The Role of Repeat DNA Sequences in Human Evolution and Disease.

Segmental chromosome duplications are an important evolutionary mechanism to produce new gene functions. Once an initial duplication takes place, the probability of a second event (structural change) increases. Segmental duplications (SDs) occur in many sizes and configurations.

A case of recurrent epilepsy-associated rosette-forming glioneuronal tumor with anaplastic transformation in the absence of therapy.

Rosette-forming glioneuronal tumor (RGNT) most commonly occurs adjacent to the fourth ventricle and therefore rarely presents with epilepsy. Recent reports describe RGNT occurrence in other anatomical locations with considerable morphologic and genetic overlap with the epilepsy-associated dysembryoplastic neuroepithelial tumor (DNET). Examples of RGNT or DNET with anaplastic change are rare, and typically occur in the setting of radiation treatment.

Interphase FISH for Residual Disease: Proposal for a Qualitative Determination of Rare Events.

Interphase fluorescence in situ hybridization (FISH) cutoff values are calculated using various mathematical methods to determine whether abnormalities seen are at reportable (statistically significant) levels. However, for interphase FISH studies of samples obtained from oncology patients who have been transplanted or treated, these cutoff values may result in reporting a false negative result due to the small percentage of residual disease that falls below such a cutoff value. Failure to detect the rare abnormal cells may impact patient care and prognosis.

MECOM (EVI1) Rearrangements: A Review and Case Report of Two MDS Patients with Complex 3q Inversion/Deletions.

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.

A New Rhesus Macaque Karyotype Based on Human-rhesus Synteny.

Rhesus macaque (Macaca mulatta), because of their similarity to humans, are often used to study complex neurobiology and anatomy, cardiovascular disease, and in vaccine development. While the rhesus genome is studied on its own by primatologists, the grand majority of rhesus macaque research is done with the intention of extrapolating the findings to human diseases and traits. As such, it makes sense that the rhesus genome and karyotype be arranged based on homology to human chromosomes in an effort to ease the comparisons between the two, and aide in interpreting data generated using rhesus macaque model systems.

The New Equivocal: Changes to HER2 FISH Results When Applying the 2013 ASCO/CAP Guidelines.

Objectives: Human epidermal growth factor receptor 2 (HER2, ERBB2) testing is an important prognostic/predictive marker in breast cancer management, especially in selecting HER2-targeted treatment. American Society of Clinical Oncology (ASCO)/College of American Pathologists (CAP) guidelines address HER2 status and were recently revised in 2013, replacing the 2007 version. For in situ hybridization interpretation, 2013 guidelines return to the prior threshold of a HER2/CEP17 ratio of 2.

ALK FISH Assays for Non-small Cell Lung Cancer Treatment Selection: Scoring Issues and Probe Design.

Lung cancer is becoming more treatable with new pharmaceuticals. There is a growing interest in FISH testing to determine which drugs to use on lung cancer patients for the best results, with a concurrent need for laboratories to provide ALK FISH testing for nonsmall-cell lung cancer. However, the test has some unique difficulties and requires a great deal of experience to interpret in some cases.

FISH testing for deletions of chromosome 6q21 and 6q23 in hematologic neoplastic disorders.

Deletions of chromosome 6q are found in many types of cancer, including melanoma, prostate cancer, fibroadenomas, and carcinoma of breast and other sites. Chromosome 6q deletions are also commonly found in lymphoid malignancies such as acute lymphocytic leukemia (ALL), chronic lymphocytic leukemia (CLL), non-Hodgkins lymphoma (NHL), multiple myeloma (MM), mantle zone lymphoma (MZL), and Waldenström's macroglobulinemia (WM). These deletions may appear to be terminal or interstitial.

Cytogenetic analysis of a hemosiderotic fibrolipomatous tumor.

