Mohapatra 2006.

Study characteristics
Patient Sampling	Inclusion/exclusion criteria Not explicitly reported, but all glioma samples had oligodendroglial features on histopathological examination. Prior testing Not explicitly reported, but presumably histopathological diagnosis.
Patient characteristics and setting	Number of participants/tumours with results for 1p/19q status by ≥ 2 DNA‐based tests: 28 Country: USA Population source and setting: Massachusetts General Hospital. 1999–2004 Age: NR Gender: NR Karnofsky performance status: NR First diagnosis/recurrent disease: NR
Index tests	3 tests: aCGH, FISH and PCR aCGH Tumour sample type: FFPE Region(s) analysed: not explicitly reported but 100 BACs (bacterial artificial chromosome) over chromosome 1, 50 BACs over chromosome 19 Cut‐off: quote: "Segments were considered to represent true losses or gains according to whether their associated absolute mean log2 ratio levels were greater than (2 × σ/√n) With σ estimated to be 0.58, the empirical estimate of the SD of the standardized segment means for 1q, and n equal to the number of clones in the given segment. For example, a 19q segment that contains 26 clones was considered to represent loss if its estimated mean level was less than −0.23. A 1p segment that contains 57 clones was considered to represent loss if its estimated mean level was less than −0.16. A 1p segment that contains 30 clones was considered to represent loss if its estimated mean level was less than −0.22". Additional details: a BAC array was constructed containing 200 targets that represented chromosomes 1, 7, 19, and X. FISH Tumour sample type: FFPE Region(s) analysed: 1p36.2/1q21, 19q13.3/19p13.3 Cut‐off: quote: "Relative copy numbers for 1p/1q and 19q/19p were counted, and a ratio of 0.7 or less for 1p:1q and/or 19q:19p was considered a loss". PCR Tumour sample type: FFPE Region(s) analysed: 1p: D1S508, D1S199, D1S2734; 19q: D19S219, D19S112, D19S412. Cut‐off: NR
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	All tests were performed on the same FFPE tissue.
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?			Unclear
DOMAIN 2: Index Test (NanoString)
DOMAIN 2: Index Test (aCGH)
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 (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?	Unclear
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?		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?	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)
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