Journal of the Association of Genetic Technologists最新文献

Objectives: Lipoblastomas are benign tumors composed of fat cells of varying degrees of maturation, from lipoblasts to mature adipocytes. These tumors typically affect young children under the age of three. Upregulation of the pleomorphic adenoma gene 1 (PLAG1), located on 8q12.1, is the primary driving force for lipoblastoma development. The most common mechanisms for PLAG1 upregulation are rearrangements of 8q11-13 and polysomy 8. We present a unique case of lipoblastoma in a three-year-old boy with a ring chromosome 8. To the best of our knowledge, this cytogenetic finding has only been described three times in the literature. We present this case to further document this rare cytogenetic abnormality in lipoblastomas and hypothesize that the formation of a ring 8 chromosome results in a promoter swapping event.

Variant databases serve as a resource for clinical molecular genetics laboratories. There is evidence of widespread interpretive and syntactic errors within the entries of both small and large-scale variant databases used for germline clinical molecular genetic interpretation reports. The over-dependence on variant databases for variant annotation, classification and reporting may be a potential source of error to clinical molecular genetics laboratories. Recent evidence suggests 12-50% of clinical test reports are in significant conflict with clinical reports from other laboratories. A non-systematic literature review of evidence of discrepancies within frequently used genetic variant databases used for generating clinical genetic tests is provided. The implications of and recommendations for addressing variant annotation, classification and interpretive errors are discussed.

DMD is a muscle-wasting disease. It is caused by mutations in the dystrophin gene which is found on the X chromosome. It has an X-linked recessive inheritance pattern and is passed on by the mother (carrier). It is a progressive disease that usually causes death in early adulthood-often in the 20s, although there have been improvements in treatment, so some patients make it into their 30s and occasionally 40s. In addition to the muscle wasting aspects, serious complications include heart or respiratory-related problems. It mostly affects boys, about 1 in every 3,500 or 5,000 male children. On September 19, 2016, the FDA approved Sarepta Therapeutics (SRPT)'s eteplirsen, which now goes by the trade name Exondys 51, to treat DMD. It is the first drug to be approved to treat the underlying causes of the disease. [http://www.biospace.com/News/victory-at-last-sarepta-stock-doublesas-the-fda/432777].

Pediatric B-cell acute lymphoblastic leukemia (B-ALL) is the most common hematological malignancy in children, and the t(12;21)(p13;q22) occurs in approximately 25% of these cases, making it is the most prevalent chromosomal abnormality. The t(12;21) which disrupts hematopoietic differentiation and proliferation, and can be present as a sole abnormality or within the context of a complex karyotype characterized by three or more chromosomal abnormalities. The prognosis of t(12;21) within a complex karyotype is extensively debated. In this review, we discuss the literature regarding t(12;21) and summarize the cytogenetic features found in 363 pediatric cases compiled from the Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer. Cytogenetically, most of the cases had secondary chromosomal abnormalities, about half of which were in the context of a complex karyotype. Trisomy 21 was found to be the most common numerical abnormality in almost one-fifth of the cases, and deletions on chromosome 12 and 6 occurred in 16.9% and 12.5% of cases, respectively. In general, t(12;21) in B-ALL is associated with a favorable prognosis. Herein, we found no significant difference in survival outcome of t(12;21) with a on-complex or complex karyotype.

Chromosomal translocations involving the short arm of chromosome 2 (p13-25) and the distal part of the long arm of chromosome 3 (q25-29) are rare and still poorly studied to date. These abnormalities are common in myeloid neoplasms and are associated with a poor prognosis. Chromosomal abnormalities within the involved range of bands may contribute to the ectopic expression or formation of fusion genes involving the EVI1 gene, but the exact mechanism by which EVI1 affects leukemogenesis remains unclear. Herein, we report an analysis of 60 patient cases presenting various myeloid malignancies with t(2;3)(p13-25;q25-29) compiled from the Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer. In these studies, this translocation has been reported as a sole abnormality or within the context of a complex karyotype. Among the analysis in which molecular cytogenetic analysis was performed in order to assess the involvement of the EVI1 (ecotropic virus integration site 1 proton homolog) locus (n=19), 16 (84%) confirmed its rearrangement. In 37% of studies, the t(2;3) was seen as a sole abnormality (n=22). The t(2;3) was secondary in 11% of cases (n=4), and in 63% of the cases the t(2;3) had additional chromosomal abnormalities (n=38). Monosomy 7, deletion of the 5q arm, and translocations involving (9;22) were most common abnormalities in order of prevalence, occurring in 29% (n=11), 26% (n=10), and 13% (n=5) of case studies, respectively. These observations in the results of the literature on t(2;3), an anomaly not otherwise molecularly characterized, adds to the discussion of this translocation's approximate incidence in myeloid disease, and specifically in acute myeloid leukemia (AML). The data highlights its nonrandom nature and suggests that it is a part of the myeloid spectrum of disorders. Considering the severe clinical outcome associated with this translocation, this data provides information about a cytogenetic biomarker as well as an understanding of the significance of this set of chromosomal anomalies in the development of myeloid disease.

