A framework for the clinical implementation of optical genome mapping in hematologic malignancies

Optical Genome Mapping (OGM) is rapidly emerging as an exciting cytogenomic technology both for research and clinical purposes. In the last 2 years alone, multiple studies have demonstrated that OGM not only matches the diagnostic scope of conventional standard of care cytogenomic clinical testing but it also adds significant new information in certain cases. Since OGM consolidates the diagnostic benefits of multiple costly and laborious tests (e.g., karyotyping, fluorescence in situ hybridization, and chromosomal microarrays) in a single cost-effective assay, many clinical laboratories have started to consider utilizing OGM. In 2021, an international working group of early adopters of OGM who are experienced with routine clinical cytogenomic testing in patients with hematological neoplasms formed a consortium (International Consortium for OGM in Hematologic Malignancies, henceforth "the Consortium") to create a consensus framework for implementation of OGM in a clinical setting. The focus of the Consortium is to provide guidance for laboratories implementing OGM in three specific areas: validation, quality control and analysis and interpretation of variants. Since OGM is a complex technology with many variables, we felt that by consolidating our collective experience, we could provide a practical and useful tool for uniform implementation of OGM in hematologic malignancies with the ultimate goal of achieving globally accepted standards.

Detection of Genomic Structural Variations Associated with Drug Sensitivity and Resistance in Acute Leukemia

Acute leukemia is a particularly problematic collection of hematological cancers, and, while somewhat rare, the survival rate of patients is typically abysmal without bone marrow transplantation. Furthermore, traditional chemotherapies used as standard-of-care for patients cause significant side effects. Understanding the evolution of leukemia to identify novel targets and, therefore, drug treatment regimens is a significant medical need. Genomic rearrangements and other structural variations (SVs) have long been known to be causative and pathogenic in multiple types of cancer, including leukemia. These SVs may be involved in cancer initiation, progression, clonal evolution, and drug resistance, and a better understanding of SVs from individual patients may help guide therapeutic options. Here, we show the utilization of optical genome mapping (OGM) to detect known and novel SVs in the samples of patients with leukemia. Importantly, this technology provides an unprecedented level of granularity and quantitation unavailable to other current techniques and allows for the unbiased detection of novel SVs, which may be relevant to disease pathogenesis and/or drug resistance. Coupled with the chemosensitivities of these samples to FDA-approved oncology drugs, we show how an impartial integrative analysis of these diverse datasets can be used to associate the detected genomic rearrangements with multiple drug sensitivity profiles. Indeed, an insertion in the gene MUSK is shown to be associated with increased sensitivity to the clinically relevant agent Idarubicin, while partial tandem duplication events in the KMT2A gene are related to the efficacy of another frontline treatment, Cytarabine.

Analytic Validation of Optical Genome Mapping in Hematological Malignancies

Structural variations (SVs) play a key role in the pathogenicity of hematological malignancies. Standard-of-care (SOC) methods such as karyotyping and fluorescence in situ hybridization (FISH), which have been employed globally for the past three decades, have significant limitations in terms of resolution and the number of recurrent aberrations that can be simultaneously assessed, respectively. Next-generation sequencing (NGS)-based technologies are now widely used to detect clinically significant sequence variants but are limited in their ability to accurately detect SVs. Optical genome mapping (OGM) is an emerging technology enabling the genome-wide detection of all classes of SVs at a significantly higher resolution than karyotyping and FISH. OGM requires neither cultured cells nor amplification of DNA, addressing the limitations of culture and amplification biases. This study reports the clinical validation of OGM as a laboratory-developed test (LDT) according to stringent regulatory (CAP/CLIA) guidelines for genome-wide SV detection in different hematological malignancies. In total, 60 cases with hematological malignancies (of various subtypes), 18 controls, and 2 cancer cell lines were used for this study. Ultra-high-molecular-weight DNA was extracted from the samples, fluorescently labeled, and run on the Bionano Saphyr system. A total of 215 datasets, Inc.luding replicates, were generated, and analyzed successfully. Sample data were then analyzed using either disease-specific or pan-cancer-specific BED files to prioritize calls that are known to be diagnostically or prognostically relevant. Sensitivity, specificity, and reproducibility were 100%, 100%, and 96%, respectively. Following the validation, 14 cases and 10 controls were run and analyzed using OGM at three outside laboratories showing reproducibility of 96.4%. OGM found more clinically relevant SVs compared to SOC testing due to its ability to detect all classes of SVs at higher resolution. The results of this validation study demonstrate the superiority of OGM over traditional SOC methods for the detection of SVs for the accurate diagnosis of various hematological malignancies.

