Complementarity of interphase and metaphase chromosome analysis in human renal tumors

1993 ◽  
Vol 6 (1) ◽  
pp. 17-23 ◽  
Author(s):  
Sandra R. Wolman ◽  
Frederic M. Waldman ◽  
Margit Balazs
Keyword(s):  
Metaphase Chromosome ◽  
Chromosome Analysis ◽  
Renal Tumors

scholarly journals Genetic Analysis Using a High Density SNP Array in Myelodysplastic Syndrome: Clinical Utility and Comparative Analysis Study Compared to Metaphase Chromosome Analysis

Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 5259-5259 ◽  
Author(s):  
Sally Jeffries ◽  
Nicola Trim ◽  
Emma Huxley ◽  
Laura Ford ◽  
Manoj Raghavan ◽  
...  
Keyword(s):  
Genetic Analysis ◽  
Metaphase Chromosome ◽  
Copy Number ◽  
Clinical Utility ◽  
Snp Array ◽  
Gene Mutations ◽  
Chromosome Analysis ◽  
Genetic Aberrations ◽  
Allelic Gene ◽  
Copy Number Changes

Abstract There is no single technology capable of detecting the various genetic and genomic aberrations observed in patients with neoplasia. Patients with myelodysplastic syndrome (MDS) may present with chromosomal copy number changes (duplication, deletion, and amplification), balanced chromosome rearrangements, copy neutral loss of heterozygosity (CN-LOH) and/or gene mutations. Currently only microscopic chromosomal changes, as dictated by the international prognostic scoring system (IPSS-R), are used to determine the genetic risk in MDS. However, different genetic aberrations, particularly gene mutations are anticipated to be incorporated into the IPSS-R in the near future. The Affymetrix CytoScan® HD Array is a high definition array with over 2.6 million markers (both copy number and SNP) allowing resolution capabilities way beyond that of metaphase chromosome analysis. The incorporation of 750,000 SNPs also allows for detection of CN-LOH, regions known to harbour bi-allelic gene mutations. A real-time comparative study using the Affymetrix CytoScan® HD Array against traditional metaphase chromosome analysis is being performed on patients with confirmed or highly suspected MDS referred for genetic analysis at the West Midlands Regional Genetics Laboratory, UK. The study is expected to utilise 600 arrays over two years at presentation and on serial surveillance samples. The preliminary results available after the first 100 patients are presented with examples demonstrating the capabilities and clinical utility of SNP array genetic analysis. The study so far, in patients with MDS at presentation, has demonstrated: An increased number of genetic aberrations (CN changes and CN-LOH) detected by SNP array (38/105 (36%) by metaphase analysis and 62/105 (60%) by SNP array analysis).The ability to reliably detect deletions at the single gene level including CUX1, TET2 and RUNX1, and rarely copy number changes within genes including duplication within KMT2A, consistent with partial tandem duplication.The detection of CN-LOH regions, which may contain bi-allelic gene mutations, in 20/105 (19%) of cases, including chromosomal regions 1p (MPL, NRAS), 4q (TET2), 7q (CUX1), 11q (CBL), 17p (TP53). Confirmatory studies are on-going.A lower failure rate for SNP array compared to metaphase analysis (1% v 4%). Of the four failed metaphase cases, three showed recurrent genetic aberrations observed in MDS including del(5q), del(20q) with CN-LOH 17p, and trisomy 8. The failed SNP array had a normal karyotype.Confirmed balanced rearrangements (without gain or loss of genetic material) are not detected.The ability to detect abnormal clones with copy number changes (deletion or gain at one or more loci) at sensitivities as low as between 5 and 20% dependent on aberration size.Twenty-two cases with a normal karyotype had abnormal genetic aberrations detected by SNP array. Two cases with an abnormal karyotype had a normal SNP array profile due to a balanced rearrangement and a low level abnormal clone (4%) beyond the sensitivity of the test.The ability to utilise peripheral blood instead of marrow as no dividing cells are required, thereby allowing genetic analysis in patients too frail or otherwise unsuitable for marrow aspirationThe ability to detect deletion or CN-LOH of the HLA gene region, which is critical in patients being considered for stem cell transplant as HLA typing may be inaccurate or ambiguous.The ability when performed as a complementary tool to metaphase analysis to detect sub-clones or concurrent clonal neoplasia with different copy number changes. Patient benefits are expected to be the potential to improve patient outcomes through improved confidence in diagnosis, prognosis and monitoring. Disclosures Jeffries: Affymetrix: Research Funding.

