James T. Mascarello

Microarray analysis for constitutional cytogenetic abnormalities

Disclaimer: This guideline is designed primarily as an educational resource for health care providers to help them provide quality medical genetic services. Adherence to this guideline does not necessarily ensure a successful medical outcome. This guideline should not be considered inclusive of all proper procedures and tests or exclusive of other procedures and tests that are reasonably directed to obtaining the same results. In determining the propriety of any specific procedure or test, the geneticist should apply his or her own professional judgment to the specific clinical circumstances presented by the individual patient or specimen. It may be prudent, however, to document in the patients record the rationale for any significant deviation from this guideline.

Second report of a translocation involving 19q13.4 in a mesenchymal hamartoma of the liver

Cytogenetic study of a mesenchymal hamartoma of the liver detected a balanced translocation between chromosomes 11 and 19 in a 6-month-old male whose constitutional karyotype was normal. The chromosome 19 breakpoint, 19q13.4, appears to be identical to one of the breakpoints identified in the only other mesenchymal hamartoma studied with cytogenetic methods.

Ring chromosome X in a child with manifestations of Kabuki syndrome

A female patient with the karyotype 45,X/46, X, r(X)(p11.2 q13) and severe developmental delay, prominent fingertip pads, long palpebral fissures, short stature, and history of hypotonia had a phenotype reminiscent of Kabuki syndrome. We hypothesized that overexpression of X chromosome-derived sequences might be associated with the Kabuki-like phenotype observed. The nature and parental origin of this small-ring X were ascertained using a combination of genotyping with microsatellite markers and quantitative Southern blotting. PCR-based genotyping demonstrated heterozygosity at X-linked loci SBMA (Xq11-q12) and DXS227 (Xq13.1). Hemizygosity was observed at several loci: DMD STR-49 (Xp21.2), DXS1003 (Xp11.23), DXS988 (Xp11.21), DXS101 (Xq21.3), FMR-1 (Xq27.3), and DXYS64 (Xq28). This ring X chromosome is paternally derived since only maternal alleles are inherited at three informative microsatellite loci. Results of FISH and RT-PCR experiments indicate that the XIST locus is missing in the ring X chromosome and not expressed. These data indicated a large deletion of the X chromosome consistent with a small-ring X chromosome with approximate breakpoints near p11.2 and q13. These results are comparable to the observation of others where an atypically severe phenotype has been associated with the presence of an r(X), or small mar(X).

Redefining the risks of prenatally ascertained supernumerary marker chromosomes: a collaborative study

Background: A marker chromosome is defined as a structurally abnormal chromosome that cannot be identified by routine cytogenetics. The risk for phenotypic abnormalities associated with a marker chromosome depends on several factors, including inheritance, mode of ascertainment, chromosomal origin, and the morphology, content, and structure of the marker. Methods: to understand the karyotype-phenotype relationship of prenatally ascertained supernumerary de novo marker chromosomes, we combined data from prenatal cases obtained from 12 laboratories with those from studies in the literature. We were able to obtain cytogenetic and phenotypic data from 108 prenatally ascertained supernumerary de novo marker chromosomes to refine the phenotypic risk associated with these markers. Because of the growing number of cases and because more techniques are available to delineate marker morphology, we have been able to group risk estimates into subcategories, such as by marker type and whether there are ultrasound abnormalities. Results: If a de novo supernumerary marker chromosome is found prenatally, our data suggest there is a 26% risk for phenotypic abnormality when there is no other information defining the marker (such as chromosomal origin or information about the existing phenotype). However, if high resolution ultrasound studies are normal, this risk reduces to 18%. Conclusions: Our findings strongly support the value of additional genetic studies for more precisely defining the risk in individual cases involving marker chromosomes.

Hepatoblastoma characterized by trisomy 20 and double minutes

Karyotypic study of two hepatoblastomas revealed trisomies for chromosome 20 and the presence of double minutes (dmin). These cases are the second and third examples of trisomy 20 in hepatoblastoma and are the first examples of dmins in this rare childhood tumor.

