Jeuken 2006.

Study characteristics
Patient Sampling	Inclusion/exclusion criteria NR. Quote: "Eighty‐eight specimens obtained from glioma patients treated in the Department of Neurosurgery of the Radboud University Nijmegen Medical Centre, The Netherlands, were selected". Prior testing Histopathological diagnosis (WHO 2000 classification). 79/88 participants were previously analysed by conventional CGH.
Patient characteristics and setting	Number of participants/tumours with results for 1p/19q status by ≥ 2 DNA‐based tests: 71 Country: the Netherlands Population source and setting: Department of Neurosurgery of the Radboud University Nijmegen Medical Center, the Netherlands. Time period NR Age: NR Gender: NR Karnofsky performance status: NR First diagnosis/recurrent disease: NR
Index tests	2 tests: CGH and MLPA CGH Tumour sample type: snap‐frozen Region(s) analysed: genome wide Cut‐off: 0.8 for losses and 1.2 for gains MLPA Tumour sample type: snap frozen or FFPE Region(s) analysed: 1p: TNFRSF4, GB1, SKII, TP72, PARK7, EPHA8, RUNX3, PTAFR, STK22C, MYCL1, FAF1, PPAP2B, CYP2J2, LPHN2, SOYS, NARS, NOTCH2; 19q: CCNE1, PDCD5, UPK1A, TGFB1, ZNF342, PPP1R15A, BAX, BC‐2 (kit P088; MRC‐Holland, Amsterdam, the Netherlands) Cut‐off: ratio ≤ 0.8 per probe. Overall results for 1p and 19q not given. We assumed that if all probes were lost, or the majority were lost and those that were not lost were flanked by probes that were that lost that loss had occurred (stated in paper: "ratios of adjacent probes should be taken into consideration for the assessment of the presence of gains or losses"). We ignored the results for the most centromeric 1p probe (NOTCH2).
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 both tests were performed on samples obtained at the same time.
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?			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)
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))
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)
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 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