Comparison of In-House Methods and Cobas BRAF V600 Mutation Assay in Melanoma Tumor Samples

Evaluation of Concordance Between the Methods Used in INCa Platforms and the Cobas® 4800 BRAF V600 Mutation Test for Detection of BRAF V600 Mutations in Melanoma in Real Life Setting

This non-interventional study will compare the Cobas BRAF V600 mutation assay with in-house methods used in molecular laboratories for the assessment of the BRAF mutation status in melanoma tumor samples. No patients will be enrolled in this study. Data will be collected for approximately 6 months.

Study Overview

• Status: Completed
• Conditions: Malignant Melanoma

• Study Type: Observational
• Enrollment (Actual): 420

Contacts and Locations

Study Locations

• France
  • Boulogne Billancourt, France, 92104
  • Colmar, France, 68024
  • Lille, France, 59037
  • Lyon, France, 69437
  • Marseille, France, 13015
  • Montpellier, France, 34295
  • Nantes, France, 44093
  • Paris, France, 75010
  • Pessac, France, 33604
  • Rouen, France, 76031
  • Vandoeuvre Les Nancy, France, 54511
  • Villejuif, France, 94505

Participation Criteria

Eligibility Criteria

• Ages Eligible for Study: Child; Adult; Older Adult
• Accepts Healthy Volunteers: No
• Genders Eligible for Study: All

• Sampling Method: Probability Sample

Study Population

No patients are enrolled in this study. Use of melanoma tumor samples.

Description

Inclusion Criteria:

No patients are enrolled. Use of tumor samples only.

• Histologically proven melanoma tumor sample
• Any type of tumor sample: biopsy or surgical specimen of primary tumor or metastasis
• Tumor samples must be fixed and paraffin-embedded.

Exclusion Criteria:

No patients are enrolled. Use of tumor samples only.

• Fixative unknown

Study Plan

How is the study designed?

Number of groups / cohorts

2

Cohorts and Interventions

Group / Cohort
INCa molecular genetics laboratory "in-house" methods; BRAF V600 mutations were analysed using INCa (Institut National du Cancer [French National Cancer Institute]) molecular genetics laboratories using "in-house" methods
Cobas 4800 Mutation Test; BRAF V600 mutations were analysed using Cobas 4800 mutation test

What is the study measuring?

Primary Outcome Measures

Outcome Measure	Measure Description	Time Frame
BRAF Mutation Status According to Cobas 4800 BRAF V600 Mutation Test vs. INCa Laboratories Molecular Genetics Laboratories	BRAF V600 mutation status was determined by INCa molecular laboratories "in-house" methods and Cobas 4800 BRAF V600 mutation test. Samples were analysed as V600 mutation, No V600 mutation and Non evaluable. Additionally, the type of V600 mutation (E, K, R, D, E2, other V600 mutation, not specified) was also evaluated only by INCa molecular laboratory "in-house" method.	Up to 6 months

