Development of a comprehensive approach to adult hereditary cancer testing in Ontario.

BACKGROUND: Genetic testing for hereditary cancer susceptibility has advanced over time due to the discovery of new risk genes, improved technology and decreased cost. In the province of Ontario, testing eligibility criteria were initially developed to include hereditary breast, ovarian and colorectal cancer syndromes. The rapid evolution of genetic technologies has facilitated the ability to interrogate a large number of genes concurrently. This, coupled with new knowledge about risk genes, necessitated a coordinated approach to expanding the scope of genes and indications tested and synchronisation of access and test utilisation across the province as required in a publicly funded universal healthcare system. METHODS: Ontario Health-Cancer Care Ontario convened expert working groups to develop a standardised and comprehensive cancer gene list for adults and accompanying hereditary cancer testing (HCT) criteria using an evidence-based framework and broad laboratory and clinical genetics engagement. RESULTS: A standardised 76-cancer-gene panel, organised into 13 larger disease site panels and 25 single/small gene panels, was developed and endorsed by the working groups. Provincial genetic testing eligibility criteria were updated to align with the new panels and to guide clinical decision-making. In the first year following the implementation of these changes, 10 564 HCT panels were performed with an overall mutation detection rate of 12.2%. CONCLUSION: Using an evidence framework and broad clinical engagement to develop and endorse an updated guidance document, cancer genetic testing for adults in Ontario is now standardised and coordinated across the province.

De novo triplication at 1p36.23p36.22 further refines the dosage sensitive region of overlap in Setleis syndrome (focal facial dermal dysplasia type III).

Setleis syndrome (SS), or focal facial dermal dysplasia type III (FFDD3, MIM #227260), is an autosomal recessive condition caused by biallelic loss-of-function variants in TWIST2. It is characterized by bitemporal atrophic skin lesions and distinctive facial features. Individuals with de novo or inherited duplication or triplication of the chromosomal region 1p36.22p36.21 have also been reported to have the SS phenotype with additional neurodevelopmental challenges (rarely seen in individuals with TWIST2 mutations) and variable expressivity and penetrance. Triplication of this region is also associated with more severe manifestations compared to a duplication. We report a 2-year-old female patient with features of SS associated with a de novo 3.603 Mb triplication at 1p36.23p36.22 identified on postnatal microarray analysis. Her triplication shares a 281.263 kb overlap with gains at 1p36.22, reported by previous groups, delineating the shortest region of overlap (SRO) to date. This SRO involves 10 RefSeq and 4 OMIM morbid map genes and highlights the candidate dosage-sensitive element(s) underlying the cardinal features of SS phenotype in individuals with gains at 1p36.

The Clinical Landscape of NRAS- mutated Juvenile Myelomonocytic Leukemia-like Myeloproliferation Includes Children With Costello Syndrome.

Juvenile myelomonocytic leukemia (JMML) is a rare, aggressive pediatric disorder characterized by pathologic myeloproliferation because of alterations in RAS pathway genes. NRAS -mutated JMML encompasses a broad range of clinical severity. Herein we describe 4 unique cases of NRAS -mutated JMML and JMML-like myeloproliferation, 2 with somatic mutations and 2 with germline mutations. These cases illustrate the diverse clinical and hematologic presentation of this subtype of JMML, including a very unusual example presenting with Auer rods. Lastly, this is the first report of patients with phenotypic Costello syndrome presenting with JMML-like myeloproliferation, highlighting an important clinical phenomenon that has not been previously described.

Practice patterns of prenatal and perinatal testing in Canadian cytogenetics laboratories.

OBJECTIVE: To survey patterns of practice in Canadian cytogenetics laboratories and evaluate whether newer technologies have influenced testing algorithms for the detection of common aneuploidies and other genomic imbalances in the prenatal and perinatal settings. METHODS: Cytogenetics laboratories across Canada were invited to participate in two patterns-of-practice surveys: one in 2016 and one in 2019. They were asked to identify the prenatal and perinatal specimen types tested at their facility and which testing methods were used for initial testing and for follow-up. RESULTS: All clinical laboratories performing prenatal testing offer rapid aneuploidy detection (RAD). Most laboratories also offer microarray analysis. A positive result is either followed up by karyotyping or no further testing is performed. For prenatal samples, a negative result may be followed up by microarray or karyotyping and is dependent on the reason for referral. For perinatal samples, availability of microarray to follow up a negative result is increasing. CONCLUSIONS: Since 2016, the availability of RAD as a first-line test in Canadian cytogenetics laboratories remains consistent, while microarray has become the preferred follow-up testing method over traditional karyotyping following a normal RAD result. Despite a universal healthcare system, disparities in prenatal and perinatal cytogenetic testing algorithms are apparent.

