Duval 2015.

Study characteristics
Patient Sampling	Inclusion/exclusion criteria NR Prior testing Not explicitly reported but presumably histopathological diagnosis
Patient characteristics and setting	Number of participants/tumours with results for 1p/19q status by ≥ 2 DNA‐based tests: 29 Country: France Population source and setting: Centre Hospitalier Universitaire de Rennes (France). 2010–2015 Age: NR Gender: NR Karnofsky performance status: NR First diagnosis/recurrent disease: NR
Index tests	2 tests: FISH (variant 1) and FISH (variant 2) FISH (variant 1) Tumour sample type: FFPE Region(s) analysed: 1p36/1q25 and 19q13/19p13 (Dual Color Probe kit, Abbott Molecular, Abbott Park, Illinois, USA). Cut‐off: combination + ratio method. Cases deleted in 1 method and normal in the other were considered deleted. Combination method: deletion status combinations (for 1p and 19q, control/test): 2/0, 2/1, 3/0, 3/1, 4/1, 4/2, 5/2, 6/2, 6/3. Normal status combinations 2/2, 1/2. (Imbalance status combinations 1/3, 1/4, 2/3, 2/4, 2/5, 3/3, 3/4, 4/3, 4/4, 4/5, 5/4, 5/5, 5/6.) The cut‐off value for the number of nuclei that had to show deletion was 55% for both 1p and 19q for deletion status (and 20% for imbalance status). Ratio method: the signal ratio of test:control probes ≤ 0.8 was considered to indicate a deletion. Additional details: automated analysis using the Metafer 4 software (Metasystem) using the "1p19q tile‐sampling classifier". FISH (variant 2) Tumour sample type: FFPE Region(s) analysed: 1p36/1q25 and 19q13/19p13 (Dual Color Probe kit, Abbott Molecular, Abbott Park, Illinois, USA). Cut‐off: combination + ratio method. Cases deleted in 1 method and normal in the other were considered deleted. Combination method: deletion status combinations (for 1p and 19q, control/test): 2/0, 2/1, 3/0, 3/1, 4/1, 4/2, 5/2, 6/2, 6/3. Normal status combinations 2/2, 1/2. (Imbalance status combinations 1/3, 1/4, 2/3, 2/4, 2/5, 3/3, 3/4, 4/3, 4/4, 4/5, 5/4, 5/5, 5/6.) The cut‐off value for the number of nuclei that had to show deletion was 55% for both 1p and 19q for deletion status (and 20% for imbalance status). Ratio method: the signal ratio of test:control probes ≤ 0.8 was considered to indicate a deletion. Additional details: manual analysis
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?	Unclear
Was a case‐control design avoided?	Yes
Did the study avoid inappropriate exclusions?	Unclear
Could the selection of patients have introduced bias?		Unclear risk
Are there concerns that the included patients and setting do not match the review question?			Low concern
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))
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?			High
DOMAIN 2: Index Test (FISH (variant 2))
If a threshold was used, was it pre‐specified?	Unclear
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?		Unclear risk
Are there concerns that the index test, its conduct, or interpretation differ from the review question?			Unclear
DOMAIN 2: Index Test (FISH (variant 3))
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?	No
Could the patient flow have introduced bias?		High risk