the application of validation and proficiency testing concepts from current clinical genetic...
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The Application of Validation and Proficiency Testing Concepts From Current Clinical Genetic Diagnostics
For the Implementation of New Genetic Technologies
Genomics 2015Kathleen S. Wilson, M.D.
The University of Texas Southwestern Medical Center
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Advent of new genetic technologies utilized for clinical diagnostics is rapid.
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Advent of new genetic technologies utilized for clinical diagnostics is rapid.
Implementation of these evolving technologies is challenging.
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Next Generation SequencingMultiple, fragmented sequence reads assembled based on overlapping areas
https://en.wikipedia.org/wiki/DNA_sequencing
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Whole Exome Sequencing
https://en.wikipedia.org/wiki/Exome_sequencing#/media/File:Exome_Sequencing_Workflow_1a.png
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College of American Pathologists/American College of Medical Genetics Cytogenetics Resource Committee
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College of American Pathologists/American College of Medical Genetics Cytogenetics Resource Committee
Fluorescence in situ hybridization (FISH)
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College of American Pathologists/American College of Medical Genetics Cytogenetics Resource Committee
Fluorescence in situ hybridization (FISH)
Cytogenomic microarray analysis (CMA)
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College of American Pathologists/American College of Medical Genetics Cytogenetics Resource Committee
Fluorescence in situ hybridization (FISH)
Cytogenomic microarray analysis (CMA)
Relevance for the rapidly evolving sequencing technologies
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Lessons learned from prior technology have relevance for the clinical genetic diagnostics of the future.
![Page 11: The Application of Validation and Proficiency Testing Concepts From Current Clinical Genetic Diagnostics For the Implementation of New Genetic Technologies](https://reader034.vdocument.in/reader034/viewer/2022051417/5697bfc51a28abf838ca6b8c/html5/thumbnails/11.jpg)
Lessons learned from prior technology have relevance for the clinical genetic diagnostics of the future.
1. Method not analyte based
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UTSW FISH Probe Validation
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UTSW FISH Probe Validation
1. Metaphase probesa. Unique sequence
1. Localization2. Analytical validation
b. Repeat sequence/whole chromosome paints1. Localization2. Analytical validation
2. Interphase probes (unique sequence and repeat sequence only)a. Localizationb. Analytical validation
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Lessons learned from prior technology have relevance for the clinical genetic diagnostics of the future.
1. Method not analyte based
Smear preparationsDropped cell suspensions from culturesMonolayer culturesUncultured amniocytesCytospin preparationsTouch preparationsFFPE (formalyn fixed parraffin embedded tissues) (CYJ/K/L)Urine
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Lessons learned from prior technology have relevance for the clinical genetic diagnostics of the future.
1. Method not analyte based
BCR/ABL1RUNX1T1/RUNX1PML/RARAMicrodeletion cocktails
ETC…
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Lessons learned from prior technology have relevance for the clinical genetic diagnostics of the future.
1. Method not analyte based
Dropped cell suspensions from cultures (CYF)Urine (Urovysion) (CYI)FFPE (formalyn fixed parraffin embedded tissues) (CYJ/K/L)HER2 (CYH)
![Page 17: The Application of Validation and Proficiency Testing Concepts From Current Clinical Genetic Diagnostics For the Implementation of New Genetic Technologies](https://reader034.vdocument.in/reader034/viewer/2022051417/5697bfc51a28abf838ca6b8c/html5/thumbnails/17.jpg)
Lessons learned from prior technology have relevance for the clinical genetic diagnostics of the future.
1. Method not analyte based
Dropped cell suspensions from cultures (CYF)Urine (Urovysion) (CYI)
![Page 18: The Application of Validation and Proficiency Testing Concepts From Current Clinical Genetic Diagnostics For the Implementation of New Genetic Technologies](https://reader034.vdocument.in/reader034/viewer/2022051417/5697bfc51a28abf838ca6b8c/html5/thumbnails/18.jpg)
Cytogenomic Microarray Analysis
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This was the fifteenth CAP/ACMG Survey mailing for whole genome copy number changes by microarray technology. This was the eleventh GRADED CYCGH Survey. The number of participants enrolled in this Survey has been 27, 34, 50, 63, 72, 80, 92, 96, 123, 124, 144, 147, 158, 161, and 170 in the first through fifteenth Surveys, respectively. CYCGH-01 and CYCGH-02 reached participant consensus of greater than 80% and were graded.