Comparative Benchmarking of Optical Genome Mapping and Chromosomal Microarray Reveals High Technological Concordance in CNV Identification and Additional Structural Variant Refinement

The recommended practice for individuals suspected of a genetic etiology for disorders including unexplained developmental delay/intellectual disability (DD/ID), autism spectrum disorders (ASD), and multiple congenital anomalies (MCA) involves a genetic testing workflow including chromosomal microarray (CMA), Fragile-X testing, karyotype analysis, and/or sequencing-based gene panels. Since genomic imbalances are often found to be causative, CMA is recommended as first tier testing for many indications. Optical genome mapping (OGM) is an emerging next generation cytogenomic technique that can detect not only copy number variants (CNVs), triploidy and absence of heterozygosity (AOH) like CMA, but can also define the location of duplications, and detect other structural variants (SVs), including balanced rearrangements and repeat expansions/contractions. This study compares OGM to CMA for clinically reported genomic variants, some of these samples also have structural characterization by fluorescence in situ hybridization (FISH). OGM was performed on IRB approved, de-identified specimens from 55 individuals with genomic abnormalities previously identified by CMA (61 clinically reported abnormalities). SVs identified by OGM were filtered by a control database to remove polymorphic variants and against an established gene list to prioritize clinically relevant findings before comparing with CMA and FISH results. OGM results showed 100% concordance with CMA findings for pathogenic variants and 98% concordant for all pathogenic/likely pathogenic/variants of uncertain significance (VUS), while also providing additional insight into the genomic structure of abnormalities that CMA was unable to provide. OGM demonstrates equivalent performance to CMA for CNV and AOH detection, enhanced by its ability to determine the structure of the genome. This work adds to an increasing body of evidence on the analytical validity and ability to detect clinically relevant abnormalities identified by CMA. Moreover, OGM identifies translocations, structures of duplications and complex CNVs intractable by CMA, yielding additional clinical utility.

Abstract 2227: Streamlined workflow for analyzing and reporting hematological malignancies in Bionano VIATM software

Cytogenetic analysis for hematological malignancies most often includes karyotyping, fluorescence in situ hybridization, and rarely, chromosomal microarray (CMA). While considered the gold standard, karyotyping and FISH have significant limitations in resolution of structural variants (SVs). CMA has a much higher resolution, but cannot detect balanced SVs, and is less commonly used in the hematologic oncology setting. Optical genome mapping (OGM) can detect all classes of SVs at high resolution (duplications, deletions, inversions, insertions, translocations), and as such, detects many copy number variants (CNVs) and SVs that have not been previously described. Although these novel SVs will help better describe genetic contributions to disease, analysis, interpretation and curation can take considerable time. A streamlined workflow has been developed for use with Bionano VIA™ software for a comprehensive analysis of relevant SVs in a hematological malignancy genome. First, by employing disease-specific decision trees for variants published in guidelines for those conditions, the software automatically flags Tier 1A variants detected according to ACMG/AMP/CGC criteria. Second, the overall genome complexity is assessed by observing chromosomal abnormalities detected by OGM. Large events (>5Mb) are counted, and complex genomes are assigned if there are more than 3 or 5 events, depending on the cancer type. Third, calls are further refined by filtering on a pan-cancer specific list to capture those variants that are then manually classified as Tier 1B or 2 by the analyst. The Bionano VIA software allows case-specific and disease subtype-specific information to be added to various sections within the software, such as the Knowledgebase, Event Table, and Sample Info fields to facilitate autopopulation of reportable data and interpretations into a formatted report template. Bionano VIA software can also accommodate multiple platforms simultaneously (e.g., NGS panels) to provide users with a comprehensive view of genomic aberrations relevant to hematological malignancies. This workflow is intended to streamline analysis and automate reporting of oncology samples, which can be extremely complex and often require extensive research.

Citation Format: Benjamin Clifford, Jen Hauenstien, Andy Wing Chun Pang, Rachel D. Burnside, Neil Miller, Alex Hastie, Alka Chaubey. Streamlined workflow for analyzing and reporting hematological malignancies in Bionano VIATM software [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2227.

Clinical Evaluation of Scout Accelerated Motion Estimation and Reduction Technique for 3D MR Imaging in the Inpatient and Emergency Department Settings

BACKGROUND AND PURPOSE

A scout accelerated motion estimation and reduction (SAMER) framework has been developed for efficient retrospective motion correction. The goal of this study was to perform an initial evaluation of SAMER in a series of clinical brain MR imaging examinations.

