Presentation is loading. Please wait.

Presentation is loading. Please wait.

Multi-Institutional FASTQ File Exchange as a Means of Proficiency Testing for Next- Generation Sequencing Bioinformatics and Variant Interpretation  Kurtis.

Published byJørn Eriksen Modified over 5 years ago

Similar presentations

Presentation on theme: "Multi-Institutional FASTQ File Exchange as a Means of Proficiency Testing for Next- Generation Sequencing Bioinformatics and Variant Interpretation  Kurtis."— Presentation transcript:

1 Multi-Institutional FASTQ File Exchange as a Means of Proficiency Testing for Next- Generation Sequencing Bioinformatics and Variant Interpretation  Kurtis D. Davies, Midhat S. Farooqi, Mike Gruidl, Charles E. Hill, Julie Woolworth-Hirschhorn, Heather Jones, Kenneth L. Jones, Anthony Magliocco, Midori Mitui, Philip H. O'Neill, Rebecca O'Rourke, Nirali M. Patel, Dahui Qin, Erica Ramos, Michael R. Rossi, Thomas M. Schneider, Geoffrey H. Smith, Linsheng Zhang, Jason Y. Park, Dara L. Aisner  The Journal of Molecular Diagnostics  Volume 18, Issue 4, Pages (July 2016) DOI: /j.jmoldx Copyright © 2016 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

2 Figure 1 Sample characteristics. A: Of the 24 sample file sets used in the proficiency test, 20 were derived from formalin-fixed, paraffin-embedded (FFPE) processed clinical samples, one was derived from a Diff-Quik slide processed clinical sample, and three were derived from commercially available calibrators (NA12878, HD129, and HD200). B: Disease type distribution for the 21 clinical samples. C: Distribution of the total number of variants (summary of all variants called by all institutions) reported per sample, including calibrator samples. The Journal of Molecular Diagnostics  , DOI: ( /j.jmoldx ) Copyright © 2016 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

3 Figure 2 Variant allele frequency (VAF) concordance. The range of VAF (highest reported minus lowest reported) was calculated for all variants reported by at least two institutions (66 variants total). The distribution of these ranges is shown. The VAF range was ≤5% for most variants (81.8%). The Journal of Molecular Diagnostics  , DOI: ( /j.jmoldx ) Copyright © 2016 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Download ppt "Multi-Institutional FASTQ File Exchange as a Means of Proficiency Testing for Next- Generation Sequencing Bioinformatics and Variant Interpretation  Kurtis."

Similar presentations

Measurement of Relative Copy Number of CDKN2A/ARF and CDKN2B in Bladder Cancer by Real-Time Quantitative PCR and Multiplex Ligation-Dependent Probe Amplification.

Measurement of Relative Copy Number of CDKN2A/ARF and CDKN2B in Bladder Cancer by Real-Time Quantitative PCR and Multiplex Ligation-Dependent Probe Amplification.
Nine Novel Germline Gene Variants in the RET Proto-Oncogene Identified in Twelve Unrelated Cases Syed A. Ahmed, Karen Snow-Bailey, W. Edward Highsmith,

Nine Novel Germline Gene Variants in the RET Proto-Oncogene Identified in Twelve Unrelated Cases Syed A. Ahmed, Karen Snow-Bailey, W. Edward Highsmith,
CyclinD1/CyclinD3 Ratio by Real-Time PCR Improves Specificity for the Diagnosis of Mantle Cell Lymphoma Carol D. Jones, Katherine H. Darnell, Roger A.

CyclinD1/CyclinD3 Ratio by Real-Time PCR Improves Specificity for the Diagnosis of Mantle Cell Lymphoma Carol D. Jones, Katherine H. Darnell, Roger A.
Quantification of Parvovirus B19 DNA Using COBAS AmpliPrep Automated Sample Preparation and LightCycler Real-Time PCR Stefan Schorling, Gunnar Schalasta,

Quantification of Parvovirus B19 DNA Using COBAS AmpliPrep Automated Sample Preparation and LightCycler Real-Time PCR Stefan Schorling, Gunnar Schalasta,
Design and Multiseries Validation of a Web-Based Gene Expression Assay for Predicting Breast Cancer Recurrence and Patient Survival Ryan K. Van Laar The.

Design and Multiseries Validation of a Web-Based Gene Expression Assay for Predicting Breast Cancer Recurrence and Patient Survival Ryan K. Van Laar The.
Prediction of Lung Cancer Histological Types by RT-qPCR Gene Expression in FFPE Specimens Matthew D. Wilkerson, Jason M. Schallheim, D. Neil Hayes, Patrick.

