Gadji 2009.

Study characteristics
Patient Sampling	Inclusion/exclusion criteria Inclusion criteria: initially diagnosed oligodendroglial or oligoastrocytomal brain tumour Prior testing Histopathological diagnosis: tumours were reviewed and classified according to the WHO 2007 classification.
Patient characteristics and setting	Number of participants/tumours with results for 1p/19q status by ≥ 2 DNA‐based tests: 11 Country: Canada Population source and setting: Sherbrooke University hospital, Canada. 1993–2007 Age: mean: 38.8 years, standard deviation: 8.3 years Gender*: 35.1% male Karnofsky performance status: NR First diagnosis/recurrent disease: NR *For whole population: 37 participants were included, but only 11 had both tests.
Index tests	2 tests: FISH and PCR FISH Tumour sample type: FFPE or fresh (touch‐preparation smear) Region(s) analysed: 1p36/1q25, 19p13/19q13 (Vysis LSI; Abbott Molecular, Des Plaines, Illinois, USA) Cut‐off: quote: "A case was considered deleted with 1p, 19q, or both when the scored nuclei displayed an imbalance between green and red signals". PCR Tumour sample type: NR Region(s) analysed: chromosome 1 (8 test markers on the short arm and 2 control markers on the long arm): D1S2795 (1p36.31), D1S2666 (1p36.23), D1S244 (1p36.22), D1S2676 (1p34.3), D1S2729 (1p34.3), D1S2722 (1p34.2), D1S508 (1p36.31~p36.21), D1S2734 (1p35.36), D1S252 (1q21), D1S2346 (1q22); chromosome 19 (9 test markers on the long arm and 1 control marker on the short arm): D19S412 (19q13.32), D19S559 (19q13.32), D19S200 (19q13.2), D19S397 (19q13.14), D19S422 (19q13.13), D19S425 (19q13.12), D19S416 (19q13.11), D19S112 (19q13.3), D19S556 (19p13.13). All markers were obtained from IDT (Coralville, Iowa, USA). Cut‐off: quote: "An absence or a significant reduction in intensity of >50% in the tumor lane compared with the corresponding blood and saliva lanes was scored as 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 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?	Yes
Was a case‐control design avoided?	Yes
Did the study avoid inappropriate exclusions?	Yes
Could the selection of patients have introduced bias?		Low 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?	Unclear
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?	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?			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?	Unclear
Could the patient flow have introduced bias?		Unclear risk