Dahlback 2011.

Study characteristics
Patient Sampling	Inclusion/exclusion criteria Inclusion criteria: Grade II glioma; aged ≥ 16 years at time of surgery Prior testing Histopathological diagnosis 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: 32 Country: Norway Population source and setting: The Department of Neurosurgery, Oslo University Hospital, Rikshospitalet, Oslo, Norway. January 2005 to October 2008 Age: mean: 38.4 years, standard deviation: 8.7 years Gender: 65.6% male Karnofsky performance status: NR First diagnosis/recurrent disease: 78.1% primary (25/32 participants with results on ≥ 2 tests), 21.9% recurrent (7/32 participants)
Index tests	3 tests: CGH, G‐banding and PCR CGH Tumour sample type: fresh‐frozen Region(s) analysed: genome wide Cut‐off: from Dahlback 2009: quote "Aberrations were scored whenever the case profile and the reference profile did not overlap with a significance level of 99%". Additional details: quote: "HR‐CGH [high‐resolution CGH] was performed according to the manufacturer's protocol and analyzed as previously described (Dahlback et al., 2009)". Dahlback 2009: quote: "CGH was performed on DNA from these samples according to the manufacturer's protocol and analyzed according to Kallioniemi et al., (1992) with the modifications described by Kraggerud et al., (2000) and Teixeira et al. (2004). Final evaluations of the CGH results used dynamic standard reference intervals (D‐SRI) as described by Ribeiro et al. (2006)". G‐banding Tumour sample type: fresh Region(s) analysed: whole genome Cut‐off: not applicable Additional details: quote: "Chromosome preparations were G‐banded using Wright stain and karyotyped according to the ISCN (2009)". PCR Tumour sample type: fresh‐frozen Region(s) analysed: at least 4 of 6 microsatellite markers on 1p35‐36 (D1S2660, D1S507, D1S199, D1S2734, D1S1676, D1S247) and 19q13 (D19S918, D19S219, D19S112, D19S412, D19S596, D19S206) used. Cut‐off: As described in Scheie D, Cvancarova M, Mork S, Skullerud K, Andresen PA, Benestad I, Helseth E, Meling T, Beiske K. 2008. Can morphology predict 1p/19q loss in oligodendroglial tumors? Histopathology 53:578‐87: 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. 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)
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 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)
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)
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 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