Srebotnik‐Kirbis 2016.

Study characteristics
Patient Sampling	Inclusion/exclusion criteria No further details reported. Included an oligodendroglial tumour and non‐oligodendroglial tumour cohort. We have only extracted data for the oligodendroglial tumour cohort. Prior testing Histopathological diagnosis, according to the WHO 2007 classification.
Patient characteristics and setting	Number of participants/tumours with results for 1p/19q status by ≥ 2 DNA‐based tests: 12 Country: Slovenia Population source and setting: tissue samples from non‐consecutive patients who underwent surgical resection or biopsy to the Institute of Pathology, Faculty of Medicine, University of Ljubljana. December 2011 to November 2015. Age: mean: 47.8 years, standard deviation: 10.5 years Gender: 50% male Karnofsky performance status: NR First diagnosis/recurrent disease: NR
Index tests	2 tests: FISH (variant 1) and FISH (variant 2) FISH (variant 1) Tumour sample type: fresh tissue cytospins Region(s) analysed: 1p36/1q25 and 19q13/19p13 (Vysis paired probes, Abbott Laboratories, Abbott Park, Illinois, USA) Cut‐off: quote: "Deletion was defined as a nucleus showing none or one target signal, and 2 or more control signals (ex. 1/2, 0/2, 1/3 etc.) … A tumour sample was considered positive for 1p or 19q deletion when it displayed a percentage of nuclei with deletion above the cut‐off value for that probe, specifically … 30% for 1p and 19% for 19q on cytospins". FISH (variant 2) Tumour sample type: FFPE tissue section Region(s) analysed: 1p36/1q25 and 19q13/19p13 (Vysis paired probes, Abbott Laboratories, Abbott Park, Illinois, USA) Cut‐off: quote: "Deletion was defined as a nucleus showing none or one target signal, and 2 or more control signals (ex. 1/2, 0/2, 1/3 etc.) … A tumour sample was considered positive for 1p or 19q deletion when it displayed a percentage of nuclei with deletion above the cut‐off value for that probe, specifically, 43% for 1p and 33% for 19q in tissue sections" and "the cut‐off value of 50 %, which is often reported in the literature, was also included in the analysis of FISH results for FFPE sections".
Target condition and reference standard(s)	Target condition was absolute 1p/19q deletion. No tests used as reference standard in 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?	No
Was a case‐control design avoided?	Yes
Did the study avoid inappropriate exclusions?	Yes
Could the selection of patients have introduced bias?		High 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))
DOMAIN 2: Index Test (Methylation array)
DOMAIN 2: Index Test (FISH)
DOMAIN 2: Index Test (FISH (variant 1))
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 2))
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 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