Erratum: Figure 1 on the last edition The Journal of the Association of Genetic Technologists. 2017;43(3): 113-127 does not contain the derivative 21. We are replacing this figure with the present one. In the section Secondary genetic aberrations we would like to add that: Deletions of 11q23 are observed in 5-6% of cases (Raynaud et al., 1999; Attarbaschi et al., 2004; Alvarez et al., 2005; Forestier et al., 2007).

Pancreatic carcinoma is a major cause of cancer-related death in the United States, with a five-year survival rate of approximately 5%. Cytogenetic analysis has identified clinically significant chromosomal abnormalities in numerous malignancies, but it is not utilized in the clinical management of pancreatic carcinoma. We performed conventional and molecular cytogenetic analysis of 16 pancreatic carcinoma cell lines using Giemsa banding and DNA-based fluorescence in situ hybridization (FISH). Conventional cytogenetic analysis revealed a diversity of recurrent and clonal numerical and structural abnormalities in all cell lines analyzed, many of which occurred at loci of genes implicated in pancreatic or related cancers. FISH analysis revealed significant decreases in copy number of numerous tumor-suppressor genes including TP53, CDKN2A, and SMAD4. In some cell lines, amplification of oncogenes HER2 and MYC was also observed. Finally, novel rearrangements involving ARID1A and TGFBR2 were identified in a small subset of cell lines by means of molecular cytogenetic analysis. All in all, these data provide additional insight into recurrent chromosomal abnormalities in pancreatic carcinoma that can potentially be utilized as biomarkers in the clinical management of the disease. Investigation of other aberrations as well as correlation of recurrent ones with clinicopathologic features is warranted in order to assess the utility of cytogenetic analysis of pancreatic carcinoma.

Lung cancer is one of the leading causes of cancer-related death worldwide. Among patients with lung cancer, approximately 85% have non-small cell lung carcinoma (NSCLC). The discovery of oncogenic driver mutations in NSCLC opened new personalized treatment options. Several methods that can identify these biomarkers are used routinely in a clinical setting to stratify patients for targeted therapy. In this review, we summarize the most clinically relevant driver genes, discuss the advantages and limitations of current clinical detection methods, and highlight the benefits of personalized treatment over standard chemotherapy.

Two recent studies demonstrated that array CGH and NGS allow identification of chromosomal abnormalities in fetal trophoblasts circulating in maternal blood. This remarkable breakthrough paves the way for an improved assay that supersedes the performance of non-invasive prenatal testing (NIPT) in cell-free fetal DNA. Furthermore, it is foreseeable to expand the use of this new genomic analysis in trophoblasts to uncover single gene mutations of clinical significance prenatally.

Acute myelogeneous leukemia (AML) with inv(3)/t(3;3)(q13q25) is associated with aberrant expression of the stem-cell regulator MECOM (aka EVI1). Two bone marrow samples received in the OHSU Knight Diagnostic Laboratories (KDL) Cytogenetics Laboratory for chromosomes and FISH for a question of progression of myelodysplastic syndrome (MDS) to AML showed complex abnormalities including a deletion of chromosome 3q, one with del(3)(q13q25) and the other with del(3)(q22q25). In light of the prognostic importance of the activation of the MECOM oncogene and the concurrent inactivation of the GATA2 tumor suppressor that occurs with the classic inversion of chromosome 3q, fluorescence in situ hybridization (FISH) was performed using two different probe designs to better define the 3q deletions in the two cases. Using the Abbott Molecular Laboratories dual fusion MECOM/RPN1 probe, interphase and metaphase cells in both patients showed a variant single fusion (orange/green/fusion) signal pattern consistent with fusion and deletion. Using the three-color (red/green/aqua) Cytocell EVI1 probe, interphase cells in both cases showed a split red/green signal with the aqua signal remaining with the green signal. The distance between the split signals was generally less than is usually seen in the commonly described inverted chromosome 3. These findings are therefore consistent with a complex inversion and concurrent deletion/deletions of chromosome 3q. Thus, the deletion 3q seen in G-banded chromosomes from bone marrow from these two patients is most consistent with the activation of MECOM and the inactivation of GATA2.