MATERIALS AND METHODS

Ninety-seven patients who underwent MR imaging in the inpatient and emergency department settings were included in the study. SAMER motion correction was retrospectively applied to an accelerated T1-weighted MPRAGE sequence that was included in brain MR imaging examinations performed with and without contrast. Two blinded neuroradiologists graded images with and without SAMER motion correction on a 5-tier motion severity scale (none = 1, minimal = 2, mild = 3, moderate = 4, severe = 5).

RESULTS

The median SAMER reconstruction time was 1 minute 47 seconds. SAMER motion correction significantly improved overall motion grades across all examinations (P < .005). Motion artifacts were reduced in 28% of cases, unchanged in 64% of cases, and increased in 8% of cases. SAMER improved motion grades in 100% of moderate motion cases and 75% of severe motion cases. Sixty-nine percent of nondiagnostic motion cases (grades 4 and 5) were considered diagnostic after SAMER motion correction. For cases with minimal or no motion, SAMER had negligible impact on the overall motion grade. For cases with mild, moderate, and severe motion, SAMER improved the motion grade by an average of 0.3 (SD, 0.5), 1.1 (SD, 0.3), and 1.1 (SD, 0.8) grades, respectively.

CONCLUSIONS

SAMER improved the diagnostic image quality of clinical brain MR imaging examinations with motion artifacts. The improvement was most pronounced for cases with moderate or severe motion.

Characterization of the G protein-coupled receptor family SREB across fish evolution

The SREB (Super-conserved Receptors Expressed in Brain) family of G protein-coupled receptors is highly conserved across vertebrates and consists of three members: SREB1 (orphan receptor GPR27), SREB2 (GPR85), and SREB3 (GPR173). Ligands for these receptors are largely unknown or only recently identified, and functions for all three are still beginning to be understood, including roles in glucose homeostasis, neurogenesis, and hypothalamic control of reproduction. In addition to the brain, all three are expressed in gonads, but relatively few studies have focused on this, especially in non-mammalian models or in an integrated approach across the entire receptor family. The purpose of this study was to more fully characterize sreb genes in fish, using comparative genomics and gonadal expression analyses in five diverse ray-finned (Actinopterygii) species across evolution. Several unique characteristics were identified in fish, including: (1) a novel, fourth euteleost-specific gene (sreb3b or gpr173b) that likely emerged from a copy of sreb3 in a separate event after the teleost whole genome duplication, (2) sreb3a gene loss in Order Cyprinodontiformes, and (3) expression differences between a gar species and teleosts. Overall, gonadal patterns suggested an important role for all sreb genes in teleost testicular development, while gar were characterized by greater ovarian expression that may reflect similar roles to mammals. The novel sreb3b gene was also characterized by several unique features, including divergent but highly conserved amino acid positions, and elevated brain expression in puffer (Dichotomyctere nigroviridis) that more closely matched sreb2, not sreb3a. These results demonstrate that SREBs may differ among vertebrates in genomic structure and function, and more research is needed to better understand these roles in fish.

Identification of Somatic Structural Variants in Solid Tumors by Optical Genome Mapping

Genomic structural variants comprise a significant fraction of somatic mutations driving cancer onset and progression. However, such variants are not readily revealed by standard next-generation sequencing. Optical genome mapping (OGM) surpasses short-read sequencing in detecting large (>500 bp) and complex structural variants (SVs) but requires isolation of ultra-high-molecular-weight DNA from the tissue of interest. We have successfully applied a protocol involving a paramagnetic nanobind disc to a wide range of solid tumors. Using as little as 6.5 mg of input tumor tissue, we show successful extraction of high-molecular-weight genomic DNA that provides a high genomic map rate and effective coverage by optical mapping. We demonstrate the system's utility in identifying somatic SVs affecting functional and cancer-related genes for each sample. Duplicate/triplicate analysis of select samples shows intra-sample reliability but also intra-sample heterogeneity. We also demonstrate that simply filtering SVs based on a GRCh38 human control database provides high positive and negative predictive values for true somatic variants. Our results indicate that the solid tissue DNA extraction protocol, OGM and SV analysis can be applied to a wide variety of solid tumors to capture SVs across the entire genome with functional importance in cancer prognosis and treatment.

