Sim 2018a.

Study characteristics
Patient Sampling	Inclusion/exclusion criteria Inclusion criteria: glioblastoma 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: 75 Country: Republic of Korea Population source and setting: Samsung Medical Center, Seoul, Korea. 2011–2014 Age: mean: 52.8 years, standard deviation: NR; range: 21–76 years Gender: 53.3% male Karnofsky performance status: NR First diagnosis/recurrent disease: not clear. We excluded recurrent samples from participants who also contributed samples from their primary tumour.
Index tests	2 tests: FISH and NGS or aCGH (or both) FISH Tumour sample type: FFPE Region(s) analysed: 1p36 and 19q13 (Vysis, Downers Grove, Illinois, USA) Cut‐off: 1p deletion as a combined target‐to‐control signal ratio < 0.75 or cut‐off of a nucleus with a 1 or 0 target signal > 50%. 19q deletion as a combined target‐to‐control signal ratio < 0.8 and a nucleus cut‐off with a 1 or 0 target signal > 30% NGS or aCGH (or both) Tumour sample type: fresh frozen Region(s) analysed: genome wide Cut‐off: whole arm losses Additional details: aCGH (Afilent SurePrint G3 Human CGH 4x180k array) or whole exome sequencing (Illumina TruSeq Exome capture kit or the Agilent SureSelect kit and either the Illumina HiSeq 2000 or HiSeq 2500) (or both)
Target condition and reference standard(s)	Target condition was absolute 1p/19q deletion. FISH 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?			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)
DOMAIN 2: Index Test (NGS or aCGH (or both))
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?			Unclear
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?		High 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