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1
Chaku, Priya, und Pooja Shah. „Automatic Karyotyping of Human Chromosomes Using Band Patterns“. International Journal of Scientific Research 2, Nr. 12 (01.06.2012): 154–56. http://dx.doi.org/10.15373/22778179/dec2013/50.
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WULF, HANS CHRISTIAN, und JOHN PHILIP. „Semi-automatic karyotyping facility-a clinical test“. Hereditas 105, Nr. 1 (14.02.2008): 37–40. http://dx.doi.org/10.1111/j.1601-5223.1986.tb00638.x.
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Urdiales García, Cristina, Antonio Bandera Rubio, Fabián Arrebola Pérez und Francisco Sandoval Hernández. „A curvature-based multiresolution automatic karyotyping system“. Machine Vision and Applications 14, Nr. 3 (Juli 2003): 145–56. http://dx.doi.org/10.1007/s00138-002-0076-z.
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4
Kleinschmidt, Peter, Ilse Mitterreiter und Christian Rank. „A hybrid method for automatic chromosome karyotyping“. Pattern Recognition Letters 15, Nr. 1 (Januar 1994): 87–96. http://dx.doi.org/10.1016/0167-8655(94)90104-x.
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5
Popescu, Mihail, Paul Gader, James Keller, Cerry Klein, Joe Stanley und Charles Caldwell. „Automatic karyotyping of metaphase cells with overlapping chromosomes“. Computers in Biology and Medicine 29, Nr. 1 (Januar 1999): 61–82. http://dx.doi.org/10.1016/s0010-4825(98)00040-7.
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Abid, Faroudja, Latifa Hamami, Faiza Badache und Houssem Derdour. „A system on chip for automatic karyotyping system“. Computers & Electrical Engineering 64 (November 2017): 1–14. http://dx.doi.org/10.1016/j.compeleceng.2017.10.001.
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Tso, Michael, Peter Kleinschmidt, Ilse Mitterreiter und Jim Graham. „An efficient transportation algorithm for automatic chromosome karyotyping“. Pattern Recognition Letters 12, Nr. 2 (Februar 1991): 117–26. http://dx.doi.org/10.1016/0167-8655(91)90057-s.
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Nanni, Loris. „A reliable method for designing an automatic karyotyping system“. Neurocomputing 69, Nr. 13-15 (August 2006): 1739–42. http://dx.doi.org/10.1016/j.neucom.2006.01.005.
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Fukui, K., und K. Kakeda. „Quantitative karyotyping of barley chromosomes by image analysis methods“. Genome 33, Nr. 3 (01.06.1990): 450–58. http://dx.doi.org/10.1139/g90-067.
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Barley chromosomes were analyzed by the chromosome image analyzing system, CHIAS. Stained and unstained diploid metaphase spreads were automatically scanned and their locations on the glass slide were detected. With stained chromosomes, detection efficiency of good metaphase plates exceeded on average 90%. Three image parameters, length, area, and density volume, of each chromosome were defined and measured for 250 haploid chromosome plates. Of these parameters, total length and the arm ratio of the length were the most informative for chromosome identification. A quantitative idiogram of the N-banded barley chromosomes was established from numerical data of phase-contrast images and the image analysis of N-banded chromosomes.Key words: Hordeum vulgare, CHIAS, image analysis, automatic scanning, quantitative idiogram.
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Ritter, Gunter, María Teresa Gallegos und Karl Gaggermeier. „Automatic context-sensitive karyotyping of human chromosomes based on elliptically symmetric statistical distributions“. Pattern Recognition 28, Nr. 6 (Juni 1995): 823–31. http://dx.doi.org/10.1016/0031-3203(94)00162-f.
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Jahani, Sahar, und S. Kamaledin Setarehdan. „AN AUTOMATIC ALGORITHM FOR IDENTIFICATION AND STRAIGHTENING IMAGES OF CURVED HUMAN CHROMOSOMES“. Biomedical Engineering: Applications, Basis and Communications 24, Nr. 06 (Dezember 2012): 503–11. http://dx.doi.org/10.4015/s1016237212500469.
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Karyotyping is a standard method for presenting the complete set of the pictures of human chromosomes in a table-like format. It is usually used by a cytogenetic expert to predict the common genetic abnormalities. Producing a Karyotype from microscopic images of human chromosomes is a tedious and time-consuming task, so an automatic Karyotyping system would help the cytogenetic expert in his/her routine work. Automatic Karyotyping algorithms usually suffer the non-rigid nature of the chromosomes, which makes them to have unpredictable shapes and sizes in the images. One such problem that usually needs the operator's interaction is the existence of curved chromosomes within the images. In this paper, an effective algorithm for identification and straightening of curved human chromosomes is presented. This will extend the domain of application of the most of the previously reported algorithms to the curved chromosomes. The proposed algorithm is applied to single chromosomes that are initially modified by means of a Median filter. The medial axis (MA) of the filtered image is then extracted using a thinning procedure, which is carried out on the binary version of the image. By comparing the Euclidean distance of the endpoints and the length of the MA, a curved chromosome is identified. For chromosome straightening, the initially extracted medial axis is then modified by extending it in both ends considering the slope of the MA. Next, the original input image is intensity sampled over many closely located perpendicular lines to the MA along the chromosome which are then mapped into a matrix (as rows) producing a vertically oriented straight chromosome. For evaluation, the algorithm is applied to 54 selected highly curved chromosomes obtained at the pro-metaphase stage, which were provided by the Cytogenetic Laboratory of Cancer Institute, Imam Hospital, Tehran, Iran. The density profile and the centromeric index of the chromosomes which are among the most important and commonly used features for chromosome identification are calculated by the expert both before and after the straightening procedure. The mean squared error and the variance of the difference between the two are then obtained and compared. The results show a good agreement between the two, hence the effectiveness of the proposed method. The proposed algorithm therefore extends the domain of application of the previously reported algorithms to the highly curved chromosomes.
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MALET, P., A. GENEIX und B. PERISSEL. „Automated karyotyping-practical applications“. Cell Biology International Reports 14 (September 1990): 218. http://dx.doi.org/10.1016/0309-1651(90)90972-2.