Simpson's paradox - aggregating and partitioning populations in health disparities of lung cancer patients

It is well known that non-small cell lung cancer (NSCLC) is a heterogeneous group of diseases. Previous studies have demonstrated genetic variation among different ethnic groups in the epidermal growth factor receptor (EGFR) in NSCLC. Research by our group and others has recently shown a lower frequency of EGFR mutations in African Americans with NSCLC, as compared to their White counterparts. In this study, we use our original study data of EGFR pathway genetics in African American NSCLC as an example to illustrate that univariate analyses based on aggregation versus partition of data leads to contradictory results, in order to emphasize the importance of controlling statistical confounding. We further investigate analytic approaches in logistic regression for data with separation, as is the case in our example data set, and apply appropriate methods to identify predictors of EGFR mutation. Our simulation shows that with separated or nearly separated data, penalized maximum likelihood (PML) produces estimates with smallest bias and approximately maintains the nominal value with statistical power equal to or better than that from maximum likelihood and exact conditional likelihood methods. Application of the PML method in our example data set shows that race and EGFR-FISH are independently significant predictors of EGFR mutation.

Juvenile idiopathic arthritis and exposure to fine particulate air pollution

OBJECTIVES

Inhalation of fine particulate matter, including particles with an aerodynamic diameter less than or equal to a 2.5-microm cut point (PM2.5), has been associated with systemic inflammation and the clinical presentation of various cardiopulmonary heath events. The urban area along Utah's Wasatch Mountains has high PM2.5 concentrations during periods of stagnant air conditions. Short-term inhalation exposures may trigger inflammatory events presenting as symptom onset in new patients with juvenile idiopathic arthritis (JIA). This study evaluated potential associations between JIA symptom onset and temporal changes in regional air pollution measured by stagnant air conditions and PM2.5 concentrations.

METHODS

A case-crossover design was used to analyze associations of regional ambient PM2.5 concentrations with onset date of 338 JIA cases living on Utah's Wasatch Front. Patients were drawn from the Intermountain States Database of Childhood Rheumatic Diseases (1993-2006). Time trends, seasonality, month, and weekday were controlled for by matching. Selected exposure windows of PM2.5 and stagnant air days were used in the model to determine the effect of short term cumulative exposure on JIA symptom onset.

RESULTS

Increased concentrations of PM2.5 and stagnant air conditions in the preceding 14 days were associated with significantly elevated risk of JIA onset in preschool aged children (RR=1.60, 95% CI 1.00-2.54) but not older children. Elevated risk was larger in males and in systemic onset JIA.

CONCLUSION

Exposure to stagnant polluted air may be an environmental risk factor for JIA in young children, potentially triggered by pollution-induced pulmonary mediated inflammation.

Lack of association between beta 2-adrenergic receptor polymorphisms and juvenile idiopathic arthritis

OBJECTIVE

Juvenile idiopathic arthritis (JIA) is a chronic autoimmune arthropathy. Beta 2-adrenergic receptors are a link between the sympathetic nervous system and the immune system. Associations between variants in the gene encoding the beta 2-adrenergic receptor (ADRB2) and autoimmune disorders such as rheumatoid arthritis (RA) have been demonstrated. We aimed to investigate ADRB2 variants for association with JIA.

METHODS

Genotypes and haplotypes of two ADRB2 variants (G16R and Q27E) were determined in 348 children with JIA and 448 healthy controls by direct molecular haplotyping using melting-curve analysis of a fluorescently labelled loci-spanning probe. Case-control analysis was performed to investigate whether ADRB2 variants were associated with JIA.

RESULTS

No association was found between JIA and alleles, genotypes, or haplotypes of ADRB2. Specifically, the haplotype that demonstrated a strong association with RA (R16/Q27) was not associated with JIA. None of the variants demonstrated association after stratification by JIA subtypes or gender.

CONCLUSIONS

Our results indicate that ADRB2 variants are not associated with JIA or any of the major JIA subtypes. These observations suggest that, although they share several clinical and pathological features, JIA and RA have unique genetic associations.

Accelerating medical research using the swift workflow system

Both medical research and clinical practice are starting to involve large quantities of data and to require large-scale computation, as a result of the digitization of many areas of medicine. For example, in brain research - the domain that we consider here - a single research study may require the repeated processing, using computationally demanding and complex applications, of thousands of files corresponding to hundreds of functional MRI studies. Execution efficiency demands the use of parallel or distributed computing, but few medical researchers have the time or expertise to write the necessary parallel programs. The Swift system addresses these concerns. A simple scripting language, SwiftScript, provides for the concise high-level specification of workflows that invoke various application programs on potentially large quantities of data. The Swift engine provides for the efficient execution of these workflows on sequential computers, parallel computers, and/or distributed grids that federate the computing resources of many sites. Last but not least, the Swift provenance catalog keeps track of all actions performed, addressing vital bookkeeping functions that so often cause difficulties in large computations. To illustrate the use of Swift for medical research, we describe its use for the analysis of functional MRI data as part of a research project examining the neurological mechanisms of recovery from aphasia after stroke. We show how SwiftScript is used to encode an application workflow, and present performance results that demonstrate our ability to achieve significant speedups on both a local parallel computing cluster and multiple parallel clusters at distributed sites.

