Broholm 2008.

Study characteristics
Patient Sampling	Inclusion/exclusion criteria NR. Quote: "46 patients were included in the study. The material consisted of 10 oligodendrogliomas (5 WHO Grade II (OII) and 5 Grade III (AOIII)), 10 mixed oligoastrocytomas (5 WHO Grade II (OAII) and 5 Grade III (AOAIII)), 10 astrocytomas (5 WHO Grade II (AII) and 5 Grade III (AAIII)) and 11 glioblastomas, WHO Grade IV (GBMIV)". 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: 38 Country: Denmark Population source and setting: FFPE tissue from the Laboratory of Neuropathology, Rigshospitalet, Copenhagen, Denmark. Time period NR Age: NR Gender: NR Karnofsky performance status: NR First diagnosis/recurrent disease: NR
Index tests	2 tests: FISH and PCR FISH Tumour sample type: FFPE Region(s) analysed: 1p36.33 and 19q13 (Vysis #40218 and #38967, Vysis, Des Plaines, Illinois, USA) Cut‐off: quote: "The FISH‐sum in % was calculated (amount of cells with only one or none fluorescence signal for the investigated probe in relation to the total cell count). The conclusion – loss (Pos.) or no loss (N) was noted. For 1p loss the FISH‐sum in % had to be higher than the calculated cut‐off level at 43.24% and for 19q more than 55.12%". PCR Tumour sample type: FFPE Region(s) analysed: D1S164 (1p34.4), D1S496 (1p34.4), D1S199 (1p36.1), D1S468 (1p36.3), D1S2736 (1p36.3); D19S867 (19q13.3), D19S888 (19q13.4), D19S572 (19q13.4), D19S210 (19q13.4) Cut‐off: allelic ratio < 0.5 or > 1.65 Additional details: PCR‐based LOH (microsatellite) without the need for comparison to normal DNA. References Hatanpaa 2003a.
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?	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)
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?	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?	No
Could the patient flow have introduced bias?		High risk