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Haferlach, Claudia, Siegfried Hänselmann, Wencke Walter, Sarah Volkert, Melanie Zenger, Wolfgang Kern, Anna Stengel, Thomas Lörch und Torsten Haferlach. „Artificial Intelligence Substantially Supports Chromosome Banding Analysis Maintaining Its Strengths in Hematologic Diagnostics Even in the Era of Newer Technologies“. Blood 136, Supplement 1 (05.11.2020): 47–48. http://dx.doi.org/10.1182/blood-2020-137463.
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Background: Chromosome banding analysis (CBA) is one of the most important techniques in diagnostics and prognostication in hematologic neoplasms. CBA is still a challenging method with very labor-intensive wet lab processes and karyotyping that requires highly skilled and experienced specialists for tumor cytogenetics. Short turnaround times (TAT) are becoming increasingly important to enable genetics-based treatment stratification at diagnosis. Aim: Improve TAT and quality of CBA by automated wet lab processes and AI-based algorithms for automatic karyotyping. Methods: In the last 15 years the CBA workflow has gradually been automated with focus on the wet lab and metaphase capturing processes. Now, a retrospective unselected digital data set of 100,000 manually arranged karyograms (KG) with normal karyotype (NKG) from routine diagnostics was used to train a deep neural network (DNN) classifier to automatically determine the class/number and orientation of the respective chromosomes (AI based classifier normal, AI-CN). With a total of 6 Mio parameters, the DNN uses two distinct output layers to simultaneously predict the chromosome number (24 classes) and the angle that is required to rotate the chromosome in its correct, vertical position (360 classes). Training of the DNN took 16 days on a Nvidia RTX 2080 Ti graphic card with 4352 cores. AI-CN was implemented into the routine workflow (including ISO 15189) after 7 months of development and intensive testing. Results: The AI-CN was tested by highly experienced staff in an independent prospective validation set of 500 NKG: 22,675/23,000 chromosomes (98.6%) were correctly assigned by AI-CN. In 369/500 (73.8%) of cells all chromosomes were correctly assigned, in an additional 20% only 2 chromosomes were interchanged. The chromosomes accounting for the majority of misclassifications were chromosomes 14 and 15 as well as 4 and 5, which are difficult to distinguish in poor quality metaphases also for humans. The 1st AI-CN was implemented into routine diagnostics in August 2019 and the 2nd AI-CN - optimized for chromosome orientation - was used since November 2019. Since then more than 17,500 cases have been processed with AI-CN (>350,000 metaphases) in routine diagnostics resulting in the following benefits: 1) Reduced working time: an experienced cytogeneticist needs - depending on chromosome quality - between 1 and 3 minutes to arrange a KG, while AI-CN needs only 1 second and the cytogeneticist about 30 seconds to review the KG. 2) Shorter TAT: The proportion of cases reported within 5 days increased from 30% before AI-CN (2019) to 36% with AI-CN1 (2019) and 45% with AI-CN2 (2019/2020), while the proportion of cases reported >7 days was reduced to 28%, 21%, and 17%, respectively (figure). Using AI-CN for aberrant karyotypes results in correct assignment of normal chromosomes and thus also correct KG in cases with solely numerical chromosome abnormalities. Derivative chromosomes derived from structural abnormalities (SA) that differ clearly from any normal chromosome are not automatically assigned but are left out for manual classification. Thus, even in cases with SA, using AI-CN saves time. To allow AI based SA assignment, two additional classifiers normal/aberrant (CNA) were built: AI-CNA1 was trained on 54,634 KG encompassing 10 different SA (AKG) and 100,000 NKG and AI-CNA2 was trained on all AKG and an equal number of NKG. First validation tests are promising and optimization is ongoing. Once the CNA has been optimized, a standardized high quality of chromosome aberration detection is feasible. A fully automated separation of chromosomes is currently in progress and will reduce the TAT by another 12-24 hours. In a fully automated workflow the detection of small subclones can be further optimized by increasing today's standard of 20 metaphases to several hundred, even without any delay in TAT and need for additional personnel. Conclusions: Implementation of AI in CBA substantially improves the quality of results and shortens turnaround times even in comparison to highly trained and experienced cytogeneticists. In the majority of cases a complete karyotype analysis can be guaranteed within 3 to 7 days, allowing CBA based treatment strategies at diagnosis. This fully automated workflow can be implemented worldwide, is rapidly scalable, can be performed cloud based and requires in the near future fewer experienced tumor cytogeneticists. Figure Disclosures Hänselmann: MetaSystems: Current Employment. Lörch:MetaSystems: Current equity holder in private company.
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van Vliet, Lucas J., Ian T. Young und Brian H. Mayall. „The athena semi-automated karyotyping system“. Cytometry 11, Nr. 1 (1990): 51–58. http://dx.doi.org/10.1002/cyto.990110107.
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Piper, J., und G. Breckon. „An automated system for karyotyping mouse chromosomes“. Cytogenetic and Genome Research 50, Nr. 2-3 (1989): 111–15. http://dx.doi.org/10.1159/000132735.
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V. Munot, Mousami, Madhuri A. Joshi und Nikhil Sharma. „Automated Karyotyping of Metaphase Cells with Touching Chromosomes“. International Journal of Computer Applications 29, Nr. 12 (29.09.2011): 14–20. http://dx.doi.org/10.5120/3700-5175.
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Lundsteen, Claes, Tommy Gerdes und Jan Maahr. „Automated multiple-cell karyotyping: a clinical feasibility study“. Clinical Genetics 39, Nr. 5 (28.06.2008): 338–46. http://dx.doi.org/10.1111/j.1399-0004.1991.tb03040.x.
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Mayall, Brian H., James D. Tucker, Mari L. Christensen, Lucas J. van Vliet und Ian T. Young. „Experience with the athena semi-automated karyotyping system“. Cytometry 11, Nr. 1 (1990): 59–72. http://dx.doi.org/10.1002/cyto.990110108.
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19
Donahue, Amber C., Adam Abdool, Jay G. Wohlgemuth und Chen-Hsiung Yeh. „Molecular Characterization of Chromosomal Abnormalities In Myelodysplastic Syndrome and Acute Myeloid Leukemia: Validation of An MLPA Protocol and Analysis Method for Use In a Diagnostic Setting“. Blood 116, Nr. 21 (19.11.2010): 4849. http://dx.doi.org/10.1182/blood.v116.21.4849.4849.