Secondary Outcome Measures

Outcome Measure	Measure Description	Time Frame
Tumor Sample Characteristics-Type of Tumor Sample	The type of tumor sample used for evaluation of BRAF V600 mutation whether it was a biopsy or surgical specimen were reported	Up to 6 months
Tumor Sample Characteristics - Source of Tumor Sample	The source of tumor sample for BRAF V600 mutation detection whether taken from internal or external pathology laboratory were reported	Up to 6 months
Type of Pathology Laboratory Performing the Fixation or Embedding-Pre-analytical Method	The external or internal pathology laboratories involved in the process of fixation or embedding of the tumor sample was evaluated.	Up to 6 months
Time From Sampling to Fixation- Pre-analytical Method	Time taken from the sampling to the fixation of the tumor sample was reported in range of 0-2 hours, 2-6 hours, >6 hours and unknown. Number of samples falling in each of the class were reported.	Up to 6 months
Type of Fixative Used- Pre-analytical Method	The different types of fixative Excell, formol, alcohol formol acetic acid and other, used to fix the tumor samples were reported.	Up to 6 months
Fixation Duration by Pre-analytical Method	Fixation duration is defined as the amount of time required in hours for the fixation of a samples. The fixation duration was categorized as <6 hours, 6-24 hours and >24 hours and unknown. Number of samples falling in each category were reported	Up to 6 months
Slice Thickness by Pre-analytical Method	Slice thickness of all the tumour samples was measured. The slice thickness was measured in micrometer.	Up to 6 months
Dewaxing by Pre-analytical Method	Dewaxing is a method to recover the DNA from samples. Dewaxing information was collected as "Yes, No or Missing"	Up to 6 Months
Necrosis Percentage Determination by Pre-analytical Method	The percentage of necrosis defined as the death of one or more cells in the analysed zone was reported.	Up to 6 months
Percentage of Tumor Cells by Pre-analytical Method	The percentage of tumor cells in the given tumor sample were reported.	Up to 6 months
Tumor Samples With Presence of Melanin by Pre-analytical Method	The tumor samples with presence of melanin were categorized as Important, Few, Medium and Absent.	Up to 6 months
DNA Extraction - Extraction Method by Pre-analytical Method	This method assessed DNA from the tumor samples was extracted by Automated method or Manual method.	Up to 6 months
Median DNA Elution Volume by Pre-analytical Method	Median DNA elution volume microliters [mcl] was reported.	Up to 6 months
Mean DNA Concentration by Pre-analytical Method	The DNA concentration in the tissue elute was measured in nanogram per microliter (ng/mcL).	Up to 6 months
Amount of DNA by Pre-analytical Method	The total DNA concentration extracted from the tissue was measured in nanogram (ng).	Up to 6 months
Size of Amplicons Used by "In-house" Analytical Method	The method described the size of amplicon used. It was measured in base pairs (bp).	Up to 6 months
Method of Mutation Detection by "In-house" Analytical Method	Allele-specific PCR, High Resolution Melting (HRM) + Sanger sequencing, Pyrosequencing, Sanger sequencing, Real time PCR, SNaPshot were used for BRAF V600 mutation detection.	Up to 6 months
Number of Samples Punched in In-house Analytical Method	Total number of samples for whom punch was used in 'in-house analytical' method are reported.	Up to 6 months
Mean Number of Slices Per Sample Used for "In-house"- Analytical Method	The mean of number of slices per sample when no punch was used are reported.	Up to 6 months
Median Time Between Receipt of Samples and Determination of Result by "In-house" Analytical Method	This In-house analytical method measured the time between receipt of samples to the result determination. It measured the time in days.	Up to 6 months
Technician Work Time Between DNA Extraction and Result by "In-house" Analytical Method	The working time required by the technician from the time of DNA extraction to the time to obtain the results was measured in hours.	Up to 6 months
Mean DNA Concentration as Measured by COBAS 4800 BRAF V600 Mutation Test-Analytical Method	The DNA concentration as assessed by COBAS 4800 BRAF V600 Mutation assay was reported. The unit used to measure the DNA concentration was nanogram/microlitre (ng/mcl)	Up to 6 months
Punch Used for Cobas 4800 BRAF V600 Mutation Test- Analytical Method	The punch done during Cobas 4800 BRAF V600 Mutation Test on the sample was described as Yes or No.	Up to 6 months
Number of Slices Used When No Punch Was Used for Cobas 4800 BRAF V600 Mutation Test- Analytical Method	This describes the Cobas 4800 BRAF V600 Mutation Test, for the mean of number of slices when No punch method, was used. Of the 420 samples, punch was Yes, for 45 samples and punch was No, for 375 samples.	Up to 6 months
Median Time Between Receipt of Sample and Determination of Result by Cobas 4800 BRAF V600 Mutation Test -Analytical Method	This analytical method for cobas 4800 BRAF V600 Mutation Test measured the time between receipt of samples to the result determination. It measured the time in days.	Up to 6 months
Technician Work Time Between DNA Extraction and Result by Cobas 4800 BRAF V600 Mutation Test - Analytical Method	This cobas 4800 BRAF V600 Mutation Test analytical method measures the working time required by the technician from the time of DNA extraction to the time to obtain the results. The time duration was measured in hours.	Up to 6 months
Management of Discordance- Method Used to Manage Discordance	Crossing DNA, DNA from In-House method analysed with cobas, SNaPshot, DNA from cobas analysed with In-House method, external site control test, Sanger sequencing, Kit CE-IVD Therascreen RGQ Qiagen, Kit Therascreen RGQ BRAF + Pyrosequencing by another platform (PF), Pyrosequencing, Mutation detection On Another Block, (primitive tumor [prm. tmr]), Sequencing And Therascreen kit (Qiagen) were used for management of discordance between "in-house" method and Cobas 4800 mutation test.	Up to 6 months
Management of Discordance-Final Result for BRAF V600 Mutation Detection	The final results obtained by discordance management of the 28 discordant samples were BRAF V600 mutation, No BRAF V600 mutation and Non-evaluable. These results were further assessed by the Investigator and interpreted as final result.	Up to 6 months

Collaborators and Investigators

• Sponsor: Hoffmann-La Roche

Study record dates

Study Major Dates

• Study Start: December 1, 2012
• Primary Completion (Actual): April 1, 2013
• Study Completion (Actual): April 1, 2013

Study Registration Dates

• First Submitted: December 6, 2012
• First Submitted That Met QC Criteria: December 6, 2012
• First Posted (Estimate): December 7, 2012

Study Record Updates

• Last Update Posted (Estimate): March 28, 2016
• Last Update Submitted That Met QC Criteria: February 25, 2016
• Last Verified: November 1, 2015

More Information

Terms related to this study

• Additional Relevant MeSH Terms: Neoplasms by Histologic Type; Neoplasms; Neuroectodermal Tumors; Neoplasms, Germ Cell and Embryonal; Neoplasms, Nerve Tissue; Neuroendocrine Tumors; Nevi and Melanomas; Melanoma
• Other Study ID Numbers: ML28471