Ronald F. Carter

Clinically detectable copy number variations in a Canadian catchment population of schizophrenia

Copy number variation (CNV) is a highly topical area of research in schizophrenia, but the clinical relevance is uncertain and the translation to clinical practice is under-studied. There is a paucity of research involving truly community-based samples of schizophrenia and widely available laboratory techniques. Our objective was to determine the prevalence of clinically detectable CNVs in a community sample of schizophrenia, while mimicking typical clinical practice conditions. We used a brief clinical screening protocol for developmental features in adults with schizophrenia for identifying individuals with 22q11.2 deletions and karyotypically detectable chromosomal anomalies in 204 consecutive patients with schizophrenia from a single Canadian catchment area. Twenty-seven (13.2%) subjects met clinical criteria for a possible syndrome, and 26 of these individuals received clinical genetic testing. Five of these, representing 2.5% of the total sample (95% CI: 0.3%-4.6%), including two of ten patients with mental retardation, had clinically detectable anomalies: two 22q11.2 deletions (1.0%), one 47, XYY, and two other novel CNVs--an 8p23.3-p23.1 deletion and a de novo 19p13.3-p13.2 duplication. The results support the utility of screening and genetic testing to identify genetic syndromes in adults with schizophrenia in clinical practice. Identifying large, rare CNVs (particularly 22q11.2 deletions) can lead to significant changes in management, follow-up, and genetic counselling that are helpful to the patient, family, and clinicians.

Morphology of acute promyelocytic leukemia with cytogenetic or molecular evidence for the diagnosis: characterization of additional microgranular variants.

Early diagnosis of t(15;17) acute promyelocytic leukemia (APL) is essential because of the associated disseminated intravascular coagulation and the unique response of the disease to all‐trans retinoic acid (ATRA) therapy. Early diagnosis depends primarily on morphological recognition. The French‐American‐British (FAB) classification, however, does not describe all morphological variations that occur in APL. In 25 cases with evidence of APL confirmed by cytogenetic and/or molecular analysis, we found a heterogeneous morphological group. The most common form of APL was heterogeneous and consisted of various combinations of cells in which hypergranular cells and some cells with multiple Auer rods were obvious. In some cases, one cell predominated. This led to the description of five subcategories. These included the classical FAB M3 with hypergranular cells and multiple Auer rods; the FAB variant with hypogranular bilobed cells; the basophilic cell type of McKenna et al. [Br. J. Haematol 50:201, 1982]; and two additional subtypes, one consisting of differentiated promyelocytes and a few blast cells (M2‐like), and the other consisting largely of blast cells and a few early promyelocytes (M1‐like). Immunophenotyping revealed a pattern of CD33 and/or CD13 positivity, and CD14 and HLA‐DR negativity in 96% of cases. CD2 was positive in the FAB variant and in the subtype with basophilic cells, but negative with other subtypes. Three out of five cases with basophilic cell predominance [McKenna et al.: Br J Haematol 50:201, 1982], and one out of two M2‐like cases, responded to ATRA therapy. Awareness of the heterogeneity and the atypical morphologic subtypes found in t(15;17) APL will contribute to improved recognition and early institution of ATRA therapy. Am. J. Hematol. 56:131–142, 1997.

Canadian Anaplastic Lymphoma Kinase Study: A Model for Multicenter Standardization and Optimization of ALK Testing in Lung Cancer

Introduction: Fluorescence in situ hybridization (FISH) is currently the standard for diagnosing anaplastic lymphoma kinase (ALK)-rearranged (ALK+) lung cancers for ALK inhibitor therapies. ALK immunohistochemistry (IHC) may serve as a screening and alternative diagnostic method. The Canadian ALK (CALK) study was initiated to implement a multicenter optimization and standardization of laboratory developed ALK IHC and FISH tests across 14 hospitals. Methods: Twenty-eight lung adenocarcinomas with known ALK status were used as blinded study samples. Thirteen laboratories performed IHC using locally developed staining protocols for 5A4, ALK1, or D5F3 antibodies; results were assessed by H-score. Twelve centers conducted FISH using protocols based on Vysis’ ALK break-apart FISH kit. Initial IHC results were used to optimize local IHC protocols, followed by a repeat IHC study to assess the results of standardization. Three laboratories conducted a prospective parallel IHC and FISH analysis on 411 consecutive clinical samples using post-validation optimized assays. Results: Among study samples, FISH demonstrated 22 consensus ALK+ and six ALK wild type tumors. Preoptimization IHC scores from 12 centers with 5A4 and the percent abnormal cells by FISH from 12 centers showed intraclass correlation coefficients of 0.83 and 0.68, respectively. IHC optimization improved the intraclass correlation coefficients to 0.94. Factors affecting FISH scoring and outliers were identified. Post-optimization concurrent IHC/FISH testing in 373 informative cases revealed 100% sensitivity and specificity for IHC versus FISH. Conclusions: Multicenter standardization study may accelerate the implementation of ALK testing protocols across a country/region. Our data support the use of an appropriately validated IHC assay to screen for ALK+ lung cancers.

Linkage analysis of 26 Canadian breast and breast-ovarian cancer families.

We have examined 26 Canadian families with hereditary breast or ovarian cancer for linkage to markers flanking the BRCA1 gene on chromosome 17q12–q21. Of the 15 families that contain cases of ovarian cancer, 94% were estimated to be linked to BRCA1. In contrast, there was no overall evidence of linkage in the group of 10 families with breast cancer without ovarian cancer. A genetic recombinant in a breast-ovarian cancer family indicates a placement of BRCA1 telomeric to D17S776, and helps to define the region of assignment of the cancer susceptibility gene. Other cancers of interest that appeared in the BRCA1-linked families included primary peritoneal cancer, cancer of the fallopian tube, and malignant melanoma.