Data sharing as a national quality improvement program: reporting on BRCA1 and BRCA2 variant-interpretation comparisons through the Canadian Open Genetics Repository (COGR).

PurposeThe purpose of this study was to develop a national program for Canadian diagnostic laboratories to compare DNA-variant interpretations and resolve discordant-variant classifications using the BRCA1 and BRCA2 genes as a case study.MethodsBRCA1 and BRCA2 variant data were uploaded and shared through the Canadian Open Genetics Repository (COGR; http://www.opengenetics.ca). A total of 5,554 variant observations were submitted; classification differences were identified and comparison reports were sent to participating laboratories. Each site had the opportunity to reclassify variants. The data were analyzed before and after the comparison report process to track concordant- or discordant-variant classifications by three different models.ResultsVariant-discordance rates varied by classification model: 38.9% of variants were discordant when using a five-tier model, 26.7% with a three-tier model, and 5.0% with a two-tier model. After the comparison report process, the proportion of discordant variants dropped to 30.7% with the five-tier model, to 14.2% with the three-tier model, and to 0.9% using the two-tier model.ConclusionWe present a Canadian interinstitutional quality improvement program for DNA-variant interpretations. Sharing of variant knowledge by clinical diagnostic laboratories will allow clinicians and patients to make more informed decisions and lead to better patient outcomes.

The clinical utility of integrative genomics in childhood cancer extends beyond targetable mutations.

We conducted integrative somatic-germline analyses by deeply sequencing 864 cancer-associated genes, complete genomes and transcriptomes for 300 mostly previously treated children and adolescents/young adults with cancer of poor prognosis or with rare tumors enrolled in the SickKids Cancer Sequencing (KiCS) program. Clinically actionable variants were identified in 56% of patients. Improved diagnostic accuracy led to modified management in a subset. Therapeutically targetable variants (54% of patients) were of unanticipated timing and type, with over 20% derived from the germline. Corroborating mutational signatures (SBS3/BRCAness) in patients with germline homologous recombination defects demonstrates the potential utility of PARP inhibitors. Mutational burden was significantly elevated in 9% of patients. Sequential sampling identified changes in therapeutically targetable drivers in over one-third of patients, suggesting benefit from rebiopsy for genomic analysis at the time of relapse. Comprehensive cancer genomic profiling is useful at multiple points in the care trajectory for children and adolescents/young adults with cancer, supporting its integration into early clinical management.

Euchromatic 9q13-q21 duplication variants are tandem segmental amplifications of sequence reciprocal to 9q13-q21 deletions.

BACKGROUND: There are four known pericentromeric euchromatic variants of chromosome 9 in the literature that are increasingly being observed in diagnostic cytogenetic laboratories. These variants pose diagnostic and counselling dilemmas, especially in prenatal settings, as distinction of a pathogenic alteration from a euchromatic variant is difficult. The molecular characterisation of three of these four variants has been reported. In this study, the genomic structure of the fourth variant, an additional G-positive band at 9q13-q21, is characterised. METHODS: Two unrelated families with the 9q13-q21 duplication variant, and a third individual with a cytogenetically visible 9q13-q21 deletion, were studied using conventional and molecular cytogenetics techniques, as well as microarrays. The highly repetitive nature of the segmental duplications in the region also necessitated the use of both interphase and metaphase fluorescence in situ hybridisation (FISH). RESULTS: It was determined that the DNA that constitutes this variant was ∼ 15-20 megabases in size and tandemly repeated as 3-4 cassettes of intrachromosomal segmental duplication. The variant appeared constitutively similar in sequence content and organisation between the two unrelated individuals, and it was inherited without apparent change. Sequences found amplified in the two duplication carriers were absent in the carrier of the deletion variant. CONCLUSIONS: The sequences involved in both the 9q13-q21 duplication and deletion appear the same, implying reciprocity and suggesting non-allelic homologous recombination as the underlying mechanism. All four known euchromatic variants of chromosome 9 have now been shown to encompass segmental duplications. Importantly, a set of validated FISH probes was defined for the detection and characterisation of this 9q13-q21 amplification in the context of other chromosome 9 variants, allowing apparently benign variants to be distinguished from pathogenic changes.