Prediction of Lung Cancer Histological Types by RT-qPCR Gene Expression in FFPE Specimens Matthew D. Wilkerson, Jason M. Schallheim, D. Neil Hayes, Patrick.
Enterococcus faecalis Induces Inflammatory Bowel Disease in Interleukin-10 Knockout Mice Edward Balish, Thomas Warner The American Journal of Pathology.

Enterococcus faecalis Induces Inflammatory Bowel Disease in Interleukin-10 Knockout Mice Edward Balish, Thomas Warner The American Journal of Pathology.
High-Quality Genotyping Data from Formalin-Fixed, Paraffin-Embedded Tissue on the Drug Metabolizing Enzymes and Transporters Plus Array  Hanneke I. Vos,

High-Quality Genotyping Data from Formalin-Fixed, Paraffin-Embedded Tissue on the Drug Metabolizing Enzymes and Transporters Plus Array  Hanneke I. Vos,
Carol Beadling, Tanaya L. Neff, Michael C

Carol Beadling, Tanaya L. Neff, Michael C
A Targeted High-Throughput Next-Generation Sequencing Panel for Clinical Screening of Mutations, Gene Amplifications, and Fusions in Solid Tumors  Rajyalakshmi.

A Targeted High-Throughput Next-Generation Sequencing Panel for Clinical Screening of Mutations, Gene Amplifications, and Fusions in Solid Tumors  Rajyalakshmi.
Genotyping of DNA Samples Isolated from Formalin-Fixed Paraffin-Embedded Tissues Using Preamplification  Renee Baak-Pablo, Vincent Dezentje, Henk-Jan.

Genotyping of DNA Samples Isolated from Formalin-Fixed Paraffin-Embedded Tissues Using Preamplification  Renee Baak-Pablo, Vincent Dezentje, Henk-Jan.
Sensitive Detection of KRAS Mutations in Archived Formalin-Fixed Paraffin-Embedded Tissue Using Mutant-Enriched PCR and Reverse-Hybridization  Christoph.

Sensitive Detection of KRAS Mutations in Archived Formalin-Fixed Paraffin-Embedded Tissue Using Mutant-Enriched PCR and Reverse-Hybridization  Christoph.
Targeted Next-Generation Sequencing for Hereditary Cancer Syndromes

Targeted Next-Generation Sequencing for Hereditary Cancer Syndromes
In Silico Proficiency Testing for Clinical Next-Generation Sequencing

In Silico Proficiency Testing for Clinical Next-Generation Sequencing
A Method to Evaluate the Quality of Clinical Gene-Panel Sequencing Data for Single- Nucleotide Variant Detection  Chung Lee, Joon S. Bae, Gyu H. Ryu, Nayoung.

A Method to Evaluate the Quality of Clinical Gene-Panel Sequencing Data for Single- Nucleotide Variant Detection  Chung Lee, Joon S. Bae, Gyu H. Ryu, Nayoung.
Laboratory Guidelines for Detection, Interpretation, and Reporting of Maternal Cell Contamination in Prenatal Analyses  Narasimhan Nagan, Nicole E. Faulkner,

Laboratory Guidelines for Detection, Interpretation, and Reporting of Maternal Cell Contamination in Prenatal Analyses  Narasimhan Nagan, Nicole E. Faulkner,
Separate Quality-Control Measures Are Necessary for Estimation of RNA and Methylated DNA from Formalin-Fixed, Paraffin-Embedded Specimens by Quantitative.

Separate Quality-Control Measures Are Necessary for Estimation of RNA and Methylated DNA from Formalin-Fixed, Paraffin-Embedded Specimens by Quantitative.
Somatic Mutation Screening Using Archival Formalin-Fixed, Paraffin-Embedded Tissues by Fluidigm Multiplex PCR and Illumina Sequencing  Ming Wang, Leire.

Somatic Mutation Screening Using Archival Formalin-Fixed, Paraffin-Embedded Tissues by Fluidigm Multiplex PCR and Illumina Sequencing  Ming Wang, Leire.
Cystic Fibrosis The Journal of Molecular Diagnostics

Cystic Fibrosis The Journal of Molecular Diagnostics
Molecular Analysis of Circulating Cell-Free DNA from Lung Cancer Patients in Routine Laboratory Practice  Stephan Bartels, Sascha Persing, Britta Hasemeier,

Molecular Analysis of Circulating Cell-Free DNA from Lung Cancer Patients in Routine Laboratory Practice  Stephan Bartels, Sascha Persing, Britta Hasemeier,

Similar presentations

Ads by Google