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Papers by Susan Crocker

Table S1. RT-PCR Targets within the Ion AmpliSeq™ Lung Fusion Research Panel. A list of all targe... more Table S1. RT-PCR Targets within the Ion AmpliSeq™ Lung Fusion Research Panel. A list of all targets in the multiplex PCR studied – including targeted fusions (genes and exons), expression control genes, and 3′and 5′regions. Table S2. ALK Clinical Samples. Table depicting details on all ALK clinical research samples analyzed in the study. Table S3. ROS1 and RET clinical samples. Table depicting details on all ROS1 and RET clinical research samples analyzed in the study. (DOCX 57 kb)

The Journal of Molecular Diagnostics, 2021

The identification of clinically significant genes recurrently mutated in myeloid malignancies ne... more The identification of clinically significant genes recurrently mutated in myeloid malignancies necessitates expanding diagnostic testing with higher throughput, such as targeted next-generation sequencing (NGS). We present validation of the Thermo Fisher Oncomine Myeloid NGS Panel (OMP), targeting 40 genes and 29 fusion drivers recurrently mutated in myeloid malignancies. The study includes data from a sample exchange between two Canadian hospitals demonstrating high concordance for detection of DNA and RNA aberrations. Clinical validation demonstrates high accuracy, sensitivity, and specificity of the OMP, with a lower limit of detection of 5% for single nucleotide variants and 10% for insertions/deletions. Prospective sequencing was performed for 187 samples from 168 unique patients presenting with suspected or confirmed myeloid malignancy and other hematological conditions to assess clinical impact of identifying variants. Of detected variants, 48% facilitated or clarified diagnoses, 29% affected prognoses, and 25% had the potential to influence clinical management. Of note, OMP was essential to identifying patients with pre-malignant clonal states likely contributing to cytopenias. We also found that the detection of even a single variant by the OMP assay, versus 0 variants, was predictive of overall survival, independent of age, sex or diagnosis (p = 0.03). This study demonstrates that molecular profiling of myeloid malignancies with the OMP represents a promising strategy to advance molecular diagnostics.

PAMJ Clinical Medicine, 2020

INTRODUCTION: The BCR-ABL1 fusion gene has been associated with poor prognosis in acute lymphobla... more INTRODUCTION: The BCR-ABL1 fusion gene has been associated with poor prognosis in acute lymphoblastic leukaemia (ALL). This study was designed to determine the presence, frequency and associated laboratory and clinical features of the BCR-ABL1 gene in Ghanaian patients diagnosed with ALL. METHODS: this was a cross-sectional study using archival methanol-fixed bone marrow aspirate slides of morphologically diagnosed ALL patients. Presence of the BCR-ABL1fusion gene was determined by fluorescent in situ hybridization. Clinical features and haematological parameters were extracted from the patients’ medical records. RESULTS: seventeen patients were studied, 13 (76.5%) males and 4 (23.5%) females. Median age was 24 years (range 15 to 67 years). A frequency of 29.4% was obtained for the BCR-ABL1 fusion gene. There was no significant association between presence of BCR-ABL1 and selected clinical features (lymphadenopathy, splenomegaly and hepatomegaly). All patients had moderate to severe anaemia with median haemoglobin concentration of 7.6 g/dL (range 3.7 to 8.7 g/dL). Median haemoglobin concentration for BCR-ABL1 positive patients was higher than that for negative patients (7.6 vs. 7.4 g/dL, p = 0.506); who also had higher median white blood cell counts (24.76 vs. 13.02 X 109/L), but lower median platelet counts (58.0 vs. 64.5 X 109/L, p = 0.721) and bone marrow blast percentages (78.5 vs. 98.0 %, p = 0.851) compared to negative patients. Conclusion: BCR-ABL1 fusion gene was detected in nearly one third of adult ALL patients in this study, with no significant association with common haematological parameters and clinical features of the disease.

Cancer Genetics, 2020

This study demonstrated the wide genomic distribution of NUP98 translocation partners in a broad ... more This study demonstrated the wide genomic distribution of NUP98 translocation partners in a broad spectrum of hematologic malignancies. Mate-pair sequencing is a powerful complementary method to identify NUP98 partners not targeted by FISH.

