Reza Shahsiah | International Congress Form
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Application Code :
762-0117-0003
Created Date : Wednesday, April 12, 2017-08:31 08:31:42Update Date : Wednesday, September 6, 2017-19:58 19:58:05
IP Address : 2.177.80.133Submit Date : Wednesday, September 6, 2017-19:58 19:58:22Email : Shahsiah@yahoo.com
Personal Information
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Name : |
Reza |
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Surname : |
Shahsiah |
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School/Research center : |
School of Medicine |
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If you choose other, please name your Research center : |
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Position : |
Associate professor |
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Tel : |
+98-21-61192425 |
Information of Congress
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Title of the Congress : |
AMP Global Congress |
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Title of your Abstract : |
Detection of Hotspot Cancer Mutations in a Clinical Laboratory Using Next Generation Sequencing on the Ion Torrent PGMâ„¢ |
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Destination Country : |
Germany |
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From : |
Monday, April 3, 2017 |
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To : |
Wednesday, April 5, 2017 |
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Abstract(Please copy/paste the abstract send to the congress) : |
Introduction:
Recent advances in sequencing technologies have enabled us to scrutinize the versatile underlying mechanisms of cancer more precisely. However, adopting these new sophisticated technologies is challenging for clinical labs as it involves complex workflows, and requires validation for diagnostic purposes. The aim of this work is towards the analytical validation of a next generation sequencing (NGS) method for cancer hotspot mutation analysis.
Methods:
Characterized formalin-fixed paraffin-embedded (FFPE) samples including biopsy specimens and cell-lines were purchased. DNA was extracted from FFPE biopsy sections or similarly prepared reference standard cell lines. After quantification of extracted DNA, multiplex PCR amplification of target regions was performed followed by library preparation, template preparation and sequencing on the Ion Torrent PGM platform using the Ion PGMâ„¢ Select Sequencing Kit and Ion 318â„¢ chip. Torrent Suite software version 4.4.3 and Ion Reporter Analysis software v4.2 were employed for sequence analysis.
Results:
The most important parameters that should be determined in the validation of any NGS assay for a clinical laboratory are coverage, threshold (cutoff point for differentiation of a positive and a negative result), sensitivity, specificity, and limit of detection (LoD). The minimum coverage and the threshold are the priority parameters because affect all others. To determine the most appropriate coverage, a difference plot was constructed showing coverage on the X-axis versus measurement-error (the deviation of the measured frequency from the expected frequency) on the Y-axis. Variant frequency calls with coverage of <100x were found to be inaccurate. Receiver operating characteristics (ROC) analysis showed the most appropriate threshold to be 2%. To determine LoD, logistic regression analysis was performed. Accordingly, the sensitivity, specificity and limit of detection of the method were of 96.1%, 97.8% and 4.3% respectively.
Conclusions:
In every validation study, the number of samples, the manner of sample selection, and the number and type of variants play a role in the outcome. Therefore, these parameters should be assessed according to the clinical needs of each laboratory undertaking the validation. The range of minimum acceptable coverage for somatic mutations varies from 100x to 500x between different laboratories in various NGS validation studies. Also in these studies, researchers have selected different thresholds typically ranging from 2 to 8 percent. Lastly, the type and amount of mutations are to be considered in the light clinical actionability and outcome when conducting a validation study. |
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Keywords of your Abstract : |
Cancer; Next Generation Sequencing; Clinical Laboratory; Test Validation; |
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Acceptance Letter : |
http://gsia.tums.ac.ir/images/UserFiles/36981/Forms/762/Gmail - AMP 2017 Global Congress Abstract Notification_2.pdf |
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The presentation : |
Poster |
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The Cover of Abstract book : |
http://gsia.tums.ac.ir/images/UserFiles/36981/Forms/762/IMG_5576.pdf |
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Published abstract in the abstract book with the related code : |
http://gsia.tums.ac.ir/images/UserFiles/36981/Forms/762/PIIS1525157817301393_1.pdf |
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Where has your abstract been indexed? : |
ISI |
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If you choose other, please name : |
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The Congress Reporting Form
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How many volunteers were present at the Congress? : |
400 |
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Delegates from which countries presented in the congress? : |
40 countries including USA, Germany, and England |
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Were the delegates of any other organizations present in the congress? : |
Yes |
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If yes, please write the names of the organizations in the box : |
ASCP, CAP |
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What were the responses to your talking points? Were specific questions or concerns raised? : |
The issue with validation of system for clinical laboratory is always selection of the characterized sample to be representative of real world samples. Companies like Horizon are always trying to manufacture those samples to be represent the clinical samples. |
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If you met staff members, please list their full names & positions. : |
Dr. Margaret L. Gulley, MD University of North Carolina at Chapel Hill |
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Please inform us if there are any follow up actions we need to talk with the members of the congress : |
I talked to AMP president about making Iranian society of pathology a member of AMP, and the idea was welcome. They are looking forward to expanding their international ties. Therefore, there is a good opportunity there. |
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Your experiences about the travel processes(Providing ticket, accommodation,...) : |
AMP had organized these things well, but membership and participation are not cheap! |
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Please give a briefing of your own observations and outcomes of the congress: : |
The conference was NGS oriented, and molecular diagnostics is becoming more and more important in clinical pathology. |