Chaturbedi 2012.

Study characteristics
Patient Sampling	Inclusion/exclusion criteria NR. Quote: "We included DNA samples from 44 OTs, 9 paired blood lymphocytes collected from patients during surgical resection of their gliomas, and 14 glioblastoma multiformes (GBMs) in this study. Breaking down of 44 OT samples included in analysis are 21 WHO grade II oligodendroglioma (OG), 8 WHO Grade II mixed oligo‐astrocytoma (OA), 15 either WHO grade III anaplastic oligodendroglioma (AO) or WHO grade III anaplastic mixed oligo‐astrocytoma (AOA)". Prior testing Histopathological diagnosis
Patient characteristics and setting	Number of participants/tumours with results for 1p/19q status by ≥ 2 DNA‐based tests: 18 Country: USA Population source and setting: University of California, Irvine, USA and University of Arkansas for Medical Sciences, USA. Time period NR Age: NR Gender: NR Karnofsky performance status: NR First diagnosis/recurrent disease: NR
Index tests	2 tests: FISH and real‐time PCR FISH Tumour sample type: FFPE Region(s) analysed: 1p36/1q24, 19q13/19p13 Cut‐off: quote: "A normal ratio is considered 1.0 and any ratio <0.80 is considered deletion of the region of interest" Real‐time PCR Tumour sample type: frozen Region(s) analysed: 1p: E2F2 (1p36) and NOTCH2 (1p13‐11) (also looked at CAMTA1 (1p36.31‐p36.23), but then excluded). 19q: PLAUR (19q13). Reference genes ERC2 (3p14.3), SPAG16 (2q34) and SPOCK1 (5q31). However: (quote) "A ratio of 1:1 between selected marker and reference genes in autosomal chromosomes is expected in normal cells while changes in this ratio in tumor DNA would suggest CNV, either deletion or amplification, in the studied gene of interest. Considering the inherent genome instability of cancer cells, we analyzed the stability of three reference genes in tumor samples and found amplification of SPAG16 in some OT. To mitigate this, we took the average of two ratios of ERC2 and SPOCK1 for most tumors. For other samples, the two reference gene ratios showing the most concordance were used to take a mean and SD. With consideration of 10%–20% variation inherited with real‐time PCR, the mean values of the marker and reference ratio was taken for determination of deletion (<0.8) or amplification (>1.2), Shown in Table 1, there was a gain at the 1p marker gene CAMTA1 (1p36.31‐23) in both GBM and OT, which were not found in other two 1p marker genes E2F2 (1p36) and NOTCH2 (1p13‐p11). Thus average of these two 1p marker genes ratio to reference gene were taken to determine 1p deletion status (value <0.80 is considered 1p deleted)". Cut‐off: marker/reference < 0.8 per gene. Mean of E2F2 (1p36) and NOTCH2 (1p13‐p11) marker genes ratio to reference gene were taken to determine 1p deletion status (value < 0.80 is considered 1p deleted). Additional details: comparative quantitative PCR
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 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?			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?	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))
DOMAIN 2: Index Test (FISH (variant 3))
DOMAIN 2: Index Test (Real‐time PCR)
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 (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