Hemosiderotic fibrolipomatous tumor is an extremely rare, nonencapsulated, fatty lesion with a consistent histologic appearance that was originally considered reactive in nature. To our knowledge, there are no previous reports on the cytogenetics of this lesion. Reported here is a case of hemosiderotic fibrolipomatous tumor arising within the subcutaneous tissue of the right foot, dorsal aspect, of an otherwise healthy 35-year-old woman.

Evaluation of Her-2/neu status in carcinomas with amplified chromosome 17 centromere locus.

Accurate assessment of Her-2/neu (erb-b2) status in breast carcinoma is essential for therapy planning. Clinical assays are targeted at protein overexpression (immunohistochemical analysis) or gene amplification (fluorescence in situ hybridization [FISH]). Cases with aberrant FISH signal patterns are problematic and may lead to underreporting of Her-2/neu amplification.

Split centromeric alpha-satellite FISH signals in a whole arm translocation 5p;10p: consequences and implications for interphase FISH studies.

This is a case report of an apparently balanced whole arm translocation between the short arms of chromosomes 5 and 10 in which the centromeric alpha-satellite DNA is split between both derivative chromosomes for both probes, leading to abnormal signal patterns. The patient requested preimplantation genetic testing for the unbalanced products of the translocation. However, using centromeric alpha-satellite DNA probes as controls for the subtelomeric-specific probes in interphase was not informative because of the split signals.

Meiotic exchange event within the stalk region of an inverted chromosome 22 results in a recombinant chromosome with duplication of the distal long arm.

Meiotic recombination occurs between homologous euchromatic regions of human chromosomes in early meiosis. However, such exchanges have been thought not to occur in the stalk regions of acrocentric chromosomes. We describe a child whose chromosome analysis suggests that crossovers do occur in homologous stalk regions.

Trisomy 8 as the sole cytogenetic abnormality in a case of extraskeletal mesenchymal chondrosarcoma.

Mesenchymal chondrosarcoma is a rare malignant tumor that comprises about 3-10% of all sarcomas. Reports of cytogenetic studies of mesenchymal chondrosarcoma are limited and no consistent cytogenetic abnormality has surfaced. Some mesenchymal chondrosarcomas have a t(11;22) translocation suggesting a relationship with the PNET/Ewing tumor family.

Y chromosome heterochromatin of differing lengths in two cell populations of the same individual.

Objective: To present a prenatal diagnosis report on a case where G-banding analysis of fetal metaphase chromosomes showed populations of cells with two different Y chromosomes; one with a short block of heterochromatin (Yqh-) and one with a longer block of heterochromatin (Yqh+).

Methods: These two populations of the Y chromosome were studied using fluorescent quinacrine banding and fluorescent in situ hybridization (FISH). A chromosome paint corresponding to the euchromatic region of the Y chromosome, and probes corresponding to the SRY, DYZ1, and DYZ3 regions were used for this study.

The role for preimplantation genetic diagnosis in balanced translocation carriers.

Objective: Preimplantation genetic diagnosis is an established technique that provides an alternative to prenatal diagnosis for patients who are at risk of transmitting a serious genetic disorder to their offspring. Preimplantation genetic diagnosis has been used for couples who have been at risk for having offspring with single gene or X-linked disorders and for screening for common age-related aneuploidy and in couples who themselves carry balanced chromosomal rearrangements. The aim of this study was to summarize our experience using preimplantation genetic diagnosis after the identification of a parental balanced translocation, specifically as it relates to the number of embryos that are suitable for transfer after preimplantation genetic diagnosis for a known translocation and aneuploidy screening.

Myxoinflammatory fibroblastic sarcoma with complex supernumerary ring chromosomes composed of chromosome 3 segments.

Myxoinflammatory fibroblastic sarcoma is a rare, recently described, and distinctive low-grade tumor of soft tissue. To our knowledge, there is only one previous report on the cytogenetics of this tumor. That case showed complex structural abnormalities, including a reciprocal translocation between chromosomes 1 and 10 [t(1;10)(p22;q24)] with loss of chromosomes 3 and 13.