Prospective validation of quantitative fluorescent polymerase chain reaction for rapid detection of common aneuploidies.

PURPOSE: To prospectively validate a quantitative fluorescent polymerase chain reaction (PCR) assay as a method of rapid prenatal aneuploidy detection for chromosomes 13, 18, 21, X, and Y. METHODS: A commercial quantitative fluorescent PCR kit was validated on 200 known, blinded, prenatal DNA specimens. The kit was then validated prospectively on 1069 amniotic fluid specimens, and the results were compared with the karyotype results and the results of interphase fluorescence in situ hybridization testing, when performed in the course of standard care. Turnaround time was monitored in a subset of the prospective specimens. RESULTS: The analytical sensitivity and specificity of testing in the validation specimens were 98.9% and 100%, respectively. There were no false positives and a single false negative, a mosaic sex chromosome aneuploidy interpreted as normal. In the prospective study, the analytical sensitivity and specificity were 98% and 100%, respectively. No false positives and a single false negative, again a sex chromosome mosaic, were detected. Overall, 72.5% of all chromosomal anomalies and 87.7% of clinically significant chromosome anomalies were detected by quantitative fluorescent PCR. The average and median turnaround times were 30.5 and 25.1 hours, respectively. CONCLUSIONS: Quantitative fluorescent PCR is a robust and accurate method of rapid prenatal aneuploidy detection.

The detection of chromosome anomalies by QF-PCR and residual risks as compared to G-banded analysis.

OBJECTIVE: To determine the detection rate of clinically significant chromosome abnormalities using quantitative fluorescent polymerase chain reaction (QF-PCR) of fetal DNA in comparison with G-banded analysis of cultured amniotic fluid cells and determine the residual risk if QF-PCR were performed alone for low-risk cases. METHODS: Amniotic fluid samples were prospectively categorized based on the likelihood of the fetus having a chromosome anomaly. QF-PCR results were compared with the G-banded findings. The distribution of patients and the rates of clinically significant anomalies in each risk category were determined. RESULTS: A total of 4176 amniotic fluid samples were studied. Among these, 331 cases with abnormalities were detected by both methods and an additional 19 abnormal cases were detected by G-banding only. Five of those undetected by QF-PCR were considered clinically significant, four of which were referred due to an elevated a priori risk (>4%). If QF-PCR is performed in all cases and G-banding performed only in higher risk cases, the residual risk for a clinically significant chromosome abnormality will be as low as 0.083%. CONCLUSIONS: This study suggests that QF-PCR alone is appropriate for patients with uncomplicated pregnancies, who are referred solely for an increased risk of a common trisomy.

Building the What Comes Next Cohort for BRCA1 and BRCA2 testing: a descriptive analysis.