Leukemia & Lymphoma, 2020

Up-regulation of BCL2 in cases of diffuse large B-cell lymphoma (DLBCL) can confer treatment resi... more Up-regulation of BCL2 in cases of diffuse large B-cell lymphoma (DLBCL) can confer treatment resistance. Quantitative immunofluorescence (QIF) histology allows objective quantification of protein-based biomarkers. We investigated the utility of QIF for evaluating BCL2 as a biomarker in DLBCL by quantifying BCL2 selectively in CD20-expressing lymphoma cells in biopsy samples from 116 cases of DLBCL in two cohorts one of which consisted of relapsed/refractory cases from a clinical trial. BCL2 protein by QIF correlated with BCL2 mRNA abundance and was associated with both translocation and copy number gain of the BCL2 gene. Elevated BCL2 protein expression by QIF, but not immunohistochemistry or mRNA quantification, was associated with inferior overall and relapse-free survival in the relapsed/refractory cohort. QIF is an effective means of quantifying BCL2 protein objectively in routine cancer biopsy specimens and shows promise for identifying relapsed/refractory DLBCL patients at risk of inferior outcomes after salvage therapy.

BMC cancer, Jan 16, 2018

Gene fusion events resulting from chromosomal rearrangements play an important role in initiation... more Gene fusion events resulting from chromosomal rearrangements play an important role in initiation of lung adenocarcinoma. The recent association of four oncogenic driver genes, ALK, ROS1, RET, and NTRK1, as lung tumor predictive biomarkers has increased the need for development of up-to-date technologies for detection of these biomarkers in limited amounts of material. We describe here a multi-institutional study using the Ion AmpliSeq™ RNA Fusion Lung Cancer Research Panel to interrogate previously characterized lung tumor samples. Reproducibility between laboratories using diluted fusion-positive cell lines was 100%. A cohort of lung clinical research samples from different origins (tissue biopsies, tissue resections, lymph nodes and pleural fluid samples) were used to evaluate the panel. We observed 97% concordance for ALK (28/30 positive; 71/70 negative samples), 95% for ROS1 (3/4 positive; 19/18 negative samples), and 93% for RET (2/1 positive; 13/14 negative samples) between t...

Diagnostic pathology, Jan 24, 2018

We report the first case of composite lymphoma consisting of chronic lymphocytic leukemia/small l... more We report the first case of composite lymphoma consisting of chronic lymphocytic leukemia/small lymphocytic lymphoma (CLL/SLL), follicular lymphoma (FL) and high-grade B-cell lymphoma with MYC and BCL2 rearrangements within the same needle biopsy in which a clonal relationship between the FL and high-grade B-cell lymphoma components was demonstrated by molecular cytogenetics. An 85-year-old man presented with masses in his neck and right groin. Cutting needle biopsy of the inguinal mass revealed the three lymphoma types which were morphologically, immunophenotypically and topographically distinct. Fluorescence in situ hybridization (FISH) identified an IGH-BCL2 rearrangement in both the FL and high-grade B-cell components while a MYC rearrangement was detected in the high-grade B-cell component alone. Our findings suggest that the high-grade lymphoma with MYC and BCL2 translocations evolved through transformation of the FL by a process that entailed acquisition of the MYC translocat...

$Research paper thumbnail of The CDK inhibitor AT7519M in patients with relapsed or refractory chronic lymphocytic leukemia (CLL) and mantle cell lymphoma. A Phase II study of the Canadian Cancer Trials Group$

Leukemia & Lymphoma, 2016

AT7519M is a small molecule inhibitor of cyclin-dependent kinases 1, 2, 4, 5, and 9 with in vitro... more AT7519M is a small molecule inhibitor of cyclin-dependent kinases 1, 2, 4, 5, and 9 with in vitro activity against lymphoid malignancies. In two concurrent Phase II trials, we evaluated AT7519M in relapsed or refractory chronic lymphocytic leukemia (CLL) and mantle cell lymphoma (MCL) using the recommended Phase II dosing of 27 mg/m 2 twice weekly for 2 of every 3 weeks. Primary objective was objective response rate (ORR). Nineteen patients were accrued (7 CLL, 12 MCL). Four CLL patients achieved stable disease (SD). Two MCL patients achieved partial response (PR), and 6 had SD. One additional MCL patient with SD subsequently achieved PR 9 months after completion of AT7519M. Tumor lysis syndrome was not reported. In conclusion, AT7519M was safely administered to patients with relapsed/refractory CLL and MCL. In CLL, some patients had tumor reductions, but the ORR was low. In MCL, activity was noted with ORR of 27%.