Section E9 of the American College of Medical Genetics technical standards and guidelines: Fluorescence in situ hybridization

This updated Section E9 has been incorporated into and supersedes the previous Section E9 in Section E: Clinical Cytogenetics of the 2008 Edition (Revised 02/2007) American College of Medical Genetics Standards and Guidelines for Clinical Genetics Laboratories. This section deals specifically with the standards and guidelines applicable to fluorescence in situ hybridization analysis.

Presence or absence of trisomy 11 is correlated with histologic subtype in congenital mesoblastic nephroma

Fluorescence in situ hybridization utilizing a probe for the alpha satellite repeat sequence on chromosome 11 was used to detect variations in the number of chromosomes 11 in 24 formalin-fixed, paraffin-embedded congenital mesoblastic nephromas. Evidence of trisomy 11 was found in nearly half of the tumors. More importantly, the presence of trisomy 11 was associated with the cellular histologic variant of this tumor.

A dysmorphic child with myelodysplasia characterized by a duplication of 1q and multiple duplications of 3q

Multiple inserted duplications of bands 3q21 through 3q27 and a duplication of the chromosome 1 long arm are reported in a karyotypically altered clone from a dysmorphic child with myelodysplasia.

Assignment of a gene for succinate dehydrogenase to human chromosome 1 by somatic cell hybridization

A Chinese hamster cell mutant has been described with little or no activity of succinate dehydrogenase (SODERBERG et al., 1977). We described here the selection and characterization of human-hamster hybrids obtained from the fusion of these mutant cells and human lymphoblasts or HT1080 fibrosarcoma cells. The presence of human chromosome 1, identified by cytogenetic techniques and isozyme analysis, is correlated with the restoration of succinate dehydrogenase activity in the hybrids, and segregants are described in which the loss of all or part of human chromosome 1 has also led to a loss of this activity. We present in one of the two structural genes for the 70,000 and 30,000 dalton peptides, respectively, which constitute succinate dehydrogenase. One of these two genes is therefore mapped on human chromosome 1.

Proficiency Testing for Laboratories Performing Fluorescence In Situ Hybridization With Chromosome-Specific DNA Probes

OBJECTIVE To assess laboratory performance, use, and limitations in the joint College of American Pathologists and American College of Medical Genetics proficiency testing program for laboratories performing cytogenetic tests based on fluorescence in situ hybridization (FISH). DATA SOURCES Eight proficiency surveys dealing with FISH detection of microdeletions or microduplications, aneuploidy in interphase cells, gene amplification, and neoplasm-specific translocations. Participating laboratories used their own DNA probes (commercial or home-brew), hybridization methods, and analytic criteria to answer clinical questions about cases represented by slides included in the survey materials. They also described their test results according to the International System for Human Cytogenetic Nomenclature (ISCN) and answered supplementary questions relating to their experience with the subject test systems. DATA EXTRACTION In addition to evaluating diagnostic accuracy, we evaluated survey use, laboratory experience, variation in methodologic approach, and the practicality of using ISCN nomenclature for describing test results. SYNTHESIS AND CONCLUSIONS With the exception of one challenge, at least 80% of the participants reached the correct diagnostic conclusion. In the sole exception, there was still a consensus of 91.7% of participants with the same (albeit erroneous) diagnostic conclusion. The overall outstanding performance of participating laboratories clearly shows the reliability of current FISH methods. Despite the fact that a large number of laboratories reported little or no experience with the specific test systems, the overwhelming majority performed very well. This result shows that the programs strategy of targeting classes of abnormalities (vs a single abnormality associated with a specific disease) did not put at a disadvantage participants who did not routinely perform all of the potential tests in the class. The extraordinary variation in ISCN descriptions submitted by participants showed that the existing system for human cytogenetic nomenclature is not suitable for facile communication of FISH test results.