Observations from a national sample exchange program for molecular haematology testing

External quality assessment programs (EQAP) for molecular haematology generally only assess the analytical phase of laboratory testing or provide limited evaluation of post-analytical components. We incorporated comprehensive post-analytical evaluation into an existing national inter-laboratory sample exchange program for molecular haematology due to the increasing complexity of diagnostic molecular testing and interpretation. We report key findings from four years of longitudinal data using this approach. Eighteen participating laboratories enrolled in an annual reciprocal sample exchange program from 2019-2022, which covered conventional and next-generation sequencing (NGS) assays. Participants submitted results on their laboratory information system-generated reports which then underwent central review. Reports were assessed according to consensus values and relevant national and international reporting standards and guidelines. A total of 680 reports were received. Laboratories had high concordance in the analytical phase of testing, with incorrect variant detection observed in a total of six of 680 (0.9%) reports. In contrast, post-analytical concordance was much lower, with at least one discordance observed in 28.9-57.6% of all conventional reports and 33.3-100% NGS reports. The most frequent post-analytical discordances were: (1) not including key technical information on reports (total 41.9% conventional, 47.2% NGS); (2) not using standard gene and variant nomenclature (total 28.2% conventional, 25.6% NGS). NGS reports also demonstrated discrepancies in variant classification (total 20.4%) and interpretation (total 10.2%). The rate of discrepancies generally improved year-on-year. Inter-laboratory concordance for molecular haematology testing is high in the analytical phase, however opportunities exist for improvement in the post-analytical phase. Given that result interpretation is crucial for clinical decision-making and that molecular testing is a complex and evolving field, we suggest that EQAPs should comprehensively evaluate both analytical and post-analytical components of laboratory performance in order to harmonise reporting and to support the accurate interpretation of molecular haematology tests.

Correlation between a 10-color flow cytometric measurable residual disease (MRD) analysis and molecular MRD in adult B-acute lymphoblastic leukemia

BACKGROUND

Measurable residual disease (MRD) monitoring in acute lymphoblastic leukemia (ALL) is an important predictive factor for patient outcome and treatment intensification. Molecular monitoring, particularly with quantitative polymerase chain reaction (qPCR) to measure immunoglobin heavy or kappa chain (Ig) or T-cell receptor (TCR) gene rearrangements, offers high sensitivity but accessibility is limited by expertise, cost, and turnaround time. Flow cytometric assays are cheaper and more widely available, and sensitivity is improved with multi-parameter flow cytometry at eight or more colors.

METHODS

We developed a 10-color single tube flow cytometry assay. Samples were subject to bulk ammonium chloride lysis to maximize cell yields with a target of 1 × 10⁶ events. Once normal maturation patterns were established, patient samples were analyzed in parallel to standard molecular monitoring.

RESULTS

Flow cytometry was performed on 114 samples. An informative immunophenotype was identifiable in all 22 patients who had a diagnostic sample. MRD analysis was performed on 87 samples. The median lower limits of detection and quantification were 0.004% (range 0.0005%-0.028%) and 0.01% (range 0.001%-0.07%) respectively. Sixty-five samples had concurrent molecular MRD testing, with good correlation (r = 0.83, p < 0.001). Results were concordant in 52 samples, and discordant in 13 samples, including one case where impending relapse was detected by flow cytometry but not Ig/TCR qPCR.

CONCLUSIONS

Our 10-color flow cytometric MRD assay provided adequate sensitivity and good correlation with molecular assays. This technique offers rapid and affordable testing in B-ALL patients, including cases where a suitable molecular assay cannot be developed or has reduced sensitivity.

T cell receptor beta locus sequencing early post-allogeneic stem cell transplant identifies patients at risk of initial and recurrent cytomegalovirus infection

Identification of patients at risk of initial & recurrent cytomegalovirus (CMV) reactivation following allogeneic stem cell transplant (alloSCT) may help guide prophylactic strategies. T-cell receptor beta (TRB) deep sequencing was used to identify and enumerate the T-cell repertoire harbouring TRB sequences with annotated specificity to CMV (pubCMVrep), as well as the overall T-cell receptor (TCR) repertoire diversity at day +30 & day +60 post-alloSCT for 65 patients. T-cells harbouring TRB sequences with annotated specificity for CMV were identifiable in all patients. 56% of patients required CMV treatment and 23% of the cohort developed recurrent CMV. PubCMVrep size at day +30 was not associated with reactivation, however amongst patients with antecedent CMV viremia a low day +60 pubCMVrep was associated with a greater incidence of recurrent CMV (75% vs. 21%, HR 6.16, 95% CI 1.29-29.40, P = 0.0008). Moreover, patients with high pubCMVrep only developed recurrent CMV in the setting of GVHD. Low TCR diversity at day +30 was associated with a greater incidence of initial CMV reactivation (71% vs. 22%, HR 5.39, 95% CI 1.70-17.09, p = 0.0002). pubCMVrep and TCR diversity are promising biomarkers to identify patients at risk of initial & recurrent CMV who may benefit from novel prophylactic strategies.

