Biomedical subjects

Jonathan P Park

Publications and source records attributed to Jonathan P Park.

5 recordsLinked to original sources

PubMed2006

Cytogenetic heteromorphisms: survey results and reporting practices of giemsa-band regions that we have pondered for years.

CONTEXT: Cytogenetic heteromorphisms (normal variants) pose diagnostic dilemmas. Common Giemsa-band heteromorphisms are not described in the literature, although Giemsa-banding is the method most frequently used in cytogenetic laboratories. OBJECTIVE: To summarize the responses from more than 200 cytogeneticists concerning the definition and reporting of cytogenetic heteromorphisms, to offer these responses as a reference for use in clinical interpretations, and to provide guidance for interpretation of newly defined molecular cytogenetic heteromorphisms. DESIGN: The Cytogenetics Resource Committee of the College of American Pathologists and the American College of Medical Genetics administered a proficiency testing survey in 1997 to 226 participant cytogenetic laboratories. Supplemental questions asked whether participants considered particular Giemsa-banded chromosomal features to be heteromorphisms and if these would be described in a cytogenetic clinical report. RESULTS: Responses were obtained from 99% of participants; 61% stated they would include selected heteromorphism data in a clinical report. More than 90% considered prominent short arms, large or double satellites, or increased stalk length on acrocentric chromosomes to be heteromorphisms; 24% to 36% stated that they would include these in a clinical report. Heterochromatic regions on chromosomes 1, 9, 16, and Y were considered heteromorphisms by 97% of participants, and 24% indicated they would report these findings. Pericentric inversions of chromosomes 1, 2, 3, 5, 9, 10, 16, and Y were considered heteromorphisms with more than 75% of respondents indicating they would report these findings. CONCLUSIONS: Responses were not unanimous, but a clear consensus is presented describing which Giemsa-band regions were considered heteromorphisms and which would be reported.

Azure Stains↗

PubMed2005

Evidence for widespread reticulate evolution within human duplicons.

Approximately 5% of the human genome consists of segmental duplications that can cause genomic mutations and may play a role in gene innovation. Reticulate evolutionary processes, such as unequal crossing-over and gene conversion, are known to occur within specific duplicon families, but the broader contribution of these processes to the evolution of human duplications remains poorly characterized. Here, we use phylogenetic profiling to analyze multiple alignments of 24 human duplicon families that span >8 Mb of DNA. Our results indicate that none of them are evolving independently, with all alignments showing sharp discontinuities in phylogenetic signal consistent with reticulation. To analyze these results in more detail, we have developed a quartet method that estimates the relative contribution of nucleotide substitution and reticulate processes to sequence evolution. Our data indicate that most of the duplications show a highly significant excess of sites consistent with reticulate evolution, compared with the number expected by nucleotide substitution alone, with 15 of 30 alignments showing a >20-fold excess over that expected. Using permutation tests, we also show that at least 5% of the total sequence shares 100% sequence identity because of reticulation, a figure that includes 74 independent tracts of perfect identity >2 kb in length. Furthermore, analysis of a subset of alignments indicates that the density of reticulation events is as high as 1 every 4 kb. These results indicate that phylogenetic relationships within recently duplicated human DNA can be rapidly disrupted by reticulate evolution. This finding has important implications for efforts to finish the human genome sequence, complicates comparative sequence analysis of duplicon families, and could profoundly influence the tempo of gene-family evolution.

Computational Biology↗

PubMed2002

An MCL1-overexpressing Burkitt lymphoma subline exhibits enhanced survival on exposure to serum deprivation, topoisomerase inhibitors, or staurosporine but remains sensitive to 1-beta-D-arabinofuranosylcytosine.

Members of the BCL2 gene family influence cell viability and can, therefore, affect the susceptibility of cancer cells to multiple chemotherapeutic agents. Thus, it is a challenge to devise approaches for inducing the death of tumor cells in which the expression of prosurvival family members is elevated or deregulated. BL41-3, a spontaneously derived subline of BL41 Burkitt lymphoma cells, was found to have amplified the prosurvival MCL1 gene (3-fold) and overexpressed the MCL1 protein. The level of MCL1 protein was 5-fold elevated compared with ML-1 cells expressing maximal MCL1 on exposure to phorbol-12-myristate-13- acetate. To assess whether this increase in MCL1 expression was associated with enhanced protection from cell death, cells were exposed to conditions of growth factor deprivation or to various cytotoxic agents. Whereas BL41-3 and BL41 cells exhibited similar growth rates in logarithmic phase, BL41-3 cells remained largely viable on reaching saturation phase in contrast to BL41 cells, which began to die. Similarly, the BL41-3 subline remained viable for an extended period under conditions of reduced serum. BL41-3 cells were also more resistant to the apoptosis-inducing effects of etoposide, camptothecin, and staurosporine (>3-fold more than BL41 cells). Unexpectedly, these cells exhibited enhanced sensitivity to 1-beta-D-arabinofuranosylcytosine, but only on exposure for an extended period (>10-fold more sensitive than BL41 cells with a 24-h but not a 6-h exposure). Thus, whereas cells expressing prosurvival BCL2 family members are frequently resistant to a variety of chemotherapeutic agents, the findings presented here, using a cell line exhibiting amplification and overexpression of MCL1, indicate that such cells may exhibit increased sensitivity to certain chemotherapeutic regimens.

Antimetabolites, Antineoplastic↗

PubMed2002

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 program's 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.

Chromosome Aberrations↗

PubMedDate not supplied

Problems with ISCN FISH Nomenclature make it not practical for use in clinical test reports or cytogenetic databases [corrected].

PURPOSE: To assess the extent and the sources of variation in ISCN nomenclature used by participants in CAP/ACMG surveys dealing with fluorescence in situ hybridization (FISH). METHODS: Over 1600 nomenclature strings from 15 challenges in seven surveys were evaluated for the contributions of diagnostic errors, syntax errors, methodological differences, and technical factors not foreseen by ISCN 1995. RESULTS: Although diagnostic errors were uncommon, syntax errors were numerous, approaching 50% of the responses for several challenges. Their frequency varied with the complexity of the nomenclature required to describe a test condition. Variation attributable to probe selection and band designation correlated with the number of probes available for addressing the diagnostic issue at hand. In the most dramatic example of this effect, a survey simulating diagnosis of trisomy 21 in uncultured amniocytes, there were 66 participants (of 99) who used the same general form for their nomenclature, but only 8 of the 66 had exactly the same nomenclature string. Participants used proprietary names, created their own nomenclature, or ignored the true complexity of probe systems when trying to describe conditions not foreseen by ISCN 1995. CONCLUSION: The use of current ISCN FISH nomenclature resulted in survey participants describing unique biological conditions in a multitude of different ways. In addition to making the nomenclature unsuitable for proficiency test purposes, this heterogeneity makes it impractical for clinical test reporting and for cytogenetic database management. Because methodological information contributes a large amount of variability, adds complexity, and increases opportunities for syntax errors, a system that excludes such information would be more effective.

Cytogenetic Analysis↗