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

Completed

Conditions: Malignant Melanoma

Registration Number: NCT01744860

Lead Sponsor: Hoffmann-La Roche

Brief Summary: 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.

Detailed Description: Not available

Recruitment & Eligibility

Status: COMPLETED

Sex: All

Target Recruitment: 420

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 & Design

Study Type: OBSERVATIONAL

Study Design: Not specified

Primary Outcome Measures

Name	Time	Method
BRAF Mutation Status According to Cobas 4800 BRAF V600 Mutation Test vs. INCa Laboratories Molecular Genetics Laboratories	Up to 6 months	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.

Secondary Outcome Measures

Name	Time	Method
Tumor Sample Characteristics-Type of Tumor Sample	Up to 6 months	The type of tumor sample used for evaluation of BRAF V600 mutation whether it was a biopsy or surgical specimen were reported
Type of Fixative Used- Pre-analytical Method	Up to 6 months	The different types of fixative Excell, formol, alcohol formol acetic acid and other, used to fix the tumor samples were reported.
Dewaxing by Pre-analytical Method	Up to 6 Months	Dewaxing is a method to recover the DNA from samples. Dewaxing information was collected as "Yes, No or Missing"
Size of Amplicons Used by "In-house" Analytical Method	Up to 6 months	The method described the size of amplicon used. It was measured in base pairs (bp).
Method of Mutation Detection by "In-house" Analytical Method	Up to 6 months	Allele-specific PCR, High Resolution Melting (HRM) + Sanger sequencing, Pyrosequencing, Sanger sequencing, Real time PCR, SNaPshot were used for BRAF V600 mutation detection.
Technician Work Time Between DNA Extraction and Result by "In-house" Analytical Method	Up to 6 months	The working time required by the technician from the time of DNA extraction to the time to obtain the results was measured in hours.
Time From Sampling to Fixation- Pre-analytical Method	Up to 6 months	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.
Number of Samples Punched in In-house Analytical Method	Up to 6 months	Total number of samples for whom punch was used in 'in-house analytical' method are reported.
Fixation Duration by Pre-analytical Method	Up to 6 months	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
Slice Thickness by Pre-analytical Method	Up to 6 months	Slice thickness of all the tumour samples was measured. The slice thickness was measured in micrometer.
Median Time Between Receipt of Samples and Determination of Result by "In-house" Analytical Method	Up to 6 months	This In-house analytical method measured the time between receipt of samples to the result determination. It measured the time in days.
Necrosis Percentage Determination by Pre-analytical Method	Up to 6 months	The percentage of necrosis defined as the death of one or more cells in the analysed zone was reported.
Percentage of Tumor Cells by Pre-analytical Method	Up to 6 months	The percentage of tumor cells in the given tumor sample were reported.
Tumor Samples With Presence of Melanin by Pre-analytical Method	Up to 6 months	The tumor samples with presence of melanin were categorized as Important, Few, Medium and Absent.
DNA Extraction - Extraction Method by Pre-analytical Method	Up to 6 months	This method assessed DNA from the tumor samples was extracted by Automated method or Manual method.
Mean DNA Concentration by Pre-analytical Method	Up to 6 months	The DNA concentration in the tissue elute was measured in nanogram per microliter (ng/mcL).
Amount of DNA by Pre-analytical Method	Up to 6 months	The total DNA concentration extracted from the tissue was measured in nanogram (ng).
Number of Slices Used When No Punch Was Used for Cobas 4800 BRAF V600 Mutation Test- Analytical Method	Up to 6 months	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.
Median Time Between Receipt of Sample and Determination of Result by Cobas 4800 BRAF V600 Mutation Test -Analytical Method	Up to 6 months	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.
Tumor Sample Characteristics - Source of Tumor Sample	Up to 6 months	The source of tumor sample for BRAF V600 mutation detection whether taken from internal or external pathology laboratory were reported
Type of Pathology Laboratory Performing the Fixation or Embedding-Pre-analytical Method	Up to 6 months	The external or internal pathology laboratories involved in the process of fixation or embedding of the tumor sample was evaluated.
Median DNA Elution Volume by Pre-analytical Method	Up to 6 months	Median DNA elution volume microliters \[mcl\] was reported.
Mean Number of Slices Per Sample Used for "In-house"- Analytical Method	Up to 6 months	The mean of number of slices per sample when no punch was used are reported.
Punch Used for Cobas 4800 BRAF V600 Mutation Test- Analytical Method	Up to 6 months	The punch done during Cobas 4800 BRAF V600 Mutation Test on the sample was described as Yes or No.
Management of Discordance-Final Result for BRAF V600 Mutation Detection	Up to 6 months	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.
Management of Discordance- Method Used to Manage Discordance	Up to 6 months	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.
Mean DNA Concentration as Measured by COBAS 4800 BRAF V600 Mutation Test-Analytical Method	Up to 6 months	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)
Technician Work Time Between DNA Extraction and Result by Cobas 4800 BRAF V600 Mutation Test - Analytical Method	Up to 6 months	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.