Utility of clinical comprehensive genomic characterization for diagnostic categorization in patients presenting with hypocellular bone marrow failure syndromes

Bone marrow failure (BMF) related to hypoplasia of hematopoietic elements in the bone marrow is a heterogeneous clinical entity with a broad differential diagnosis including both inherited and acquired causes. Accurate diagnostic categorization is critical to optimal patient care and detection of genomic variants in these patients may provide this important diagnostic and prognostic information. We performed real-time, accredited (ISO15189) comprehensive genomic characterization including targeted sequencing and whole exome sequencing in 115 patients with BMF syndromes (median age 24 years, range: 3 months - 81 years). In patients with clinical diagnoses of inherited BMF syndromes, acquired BMF syndromes or clinically unclassifiable BMF we detected variants in 52% (12 of 23), 53% (25 of 47) and 56% (25 of 45) respectively. Genomic characterization resulted in a change of diagnosis in 30 of 115 (26%) including the identification of germline causes for 3 of 47 and 16 of 45 cases with pre-test diagnoses of acquired and clinically unclassifiable BMF respectively. The observed clinical impact of accurate diagnostic categorization included choice to perform allogeneic stem cell transplantation, disease-specific targeted treatments, identification of at-risk family members and influence of sibling allogeneic stem cell donor choice. Multiple novel pathogenic variants and copy number changes were identified in our cohort including in TERT, FANCA, RPS7 and SAMD9. Whole exome sequence analysis facilitated the identification of variants in two genes not typically associated with a primary clinical manifestation of BMF but also demonstrated reduced sensitivity for detecting low level acquired variants. In conclusion, genomic characterization can improve diagnostic categorization of patients presenting with hypoplastic BMF syndromes and should be routinely performed in this group of patients.

Sensitive NPM1 Mutation Quantitation in Acute Myeloid Leukemia Using Ultradeep Next-Generation Sequencing in the Diagnostic Laboratory

Context Detection of measurable residual disease after therapy is an important predictor of outcome in acute myeloid leukemia. Objective To investigate the feasibility of using next-generation sequencing (NGS) in the diagnostic laboratory to perform quantitative NPM1 mutation assessment using ultradeep (approximately 300 000×-500 000×) sequencing (NGS-q NPM1) as a method of assessing residual disease burden in patients with acute myeloid leukemia. Design A flexible NGS-based assay for the detection and quantitation of NPM1 mutations was developed by polymerase chain reaction amplification of target DNA sequences, sequencing on an Illumina (San Diego, California) MiSeq, and analyzing data with an in-house-designed bioinformatic pipeline. NGS-q NPM1 was compared with current NPM1 quantitation methods (real-time quantitative-polymerase chain reaction and multiparameter flow cytometry). Results The NGS-q NPM1 assay had a sensitivity of between 10^-4 and 10^-5 and showed high concordance and correlation with reference methodologies. Moreover, the NGS-q NPM1 assay was able to be integrated into the laboratory's existing, targeted amplicon-based sequencing workflow. Conclusions An NGS-based, quantitative NPM1-mutation assessment can be used to monitor patients with acute myeloid leukemia, and it has some practical advantages over existing modalities.

Incidental detection of germline variants of potential clinical significance by massively parallel sequencing in haematological malignancies

Massively parallel sequencing (MPS) technology has become routinely available for diagnosis, prognostication and therapeutic decision-making in haematological malignancies. However, increased throughput and wider coverage of genes can have unintended consequences. Germline variants of potential clinical significance (GVPCSs) detected during cancer testing may have implications for patients and families beyond the biological evaluation of a specific tumour. 721 reports generated from MPS panels used in the routine testing of myeloid and lymphoid malignancies were reviewed and variants within genes of potential germline relevance (TP53, RUNX1, GATA2 and WT1 in all contexts and CBL, KRAS and NRAS in the setting of juvenile myelomonocytic leukaemia) were analysed. A variant allele fraction threshold of ≥33.09% for considering germline origin of variants within cancer samples was established. The detection rate of incidental, pathogenic germline variants was 0.42%. Patient education and confirmatory germline sample testing of GVPCSs in appropriate circumstances are recommended.

