Archival Bone Marrow Smears Research Articles

Archival bone marrow smears are useful in targeted next-generation sequencing for diagnosing myeloid neoplasms.

Gene abnormalities, including mutations and fusions, are important determinants in the molecular diagnosis of myeloid neoplasms. The use of bone marrow (BM) smears as a source of DNA and RNA for next-generation sequencing (NGS) enables molecular diagnosis to be done with small amounts of bone marrow and is especially useful for patients without stocked cells, DNA or RNA. The present study aimed to analyze the quality of DNA and RNA derived from smear samples and the utility of NGS for diagnosing myeloid neoplasms. Targeted DNA sequencing using paired BM cells and smears yielded sequencing data of adequate quality for variant calling. The detected variants were analyzed using the bioinformatics approach to detect mutations reliably and increase sensitivity. Noise deriving from variants with extremely low variant allele frequency (VAF) was detected in smear sample data and removed by filtering. Consequently, various driver gene mutations were detected across a wide range of allele frequencies in patients with myeloid neoplasms. Moreover, targeted RNA sequencing successfully detected fusion genes using smear-derived, very low-quality RNA, even in a patient with a normal karyotype. These findings demonstrated that smear samples can be used for clinical molecular diagnosis with adequate noise-reduction methods even if the DNA and RNA quality is inferior.

Archived Bone Marrow Smears Are an Excellent Source for NGS-Based Mutation Detection in Acute Myeloid Leukemia

Acute myeloid leukemia (AML) is a heterogeneous disease with a great variety of somatic driver mutations. Each AML carries specific (combinations of) acquired mutations, which enables minimal residual disease (MRD) detection in virtually every patient with next-generation sequencing (NGS). In recent years there has been an increasing interest to conduct longitudinal molecular MRD detection to better estimate prognosis, monitor treatment efficacy, as well as prediction of an impending relapse. The development of molecular monitoring on archived samples has been slow because only limited numbers of samples collected during the course of the disease were biobanked. We have systematically investigated whether archived May-Giemsa Grünwald (MGG)-stained bone marrow slides could be an alternative source of material to conduct NGS-based molecular MRD detection in AML. Since MGG-stained bone marrow evaluations are performed at high frequency to evaluate the response on therapy and repopulation of the bone marrow, we focused on these bone marrow slides taken at regular intervals during treatment.We initial tested DNA isolation protocol on MGG-stained and unstained morphology slides, which were archived over the years. The DNA could be isolated from the MGG-stained (n=16) and unstained bone marrow slides (n=16). However, we were unable to isolate genomic DNA from all of the unstained slides (11 out of 16). Furthermore, the DNA concentration from the unstained slides was much lower than the MGG-stained slides. We next isolated DNA from MGG-stained bone marrow slides of 43 AML samples at diagnosis and relapse of which the mutation status of genes frequently mutated in myeloid diseases was known. DNA isolated from Ficoll-purified mononuclear cells of the same pairs was previously sequenced by NGS using the Illumina Trusight Myeloid panel. NGS-based mutation screening with the same panel on DNA obtained from morphology slides revealed that detection of the driver mutations was feasible. In fact, all known mutations were detectable at diagnosis and relapse. Interestingly, in 91% (39 out of 43) of cases, the variant allele frequency (VAF) of the mutations were virtually identical to those detected using the DNA from MNCs. Representative examples are shown in Figure 1 (A and B). In a minority of samples, the VAFs differed between MNCs and bone marrow slides (3 cases VAF higher in MNCs and 1 case VAF lower in MNCs). These findings indicate that DNA isolated from bone marrow slides are a rich source for NGS-based mutation detection in AML at diagnosis and relapse.We next sought to evaluate the use of MGG-stained bone marrow slides to study the mutations kinetics in time from AML diagnosis to relapse. To perform this analysis 30 paired-AML (diagnosis - relapse) with variable time to relapse (range: 200 to 4004 days) were selected. We collected the archived bone marrow slides at different time points between diagnosis and relapse, isolated DNA and performed NGS-based mutation detection. The NGS analysis of the 30 paired-AML cases showed different patterns of mutation dynamics and clonal evolution. Representative examples are shown in Figure 1 (C and D). Interestingly, by this systematic analyses of somatic mutations at various time points clear distinction could be made between leukemia-specific mutations and mutations associated with clonal hematopoiesis at the time of complete remission in the individual AML cases.Our study uncovers an unutilized source of material for mutation detection at diagnosis and relapse in AML. These materials are widely available and well archived. Furthermore, our study reveals the potential use of MGG stained bone marrow morphology slides to track mutations and (sub)clones in AML, which is applicable to virtually every AML patient and possibly valuable for other hematological malignancies as well. [Display omitted] DisclosuresNo relevant conflicts of interest to declare.

