Ghasimi 2016.

Study characteristics
Patient Sampling	Inclusion/exclusion criteria Inclusion criteria: availability of FFPE tissue. No other criteria were reported. This study included 33 grade II–III gliomas and 58 glioblastomas. Prior testing Presumably histopathological diagnosis, although not explicitly reported.
Patient characteristics and setting	Number of participants/tumours with results for 1p/19q status by ≥ 2 DNA‐based tests: 55 Country: Sweden Population source and setting: Umeå University Hospital, Sweden. Time period NR Agea: median: 58 years, interquartile range: NR; range: 15–80 years Gendera: 59.3% male Karnofsky performance status: NR First diagnosis/recurrent disease: NR aFor whole population: the data are for the 59 participants who had SNP array data, of whom 55 also had FISH data.
Index tests	2 tests: FISH and SNP array FISH Tumour sample type: FFPE Region(s) analysed: 1p36/1q13, 19p13/19q13 (Vysis, Illinois, USA) Cut‐off: 1p36/1q25 ratios < 0.88 and 19q13/19p13 ratios < 0.74 in > 12% of the cells were considered as deleted. SNP array Tumour sample type: FFPE Region(s) analysed: regions corresponding to the location of the FISH probes Cut‐off: quote: "For comparison between FISH and ASCAT, we extracted the median total copy number from the ASCAT profiles for the genomic regions corresponding to the FISH probes. These copy number data were subsequently used to mimic the sample classification based on FISH data, by calculating the same ratios and using the same cutoff values that had been used for classification by FISH". Additional details: "Illumina HumanOmni1‐Quad BeadChips. The ASCAT algorithm [26] (version 2.0) was used to calculate somatic whole‐genome allele‐specific copy number profiles (ASCAT‐profiles), as well as estimates of tumor cell content and tumor cell ploidy".
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?	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?	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 (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))
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