Horbinski 2012.

Study characteristics
Patient Sampling	Inclusion/exclusion criteria Inclusion criteria: oligodendrogliomas. Exclusion criteria: recurrent or treated (or both) gliomas; children aged < 18 years Prior testing Histopathological diagnosis according to WHO criteria at the time of initial biopsy.
Patient characteristics and setting	Number of participants/tumours with results for 1p/19q status by ≥ 2 DNA‐based tests: 111 Country: USA Population source and setting: University of Pittsburgh. 2002–2010 Age: median: Grade II oligodendroglioma: 42 years. Grade III oligodendroglioma: 49 years. Interquartile range: NR; range: 19–80 years (Grade II oligodendroglioma 19–79 years; Grade III oligodendroglioma 25–80 years) Gender: 56.8% male Karnofsky performance status: NR First diagnosis/recurrent disease: first diagnosis (cases of recurrent glioma were excluded)
Index tests	3 tests: FISH (variant 1), FISH (variant 2) and PCR FISH (variant 1) (referred to as FISH below. Note: the risk of bias and applicability judgements for this FISH variant appear inFigure 7) Tumour sample type: FFPE Region(s) analysed: 1p36/1q25 19q13 /19p13 (Abbott Molecular, Des Plaines, Illinois, USA) Cut‐off: target‐ploidy control ratio was < 0.87, with ≥ 20% of nuclei showing deletion FISH (variant 2) Tumour sample type: FFPE Region(s) analysed: 1p36/1q25 19q13 /19p13 (Abbott Molecular, Des Plaines, Illinois) Cut‐off: target‐ploidy control ratio was < 0.75, with ≥ 20% of nuclei showing deletion PCR Tumour sample type: FFPE Region(s) analysed: chromosome 1: D1S1172, D1S226, D1S162, D1S1161, D1S199, D1S407, D1S171; chromosome 19: D19S112, D19S206 Cut‐off: at least half of all informative microsatellite loci on both 1p and 19q had to show LOH to be designated as having 1p/19q codeletion. Quote: "When available, patient‐matched germline DNA from a peripheral blood sample was used as a control. When normal tissue was not available, peak height ratios falling outside 2 SDs beyond the mean of previously validated normal values for each polymorphic allele paring were assessed as showing LOH". Additional details: from Horbinski C, Hamilton RL, Nikiforov Y, Pollack IF. Association of molecular alterations, including BRAF, with biology and outcome in pilocytic astrocytomas. Acta Neuropathologica 2010;119:641‐49) "Polymerase chain reaction was performed, and the products were analyzed using capillary gel electrophoresis on GeneMapper ABI 3730 (Applied Biosystems, Foster City, CA)".
Target condition and reference standard(s)	Target condition was absolute 1p/19q deletion. FISH or 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?			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)
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 (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))
If a threshold was used, was it pre‐specified?	No
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?		High 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?	Yes
Could the patient flow have introduced bias?		Low risk