Paediatric leukaemia DNA methylation profiling using MBD enrichment and SOLiD sequencing on archival bone marrow smears.

BackgroundAcute Lymphoblastic Leukaemia (ALL) is the most common cancer in children. Over the past four decades, research has advanced the treatment of this cancer from a less than 60% chance of survival to over 85% today. The causal molecular mechanisms remain unclear. Here, we performed sequencing-based genomic DNA methylation profiling of eight paediatric ALL patients using archived bone marrow smear microscope slides.FindingsSOLiD™ sequencing data was collected from Methyl-Binding Domain (MBD) enriched fractions of genomic DNA. The primary tumour and remission bone marrow sample was analysed from eight patients. Four patients relapsed and the relapsed tumour was analysed. Input and MBD-enriched DNA from each sample was sequenced, aligned to the hg19 reference genome and analysed for enrichment peaks using MACS (Model-based Analysis for ChIP-Seq) and HOMER (Hypergeometric Optimization of Motif EnRichment). In total, 3.67 gigabases (Gb) were sequenced, 2.74 Gb were aligned to the reference genome (average 74.66% alignment efficiency). This dataset enables the interrogation of differential DNA methylation associated with paediatric ALL. Preliminary results reveal concordant regions of enrichment indicative of a DNA methylation signature.ConclusionOur dataset represents one of the first SOLiD™MBD-Seq studies performed on paediatric ALL and is the first to utilise archival bone marrow smears. Differential DNA methylation between cancer and equivalent disease-free tissue can be identified and correlated with existing and published genomic studies. Given the rarity of paediatric haematopoietic malignancies, relative to adult counterparts, our demonstration of the utility of archived bone marrow smear samples to high-throughput methylation sequencing approaches offers tremendous potential to explore the role of DNA methylation in the aetiology of cancer.

Archival bone marrow samples: suitable for multiple biomarker analysis.

AB Archival samples represent a significant potential for genetic studies, particularly in severe diseases with risk of lethal outcome, such as in cancer. In this pilot study, we aimed to evaluate the usability of archival bone marrow smears and biopsies for DNA extraction and purification, whole genome amplification (WGA), multiple marker analysis including 10 short tandem repeats, and finally a comprehensive genotyping of 33,683 single nucleotide polymorphisms (SNPs) with multiplexed targeted next-generation sequencing. A total of 73 samples from 21 bone marrow smears and 13 bone marrow biopsies from 18 Danish and Norwegian childhood acute lymphoblastic leukemia patients were included and compared with corresponding blood samples. Samples were grouped according to the age of sample and whether WGA was performed or not. We found that measurements of DNA concentration after DNA extraction was dependent on detection method and that spectrophotometry overestimated DNA amount compared with fluorometry. In the short tandem repeat analysis, detection rate dropped slightly with longer fragments. After WGA, this drop was more pronounced. Samples stored for 0 to 3 years showed better results compared with samples stored for 4 to 10 years. Acceptable call rates for SNPs were detected for 7 of 42 archival samples. In conclusion, archival bone marrow samples are suitable for DNA extraction and multiple marker analysis, but WGA was less successful, especially when longer fragments were analyzed. Multiple SNP analysis seems feasible, but the method has to be further optimized.

A Preliminary Study of the Suitability of Archival Bone Marrow and Peripheral Blood Smears for Diagnosis of CML Using FISH.

Background. FISH is a molecular cytogenetic technique enabling rapid detection of genetic abnormalities. Facilities that can run fresh/wet samples for molecular diagnosis and monitoring of neoplastic disorders are not readily available in Ghana and other neighbouring countries. This study aims to demonstrate that interphase FISH can successfully be applied to archival methanol-fixed bone marrow and peripheral blood smear slides transported to a more equipped facility for molecular diagnosis of CML. Methods. Interphase FISH was performed on 22 archival methanol-fixed marrow (BM) and 3 peripheral blood (PB) smear slides obtained at diagnosis. The BM smears included 20 CML and 2 CMML cases diagnosed by morphology; the 3 PB smears were from 3 of the CML patients at the time of diagnosis. Six cases had known BCR-ABL fusion results at diagnosis by RQ-PCR. Full blood count reports at diagnosis were also retrieved. Result. 19 (95%) of the CML marrow smears demonstrated the BCR-ABL translocation. There was a significant correlation between the BCR-ABL transcript detected at diagnosis by RQ-PCR and that retrospectively detected by FISH from the aged BM smears at diagnosis (r = 0.870; P = 0.035). Conclusion. Archival methanol-fixed marrow and peripheral blood smears can be used to detect the BCR-ABL transcript for CML diagnosis.

