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

Advent of new genetic technologies utilized for clinical diagnostics is rapid.

Advent of new genetic technologies utilized for clinical diagnostics is rapid.

Implementation of these evolving technologies is challenging.

Next Generation SequencingMultiple, fragmented sequence reads assembled based on overlapping areas

https://en.wikipedia.org/wiki/DNA_sequencing

Whole Exome Sequencing

https://en.wikipedia.org/wiki/Exome_sequencing#/media/File:Exome_Sequencing_Workflow_1a.png

College of American Pathologists/American College of Medical Genetics Cytogenetics Resource Committee

College of American Pathologists/American College of Medical Genetics Cytogenetics Resource Committee

Fluorescence in situ hybridization (FISH)

College of American Pathologists/American College of Medical Genetics Cytogenetics Resource Committee

Fluorescence in situ hybridization (FISH)

Cytogenomic microarray analysis (CMA)

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

Lessons learned from prior technology have relevance for the clinical genetic diagnostics of the future.

Lessons learned from prior technology have relevance for the clinical genetic diagnostics of the future.

1. Method not analyte based

UTSW FISH Probe Validation

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

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

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…

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)

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)

Cytogenomic Microarray Analysis

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.

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

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

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

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

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

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

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

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