Natte 2005.

Study characteristics
Patient Sampling	Inclusion/exclusion criteria NR. 19 oligodendroglial tumours from 19 participants were analysed. Prior testing Histopathological diagnosis according to WHO classification. Quote: "From all tumors FISH data were available".
Patient characteristics and setting	Number of participants/tumours with results for 1p/19q status by ≥ 2 DNA‐based tests: 19 Country: the Netherlands Population source and setting: NR Age: NR Gender: NR Karnofsky performance status: NR First diagnosis/recurrent disease: NR
Index tests	2 tests: FISH and MLPA FISH Tumour sample type: FFPE Region(s) analysed: 1p36(D1S32)/1cen(PUC 1.77) and 19q13(BAC127F23)/19p13(BAC2310A1) Cut‐off: 0.8 MLPA Tumour sample type: FFPE Region(s) analysed: 1p36.33, 1p36, 1p36.3,1p34.3‐1p32.1, 1p13.2, 1p22‐21, 1p13.3, 19q13.3, 19q13.3, 19q13, 19q13.43. Quote: "The MLPA kit was assembled by MRC‐Holland (Amsterdam, The Netherlands). Details of MLPA and probes can be found at http://www.mlpa.com". Cut‐off: the principal decision rule for a deletion was that for 1p ≥ 4 probes (of 7?) and for 19q ≥ 2 focus probes (of 4?) had normalised peak heights ≥ 0.25 below the median normalised peak height of the reference probes.
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?	Unclear
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))
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?	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 (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)
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 (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