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Abstract Abstract 4849 Introduction: Current diagnostic screening strategies for copy number variations (CNVs) in myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML) include fluorescence in situ hybridization (FISH) or karyotyping, both of which are time-consuming, costly, laborious, and lacking in resolution. Multiplex ligation-dependent probe amplification (MLPA) can be used to detect copy number changes in multiple loci simultaneously in a single PCR reaction, and boasts a resolution down to single exons. To adapt MLPA for use in routine clinical diagnostics, we have developed and validated a protocol for automatic data analysis and interpretation of common chromosomal abnormalities in MDS/AML. Patients and Methods: The study used a training set of 45 healthy subjects to establish a normal reference range for each individual probe. Using these ranges we built an automated Excel spreadsheet-based analysis system, which included multiple quality checks, and flagged samples failing these quality controls. Each probe was given a call of “no mutation detected,” “deletion,” or “gain,” based on whether the normalized ratio fell within or outside of the empirically-determined normal range for that probe. We then analyzed over 100 leukemia cases tested by FISH, including both suspected myeloid leukemia samples and suspected chronic lymphocytic leukemia (CLL) samples. Documented chromosomal abnormalities in CLL include 11q-, 17p- (loss of TP53), and trisomy 12, all of which had the potential to be detected by the probes in the MDS MLPA probemix. The greater prevalence of CLL and its associated CNVs provided additional positive controls for the validation of the MDS MLPA probemix and our analysis method. Results: The empirically-determined normal ranges demonstrated that some probes varied widely (3 standard deviation [3SD] normal range of 0.46–1.54), while others were extremely reliable (3SD normal range of 0.84–1.16). The MLPA assay demonstrated excellent overall accuracy (>90%) and specificity (>93%) for both suspected myeloid and CLL samples when compared to FISH. The sensitivity of the MLPA assay is somewhat lower than that of FISH, requiring a probe-dependent 20–40% positivity for a given CNV to be detected. However in several cases, the MDS MLPA assay was able to detect additional lesions too small to be seen by FISH. Conclusions: For MLPA, the total process-to-report time, including data analysis, is 2–3 days, versus the 7–10 days required for FISH analysis. In addition, the MLPA assay is substantially cheaper and considerably less labor-intensive than FISH. Our improved MLPA assay protocol and analysis method provides a clinically robust, multiplexed, high-throughput, high-resolution, and low-cost solution for detection of copy number changes in MDS/AML, and can therefore be used as a first-line screening test in a clinical laboratory. Disclosures: Donahue: Quest Diagnostics Inc.: Employment. Abdool: Quest Diagnostics Inc.: Employment. Wohlgemuth: Quest Diagnostics Inc.: Employment. Yeh: Quest Diagnostics Inc.: Employment.
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Munot, Mousami V., Jayanta Mukherjee und Madhuri Joshi. „A novel approach for efficient extrication of overlapping chromosomes in automated karyotyping“. Medical & Biological Engineering & Computing 51, Nr. 12 (20.08.2013): 1325–38. http://dx.doi.org/10.1007/s11517-013-1105-y.
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Hieber, Ludwig, Reinhard Huber, Verena Bauer, Quirin Schäffner, Herbert Braselmann, Geraldine Thomas, Tatjana Bogdanova und Horst Zitzelsberger. „Chromosomal Rearrangements in Post-Chernobyl Papillary Thyroid Carcinomas: Evaluation by Spectral Karyotyping and Automated Interphase FISH“. Journal of Biomedicine and Biotechnology 2011 (2011): 1–7. http://dx.doi.org/10.1155/2011/693691.
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Structural genomic rearrangements are frequent findings in human cancers. Therefore, papillary thyroid carcinomas (PTCs) were investigated for chromosomal aberrations and rearrangements of the RET proto-oncogene. For this purpose, primary cultures from 23 PTC have been established and metaphase preparations were analysed by spectral karyotyping (SKY). In addition, interphase cell preparations of the same cases were investigated by fluorescencein situhybridisation (FISH) for the presence of RET/PTC rearrangements using RET-specific DNA probes. SKY analysis of PTC revealed structural aberrations of chromosome 11 and several numerical aberrations with frequent loss of chromosomes 20, 21, and 22. FISH analysis for RET/PTC rearrangements showed prevalence of this rearrangement in 72% (16 out of 22) of cases. However, only subpopulations of tumour cells exhibited this rearrangement indicating genetic heterogeneity. The comparison of visual and automated scoring of FISH signals revealed concordant results in 19 out of 22 cases (87%) indicating reliable scoring results using the optimised scoring parameter for RET/PTC with the automated Metafer4 system. It can be concluded from this study that genomic rearrangements are frequent in PTC and therefore important events in thyroid carcinogenesis.
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Al-Kharraz, Mona Salem, Lamiaa A. Elrefaei und Mai Ahmed Fadel. „Automated System for Chromosome Karyotyping to Recognize the Most Common Numerical Abnormalities Using Deep Learning“. IEEE Access 8 (2020): 157727–47. http://dx.doi.org/10.1109/access.2020.3019937.
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Legrand, B., Che Sau Chang, Sim-Heng Ong, Soek-Ying Neo und N. Palanisamy. „Automated Identification of Chromosome Segments Involved in Translocations by Combining Spectral Karyotyping and Banding Analysis“. IEEE Transactions on Systems, Man, and Cybernetics - Part A: Systems and Humans 38, Nr. 6 (November 2008): 1374–84. http://dx.doi.org/10.1109/tsmca.2008.2003963.
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Lekha, K. S., V. Bhagyam, P. D. Varghese und M. Manju. „Genital ambiguity: a cytogenetic evaluation of gender“. International Journal of Research in Medical Sciences 9, Nr. 2 (29.01.2021): 364. http://dx.doi.org/10.18203/2320-6012.ijrms20210050.