BACKGROUND: Our understanding of how testing for and mutations of the BRCA1 and BRCA2 genes affect cancer risk and the use of risk-reduction strategies comes largely from studies of women recruited from specialized genetics clinics. Our aim was to assemble a generalizable cohort of women who underwent BRCA1/BRCA2 testing (the What Comes Next Cohort), irrespective of test result, to enable study of health care utilization and outcomes after testing. METHODS: This descriptive study included adult women (≥ 18 yr) who met at least 1 of 13 provincial criteria for BRCA1/BRCA2 testing and who underwent genetic testing at sites in Ontario, Canada, from 2007 to 2016. Most of the women were tested at 1 of 2 main sites, which together capture about 70% of all BRCA1/BRCA2 testing in the province. We collected detailed demographic, genetic testing and family history data through chart review for linkage with data from administrative health databases providing information on cancer history before and after testing. We followed all women to September 2019, evaluating the demographic characteristics of the cohort, indications for testing and test results. RESULTS: We identified 15 986 women (mean age 52.5 [standard deviation 13.9] yr) who underwent BRCA1/BRCA2 testing. Of these, 2033 women had positive results, 1175 women had variants of uncertain significance, and 12 778 women had negative results. Positive yields were 41.0% (955/2329) for predictive testing (for familial variants), 10.4% (216/2072) for Ashkenazi Jewish founder testing and 7.4% (862/11 585) for complete gene analysis. Six of the 13 provincial testing criteria had less than 10% positive yield. Among 403 women who tested negative for Ashkenazi Jewish founder mutations and subsequently underwent complete gene analysis, 12 (3.0%) tested positive for alternate pathogenic or likely pathogenic variants in the BRCA1 or BRCA2 gene. INTERPRETATION: Several provincial eligibility criteria for BRCA1/BRCA2 testing led to positive results in less than 10% of cases. How testing influences women's health care behaviours, particularly those with negative results and those found to carry variants of uncertain significance, is unknown; the What Comes Next Cohort will be instrumental in the study of long-term implications of BRCA1/BRCA2 testing.

Src promotes estrogen-dependent estrogen receptor alpha proteolysis in human breast cancer.

Estrogen drives both transcriptional activation and proteolysis of estrogen receptor alpha (ER alpha; encoded by ESR1). Here we observed variable and overlapping ESR1 mRNA levels in 200 ER alpha-negative and 50 ER alpha-positive primary breast cancers examined, which suggests important posttranscriptional ER alpha regulation. Our results indicate that Src cooperates with estrogen to activate ER alpha proteolysis. Inducible Src stimulated ligand-activated ER alpha transcriptional activity and reduced ER alpha t(1/2). Src and ER alpha levels were inversely correlated in primary breast cancers. ER alpha-negative primary breast cancers and cell lines showed increased Src levels and/or activity compared with ER alpha-positive cancers and cells. ER alpha t(1/2) was reduced in ER alpha-negative cell lines. In both ER alpha-positive and -negative cell lines, both proteasome and Src inhibitors increased ER alpha levels. Src inhibition impaired ligand-activated ER alpha ubiquitylation and increased ER alpha levels. Src siRNA impaired ligand-activated ER alpha loss in BT-20 cells. Pretreatment with Src increased ER alpha ubiquitylation and degradation in vitro. These findings provide what we believe to be a novel link between Src activation and ER alpha proteolysis and support a model whereby crosstalk between liganded ER alpha and Src drives ER alpha transcriptional activity and targets ER alpha for ubiquitin-dependent proteolysis. Oncogenic Src activation may promote not only proliferation, but also estrogen-activated ER alpha loss in a subset of ER alpha-negative breast cancers, altering prognosis and response to therapy.

Associations between the uptake of 111In-DTPA-trastuzumab, HER2 density and response to trastuzumab (Herceptin) in athymic mice bearing subcutaneous human tumour xenografts.

PURPOSE: The purpose of the study was to investigate the associations between uptake of (111)In-DTPA-trastuzumab, tumour HER2 density and response to trastuzumab (Herceptin) of human breast cancer (BC) xenografts in athymic mice. MATERIALS AND METHODS: The tumour uptake of (111)In-DTPA-trastuzumab in athymic mice bearing BC xenografts with increasing HER2 density (0 to 3+) was evaluated. Specific uptake ratios were established in biodistribution (SUR) and imaging studies (ROI-SUR) using (111)In-labeled mouse IgG ((111)In-DTPA-mIgG). Further corrections were made for circulating radioactivity using tumour-to-blood ratios defined as a localization index (LI) and region-of-interest localization index (ROI-LI), respectively. Mice were treated with trastuzumab (Herceptin). A tumour growth inhibition index (TGI) was calculated and relative TGIs calculated by dividing the TGI of control by that of trastuzumab-treated mice. RESULTS: Strong, nonlinear associations with HER2 density were obtained if the uptake of (111)In-DTPA-trastuzumab was corrected for nonspecific IgG localization (i.e., SUR; r (2) = 0.99) and circulating radioactivity (i.e., LI; r (2) = 0.87), but without these corrections, the association between HER2 density and tumour uptake was poor (r (2) = 0.22). There was a strong association between ROI-SUR and ROI-LI values and HER2 expression (r (2) = 0.90 and r (2) = 0.95, respectively. All tumours were imaged. Relative TGI values were associated with increasing uncorrected tumour uptake of (111)In-DTPA-trastuzumab but not always with HER2 density (i.e., MCF-HER2-18 cells with trastuzumab-resistance). CONCLUSION: HER2 expression (0 to 3+) can be differentiated using (111)In-DTPA-trastuzumab, but requires correction of tumour uptake for nonspecific IgG localization and circulating radioactivity. The uncorrected uptake of (111)In-DTPA-trastuzumab was associated with tumour response to trastuzumab.

