistani population: a step towards formulation of hospital cancer registry

PO-52 Immunophenotypic analysis of haematological malignancies in a Pakistani population: a step towards formulation of hospital cancer registry

49. Whole genome optical mapping: A high-resolution technology for cytogenetic analysis of hematological malignancies (HM)

49. Whole genome optical mapping: A high-resolution technology for cytogenetic analysis of hematological malignancies (HM)

Case-series analysis of haematological malignancies in gold mining areas in South Africa

Introduction South Africa has a long history of uranium (U) production from gold mining and milling that has resulted in locally high-levels of environmental contamination from uranium and its decay products (radium 226 and radon 222). Due to short distances from mining tailings to residential areas, populations living around gold mine tailings of the Witwatersrand goldfields may be exposed to uranium and its decay products from the tailings through multiple pathways, including ingestion of contaminated water and food grown in contaminated areas, direct consumption of soil (geophagia) and inhalation of dust, raising concern about potential health risks associated with environmental U-exposure, and in particular regarding haematological malignancies (HM). We designed a case-series study of HM from Chris Hani Baragwanath Academic Hospital (CHBAH), South Africa, to assess the feasibility of an analytical study on the association between U-exposure and HM risk in this setting. Methods First, patient and cancer characteristics and spatial distribution were retrospectively reviewed from patient files of the HM cases diagnosed between 2004 and 2013 at CHBAH. Spatial relations between residential addresses of patients and location of mine tailings and other U-sources were analysed using a specifically designed GIS-supported virtual geographical environment. Then, we assessed the feasibility of collecting additional information, from patients newly diagnosed with a HM at CHBAH (in 2014–2015), on potential environmental U-exposure pathways and referral patterns from interviewer-administered questionnaires. Results Among the 1880 cases aged 18–94 years and retrospectively identified from CHBAH's patient files, 44% were diagnosed with Non-Hodgkin lymphoma (NHL), 26% with leukemia and 17% with myeloma. Referral from distant provinces was not uncommon but more than 90% of patients lived within 50 km of the hospital. Human immunodeficiency virus (HIV) status was known for 94%, of which 44% were HIV-positive. No clear and consistent spatial relations between patient's residences and mine tailings deposits could be established. A total of 196 haematological cancer cases aged 18–90 were prospectively diagnosed between 2014 and 2015 at CHBAH, with NHL (35%), leukemia (34%) and myeloma (16%). HIV status was available for all patients, 41% being HIV-positive. Working in gold mines was reported by 12 cases (6%), all men. Soil consumption was a habit for 53 cases (27%), mostly women, and came from backyards and road vendors. Soil consumption occurred more frequently during adulthood and pregnancy. Drinking water came from piped water; untreated water from nearby rivers was not drunk. Animal products and vegetables came from stores and backyards. At the time of interview, 95% of cases were living in Gauteng Province, in Soweto (58%). Half of the cases were living at their current residence for 20 years or more. Cases were referred to CHBAH by governmental clinic doctors (44%), referral hospitals (25%) and private doctors (20%). Most cases lived less than one hour from CHBAH (77%). Conclusions This case-series analysis showed the capacity of CHBAH to recruit HM patients and allowed the description of the HM burden of the area. Caution is required when interpreting the spatial distributions of patients; our results may not reflect population-incidence rates due to referral patterns to the hospital and inaccuracies in residential addresses retrospectively collected from clinical records. This needs to be considered when analyzing spatial relations related to various exposure pathways. The questionnaire administered to the prospective cases allowed collecting information on U-related exposure, although results generally showed low exposure prevalence in our study population. As infections, such as HIV, may be a risk factor for some HM, collecting clinical data on infections and subtypes of HM needs to be considered in the investigation of HM risk.