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Background: Genital ambiguity is a complex genetic disorder of sexual differentiation into male or female. The purpose of the present study is to correlate the sex of rearing with the genetic sex and to find out the prevalence of chromosomal anomalies in patients with ambiguous genitalia. The findings can help in proper diagnosis, genetic counselling, and the reassignment of sex, if necessary. Methods: In this cross-sectional study, 22 patients from north Kerala, ranging in age from 17 days to 17 years, were included. All cases were subjected to the following: a detailed history, physical examination, evaluation of clinical data, and cytogenetic analysis. Based on the standard protocol, peripheral blood lymphocyte culture was done. Chromosomal analysis was carried out with the help of an automated karyotyping system after G-banding of chromosomes.Results: Out of the 22 patients with ambiguous genitalia, 12 patients were genetic females with karyotype 46, XX, and nine patients were genetic males with 46, XY karyotype. One was a rare variant of Klinefelter syndrome with karyotype 49, XXXXY. The most common diagnosis was congenital adrenal hyperplasia, followed by partial androgen insensitivity syndrome. Discrepancies between genetic sex and sex of rearing were noted in 27% of the cases.Conclusions: This study unfolds the variable etiology of ambiguous genitalia and emphasizes the importance of karyotyping in diagnosis, proper assignment of the sex, and appropriate management of patients with genital ambiguity.
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Bai, Qikun, Lili Wang, Zongqing Wang, Nathan Lo und Yanli Che. „Exploring the diversity of Asian Cryptocercus (Blattodea : Cryptocercidae): species delimitation based on chromosome numbers, morphology and molecular analysis“. Invertebrate Systematics 32, Nr. 1 (2018): 69. http://dx.doi.org/10.1071/is17003.
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Woodroaches from the genus Cryptocercus Scudder, 1862 are known to display low levels of morphological divergence, yet significant genetic divergence and variability in chromosome number. Compared with Cryptocercus taxa from North America, the diversity of the genus in Asia has received relatively little attention. We performed morphological and karyotypic examinations of multiple taxa from several previously unsampled mountainous areas of central and south-western China, and identified nine candidate species primarily on the basis of chromosome number. We then investigated diversity across all Asian Cryptocercus, through phylogenetic analyses of 135 COI sequences and 74 28S rRNA sequences from individuals of 28 localities, including species delimitation analysis in General Mixed Yule Coalescent (GMYC) and Automatic Barcode Gap Discovery (ABGD). Phylogenetic results indicated that individuals from the same locality constituted well supported clades. The congruence of GMYC and ABGD results were in almost perfect accord, with 28 candidate species described on the basis of karyotypes (including the nine identified in this study). We provide evidence that each valley population in the Hengduan Mountains contains a separate evolving lineage. We conclude that the principal cause of the rich Cryptocercus diversity in China has been the uplift of the Qinghai-Tibet Plateau.
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Caudill, Jonathan S., Ruchira Sood, James L. Zehnder, Erik C. Thorland, Vilmarie Rodriguez, Rajiv K. Pruthi und David P. Steensma. „Severe Factor V Deficiency Associated with Chromosome 1q Deletion.“ Blood 108, Nr. 11 (16.11.2006): 1043. http://dx.doi.org/10.1182/blood.v108.11.1043.1043.
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Abstract Background: Coagulation factor V (FV) is an essential cofactor of the prothrombinase complex, catalyzing conversion of prothrombin to thrombin. Severe FV deficiency is a rare coagulation defect with a prevalence in the general population of approximately 1 in 1,000,000 and a variable bleeding risk (Asselta R et al. J Thromb Haemostas 2006). Genetic mutations underlying a FV-deficient hemorrhagic diathesis have been described in a limited number of cases, display considerable allelic heterogeneity, and have been due to point mutations in the FV gene located at chromosome 1q23. Here, we report a 15 year-old girl with psychomotor delay, CNS abnormalities, and a solitary left kidney - features consistent with a congenital 1q deletion including band 1q23 - who was found to have severely reduced plasma FV activity after a routine preoperative laboratory evaluation prior to an elective spinal stabilization surgery revealed a mildly prolonged prothrombin (PT, 13.2 seconds; normal 8.4 – 12 seconds) and activated partial thromboplastin (aPTT, and 38 seconds; normal 21 – 33 seconds) time. She had undergone minor surgical procedures in the past without reports of significant bleeding, and her family members were also clinically unaffected. Methods: FV procoagulant activity level was measured in the patient with an MDA-180 automated coagulation analyser (Trinity Biotech, Ireland). The patient’s peripheral blood leukocytes were separated by density centrifugation and fixed in methanol:glacial acetic acid (2:1). We then performed interphase fluorescent in-situ (FISH) analysis using probes covering the FV gene and the more telomeric HPC1 gene as a control. Genomic DNA was also isolated from the patient, and the coding region (25 exons) of the FV gene amplified by polymerase chain reaction (PCR) and sequenced. Results: FV activity assays revealed a severely reduced level of 9% (normal range: 60–130%). Factor V activity levels in the patient’s family members were not assessed. Peripheral blood karyotyping revealed an interstitial deletion of 1q: 46,XX,del(1)(q24.2q25.3 or q23.3q25.1). Interphase FISH analysis was performed. Red signals corresponded to the FV probe and green signals corresponded to HPC1, which is approximately 13 MB telomeric to FV. In contrast to healthy controls, the patient had a signal pattern of only 1 green HPC1 signal and 1 red FV signal, corresponding to heterozygous loss of the FV gene and adjacent chromosomal material. Sequencing of the retained allele revealed a novel hemizygous S234W mutation (encoded by exon 6). The lost serine is part of a conserved “SGP” peptide segment predicted to be a solvent-exposed region of the heavy chain of the FV protein. Conclusion: Most mutations causing FV deficiency are autosomal recessive and introduce frame shifts resulting in the generation of a premature termination codon. Karyotypic and FISH analysis of this patient revealed a novel mechanism for FV deficiency: loss of an entire FV allele as part of a chromosomal deletion, coupled with a point mutation in the other allele. Structural modeling of the consequences of the S234W point mutation, which is predicted to alter the hydrophobicity of the protein, is ongoing. Syndromes involving an interstitial deletion of 1q have been described in association with ATIII deficiency (Pallotta, Dalpra et al. 2001), but to our knowledge, this is the first description of a 1q deletion with FV deficiency.
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Kawata, Eri, Benjamin Hedley, Benjamin Chin-Yee, Anargyros Xenocostas, Alejandro Lazo-Langner, Cyrus C. Hsia, Kang Howson-Jan et al. „Reducing Cytogenetic Testing in the Era of Next Generation Sequencing (NGS); Are We Choosing Wisely?“ Blood 136, Supplement 1 (05.11.2020): 12–13. http://dx.doi.org/10.1182/blood-2020-138667.