A single nucleotide polymorphism chip-based method for combined genetic and epigenetic profiling: validation in decitabine therapy and tumor/normal comparisons.

Progress on several unresolved issues in cancer epigenetics will benefit from rapid and standardized methods for profiling DNA methylation genome-wide. In the area of epigenetic therapy, the demethylating drug decitabine (5-aza-2'-deoxycytidine) is increasingly used to treat acute myelogenous leukemia and myelodysplastic syndrome, but the mechanisms of its anticancer activity have remained unclear. Given the clinical efficacy of decitabine and the uncertainties about its mode of action, it will be useful to optimize methods for following DNA methylation as a biochemical response in individual patients. Here, we describe a single nucleotide polymorphism (SNP) chip-based method (MSNP) for profiling DNA methylation. Using this procedure, the extent of demethylation in bone marrow aspirates from patients with leukemia receiving decitabine can be assessed genome-wide using commercially available (Affymetrix) SNP chips. We validated the accuracy of MSNP by comparing the results with combined bisulfite restriction analysis and by sequencing cloned PCR products from bisulfite-converted DNA. We further validated MSNP in a Wilms' tumor/normal kidney comparison, comparing the results with methylation-sensitive Southern blotting. MSNP simultaneously detects aberrations in DNA copy number and loss of heterozygosity, making it a generally useful approach for combined genetic and epigenetic profiling in tissue samples from cancer patients.

Assessing copy number aberrations and copy-neutral loss-of-heterozygosity across the genome as best practice: An evidence-based review from the Cancer Genomics Consortium (CGC) working group for chronic lymphocytic leukemia.

The prognostic role of cytogenetic analysis is well-established in B-cell chronic lymphocytic leukemia (CLL). Approximately 80% of patients have a cytogenetic aberration. Interphase FISH panels have been the gold standard for cytogenetic evaluation, but conventional cytogenetics allows detection of additional abnormalities, including translocations, complex karyotypes and multiple clones. Whole genome copy number assessment, currently performed by chromosomal microarray analysis (CMA), is particularly relevant in CLL for the following reasons: (1) copy number alterations (CNAs) represent key events with biologic and prognostic significance; (2) DNA from fresh samples is generally available; and (3) the tumor burden tends to be relatively high in peripheral blood. CMA also identifies novel copy number variants and copy-neutral loss-of-heterozygosity (CN-LOH), and can refine deletion breakpoints. The Cancer Genomics Consortium (CGC) Working Group for CLL has performed an extensive literature review to describe the evidence-based clinical utility of CMA in CLL. We provide suggestions for the integration of CMA into clinical use and list recurrent copy number alterations, regions of CN-LOH and mutated genes to aid in interpretation.

Characteristics and outcomes of acute myelogenous leukemia patients with very late relapse (>5 years).

The clinical characteristics and outcome of 15 patients with acute myelogenous leukemia (AML) who experienced relapse at least 5 years after induction of complete remission (very late-relapse AML) are described. This subgroup represented 3% of all relapsed patients seen at this institution over the same time period. There were eight males in this cohort and the median age at diagnosis was 48 years (range 13 - 77 years). Nine patients had M4/M5 French - American - British (FAB) classification subtype and most had intermediate risk cytogenetics. The median duration of first complete remission (CR-1) was 9 years (range 5.2 - 11.5 years). Thirteen patients (86%) achieved CR-2 with reinduction therapy. The 5-year relapse-free survival and overall survival rates of this cohort were 59% and 51%, respectively. We conclude that very late-relapse AML is a rare event, and that reinduction in these patients is associated with very high CR rates and a potential cure fraction.