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Lessons learned from prior technology have relevance for the clinical genetic diagnostics of the future.
1. Method not analyte based
2. Vendor provided Quality Control measures as part of assay development and validation
![Page 21: The Application of Validation and Proficiency Testing Concepts From Current Clinical Genetic Diagnostics For the Implementation of New Genetic Technologies](https://reader034.vdocument.in/reader034/viewer/2022051417/5697bfc51a28abf838ca6b8c/html5/thumbnails/21.jpg)
Lessons learned from prior technology have relevance for the clinical genetic diagnostics of the future.
1. Method not analyte based
2. Vendor provided Quality Control measures as part of assay development and validation
![Page 22: The Application of Validation and Proficiency Testing Concepts From Current Clinical Genetic Diagnostics For the Implementation of New Genetic Technologies](https://reader034.vdocument.in/reader034/viewer/2022051417/5697bfc51a28abf838ca6b8c/html5/thumbnails/22.jpg)
Lessons learned from prior technology have relevance for the clinical genetic diagnostics of the future.
1. Method not analyte based
2. Vendor provided Quality Control measures as part of assay development and validation
![Page 23: The Application of Validation and Proficiency Testing Concepts From Current Clinical Genetic Diagnostics For the Implementation of New Genetic Technologies](https://reader034.vdocument.in/reader034/viewer/2022051417/5697bfc51a28abf838ca6b8c/html5/thumbnails/23.jpg)
Lessons learned from prior technology have relevance for the clinical genetic diagnostics of the future.
1. Method not analyte based
2. Vendor provided Quality Control measures as part of assay development and validation
3. DNA quality
![Page 24: The Application of Validation and Proficiency Testing Concepts From Current Clinical Genetic Diagnostics For the Implementation of New Genetic Technologies](https://reader034.vdocument.in/reader034/viewer/2022051417/5697bfc51a28abf838ca6b8c/html5/thumbnails/24.jpg)
Lessons learned from prior technology have relevance for the clinical genetic diagnostics of the future.
1. Method not analyte based
2. Vendor provided Quality Control measures as part of assay development and validation
3. DNA quality
![Page 25: The Application of Validation and Proficiency Testing Concepts From Current Clinical Genetic Diagnostics For the Implementation of New Genetic Technologies](https://reader034.vdocument.in/reader034/viewer/2022051417/5697bfc51a28abf838ca6b8c/html5/thumbnails/25.jpg)
Lessons learned from prior technology have relevance for the clinical genetic diagnostics of the future.
1. Method not analyte based
2. Vendor provided Quality Control measures as part of assay development and validation
3. DNA quality
4. Computer technology
![Page 26: The Application of Validation and Proficiency Testing Concepts From Current Clinical Genetic Diagnostics For the Implementation of New Genetic Technologies](https://reader034.vdocument.in/reader034/viewer/2022051417/5697bfc51a28abf838ca6b8c/html5/thumbnails/26.jpg)
Lessons learned from prior technology have relevance for the clinical genetic diagnostics of the future.
1. Method not analyte based
2. Vendor provided Quality Control measures as part of assay development and validation
3. DNA quality
4. Computer technology-interface checks
![Page 27: The Application of Validation and Proficiency Testing Concepts From Current Clinical Genetic Diagnostics For the Implementation of New Genetic Technologies](https://reader034.vdocument.in/reader034/viewer/2022051417/5697bfc51a28abf838ca6b8c/html5/thumbnails/27.jpg)
Lessons learned from prior technology have relevance for the clinical genetic diagnostics of the future.
1. Method not analyte based
2. Vendor provided Quality Control measures as part of assay development and validation
3. DNA quality
4. Computer technology-interface checks
5. Scope of validation
![Page 28: The Application of Validation and Proficiency Testing Concepts From Current Clinical Genetic Diagnostics For the Implementation of New Genetic Technologies](https://reader034.vdocument.in/reader034/viewer/2022051417/5697bfc51a28abf838ca6b8c/html5/thumbnails/28.jpg)