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Background: The combination of automation and expanding panel of target genes has improved utility and reduced costs of Next Generation Sequencing (NGS), leading to its widespread adoption in the clinical laboratory. In most laboratories, NGS has been added without consideration for redundancy or relative value compared to traditional genomic assays such as G-band karyotyping and FISH. At our centre, most patients with suspected hematologic malignancies receive both conventional cytogenetics (CG) and NGS assessment in addition to bone marrow morphology and flow cytometry. Appropriate test utilization is a high priority highlighted by campaigns such as Choosing Wisely, which often disproportionally focus on appropriate utilization of "routine" high volume tests rather than new test modalities. We implemented NGS screening in patients with suspected hematologic malignancies (Levi et al. 2019), and demonstrated enhanced diagnostic and prognostic yield of NGS, supporting the efficacy and cost-effectiveness of an 'NGS first' approach with CG restricted to samples with morphologic abnormalities in MDS (Kawata et al. BJH 2020). In this follow up study, we further expanded our Morphologic Flow Triage/NGS first (MFT-NGS1) algorithm to investigate patients with suspected hematological diseases. The main objective of our study was to evaluate this rationalized molecular diagnostic testing "MFT-NGS1" algorithm for its feasibility, acceptability and cost impact. Methods: Using the results from morphologic interpretation of aspirate and flow cytometry, patient samples were triaged into 4 groups. Group 1: Patients with dysplastic features in the marrow or excess blasts were triaged to Bone Marrow Molecular Diagnostic 1 (BMD1) and had both NGS and G-band karyotyping. Group 2: Patients with no excess blasts or dysplasia (BMD2), had NGS only with CG sample held for 3 months in case testing was required in follow up. Group 3: Patients who had NGS and/or CG on a previous BM aspirate were triaged to (BMD3), with the comment that NGS and CG should not be repeated unless results will influence patient management. These samples were held for 4 weeks and testing was performed only if specifically requested. Group 4: Patients with suspected myeloma where the proportion of plasma cells was less than 5% were triaged to (BMD4), and FISH testing was cancelled. These samples were held for 3 months in case subsequent biopsy showed an increased proportion of plasma cells in keeping with myeloma. Results: Over a 9-month period between August 2019 to April 2020 a total of 599 adult BM samples were assessed; 549 (91.7%) were ordered by hematologists and 331 (60.1%) meeting study criteria for MFT-NGS1 algorithm. Of those, 115 (34.7%) samples showed morphologic abnormalities and triaged to BMD1; 61 (18.4%) samples showed no morphologic abnormalities and were triaged to BMD2; 116 (35%) had previous CG and/or NGS tested and triaged to BMD3; and 39 (11.8%) samples were from patients with suspected myeloma had less than 5% of plasma cells and were triaged into BMD4 group. (Figure 1) Overall the MFT-NGS1 algorithm decreases G band karyotyping or FISH analysis in 149/331 (45%) samples. Only 11 / 216 (5.5%) hematologist overruled triage comment and requested CG testing for a specific indication either suspected progression of known diseases or for a therapeutic decision (e.g. drug approval). CG and FISH were mistakenly performed without the necessary reconfirmation in 26/216 (12%). Conclusion: The proposed approach combining morphologic and flow triage and NGS as the primary genomic test (MFT-NGS) is both feasible and well accepted by clinical teams. We estimated that approximately 40% of all CG testing could be reduced primarily by reducing repeat testing which offsets a large proportion of the cost of implementation of NGS testing, while increasing both diagnostic and prognostic yield. Key factors for the success of this quality improvement project were involvement of clinical and genomic teams in developing the triage algorithm, rapid turnaround time (less than 24 to 48 hours) for aspirate interpretation and flow for triage and communication between laboratories within a fully integrated healthcare centre. Figure 1 Disclosures No relevant conflicts of interest to declare.
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Abdool, Adam, Amber C. Donahue, Jay G. Wohlgemuth und Chen-Hsiung Yeh. „Detection, Comprehensive Analysis and Clinical Validation of Chromosomal Aberrations by Multiplex Ligation-Dependent Probe Amplification In Chronic Lymphocytic Leukemia“. Blood 116, Nr. 21 (19.11.2010): 2716. http://dx.doi.org/10.1182/blood.v116.21.2716.2716.
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Abstract Abstract 2716 Background: Current strategies based on karyotyping or fluorescent in situ hybridization (FISH) for detection of chromosomal abnormalities in chronic lymphocytic leukemia (CLL) are laborious, time-consuming, and costly and have limitations in resolution. Multiplex ligation-dependent probe amplification (MLPA) can simultaneously detect copy number changes of multiple loci in a single PCR, making it an attractive alternative. We developed and validated an MLPA protocol for comprehensive, automated data analysis and interpretation of chromosome abnormalities associated with CLL. Patients and Methods: Reference ranges for individual MLPA probes were established from a group of 50 healthy control subjects. Using these ranges we built an automated spreadsheet-based analysis system that includes multiple quality checks; samples that fail these checks are flagged and not reported. Each target was given a call of “deletion,” “normal,” or “amplification,” depending on whether the normalized ratio fell within or outside of the established normal range (mean ± 2SD or mean ± 3SD). After establishing the normal references ranges for each probe, we used the MLPA assay to characterize chromosome abnormalities in blood samples from 100 patients with suspected CLL that had been previously tested with FISH. Results: The maximum normal ranges were distributed between 0.82 and 1.18 for the mean ± 2SD values (ie, 95% CI, P = 0.05), and between 0.73 and 1.27 for the mean ± 3SD values (ie, 99.7% CI, P = 0.01). MLPA showed good concordance with FISH results in the 100 clinically suspected CLL cases. In 6 of these cases, abnormalities detected by MLPA were in regions not covered by FISH, including additional copy number gains on chromosomes 18q21.1 and 19, and novel micro-deletions at 19q13.43 and 19p13.2 loci. Excluding these cases, MLPA showed 94% sensitivity, 94% concordance, and 93% specificity relative to FISH. MLPA detected abnormalities in 3 FISH-negative cases and failed to detect abnormalities in three 13q- cases with low percentages of leukemic cells (7%, 12% and 19%). The limit of detection of the CLL MLPA assay was about 20% leukemic clones. Conclusions: This MLPA-based assay for chromosome abnormalities in CLL showed excellent concordance with FISH. This multiplex assay represents a fast (roughly 2–3 days total process to report time vs 7–10 days for FISH), high-throughput, accurate, and user-friendly process for that has potential for use as a first-line screening test for detection of chromosome abnormalities associated with CLL in the clinical laboratory. Disclosures: No relevant conflicts of interest to declare.