Development and evaluation of a secondary reference panel for BCR-ABL1 quantification on the International Scale

Molecular monitoring of chronic myeloid leukemia patients using robust BCR-ABL1 tests standardized to the International Scale (IS) is key to proper disease management, especially when treatment cessation is considered. Most laboratories currently use a time-consuming sample exchange process with reference laboratories for IS calibration. A World Health Organization (WHO) BCR-ABL1 reference panel was developed (MR¹–MR⁴), but access to the material is limited. In this study, we describe the development of the first cell-based secondary reference panel that is traceable to and faithfully replicates the WHO panel, with an additional MR^4.5 level. The secondary panel was calibrated to IS using digital PCR with ABL1, BCR and GUSB as reference genes and evaluated by 44 laboratories worldwide. Interestingly, we found that >40% of BCR-ABL1 assays showed signs of inadequate optimization such as poor linearity and suboptimal PCR efficiency. Nonetheless, when optimized sample inputs were used, >60% demonstrated satisfactory IS accuracy, precision and/or MR^4.5 sensitivity, and 58% obtained IS conversion factors from the secondary reference concordant with their current values. Correlation analysis indicated no significant alterations in %BCR-ABL1 results caused by different assay configurations. More assays achieved good precision and/or sensitivity than IS accuracy, indicating the need for better IS calibration mechanisms.

Quantitative threefold allele-specific PCR (QuanTAS-PCR) for highly sensitive JAK2 V617F mutant allele detection

Background

The JAK2 V617F mutation is the most frequent somatic change in myeloproliferative neoplasms, making it an important tumour-specific marker for diagnostic purposes and for the detection of minimal residual disease. Sensitive quantitative assays are required for both applications, particularly for the monitoring of minimal residual disease, which requires not only high sensitivity but also very high specificity.

Methods

We developed a highly sensitive probe-free quantitative mutant-allele detection method, Quantitative Threefold Allele-Specific PCR (QuanTAS-PCR), that is performed in a closed-tube system, thus eliminating the manipulation of PCR products. QuantTAS-PCR uses a threefold approach to ensure allele-specific amplification of the mutant sequence: (i) a mutant allele-specific primer, (ii) a 3′dideoxy blocker to suppress false-positive amplification from the wild-type template and (iii) a PCR specificity enhancer, also to suppress false-positive amplification from the wild-type template. Mutant alleles were quantified relative to exon 9 of JAK2.

Results

We showed that the addition of the 3′dideoxy blocker suppressed but did not eliminate false-positive amplification from the wild-type template. However, the addition of the PCR specificity enhancer near eliminated false-positive amplification from the wild-type allele. Further discrimination between true and false positives was enabled by using the quantification cycle (Cq) value of a single mutant template as a cut-off point, thus enabling robust distinction between true and false positives. As 10,000 JAK2 templates were used per replicate, the assay had a sensitivity of 1/10^-4 per replicate. Greater sensitivity could be reached by increasing the number of replicates analysed. Variation in replicates when low mutant-allele templates were present necessitated the use of a statistics-based approach to estimate the load of mutant JAK2 copies. QuanTAS-PCR showed comparable quantitative results when validated against a commercial assay.

Conclusions

QuanTAS-PCR is a simple, cost-efficient, closed-tube method for JAK2 V617F mutation quantification that can detect very low levels of the mutant allele, thus enabling analysis of minimal residual disease. The approach can be extended to the detection of other recurrent single nucleotide somatic changes in cancer.

Administrative data for public health surveillance and planning

Electronically available administrative data are increasingly used by public health researchers and planners. The validity of the data source has been established, and its strengths and weaknesses relative to data abstracted from medical records and obtained via survey are documented. Administrative data are available from a variety of state, federal, and private sources and can, in many cases, be combined. As a tool for planning and surveillance, administrative data show great promise: They contain consistent elements, are available in a timely manner, and provide information about large numbers of individuals. Because they are available in an electronic format, they are relatively inexpensive to obtain and use. In the United States, however, there is no administrative data set covering the entire population. Although Medicare provides health care for an estimated 96% of the elderly, age 65 years and older, there is no comparable source for those under 65.