scholarly journals Evaluations of Auto-Focusing Methods under a Microscopic Imaging Modality for Metaphase Chromosome Image Analysis

2013 ◽  
Vol 36 (1-2) ◽  
pp. 37-44 ◽  
Author(s):  
Yuchen Qiu ◽  
Xiaodong Chen ◽  
Yuhua Li ◽  
Wei R. Chen ◽  
Bin Zheng ◽  
...  
Keyword(s):  
Bone Marrow ◽  
High Throughput ◽  
Metaphase Chromosome ◽  
Imaging Modality ◽  
Digital Pathology ◽  
Chromosome Analysis ◽  
Blood Specimens ◽  
Time Accuracy ◽  
High Throughput Imaging ◽  
Auto Focusing

Background: Auto-focusing is an important operation in high throughput imaging scanning. Although many auto-focusing methods have been developed and tested for a variety of imaging modalities, few investigations have been performed on the selection of an optimal auto-focusing method that is suitable for the pathological metaphase chromosome analysis under a high resolution scanning microscopic system.Objective: The purpose of this study is to investigate and identify an optimal auto-focusing method for the pathological metaphase chromosome analysis.Methods: In this study, five auto-focusing methods were applied and tested using metaphase chromosome images acquired from bone marrow and blood specimens. These methods were assessed by measuring a number of indices including execution time, accuracy, number of false maxima, and full width at half maximum (FWHM).Results: For the specific condition investigated in this study, the results showed that the Brenner gradient and threshold pixel counting methods were the optimal methods for acquiring high quality metaphase chromosome images from the bone marrow and blood specimens, respectively.Conclusions: Selecting an optimal auto-focusing method depends on the specific clinical tasks. This study also provides useful information for the design and implementation of the high throughput microscopic image scanning systems in the future digital pathology.

Chromosome Analysis of Oncocytic Renal Tumors

1987 ◽  
Vol 137 (6) ◽  
Author(s):  
Jaraes A. Reynolds ◽  
Sheila Dobin ◽  
K. Scott Coffield
Keyword(s):  
Chromosome Analysis ◽  
Renal Tumors

scholarly journals Interphase Chromosome Profiling: A Method for Conventional Banded Chromosome Analysis Using Interphase Nuclei

2017 ◽  
Vol 142 (2) ◽  
pp. 213-228 ◽  
Author(s):  
Ramesh Babu ◽  
Daniel L. Van Dyke ◽  
Vaithilingam G. Dev ◽  
Prasad Koduru ◽  
Nagesh Rao ◽  
...  
Keyword(s):  
Bone Marrow ◽  
Peripheral Blood ◽  
Metaphase Chromosome ◽  
Spectral Characteristics ◽  
Chromosome Analysis ◽  
Artificial Chromosome ◽  
Turnaround Time ◽  
Interphase Nuclei ◽  
Interphase Chromosome

Context.— Chromosome analysis on bone marrow or peripheral blood samples fails in a small proportion of attempts. A method that is more reliable, with similar or better resolution, would be a welcome addition to the armamentarium of the cytogenetics laboratory. Objective.— To develop a method similar to banded metaphase chromosome analysis that relies only on interphase nuclei. Design.— To label multiple targets in an equidistant fashion along the entire length of each chromosome, including landmark subtelomere and centromere regions. Each label so generated by using cloned bacterial artificial chromosome probes is molecularly distinct with unique spectral characteristics, so the number and position of the labels can be tracked to identify chromosome abnormalities. Results.— Interphase chromosome profiling (ICP) demonstrated results similar to conventional chromosome analysis and fluorescence in situ hybridization in 55 previously studied cases and obtained useful ICP chromosome analysis results on another 29 cases in which conventional methods failed. Conclusions.— ICP is a new and powerful method to karyotype peripheral blood and bone marrow aspirate preparations without reliance on metaphase chromosome preparations. It will be of particular value for cases with a failed conventional analysis or when a fast turnaround time is required.

919: Ureteral Extension in Childhood Renal Tumors: A Report From the National Wilms Tumor Study Group (NWTSG)

2007 ◽  
Vol 177 (4S) ◽  
pp. 305-305
Author(s):  
Shane Daley ◽  
Michael Ritchey ◽  
Robert Shamberger ◽  
Robert Sawin ◽  
Thomas Hamilton ◽  
...  
Keyword(s):  
Wilms Tumor ◽  
Renal Tumors ◽  
Study Group ◽  
Tumor Study ◽  
Tumor Study Group
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