Journal of Pediatric Hematology/Oncology, 2011

We report a unique pediatric case of hypergranular acute myeloid leukemia with myelodysplasia-rel... more We report a unique pediatric case of hypergranular acute myeloid leukemia with myelodysplasia-related changes. The patient presented with moderate leukocytosis with neutrophilia with left-shift maturation and dysplasia, anemia, and multiple sclerotic bone lesions. The bone marrow was hypercellular with a predominance of myeloblast cells and/or abnormal promyelocytes with hypergranular cytoplasm. Flow cytometric immunophenotyping showed that the leukemic cells were positive for CD13, CD33, and myeloperoxidase, and negative for HLA-DR and CD34. Morphology and immunophenotyping were highly suggestive of acute promyelocytic leukemia. The classic t(15;17) or other RARa rearrangements were not detected by cytogenetic or molecular assays, ruling out acute promyelocytic leukemia. Standard cytogenetic analysis showed that the karyotype of the predominant clone was 47, XY,+6 with evidence of clonal evolution to 47, XY,+6,del(5)(q22q33). A literature and database review showed that trisomy 6 is a rare occurrence in hematological malignancies and, to our knowledge, has never been reported in association with del(5)(q22q33) in a child presenting with hypergranular acute myeloid leukemia with myelodysplasia-related changes. We present a current review of the literature and summarize the clinical features of 57 cases of trisomy 6 as the primary chromosomal abnormality in hematological disease.

Human Molecular Genetics, 2005

Huntington disease (HD) results from polyglutamine expansion in the huntingtin protein (htt). Des... more Huntington disease (HD) results from polyglutamine expansion in the huntingtin protein (htt). Despite the widespread tissue expression pattern of htt, neuronal loss is highly selective to medium spiny neurons of the striatum. Huntingtin is phosphorylated on serine-421 (S421) by the pro-survival signaling protein kinase Akt (PKB) and this has been previously shown to be protective against the toxicity of polyglutamine-expanded htt in cell culture. Using an antibody specific for htt phosphorylated on S421, we now demonstrate that htt phosphorylation is present at significant levels under normal physiological conditions in human and mouse brain. Furthermore, htt phosphorylation shows a regional distribution with the highest levels in the cerebellum, less in the cortex, and least in the striatum. In cell cultures and in YAC transgenic mice, the endogenous phosphorylation of polyglutamine-expanded htt is significantly reduced relative to wild-type htt. The presence and pattern of significant htt phosphorylation in the brain indicates that this dynamic post-translational modification is important for the regulation of htt and may contribute to the selective neurodegeneration seen in HD.

Clinical Neurophysiology, 2000

We investigated event-related brain potentials (ERPs) elicited by a novel speech comprehension pa... more We investigated event-related brain potentials (ERPs) elicited by a novel speech comprehension paradigm modelled after the neuropsychological Token Test. The objective of the study was to determine whether the ERPs were sensitive to differences in the initial phonemes of the speech stimuli. Twenty-seven healthy subjects identified incorrect spoken sentences on the computerised Token Test (CTT). The incorrect spoken sentences contained one word that did not match the previously studied animations. The initial phonemes of these words were either different than or similar to the initial phonemes of their correct counterparts. Different initial phonemes were associated with an early N2b, while words having similar initial phonemes resulted in a substantially delayed N2b. The delayed latency effect was due to whether the incorrect word's initial phoneme matched or mismatched that of the expected word. In both cases, this component reflected a mismatch with an existing cognitive template maintained in phonological working memory. The results indicate that this mismatching effect reflected primarily attentional detection rather than language processing.

Clinical Chemistry, 2009

Background: The use of fetal DNA in maternal plasma for noninvasive prenatal diagnosis of trisomy... more Background: The use of fetal DNA in maternal plasma for noninvasive prenatal diagnosis of trisomy 21 (T21) is an actively researched area. We propose a novel method of T21 detection that combines fetal-specific epigenetic and genetic markers. Methods: We used combined bisulfite restriction analysis to search for fetal DNA markers on chromosome 21 that were differentially methylated in the placenta and maternal blood cells and confirmed any target locus with bisulfite sequencing. We then used methylation-sensitive restriction endonuclease digestion followed by microfluidics digital PCR analysis to investigate the identified marker. Chromosome-dosage analysis was performed by comparing the dosage of this epigenetic marker with that of the ZFY (zinc finger protein, Y-linked) gene on chromosome Y. Results: The putative promoter of the HLCS (holocarboxylase synthetase) gene was hypermethylated in the placenta and hypomethylated in maternal blood cells. A chromosome-dosage comparison of t...

Brain Research, 2006

Huntington's disease (HD) is an inherited, progressive neurodegenerative disorder caused by CAG r... more Huntington's disease (HD) is an inherited, progressive neurodegenerative disorder caused by CAG repeat expansion in the gene that codes for the protein huntingtin. The underlying neuropathological events leading to the selectivity of striatal neuronal loss are unknown. However, the huntingtin mutation interferes at several levels of normal cell function. The complexity of this disease makes microarray analysis an appealing technique to begin the identification of common pathways that may contribute to the pathology. In this study, striatal tissue was extracted for gene expression profiling from wild-type and symptomatic transgenic Huntington mice (R6/2) expressing part of the human Huntington's disease gene. We interrogated a 15 K high-density mouse EST array not previously used for HD and identified 170 significantly differentially expressed ESTs in symptomatic R6/2 mice. Of the 80 genes with known function, 9 genes had previously been identified as altered in HD. 71 known genes were associated with HD for the first time. The data obtained from this study confirm and extend previous observations using DNA microarray techniques on genetic models for HD, revealing novel changes in expression in a number of genes not previously associated with HD. Further bioinformatic analysis, using software to construct biological association maps, focused attention on proteins such as insulin and TH1-mediated cytokines, suggesting that they may be important regulators of affected genes. These results may provide insight into the regulation and interaction of genes that contribute to adaptive and pathological processes involved in HD.

