Duval 2014.

Study characteristics
Patient Sampling	Inclusion/exclusion criteria Inclusion criteria: oligodendrogliomas with FFPE tissue with previously established 1p/19q status by FISH. Prior testing Histopathological diagnosis according to WHO 2007 classification. Previously established 1p/19q status by FISH.
Patient characteristics and setting	Number of participants/tumours with results for 1p/19q status by ≥ 2 DNA‐based tests: 36 Country: Canada Population source and setting: NR Age: median: 55 years, interquartile range: NR; range: 26–82 years Gender: 38.9% male Karnofsky performance status: NR First diagnosis/recurrent disease: 16.7% recurrent tumours
Index tests	4 tests: FISH (variant 1), FISH (variant 2), FISH (variant 3) and FISH (variant 4) FISH (variant 1) Tumour sample type: FFPE Region(s) analysed: 1p36/19q13 Dual‐Color Probe kit (Abbott Molecular, Abbott Park, Illinois, USA) Cut‐off: combination cut‐off: quote: "The cut‐off of nuclei that had to show deletion was calculated on a series of 10 non‐neoplastic brain tissue samples (from epilepsy surgery cases and autopsy brains). This cut‐off was calculated using mean +3 SD and was set at 50% for both 1p and 19q. Cases above the cutoff were considered deleted and those under the cut‐off were considered normal or imbalanced according to the literature guidelines [43,44]". FISH (variant 2) Tumour sample type: FFPE Region(s) analysed: 1p36/19q13 Dual‐Color Probe kit (Abbott Molecular, Abbott Park, Illinois, USA) Cut‐off: ratio cut‐off: ratio ≤ 0.8 was considered to indicate a deletion; quote: "For each case the signal ratio of red signals to green signals per cell was also established. A ratio ≤0.8 was considered to indicate a deletion whereas a ratio between 0.8 and 1.1 was considered to indicate a normal status on the chromosomal arm. A ratio over 1.1 was considered to indicate polysomy and was classified in the imbalanced status subgroup [2,30]". FISH (variant 3) Tumour sample type: FFPE Region(s) analysed: 1p36/19q13 Dual‐Color Probe kit (Abbott Molecular, Abbott Park, Illinois, USA) Cut‐off: combination cut‐off: quote: "cut‐off at the median value of our tumor series which corresponds to a value of 65% for both 1p and 19q". Additional details: ImmunoFISH. IHC performed against Ki67 (MIB‐1). FISH (variant 4) Tumour sample type: FFPE Region(s) analysed: 1p36/19q13 Dual‐Color Probe kit (Abbott Molecular, Abbott Park, Illinois, USA) Cut‐off: ratio cut‐off: ratio ≤ 0.8 was considered to indicate a deletion; quote: "For the ratio method, established values were the same as for the FISH". Additional details: ImmunoFISH. IHC performed against Ki67 (MIB‐1).
Target condition and reference standard(s)	Target condition was absolute 1p/19q deletion. No tests used as reference standard in our analyses.
Flow and timing	We presumed that all tests were performed on biopsied tumour material collected on 1 occasion.
Comparative
Notes
Methodological quality
Item	Authors' judgement	Risk of bias	Applicability concerns
DOMAIN 1: Patient Selection
Was a consecutive or random sample of patients enrolled?	No
Was a case‐control design avoided?	Yes
Did the study avoid inappropriate exclusions?	Unclear
Could the selection of patients have introduced bias?		High risk
Are there concerns that the included patients and setting do not match the review question?			High
DOMAIN 2: Index Test (NanoString)
DOMAIN 2: Index Test (aCGH)
DOMAIN 2: Index Test (NGS)
DOMAIN 2: Index Test (G‐banding)
DOMAIN 2: Index Test (FISH (variant 4))
If a threshold was used, was it pre‐specified?	Yes
Were the index test results interpreted without knowledge of the results of the other tests being compared?	Yes
Could the conduct or interpretation of the index test have introduced bias?		Low risk
Are there concerns that the index test, its conduct, or interpretation differ from the review question?			Low concern
DOMAIN 2: Index Test (SNP array)
DOMAIN 2: Index Test (PCR (with comparison to normal DNA))
DOMAIN 2: Index Test (PCR (without comparison to normal DNA))
DOMAIN 2: Index Test (CISH)
DOMAIN 2: Index Test (MS)
DOMAIN 2: Index Test (RFLP)
DOMAIN 2: Index Test (PCR‐based LOH)
DOMAIN 2: Index Test (NGS or aCGH (or both))
DOMAIN 2: Index Test (Methylation array)
DOMAIN 2: Index Test (FISH)
DOMAIN 2: Index Test (FISH (variant 1))
If a threshold was used, was it pre‐specified?	Yes
Were the index test results interpreted without knowledge of the results of the other tests being compared?	Yes
Could the conduct or interpretation of the index test have introduced bias?		Low risk
Are there concerns that the index test, its conduct, or interpretation differ from the review question?			Low concern
DOMAIN 2: Index Test (FISH (variant 2))
If a threshold was used, was it pre‐specified?	Yes
Were the index test results interpreted without knowledge of the results of the other tests being compared?	Yes
Could the conduct or interpretation of the index test have introduced bias?		Low risk
Are there concerns that the index test, its conduct, or interpretation differ from the review question?			Low concern
DOMAIN 2: Index Test (FISH (variant 3))
If a threshold was used, was it pre‐specified?	Yes
Were the index test results interpreted without knowledge of the results of the other tests being compared?	Yes
Could the conduct or interpretation of the index test have introduced bias?		Low risk
Are there concerns that the index test, its conduct, or interpretation differ from the review question?			Low concern
DOMAIN 2: Index Test (Real‐time PCR)
DOMAIN 2: Index Test (MLPA)
DOMAIN 2: Index Test (CGH)
DOMAIN 3: Reference Standard
Is the reference standards likely to correctly classify the target condition?	No
Could the reference standard, its conduct, or its interpretation have introduced bias?		High risk
Are there concerns that the target condition as defined by the reference standard does not match the question?			Low concern
DOMAIN 4: Flow and Timing
Was there an appropriate interval between index test and reference standard?	Yes
Were all patients included in the analysis?	Yes
Could the patient flow have introduced bias?		Low risk