Scheie 2006.

Study characteristics
Patient Sampling	Inclusion/exclusion criteria Inclusion criteria: people with a supratentorial oligodendroglial tumour Prior testing Histopathological diagnosis according to WHO 2000 classification.
Patient characteristics and setting	Number of participants/tumours with results for 1p/19q status by ≥ 2 DNA‐based tests: 40 Country: Norway Population source and setting: Rikshospitalet‐Radiumhospitalet Medical Center (Oslo, Norway). 2000–2004. Age: mean: 43.1 years, standard deviation: NR; range: 19–66 years Gender: NR Karnofsky performance status: NR First diagnosis/recurrent disease: 95% first diagnosis (38/40); 5% recurrent disease (2/40)
Index tests	2 tests: FISH and PCR FISH Tumour sample type: fresh or fresh‐frozen Region(s) analysed: 1p36.3 (D1Z2)/D1Z hybridising to the pericentric region (Q‐biogene, Heidelberg, Germany), 19q (D19S238E)/telomeric region on chromosome 19p (Vysis Inc, Downers Grove, Illinois, USA). Cut‐off: a tumour was defined as FISH positive when FISH‐sum (proportion of cells with FISH‐LOH and FISH‐imbalance) exceeded the mean plus 3 standard deviations value in control specimens from non‐neoplastic brain tissue. The presence of 0 or 1 1p36‐ or 19q‐ signal was reported as FISH‐LOH. Losses with any disproportion (signal ratios 3/2, 4/3, 4/2, 5/3, etc. were defined as FISH‐imbalance. Cut‐offs: 27.7% for 1p and 33.2% for 19q Additional details: FISH on touch preparations PCR Tumour sample type: fresh‐frozen or FFPE Region(s) analysed: ≥ 4 of the following for chromosome 1 and 19: chromosome 1: D1S2660, D1S507, D1S199, D1S2734, D1S1676, D1S247; chromosome 19: D19S918, D19S219, D19S112, D19S412, D19S596, D19S206 Cut‐off: results were defined as LOH‐positive when the peak areas of fluorescent intensity curves, corresponding to PCR products from individual primer sets, showed a relative reduction of ≥ 40% when the products from tumour DNA were compared with those from normal DNA. Unclear how many markers had to display LOH.
Target condition and reference standard(s)	Target condition was absolute 1p/19q deletion. FISH or PCR‐based LOH used as reference standard in some of our analyses.
Flow and timing	We presumed that both tests were performed on the same sample for each participant.
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?	Yes
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?			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))
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)
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?	Unclear
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?			Low concern
DOMAIN 2: Index Test (NGS or aCGH (or both))
DOMAIN 2: Index Test (Methylation array)
DOMAIN 2: Index Test (FISH)
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?	Unclear
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?			Low concern
DOMAIN 2: Index Test (FISH (variant 1))
DOMAIN 2: Index Test (FISH (variant 2))
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?	Yes
Could the patient flow have introduced bias?		Low risk