Application of fluorescence in situ hybridization on archived bone marrow smears in retrospective diagnosis of hematologic malignancies

Application of fluorescence in situ hybridization on archived bone marrow smears in retrospective diagnosis of hematologic malignancies

Successful Application of a Direct Detection Slide-Based Sequential Phenotype/Genotype Assay Using Archived Bone Marrow Smears and Paraffin Embedded Tissue Sections

Successful Application of a Direct Detection Slide-Based Sequential Phenotype/Genotype Assay Using Archived Bone Marrow Smears and Paraffin Embedded Tissue Sections

Successful Application of a Direct Detection Slide-Based Sequential Phenotype/Genotype Assay Using Archived Bone Marrow Smears and Paraffin Embedded Tissue Sections

Identification of genetic abnormalities in pathological samples is critical for accurate diagnosis, risk stratification, detection of minimal residual disease, and assessment of response to therapy. Interphase fluorescence in situ hybridization analysis is the standard cytogenetic assay used by many laboratories to detect specific clonal karyotypic aberrations in formalin-fixed, paraffin-embedded tissue. However, direct correlation with immunophenotype or morphology in individual cells is rarely performed because the procedural steps are labor intensive and usually require extensive troubleshooting. In this study, we present a sequential fluorescence in situ hybridization-based technique that uses the identical archived bone marrow smears or paraffin-embedded tissue sections previously evaluated by a pathologist for morphological or immunohistochemical characteristics. This approach is relatively straightforward, using uncomplicated pretreatment and hybridization conditions and basic equipment attached to an automated image analyzer with image capture software to record the location of targeted cells for genotypic/phenotype correlation. Furthermore, the method has proved reliable and reproducible on test samples regardless of specimen age, tissue type, or referring institution.

No evidence of association of methylenetetrahydrofolate reductase polymorphism with occurrence of second neoplasms after treatment of childhood leukemia

Methylenetetrahydrofolate reductase (MTHFR) polymorphisms have been associated not only with the risk for acute lymphoblastic leukemia (ALL) in adults and children, but also with increased methotrexate toxicity. The present study aimed to investigate whether MTHFR polymorphisms modify the risk for development of secondary malignancies in children treated for ALL with protocols that included high-dose methotrexate. MTHFR genotypes were determined in DNA samples isolated from archived bone marrow smears of 15 patients with a second malignancy and a matched control group of 30 patients who did not developed a second malignancy after the treatment for ALL. The frequencies of MTHFR C677T and A1298C genotypes in all patients were: C677T: CC 40%, CT 46.7% and TT 13.3% and A1298C: AA 46.7%, AC 44.4% and CC 8.9%. The relative risk for second malignancy was not significantly increased in ALL patients having at least one polymorphic C667T [odds ratio (OR) 1.51; 95% confidence interval (CI) 0.43-5.31] or one polymorphic A1298C allele (OR 1; 95% CI 0.29?-?3.46). Our study suggests that MTHFR polymorphisms are not associated with increased risk of second cancer in children treated with high-dose methotrexate.

Single cell PCR from archival stained bone marrow slides: a method for molecular diagnosis and characterization.

Molecular analysis of isolated single cells is a powerful tool for clarifying issues of cell origin and clonality. Previous reports have described PCR amplifications from total DNA and RNA extracted from archival bone marrow and peripheral blood smears and have also shown the feasibility of amplifications from single cells, microdissected from stained histological sections. In this study, a method is described for performing PCR from morphologically defined single cells isolated from archival May-Gruenwald-Giemsa-stained bone-marrow and blood smears. Using three DNA extraction procedures, the organic lysis showed reproducible high efficiencies of amplifications. With this method, we were able to amplify long range amplicons up to 14.5 kb from mitochondrial DNA as well as PCR products of conventional length. The usability of such products for molecular diagnosis is demonstrated by restriction fragment length polymorphism (RFLP)characterization of a mitochondrial disorder. In conclusion, this method has the power to perform molecular diagnosis and characterization of diseases on the single cell level, and should provide valuable information to aid disease treatment and prognosis of hematological disorders.