A genetic approach to stratification of risk for age-related macular degeneration

The genetic determinants of age-related macular degeneration (AMD) are reviewed and a novel approach to risk determination based upon inherited genetic polymorphisms and smoking history is presented. Although AMD was long thought to have primarily an environmental etiology, genetic variation is now known to account for the majority of the disease risk, with variations in the genes of the complement pathways playing a prominent role. Independent and validated clinical studies have implicated the C3 gene and its regulator, complement factor H (1q31.1), complement component 2 (6q21.33), and complement factor B (6q21.33). Subtle variations in complement activity increase the risk of symptomatic macular inflammation with age. A second group of AMD-associated genetic markers may aggravate complement-mediated inflammation by permitting retinal oxidative damage. Variation within the chromosomal site (10q26) coding a mitochondrial-associated protein (age-related maculopathy susceptibility 2) and an independent variation within the mitochondrial genome itself (A4917G) suggest a contributing pathophysiological role of retinal oxidative stress. A genetic panel of disease-susceptibility markers and smoking history can identify a group of individuals with greater than 65% lifetime risk of AMD. The introduction of genetic marker testing into clinical practice may identify patients with early disease who may be aided by presymptomatic monitoring or inclusion into trials of newer prophylactic agents.

A male phenotype with Aicardi syndrome.

Aicardi syndrome is a rare neurodevelopmental condition that occurs almost exclusively in women. We report a second male phenotype and 47,XXY karyotype with a typical presentation of the Aicardi syndrome including a midline arachnoid cyst.

Nonrandom chromosomal abnormalities in bovine lymphoma

Despite detailed knowledge of the genetic map of the bovine leukemia virus (BLV), the mechanism whereby BLV infection results in transformation and B-lineage restriction of tumors is poorly understood. The aim of this study was to gain new insight into pathogenetic mechanisms of BLV-induced tumorigenesis by determining the karyotypes of BLV-associated lymphomas in cattle. Metaphases in cells from lymphoid tumors from 20 mature dairy cows were banded and analyzed after short-term, unstimulated culture. Nineteen out of twenty cases exhibited clonal abnormalities, 17 cases were hyperdiploid, and 16 cases had extremely complex chromosomal changes. Recurrent chromosomal anomalies were identified and there was clear evidence for the evolution of increasing chromosomal instability in 12 cases. The most common abnormalities were the acquisition of additional small chromosomes (23-29); trisomy of chromosomes 5 and 7, and Robertsonian translocations and isochromosome rearrangements involving chromosomes 10, 12, 23, and 26. Monosomy X, trisomy X, and translocations involving the X chromosome were also detected. Chromosomes 2, 3, 4, 6, 8, 9, 11, 13, 14, 19, and 21 were infrequently involved in either structural or numerical changes. Structural rearrangements of chromosomes 10, 12, 23, and 26 may reflect primary abnormalities occurring relatively early in transformation, whereas trisomy 5 may be an extremely common secondary abnormality. While comparison of these findings with the current bovine gene map raises intriguing possibilities for pathogenetic mechanisms, further studies are needed before hypothetical mechanisms linking chromosomal abnormalities with BLV-induced transformation can be made.

Gender and BCR‐ABL transcript type are correlated with molecular response to imatinib treatment in patients with chronic myeloid leukemia

Achieving a major molecular response (MMR) is the goal of imatinib therapy for chronic myeloid leukemia. However, the association between gender, BCR‐ABL transcript type, and age with MMR is not well understood and often controversial.

Boy with 47,XXY,del(15)(q11.2q13) karyotype and Prader-Willi syndrome: a new case and review of the literature.

We report on a 10‐year‐old boy with a 47,XXY,del(15)(q11.2q13) karyotype and a Prader–Willi syndrome phenotype. His medical history and physical examination conformed to all of the major clinical criteria for Prader–Willi syndrome, but his height was taller than expected based on his hand and foot sizes. The deleted chromosome 15 was paternal in origin and molecular analysis showed maternal origin for the additional X chromosome. These findings suggest that the presence of these two disorders was coincidental in our patient. This supports the findings in the two other 47,XXY and Prader–Willi cases for which parent of origin studies have been published. Given the information from the literature and presented herein, we suggest that genetic counseling for cases of PWS and 47,XXY should address these two conditions separately.

Improving molecular testing and personalized medicine in non-small-cell lung cancer in Ontario

BACKGROUND Although molecular testing has become standard in managing advanced nonsquamous non-small-cell lung cancer (nsclc), most patients undergo minimally invasive procedures, and the diagnostic tumour specimens available for testing are usually limited. A knowledge translation initiative to educate diagnostic specialists about sampling techniques and laboratory processes was undertaken to improve the uptake and application of molecular testing in advanced lung cancer. METHODS A multidisciplinary panel of physician experts including pathologists, respirologists, interventional thoracic radiologists, thoracic surgeons, medical oncologists, and radiation oncologists developed a specialty-specific education program, adapting international clinical guidelines to the local Ontario context. Expert recommendations from the program are reported here. RESULTS Panel experts agreed that specialists procuring samples for lung cancer diagnosis should choose biopsy techniques that maximize tumour cellularity, and that conservation strategies to maximize tissue for molecular testing should be used in tissue processing. The timeliness of molecular reporting can be improved by pathologist-initiated reflex testing upon confirmation of nonsquamous nsclc and by prompt transportation of specimens to designated molecular diagnostic centres. To coordinate timely molecular testing and optimal treatment, collaboration and communication between all clinicians involved in diagnosing patients with advanced lung cancer are mandatory. CONCLUSIONS Knowledge transfer to diagnostic lung cancer specialists could potentially improve molecular testing and treatment for advanced lung cancer patients.