Harada 2011.

Study characteristics
Patient Sampling	Inclusion/exclusion criteria Inclusion criteria: samples submitted for routine clinical analysis of 1p/19q loss. Prior testing Not explicitly reported, but presumably histopathological diagnosis.
Patient characteristics and setting	Number of participants/tumours with results for 1p/19q status by ≥ 2 DNA‐based tests: 29 Country: USA Population source and setting: Johns Hopkins Medical Institutions. 2010 Agea: mean: 42.7 years (48.3 years in participants with oligodendrogliomas, 37.7 years in participants with non‐oligodendroglioma tumours, standard deviation: 15.3 yearsb; range: 14–82 years Gendera: 53.3% male Karnofsky performance status: NR First diagnosis/recurrent disease: NR aIncluded 1 participant with pineal parenchymal tumour of intermediate differentiation, who was excluded. bThe standard error of the mean was 4.47 years in participants with oligodendrogliomas and 3.35 years in participants with non‐oligodendroglioma tumours. The standard deviation was calculated from these figures.
Index tests	2 tests: PCR and SNP array PCR Tumour sample type: FFPE Region(s) analysed: chromosome 1: D1S199, D1S186, D1S162, D1S312, D1S226; chromosome 19: D19S918, D19S112, D19S206 Cut‐off: NR Additional details: Multiplex PCR (as described in Hatanpaa 2003a and Hatanpaa 2003b). Fluorescent labelled PCR products were detected by capillary electrophoresis with use of the ABI 3130 Genetic Analyzer and GeneMapper software version 4 (Applied Biosystems, Carlsbad, California, USA). SNP array Tumour sample type: FFPE Region(s) analysed: genome wide Cut‐off: NR Additional details: quote: "Illumina Infinium II SNP array with 300K markers (HumanCytoSNP‐12, Illumina Inc., San Diego, CA)".
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?	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?			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)
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 (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)
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?	Yes
Could the patient flow have introduced bias?		Low risk