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Dudareva, Yu A., und A. A. Shipilov. „Efficacy of prenatal diagnostic in mothers of children with chromosomal aberrations diagnosed postnatally“. Russian Journal of Woman and Child Health 4, Nr. 1 (2021): 42–45. http://dx.doi.org/10.32364/2618-8430-2021-4-1-42-45.
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Aim: to assess the efficacy of prenatal screening in women those children were diagnosed with chromosomal aberrations postnatally. Patients and Methods: this descriptive cross-sectional retrospective study was performed to analyze medical records, obstetric gynecological database, and the results of prenatal screening in women (Altay Region residents) who gave birth to children with chromosomal aberrations in 2017–2019. The examination also included the calculation of the individual risk of fetal chromosomal aberrations using Astraia and PRISCA software. Results: in 2017–2019, sixty-nine children with chromosomal aberrations were born in the Altay Region. Most (90%) children were diagnosed with Down’s syndrome. More girls were born than boys (1.7:1). The mean age of women who gave birth to children with chromosomal aberrations diagnosed postnatally was 35 years. In 4.3%, mean mother’s age was 21.3 years. In 40.6%, mean mother’s age was 31.2 years. Every second woman (55.1%) was older than 35 years. A retrospective analysis of pathological prenatal markers and automated calculation of individual risk have demonstrated that the risk of fetal chromosomal aberrations was moderate to high in 79.7%. In this risk score, the diagnosis can be verified prenatally. Sonographic and biochemical markers of fetal chromosomal aberrations were lacking in 20.3%. Early prenatal screening was not performed in 20.3% due to late referral to the maternity clinic. Sonographic markers, diagnosed congenital anomalies, and biochemical tests in the second trimester were the most effective prenatal markers of chromosomal aberrations. Conclusions: following the technology of prenatal screening to identify fetal chromosomal aberrations allows for verifying the diagnosis and granting the families the right to decide on the utility to prolong pregnancy. KEYWORDS: prenatal screening, chromosomal aberrations, congenital anomalies, karyotyping, genetic counseling, noninvasive prenatal testing. FOR CITATION: Dudareva Yu.A., Shipilov A.A. Efficacy of prenatal diagnostic in mothers of children with chromosomal aberrations diagnosed postnatally. Russian Journal of Woman and Child Health. 2021;4(1):42–45. DOI: 10.32364/2618-8430-2021-4-1-42-45.
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De Weer, An, Bruce Poppe, Pieter Mestdagh, Katleen De Preter, Pieter Van Vlierberghe, Barbara Cauwelier, Nadine Van Roy et al. „MicroRNA Profiling of EVI1 Deregulated Myeloid Leukemia“. Blood 112, Nr. 11 (16.11.2008): 5322. http://dx.doi.org/10.1182/blood.v112.11.5322.5322.
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Abstract Chromosomal rearrangements involving the EVI1 gene are a recurrent finding in malignant myeloid disorders. These translocations or inversions contribute to ectopic expression of, or to the formation of fusion genes involving the EVI1 gene. EVI1 transcriptional activation has been reported in up to 10% of acute myeloid leukemia (AML) patients, and is a prognostic marker predictive of a poor outcome. Recently, microRNA deregulation was identified as a major contributor to cancer initiation and progression. Furthermore, miRNA genes were shown to be directly regulated by activated proto-oncogenes. In this study, we investigated which miRNAs are implicated in the transcriptional pathways governed by the EVI1 oncogene as well as possible microRNAs regulating the expression of the EVI1 gene itself. A total of 384 miRNAs were profiled through automated qRT-PCR using high-throughput quantitative stem-loop RT-PCR. Our patient series consisted of 18 EVI1 rearranged and overexpressing samples confirmed by FISH, karyotyping and qRT-PCR, 11 normal bone marrow samples and 2 CD34+ cord blood fractions. Through integrated statistical analysis we were able to identify 36 significantly upregulated and 44 significantly downregulated miRNAs (p<0.05) in EVI1 rearranged samples compared to normal bone marrow samples. Among these up- and downregulated miRNAs several have already been associated with leukemia or other types of cancer acting as oncogenes or tumor suppressor genes, respectively. Interestingly, in the panel of downregulated miRNAs, we found 3 miRNAs that have predicted binding sites on the 3′UTR of the EVI1 gene. Currently, no mechanism has been described to explain EVI1 overexpression, therefore loss of the inhibitory effect of miRNAs targeting the 3′UTR of EVI1 might be an important mechanism contributing to EVI1 ectopic expression. Further analyses will include vector based luminescence experiments to confirm the association between EVI1 and the 3 downregulated miRNAs. Functional studies will also be performed in order to assess the contribution of the differentially expressed miRNAs to the leukemic phenotype. Since patients with EVI1 involvement have a poor prognosis, elucidating the downstream EVI1 controlled miRNA targets and pathways could not only yield new insights into EVI1 etiogenesis, but could also add additional prognostic and diagnostic information. We anticipate that these findings could provide new targets for therapeutic intervention.
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Schnerch, Dominik, Julia Felthaus, Monika Engelhardt und Ralph M. Waesch. „Unscheduled Sister-Chromatid-Separation in the Presence of Spindle Disruption in Acute Myelogenous Leukemia“. Blood 112, Nr. 11 (16.11.2008): 3114. http://dx.doi.org/10.1182/blood.v112.11.3114.3114.