Pre-natal, Clonal Origin of Acute Lymphoblastic Leukaemia in Triplets

A unique case of ALL in three monozygotic triplets diagnosed at the age of 24, 27 and 37 months is described. Archived bone marrow smears were available for molecular analysis of immunoglobulin heavy chain (IGH) and IGK genes and T-cell receptor (TCR)-delta and gamma gene rearrangements. A shared IGH rearrangement was found in triplets "A" and "B", and an identical rearrangement of TCR-delta in triplets "B" and "C". These data suggest a common, monoclonal initiation of ALL in one of these three triplets, followed by dissemination of clonal progeny to the other twins via vascular anastomoses within the single, monochorionic placenta that they shared in utero. Differences in IGH rearrangements in diagnostic samples also indicates divergent subclonal evolution of the original "pre-leukaemic" clone.

Increased incidence of spontaneous apoptosis in the bone marrow of hyperdiploid childhood acute lymphoblastic leukemia

Hyperdiploidy of 51-65 chromosomes is associated with a good prognosis in childhood B-lineage acute lymphoblastic leukemia (ALL). Blasts from childhood ALL patients with a hyperdiploid karyotype have a tendency to apoptosis when cultured on stromal layers in vitro. In this study, we apply a novel method to investigate the relationship between apoptosis and hyperdiploidy in lymphoblasts of childhood ALL. The DNA content of individual ALL blasts in Feulgen-stained archival bone marrow smears can be determined by static cytometry. TUNEL (TdT-mediated dUTP-biotin nick end labeling) detects the DNA degradation associated with apoptosis. We performed TUNEL in situ sequential to DNA ploidy analysis in archival bone marrow smears from 12 patients with childhood ALL. Five patients were diploid and seven were hyperdiploid (51-65 chromosomes) by conventional cytogenetic analysis. In the five diploid cases, the percentage of TUNEL-positive blasts ranged from 1.0% to 1.3%; in the seven hyperdiploid cases, the percentage of TUNEL-positive blasts ranged from 3.6% to 9.0%. Comparing TUNEL and corresponding Feulgen images, we found that apoptotic blasts were predominantly of high DNA ploidy in both diploid and hyperdiploid cases. The mean DNA value of apoptotic blasts was larger than that of the total blast population in each case. The results demonstrate an increased incidence of spontaneous apoptosis in situ of hyperdiploid blasts in ALL bone marrow and indicate that this phenomenon is not restricted to in vitro cultures. The findings provide a possible rationale for the good prognosis associated with hyperdiploid childhood ALL.

Detection of microsatellite markers in leukaemia using DNA from archival bone marrow smears

We describe a simple PCR method to detect highly polymorphic repetitive DNA markers (microsatellites) in leukaemia using DNA from fresh and archival bone marrow smears. Neither the period of storage nor staining of the slides affected microsatellite PCR. Comparison of slide DNA with constitutive DNA from buccal epithelium revealed loss of heterozygosity (LOH) with at least one marker in four of 11 leukaemias. Marrow smears offer an attractive archival source of DNA for the detection of microsatellite markers. Applications include detection of LOH or tracing the origin of cell populations, e.g. in bone marrow transplant recipients.

Application of fluorescence in situ hybridisation to chromosome analysis of aged bone marrow smears.

To evaluate the reliability of fluorescence in situ hybridisation (FISH) in the retrospective cytogenetic assessment of old bone marrow smears stored for periods of up to 20 years. A series of bone marrow smears either Romanowsky stained, or frozen and unstained, and aged from one month to 20 years were hybridised with biotin labelled probes specific for the centromeric regions of human chromosomes X, 6, and 18. Sites of hybridisation were detected with fluoresceinated avidin. One hundred to 400 cells from each preparation were examined and the number of signals observed was recorded. All smears exhibited signals in most cells examined. In cytogenetically normal cases, an average 67.6% of cells (range 36%-90%) demonstrated the appropriate number of X centromere signals. In those samples known to contain extra chromosomes X, 6, or 18 the presence of cells with the abnormal copy number was clearly detected in each case. When applied in the way described, FISH can give consistent and accurate results with a variety of archival bone marrow smears, including aged prestained material. This will permit retrospective assessment of specific cytogenetic abnormalities in patients with leukaemia using their initial diagnostic slides even where these are several years old.