Association of two functional polymorphisms in the CCR5 gene with juvenile rheumatoid arthritis

Juvenile rheumatoid arthritis (JRA) is mediated by Th1-immune responses. In children with JRA, synovial T cells express high levels of the Th1-chemokine receptor CC chemokine receptor 5 (CCR5), which has been implicated in susceptibility to rheumatoid arthritis. To test the hypothesis that genetic variation in CCR5 is associated with susceptibility to JRA, we analyzed patterns of variation in the 5'cis-regulatory region of CCR5 in 124 multiplex families from a JRA-affected sibpair registry. After sequencing the upstream region of CCR5, variants were tested for association with JRA by transmission disequilibrium testing. A single nucleotide polymorphism, C-1835T, was significantly undertransmitted to children with early-onset JRA (P<0.01). C-1835T was genotyped in 424 additional simplex and multiplex families. CCR5-1835T allele was undertransmitted in the cohort of all probands with JRA (P<0.02), as well as in those with early-onset (P<0.01) or pauciarticular JRA (P<0.05). Another variant, a 32-bp deletion in the open reading frame of CCR5 (CCR5-Delta32) was also tested in approximately 700 simplex and multiplex families. CCR5-Delta32 was also significantly undertransmitted to probands with early-onset JRA (P<0.05). Both variants are in regions under natural selection, and result in functional consequences. Our results suggest these CCR5 variants are protective against early-onset JRA.

The New South Wales Fire Brigades' critical incident stress management response to the Thredbo Landslide

The Thredbo Landslide occurred just before midnight on Wednesday, July 30th, 1997. The first call was received by the Regional Fire Communications and subsequently to Sydney where a multiagency response to the first Urban Search and Rescue (USAR) incident in Australia occurred. After ten days, eighteen bodies had been recovered and one survivor rescued, with one of those victims a member of the Thredbo Fire Brigade. Although some 2000 emergency service personnel were involved in the overall operation, 120 firefighters were at the forefront of the "hands on" rescue throughout the incident. In New South Wales the emergency services each have their own Critical Incident Stress Management (CISM) programs which operate independently from each other, and this was the case at Thredbo. This paper will describe how the New South Wales Fire Brigades CISM Program managed the Thredbo incident for the 120 New South Wales Fire Brigades firefighters and officers who attended the rescue operation. We are pleased to share this experience and what we have learned in the hope that it might be helpful to others.

VACTERL with hydrocephalus: spontaneous chromosome breakage and rearrangement in a family showing apparent sex-linked recessive inheritance

The rate of spontaneous and mitomycin C induced chromosome breakage and sister chromatid exchange (SCE) was studied in three related cases diagnosed with VACTERL-H syndrome. There have been recent reports of sporadic patients with VACTERL-H in whom high rates of chromosome breakage were observed. This has led to the suggestion that some of these patients may represent the severe expression of Fanconi anemia. The pattern of inheritance in our family is highly suggestive of X-linked recessive inheritance supporting the hypothesis that VACTERL-H is, at least in some cases, a syndrome and not an association.

The characteristic physiognomy and tissue specific karyotype distribution in the Pallister-Killian syndrome

We report a child with clinical features remarkably similar to those of our patient reported as tetrasomy 21 in 1982. Improved banding in this, and the previous case, together with gene dosage studies, and subsequent reports in the literature lead us to conclude that these patients are in fact tetrasomic for 12p. The clinical features of these children are most distinctive and the importance of their recognition lies in the fact that the abnormal cell line is virtually confined to fibroblast studies.

Detection at amniocentesis of a maternally inherited X;Y translocation

G banded chromosomal analysis of cells from a routine amniocentesis revealed a Y to X translocation in the fetus. The same unbalanced translocation was found in the mother who was disproportionately short. H-Y antigen titers in the mother were intermediate and steroid sulfatase activity was in the normal female range. At birth the baby exhibited few dysmorphic features but appeared to have short limbs.