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Abstract Mitosis is known to be one of the most critical events in the cell cycle. The spindle assembly checkpoint (SAC) is required for proper chromosome segregation during mitosis. The SAC serves as a mitotic surveillance mechanism responsible for detection of misassembly of chromosomes to the mitotic spindle. Lack of chromosome attachment and spindle tension generate a specific „wait-anaphase-signal“. This particular signal interferes with proteolysis, depending on the ubiquitin-ligase APCCdc20, thereby inhibiting mitotic progression through stabilization of mitotic regulators. We found several AML cell lines to be incapable of properly accumulating in mitosis upon nocodazole-induced spindle disruption when compared to a set of Burkitt’s lymphoma cell lines. This result was further supported by the degradation of the mitotic regulators Cyclin B and Securin in synchronized Kasumi-1 cells in the presence of nocodazole shortly after entering mitosis. Interestingly, the SAC proteins BubR1 and Bub1 were found at low expression levels in AML cell lines in comparison to Burkitt’s lymphoma cell lines. We established a shRNA-based model to evaluate the effects of BubR1- and/or Bub1-repression to levels found in AML cell lines to directly compare the Bub1/BubR1 knockdown phenotype with the investigated AML cell lines. Our findings support the view that BubR1 repression alone is sufficient to confer SAC deficiency. To determine the frequency of BubR1 repression in patient-derived primary cells, AML blasts were cytokine-stimulated to enter the cell cycle. Flow cytometry-based G2/M-specific expression analysis of BubR1 in primary AML blasts revealed lower expression in most analyzed cell populations. To further test the hypothesis that AML cells override the metaphase-to-anaphase-transition despite spindle damage, we performed Giemsa staining of cells that were incubated in nocodazole containing growth medium. In AML cell lines, unlike the analyzed Burkitt’s lymphoma cell lines, a significant number of metaphase-like cells contained single chromatids, suggesting premature sister chromatid separation in the presence of spindle damage. Premature sister-chromatid-separation in the presence of chromosomal misalignment would lead to aneuploidy and favor the onset of genomic instability. Our recent efforts focus on high-throughput automated live cell scanning, promising a better understanding of cell division and chromosome separation in the context of different challenges, such as spindle damage. This powerful tool allows a more precise characterization of our knockdown phenotypes in the double-knockdown system, which is a prerequisite for comparison of our model system with AML cell lines. Finally, this new technique might also prove useful to extend our analyses to patient derived AML blasts. As we observed deregulation of SAC protein levels in AML cell lines and primary AML blasts, our findings of premature degradation of cell cycle regulators and unscheduled sister-chromatid-separation suggest an important role for SAC malfunction in the development of AML with karyotypic abnormalities. Mitotic kinases, such as Plk1 and Aurora, are already promising targets for modern antineoplastic therapies. A deeper understanding of mitotic control in AML might contribute to even more sophisticated targeted therapeutic approaches.
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Rauh, Michael J., Juraj Bodo, Eric Hsi, Bill Richendollar, Yuka Sugimoto, Jaroslaw P. Maciejewski, Christine L. O'Keefe und Stephen D. Smith. „Single Nucleotide Polymorphism Array (SNP-A) Genomic Profiling of Mantle Cell Lymphoma (MCL) Against a Large Control Database Reveals Recurring Copy Number Alterations (CNAs) and Copy Neutral Loss of Heterozygosity (CN-LOH)“. Blood 116, Nr. 21 (19.11.2010): 2001. http://dx.doi.org/10.1182/blood.v116.21.2001.2001.
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Abstract Abstract 2001 Background: MCL is characterized by extreme genomic instability. Conventional techniques such as metaphase cytogenetics are unable to detect small deletions, amplifications, or uniparental disomy (UPD) in the MCL tumor genome. SNP-A analysis permits high resolution karyotyping and detection of unbalanced DNA defects, including somatic UPD. We performed SNP-A analysis on MCL tumor samples, excluded CNA present in normal controls, and assessed our results in context of clinical outcome and Ki-67 index. Methods: With IRB approval, available frozen tissue from 18 patients diagnosed with cyclin D1-positive MCL between 1997–2006 was analyzed using high-resolution genome-wide human SNP Array 6.0 (Affymetrix). Signal intensity and SNP calls were determined using the Gene Chip Genotyping Analysis Software Version 4.0 (GTYPE) (Affymetrix). Copy number was also determined. Somatic MCL CNAs and CN-LOH were discerned from germline variants (CNV) by comparing to a database of 1535 normal controls subjected to 250K and/or SNP Array 6.0 analysis. Clinical data was available for all patients, and 15/18 samples were subject to immunohistochemistry (IHC) for Ki67 using an automated immunostainer (Discovery; Ventana Medical Systems). Kaplan-Meier survival analysis was performed. Results: Analysis of 18 MCL patient samples revealed an average 13 CNAs (6.2 gains, 6.4 losses) and 0.4 CN-LOH per patient (Figure 1). Gains were frequently observed in 3q (33%), 8q (22%), 12q (17%), and 18q (11%). A unique 12q micro-gain in one patient narrowed the minimal common region (MCR) to linear region 130.4 – 131.3 Mbp, overlapping with an area of CN-LOH, and including candidate genes MMP17 (upregulated in invasive breast cancer), ULK1 (regulator of autophagy), and EP400 (regulator of chromatin remodeling, proliferation and apoptosis). Recurring deletions were observed at 11q (50%), 1p, 6q (39%), 9p (33%), 13 q (28%), 9q (22%), 7q, and 17p (17%). Similar to prior studies, losses at 1p encompassing CDKN2C and FAF were seen though we further narrowed a common MCR, spanning 93.1–99.7 Mpb and including ARHGAP29 (PARG1)—previously identified in MCL by aCGH/gene expression, whose promoter is a frequent target of MCL methylation. As previously reported, losses in components of the Hippo tumor suppressor pathway were frequently affected by these recurring deletions (6q: LATS1, 9p: MOBKL2B) and by one deletion on 19p (MOBK2LA). Other high-frequency losses encompassed CDKN2A, CDKN2B, and MTAP (on 9p), RB1 and DLEU1/2/miR15a/16-1 (13q), and TP53 (17p). Unique homozygous losses were detected at 9p (3.2-3.3 Mbp; involving only RFX3), 11q (94.5-111.7 Mbp; spanning the ATM region), and 13q (82.7-99.5 Mbp; including the miR17-92 region), and micro-deletions at 6q (121.1-121.9; GJA1/Cx43), 12p (7.5-7.6; CD163), and 13q (73.3-73.4; KLF12, and 75.2–75.3; LMO7). CN-LOH was observed at 6p, similar to prior studies, though we found novel regions of UPD at 4p, 8q, 18q, 19q, and 22q. An overall survival of 3.6 years and relapse-free survival of 1.3 years was observed. Survival was significantly worse among 8 pts with Ki67 >75% (OS 1.4 years, p=.003), but was unaffected by del 11q, del 9p, gain 3q, or gain 8q. Conclusions: SNP-A analysis of 18 primary samples confirms that gains in 3q and 8q and losses in 11q, 6q, and 9p represent common secondary genetic lesions in MCL, and are not frequent in normal controls. We narrowed the MCR of several deletions, potential targets for gene sequencing, and confirm the presence of deletions of potential relevance to the Hippo pathway. Further analysis of our findings in light of tissue micro-array and fluorescence in-situ hybridization studies is underway, to assess pathobiologic consequences of genomic lesions as well as potential therapeutic targets. Disclosures: No relevant conflicts of interest to declare.