Progression of myelodysplasia to acute lymphoblastic leukaemia: implications for disease biology.

Myelodysplastic syndrome (MDS) comprises a group of clonal haematopoietic disorders characterized by peripheral blood cytopenias, bone marrow hypercellularity, and abnormal blood cell differentiation. Approximately 30% of cases of MDS eventually progress to acute myelogenous leukemia (AML), while progression of MDS into acute lymphoblastic leukemia (ALL) is rare. In this report, we describe a case of MDS that progressed to ALL, and review the 21 previously reported cases of MDS to ALL transformation. We review the cancer stem cell model and its application to these disorders, and discuss the implications of the rarity of transformation of MDS to ALL for the biology of MDS and the pathogenesis of ALL.

Extramedullary infiltrates of AML are associated with CD56 expression, 11q23 abnormalities and inferior clinical outcome.

We evaluated the frequency and prognostic significance of extramedullary infiltrates (EMI) at presentation of acute myeloid leukemia (AML) in adult patients. Of 331 cases with de novo AML, 101(30.5%) had extramedullary infiltrates at diagnosis. The extramedullary manifestations included: lymphadenopathy, splenomegaly, hepatomegaly, gingival hypertrophy, skin infiltrates and involvement of central nervous system (CNS). Patients with EMI had a high initial WBC count and a high proportion of M4/M5 morphological variants. The complete remission rate (CR) with induction chemotherapy was lower in patients with EMI (P=0.0077) and their overall survival was also inferior (P=0.0017). Flow cytometric evaluation of the surface antigens expressed by the leukemic blasts for CD34, TdT, HLADR, CD7, CD19 and CD56 found that only CD56 expression was associated with EMI. The association of CD56 expression with lymphadenopathy was statistically significant (P=0.035). Abnormal karyotypes were found in 50.6% of patients with EMI and 49.7% of patients without EMI. Only 11q23 abnormalities were associated with specific sites of EMI; lymphadenopathy (P=0.0111) and gingival hypertrophy (P=0.0016). Our study of adult AML patients demonstrates that EMI at diagnosis is associated with CD56 expression by leukemic blasts, 11q23 karyotypic abnormalities, low complete remission rate and poor overall survival.

Prognostic significance of trisomy 4 as the sole cytogenetic abnormality in acute myeloid leukemia.

Trisomy 4 is a recurrent but rare cytogenetic abnormality reported in patients with acute myeloblastic leukemia (AML). The prognostic significance of this abnormality in patients with AML is not clear. We report here four cases of trisomy 4 as the sole cytogenetic abnormality in AML patients treated at our institute during the last 15 years and systematically review all reported cases of trisomy 4 as a solitary cytogenetic abnormality in AML with the aim of studying the disease demography and prognostic significance of this abnormality. Collective data on 30 patients (including four in the present report) showed complete remission (CR) rates of 76.6%. Median relapse free survival and overall survival were 7 months (95% CI 5-17) and 9 months (95% CI 3-17), respectively. Given the limitations of reported literature, the prognosis of AML patients with trisomy 4 appears to be poor compared with the intermediate risk cytogenetics. Collaborations between major institutions and cooperative groups are needed to collect better quality data to understand the prognostic significance of such rare karyotypic abnormalities.

Acute leukemia of donor origin arising after stem cell transplantation for acute promyelocytic leukemia.

We report a patient with PML/RARalpha-positive acute promyelocytic leukemia (APL) who developed PML/RARalpha-negative acute myeloid leukemia 37 months after allogeneic bone marrow (BMT) transplant for molecular relapse. Features of myelodysplasia were noted 11 months earlier, chimerism testing by analysis of short tandem repeats was consistent with development of myelodysplasia and acute leukemia within cells of donor origin. To our knowledge, this is the first report of donor cell leukemia following BMT for APL. We hypothesize that replicative stress may lead to the development of some cases of donor cell acute leukemia.