Increasing rates of hospitalization due to septicemia in the US elderly population, 1986-1997

Rates of hospitalization due to septicemia (International Classification of Diseases, Ninth Revision, Clinical Modification, code 038) in the US elderly population for 1986-1997 were examined, using Medicare administrative data. Age group-, sex-, and race-adjusted rates more than doubled from 1986 through 1997, from 3.42 to 7.42 per 1000 beneficiaries. The 1997 rates of septicemia increased with age, from 4.47 per 1000 beneficiaries among persons 65-74 years old to 18.1 per 1000 beneficiaries among persons > or =85 years old. The rates of septicemia were slightly greater among men (7.46 per 1000 beneficiaries) than among women (7.39 per 1000 beneficiaries) and were higher among blacks (13.61 per 1000 beneficiaries) than among whites (6.89 per 1000 beneficiaries). The most likely sites of the origin of the septicemia were the urinary tract (40.1%) and lungs (15.3%). Escherichia coli and Staphylococcus species were the most frequently reported organisms. Diabetes was listed as a comorbidity in 24.5% of the hospitalizations. We estimate that the cost to Medicare for septicemia hospitalizations in 1997 was >$1.8 billion.

Geographic variation in hospice use prior to death

OBJECTIVES

To examine national variation in use of the Medicare hospice benefit by older individuals before their death, and to identify individual characteristics and local market factors associated with hospice use.

DESIGN

Retrospective analysis of Medicare administrative data.

SETTING

Hospice care.

PARTICIPANTS

Older Medicare enrollees who died in 1996.

MEASUREMENTS

Rate of hospice use per 1,000 older Medicare beneficiary deaths.

RESULTS

Overall, 155 of every 1,000 older Medicare beneficiaries who die use hospice before death. This rate is significantly higher among younger older persons (P < .001), non-blacks (P < .001), persons living in wealthier areas (P < .001), and persons in urban areas (P < .001). Areas with a higher proportion of non-cancer diagnoses among hospice users have higher rates of hospice use for both cancer and non-cancer reasons than areas with a majority of hospice users having cancer diagnoses (P < .001). Hospice use is higher in areas with fewer hospital beds per capita (P < .001), areas with lower in-hospital death rates (P < .001), and areas with higher HMO enrollment (P < .001). Rates of hospice use are also positively related to average reimbursements for health care (P < .001) and to physicians per capita (P < .001). In the largest metropolitan statistical areas (MSAs), rates of hospice use vary more than 11-fold from a low of 35.15 (Portland, ME) to a high of 397.2 per 1,000 deaths (Ft. Lauderdale, FL).

CONCLUSIONS

The wide variation in hospice use suggests that there is great potential to increase the number of users of the Medicare hospice benefit.

Teaching medical students how to perform a clinical breast examination

BACKGROUND

One challenge in medical education is to provide training in physical examination skills. The authors conducted a randomized study to compare standardized and unstandardized methods of teaching clinical breast examinations and to determine whether trained non-medical women could teach as well as medical faculty.

METHOD

Sensitivity, specificity, and examination techniques were compared between first-year students at the University of Calgary Faculty of Medicine who in 1992-93 received standardized teaching from family medicine faculty or well women teachers and 70 second-year students who received unstandardized teaching during their clinical rotations. Standardized teaching included a specific examination technique using silicone breast models. The students taught by the well women teachers also examined the women's breasts.

RESULTS

The standardized-teaching group had more consistent examination techniques and significantly higher sensitivity but lower specificity. The students taught by the well women teachers performed as well as those taught by the family medicine faculty.

CONCLUSIONS

The teaching methods used by trained teachers and standardized models improved the students'accuracy of breast lump detection and examination skills.

Medicare beneficiaries: adverse outcomes after hospitalization for eight procedures

Rehospitalization following surgery is widely recognized as an important outcome measure. The purpose of this study was to identify rehospitalizations for adverse events following 8 procedures, using diagnosis and procedure codes contained in Medicare claims files. Adverse events were broadly defined as: 1) complications; 2) failure of the procedure to achieve its therapeutic goal; and 3) untoward events associated with the natural history of the disease being treated with the procedure. Expert panels identified specific diagnosis and procedure codes that might indicate an adverse event if they appeared on the Medicare record of a rehospitalization. Among patients undergoing percutaneous transluminal coronary angioplasty, almost 36% were rehospitalized for an adverse event within a year of surgery; among patients undergoing coronary artery bypass graft surgery, 20% were rehospitalized for an adverse event. Following the other 6 procedures (cholecystectomy, partial excision of the large intestine, total knee replacement, total hip replacement, replacement of the head of the femur, and reduction of fracture of the femur) between 4% and 9% of patients were rehospitalized for an adverse event. Findings from this exploratory study indicate that rehospitalizations for adverse events appear to be a useful outcome measure for the cardiac procedures; they appear to be less useful for the other procedures, at least at the individual hospital or small area level, because of their relative rarity. Future studies should investigate procedures associated with more frequent rehospitalizations, and medical admissions, which often tend to be associated with higher rehospitalization levels.