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Do, Cuc Hoang, Karen M. Lower, Cindy C. Macardle und Bryone Jean Kuss. „The Detection and Determination of the Genomic Profile of Low-Frequency 17p Deletion Clones in Chronic Lymphocytic Leukaemia (CLL)“. Blood 128, Nr. 22 (02.12.2016): 2021. http://dx.doi.org/10.1182/blood.v128.22.2021.2021.
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Abstract Novel gene mutation discovery has resulted in the increasing utility of targeted therapies. This is of particular relevance where traditional therapies have failed, resulting in increasing drug resistance and genetic instability. The incremental rise of subclonal populations of drug resistant cells is well recognized in CLL, however exactly how these subclones contribute to the overall disease course of the patient is unknown. Critical to further understanding the relevance of early minor subclones is the determination of the genetic profiles of these subclones and the identification of potential driver mutations. While a high level of resolution of genetic mutations can be revealed using ultra-deep next generation sequencing of CLL cells, this method does not determine which actual subclone contain the mutations, and requires approximately 2000 fold coverage. One of the most important prognostic markers in CLL is a deletion of the short arm of chromosome 17 (del17p), which includes deletion of TP53 gene. Whilst del17p is uncommon at diagnosis (only 5%-10% of all CLL patients), this proportion significantly increases to rougly 40-50% of chemo-refractory CLL. Therefore, we hypothesise that there are specific mutations in the del17p cells, including but not limited to TP53, which drive these subclones through clonal evolution, creating genetically unstable cells which are then refractory to treatment. We are particularly interested in those cases of CLL that carry a low frequency del17p subclone (<20% CLL cells), as these patients represent the greatest challenge to clinicians to decide the most appropriate course of treatment. Current methods to detect these 17p-deleted cells, such as microscopy-based fluorescence in situ hybridization (FISH) and karyotyping, have restrictions on their lower limit of detection due to the low number of cells targeted. We have developed a sensitive method of detecting and flow sorting del17p cells to facilitate specific subclone analysis. FISH in suspension (FISH-IS) incorporates a flow cytometry-based imaging approach with automated analysis of thousands of cells, and is highly applicable to detecting del17p in CLL samples. Methods: The FISH-IS workflow was used with 17p locus-specific identifier (LSI) probes in CLL samples. A fluorescently labelled contig of multiple BAC clones covering the TP53 region was hybridised to CLL cells in suspension. Data was collected through the Image Stream X flow cytometer (Amnis) and IDEAS software was used to carry out the analysis. Results: In preliminary experiments CLL cells were mixed in fixed ratios with wild type 17p cells (wt 17p). We have shown that FISH-IS is able to accurately enumerate the 17p allele status (monoallelic vs biallelic) based on fluorescence intensity. Furthermore, the sensitivity of detection of del17p cells amongst 20,000 analysed cells was precisely identified to a 5% limit (Figure 1). The second phase involved developing a methodology capable of enriching del17p low-frequency subclones in CLL samples by standard flow cytometry. Flow cytometry was used to sort cells based on their mean fluorescence intensity. Analysis of common polymorphisms within TP53 were used to demonstrate enrichment by collecting predefined fractions from the flow cytometer, based on fluorescence intensity and predicted 17p deletion status. We confirmed this method on CLL samples carrying high-frequency del17p clones due to sample availability. Our data clearly shows that this method is able to enrich for the low frequency clone as evidenced by analysis of targeted heterozygous SNPs located in the deleted region of 17p (Figure 2). Further sample analysis and exome sequencing is underway to determine sub-clonal mutation architecture. Original findings in this specific and novel approach to sub-clone analysis will be presented. Conclusion: This is the first time the genomic landscape of these low-frequency subclones has been interrogated in an unbiased manner. This data will enable a specific and in-depth genetic analysis of the untreated low-frequency del17p subclone, with a view to being able to identify the mechanisms of development of a chemorefractory and aggressive CLL phenotype. Figure 1 Sensitivity of FISH-IS with a predictable mixing model. Figure 1. Sensitivity of FISH-IS with a predictable mixing model. Figure 2: Successful enrichment of low frequency CLL subclones based on 17p status. (A) FISH-IS images. (B) Flow sorting. (C) Validation of enrichment by SNPs within TP53. Figure 2: Successful enrichment of low frequency CLL subclones based on 17p status. (A) FISH-IS images. (B) Flow sorting. (C) Validation of enrichment by SNPs within TP53. Disclosures No relevant conflicts of interest to declare.
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„Development of Semi-Automatic Karyotyping System Using Image Processing“. Journal of Control, Automation and Systems Engineering 9, Nr. 10 (01.10.2003): 844–51. http://dx.doi.org/10.5302/j.icros.2003.9.10.844.
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Remya, R. S., S. Hariharan, V. Keerthi und C. Gopakumar. „Preprocessing G-banded metaphase: towards the design of automated karyotyping“. SN Applied Sciences 1, Nr. 12 (28.11.2019). http://dx.doi.org/10.1007/s42452-019-1754-z.
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Remani Sathyan, Remya, Gopakumar Chandrasekhara Menon, Hariharan S, Rakhi Thampi und Jude Hemanth Duraisamy. „Traditional and deep‐based techniques for end‐to‐end automated karyotyping: A review“. Expert Systems, 30.08.2021. http://dx.doi.org/10.1111/exsy.12799.
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