American Journal of Medical Genetics, 2000

During a recent trip to the Palestinian city of Nablus, I examined a 4-year-old boy (JH) with str... more During a recent trip to the Palestinian city of Nablus, I examined a 4-year-old boy (JH) with strikingly unusual facial appearance; he appeared as if he was wearing a mask. The parents were phenotypically normal and nonconsanguineous. The father was 32 and the mother 25 years old at the time of JH's birth. JH is one of twins; his twin sister is phenotypically normal. The twins have a 7-year-old brother who is normal. There is no family history of a similar condition or other birth defects. Pregnancy history was unremarkable and delivery was normal at term. JH appeared unusual at birth, whereas his twin sister appeared normal. Birth weight was 2.6 kg and his sister's was 2.9 kg. JH's psychomo

American Journal of Audiology, 2014

Purpose The authors report on a 7-year-old male, designated FR, who has severe sensorineural hear... more Purpose The authors report on a 7-year-old male, designated FR, who has severe sensorineural hearing loss. Features include a round face, hypertelorism, epicanthal folds, and flat nasal root. Although there were early developmental concerns regarding FR, all but his speech delay resolved when he was placed in an educational program that accommodated his hearing loss. Genetic studies were performed to investigate genetic causes for his hearing loss. Method History, physical examination, audiologic assessment, and imaging were performed according to usual practice. FMR1, GJB2, GJB6, and POU3F4 genes were sequenced. Chromosomal studies consisted of karyotyping and breakpoint analysis by fluorescence in situ hybridization (FISH). Results Results from FMR1, GJB2, GJB6, and POU3F4 sequencing and echocardiography, electrocardiogram, and abdominal ultrasound were normal. A computed tomography (CT) scan revealed a large fundus of the internal auditory canals and absence of the bony partition...

Blood, 2014

Introduction: The prognosis of patients (pts) with relapsed or refractory (rel/ref) Chronic Lymph... more Introduction: The prognosis of patients (pts) with relapsed or refractory (rel/ref) Chronic Lymphocytic Leukemia (CLL) is poor. AT7519M is a small molecule inhibitor of cyclin-dependent kinases (CDKs) 1, 2, 4, 5 and 9 with lower potency against CDKs 3, 6 and 7. AT7519 has potent anti-proliferative activity against peripheral blood mononuclear cells isolated from CLL patients. Exposure of CLL cells to AT7519 results in cell cycle arrest and, ultimately, cell death by apoptosis. Based on the results of a NCIC CTG phase I study in advanced malignancies, the recommended phase II dose (RP2D) was 27 mg/m2 given as a 1 hour infusion twice weekly for 2 out of every 3 weeks. Using this schedule, Tumor Lysis Syndrome (TLS) and QTc prolongation were not observed. Methods: In a phase II clinical trial, we evaluated the clinical and pharmacodynamic effects of AT7519 using the RP2D schedule in pts with rel/ref CLL. Eligible patients were those with documented CLL with at least one prior systemic ...

American Journal of Medical Genetics Part A, 2012

Nablus mask-like facial syndrome (NMLFS) has many distinctive phenotypic features, particularly t... more Nablus mask-like facial syndrome (NMLFS) has many distinctive phenotypic features, particularly tight glistening skin with reduced facial expression, blepharophimosis, telecanthus, bulky nasal tip, abnormal external ear architecture, upswept frontal hairline, and sparse eyebrows. Over the last few years, several individuals with NMLFS have been reported to have a microdeletion of 8q21.3q22.1, demonstrated by microarray analysis. The minimal overlapping region is 93.98-96.22 Mb (hg19). Here we present clinical and microarray data from five singletons and two mother-child pairs who have heterozygous deletions significantly overlapping the region associated with NMLFS. Notably, while one mother and child were said to have mild tightening of facial skin, none of these individuals exhibited reduced facial expression or the classical facial phenotype of NMLFS. These findings indicate that deletion of the 8q21.3q22.1 region is necessary but not sufficient for development of the NMLFS. We discuss possible genetic mechanisms underlying the complex pattern of inheritance for this condition.