Comprehensive whole-genome sequencing of an early-stage primary myelofibrosis patient defines low mutational burden and non-recurrent candidate genes

In order to identify novel somatic mutations associated with classic BCR/ABL1-negative myeloproliferative neoplasms, we performed high-coverage genome sequencing of DNA from peripheral blood granulocytes and cultured skin fibroblasts from a patient with MPL W515K-positive primary myelofibrosis. The primary myelofibrosis genome had a low somatic mutation rate, consistent with that observed in similar hematopoietic tumor genomes. Interfacing of whole-genome DNA sequence data with RNA expression data identified three somatic mutations of potential functional significance: i) a nonsense mutation in CARD6, implicated in modulation of NF-kappaB activation; ii) a 19-base pair deletion involving a potential regulatory region in the 5'-untranslated region of BRD2, implicated in transcriptional regulation and cell cycle control; and iii) a non-synonymous point mutation in KIAA0355, an uncharacterized protein. Additional mutations in three genes (CAP2, SOX30, and MFRP) were also evident, albeit with no support for expression at the RNA level. Re-sequencing of these six genes in 178 patients with polycythemia vera, essential thrombocythemia, and myelofibrosis did not identify recurrent somatic mutations in these genes. Finally, we describe methods for reducing false-positive variant calls in the analysis of hematologic malignancies with a low somatic mutation rate. This trial is registered with ClinicalTrials.gov (NCT01108159).

Molecular genetic analysis of haematological malignancies: I. Acute leukaemias and myeloproliferative disorders

Molecular genetic techniques are now routinely applied to haematological malignancies within a clinical laboratory setting. The detection of genetic rearrangements not only assists with diagnosis and treatment decisions, but also adds important prognostic information. In addition, genetic rearrangements associated with leukaemia can be used as molecular markers allowing the detection of low levels of residual disease. This review will concentrate on the application of molecular genetic techniques to the acute leukaemias and myeloprolferative disorders.

Clinically useful information provided by the flow cytometric immunophenotyping of hematological malignancies: current status and future directions.

At present, immunophenotyping of hematological malignancies represents one of the most relevant clinical applications of flow cytometry. In recent years, its use has extended from clinical research to diagnostic laboratories. The aim of this report is to critically review the type of information provided by the flow cytometric immunophenotyping of hematological malignancies and its clinical impact as well as to highlight its potential future applications. The currently available information, including that provided by different international consensus groups on the phenotypic characterization of hematologic malignancies, was reviewed. Additionally, recent reports on the immunophenotypic analysis of hematological malignancies published in hematology, oncology, pathology, immunology, and cell biology journals were also analyzed. A careful review of the literature showed that in spite of the well-established utility of immunophenotyping for the diagnosis, classification, prognostic stratification, and monitoring of hematological malignancies, only a small part of the information on the immunophenotypic characteristics of pathological hemopoietic cells has been used routinely. Specific and sensitive identification of neoplastic cells and their accurate enumeration and phenotypic characterization represent the major aims of these procedures. Similarities between leukemic and healthy cells allow the establishment of the lineage and maturation stage of the pathologic cells, this information being of great utility for the diagnosis, classification, and prognostic evaluation of different subtypes of hematological malignancies. On the other hand, the phenotypic aberrations displayed by leukemic cells could allow the selection of cases carrying specific genetic abnormalities in which further confirmatory molecular studies will be performed. The information provided by the flow cytometric immunophenotyping of hematological malignancies is of great clinical utility, with a major challenge for the near future being the standardization of technical procedures, data interpretation, and reporting.

Hairy cell leukemia has a B-cell genotype.

The phenotype and, by inference, the cell of origin of some lymphocytic neoplasms has been defined by surface marker studies; however, the precise cellular origin of other neoplasms of the lymphoid system is still unknown. For example, with reference to hairy cell leukemia (HCL), cell marker data has been used in support of a monocytic, a T cell, or a B cell origin. If hairy cell leukemia is a B cell-derived neoplasm, the controversy may be resolved by genotyping the cells, using the rearrangement of immunoglobulin genes as a marker of the B cell nature of the process. Rearrangement of these genes is detected using the Southern blot technique and cloned probes specific for the JH segment of the immunoglobulin genes. In this study, the arrangement of the immunoglobulin genes was analysed in normal tissue, in two accepted B cell lymphomas and in nine cases of hairy cell leukemia. DNA from peripheral blood leukocytes (two patients) and from the spleen (seven patients) revealed a discrete new JH restriction fragment length in the leukocytes of hairy cell leukemia cases. The presence of rearranged restriction fragments is interpreted as evidence of the existence of clonal B cell populations. Three of six samples had rearranged kappa light chain fragments. We conclude that most cases of hairy cell leukemia have a B cell genotype. The use of genotyping has wider application in the analysis of hematological malignancies.