Clark 2013.

Study characteristics
Patient Sampling	Inclusion/exclusion criteria Inclusion criteria: glioblastoma cases in the Hillman Cancer registry. Exclusion criteria: cases of recurrent or treated (or both) glioma. Prior testing Histopathological diagnosis (WHO 2007 classification).
Patient characteristics and setting	Number of participants/tumours with results for 1p/19q status by ≥ 2 DNA‐based tests: 446 Country: USA Population source and setting: Hillman Cancer Registry, University of Pittsburgh, USA. 2002–2010 Agea: median: 63 years, interquartile range: NR; range: 18–89 years Gendera: 58.5% male Karnofsky performance status: NR First diagnosis/recurrent disease: 100% first diagnosis. Cases of recurrent glioma were excluded. aFor whole population: there were 532 cases in the complete glioblastoma cohort, 491 had upfront 1p/19q testing, 446 had results for both tests.
Index tests	2 tests: FISH and PCR FISH Tumour sample type: FFPE Region(s) analysed: 1p36/1q25, 19q13/19p36 (Abbott Molecular, Des Plaines, Illinois, USA). Cut‐off: quote: "Codeletion was counted if the 1p36/1q25 and 19q13/19p13 ratios were both below 0.87 and at least 20% of tumour nuclei showed relative deletion". PCR Tumour sample type: FFPE Region(s) analysed: D1S1172, D1S226, D1S162, D1S1161, D1S199, D1S407, D1S171, D19S112, D19S206, D19S559 (from 2007 onwards, comprising 75% of the total cohort) Cut‐off: quote: "To be considered codeleted the majority of informative microsatellite loci on both 1p and 19q had to show 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?	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?	No
Could the patient flow have introduced bias?		High risk