Belaud‐Rotureau 2006.

Study characteristics
Patient Sampling	Inclusion/exclusion criteria Inclusion criteria: grade II or III glioma, sufficient frozen material for FISH analysis and histological control of frozen sections performed during the imprint procedure. Prior testing Examination of haematoxylin and eosin‐stained paraffin sections. Glial‐fibrillary acid‐protein and MIB‐1 immunostaining. Classified and graded according to WHO 2000.
Patient characteristics and setting	Number of participants/tumours with results for 1p/19q status by ≥ 2 DNA‐based tests: 23 Country: France Population source and setting: Neurosurgery Department of the University Hospital Centre of Bordeaux, France. July 1995 to September 2002 Age: NR Gender: NR Karnofsky performance status: NR First diagnosis/recurrent disease: unclear. Previously untreated glioma
Index tests	3 tests: FISH (variant 1), FISH (variant 2) and FISH (variant 3) FISH (variant 1) Tumour sample type: touch imprints of frozen tumours Region(s) analysed: 1p36.3 (D1Z2)/1q12 (D1Z1), 19q13.3/19pter Cut‐off: quote: "For each chromosome probe mix, hybridization signals of control and test probes were counted per nucleus, which was classified as follows: (1) In case of deletion, the ratio of control and test probes was 2/1, partially in conjunction with 4/2, 3/1, 4/1 ratios. (2) An imbalance hybridization pattern was associated to a disproportion of the ratio of control and test probes signals (3/2, 4/3, 5/3, etc.). Such pattern does not prove an LOH, which should be further determined by ancillary techniques. (3) A normal pattern (no deletion, no imbalance) was associated to an equal ratio of control and test probes signals (2/2, 4/4). At least 200 tumour cell nuclei were assessed. The cut‐off values, i.e. the percentage of deleted patterns required to assess a deletion for each 1p36 or 19q13 probes were determined to be the mean + 3 SD of the percentage of deleted nuclei on control tissues (reactive lymphadenitis, n=5) [45]. A tumour was classified as deleted if the percentage (%) of deleted nuclei exceeded the cut‐off value of the probe set. In the other cases, it was classified as (1) normal if the percentage of deleted plus imbalanced nuclei was less than the cutoff or (2) imbalanced if the percentage of imbalanced nuclei or the sum of imbalanced plus deleted nuclei was greater than or equal to the cut‐off". Comment: cut‐off determined to be 10%. Additional details: manual analysis with 1p36.3 (D1Z2)/1q12 (D1Z1) and 19q13.3/19pter probe set FISH (variant 2) Tumour sample type: touch imprints of frozen tumours Region(s) analysed: 1p36/1q25, 19q13/19p13 (Abbott Vysis) Cut‐off: quote: "For each chromosome probe mix, hybridization signals of control and test probes were counted per nucleus, which was classified as follows: (1) In case of deletion, the ratio of control and test probes was 2/1, partially in conjunction with 4/2, 3/1, 4/1 ratios. (2) An imbalance hybridization pattern was associated to a disproportion of the ratio of control and test probes signals (3/2, 4/3, 5/3, etc.). Such pattern does not prove an LOH, which should be further determined by ancillary techniques. (3) A normal pattern (no deletion, no imbalance) was associated to an equal ratio of control and test probes signals (2/2, 4/4). At least 200 tumour cell nuclei were assessed. The cut‐off values, i.e. the percentage of deleted patterns required to assess a deletion for each 1p36 or 19q13 probes were determined to be the mean + 3 SD of the percentage of deleted nuclei on control tissues (reactive lymphadenitis, n=5) [45]. A tumour was classified as deleted if the percentage (%) of deleted nuclei exceeded the cut‐off value of the probe set. In the other cases, it was classified as (1) normal if the percentage of deleted plus imbalanced nuclei was less than the cut‐off or (2) imbalanced if the percentage of imbalanced nuclei or the sum of imbalanced plus deleted nuclei was greater than or equal to the cut‐off". Comment: cut‐off determined to be 6%. Additional details: manual analysis with the 1p36/1q25 and 19q13/19p13 Abbott Vysis probe set. FISH (variant 3) Tumour sample type: touch imprints of frozen tumours Region(s) analysed: 1p36/1q25, 19q13/19p13 (Abbott Vysis) Cut‐off: quote: "For each chromosome probe mix, hybridization signals of control and test probes were counted per nucleus, which was classified as follows: (1) In case of deletion, the ratio of control and test probes was 2/1, partially in conjunction with 4/2, 3/1, 4/1 ratios. (2) An imbalance hybridization pattern was associated to a disproportion of the ratio of control and test probes signals (3/2, 4/3, 5/3, etc.). Such pattern does not prove an LOH, which should be further determined by ancillary techniques. (3) A normal pattern (no deletion, no imbalance) was associated to an equal ratio of control and test probes signals (2/2, 4/4). At least 200 tumour cell nuclei were assessed. The cut‐off values, i.e. the percentage of deleted patterns required to assess a deletion for each 1p36 or 19q13 probes were determined to be the mean + 3 SD of the percentage of deleted nuclei on control tissues (reactive lymphadenitis, n=5) [45]. A tumour was classified as deleted if the percentage (%) of deleted nuclei exceeded the cut‐off value of the probe set. In the other cases, it was classified as (1) normal if the percentage of deleted plus imbalanced nuclei was less than the cut‐off or (2) imbalanced if the percentage of imbalanced nuclei or the sum of imbalanced plus deleted nuclei was greater than or equal to the cut‐off". Comment: cut‐off determined to be 6%. Additional details: automatic analysis (Metafer 4, Metasystems, Althlussheim, Germany) with the 1p36/1q25 and 19q13/19p13 Abbott Vysis probe se
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	All tests were performed on frozen tissue samples.
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?	No
Was a case‐control design avoided?	Yes
Did the study avoid inappropriate exclusions?	Unclear
Could the selection of patients have introduced bias?		High 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)
DOMAIN 2: Index Test (FISH (variant 1))
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 2))
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 3))
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 (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