Blesa 2009.

Study characteristics
Patient Sampling	Inclusion/exclusion criteria Not explicitly reported but only oligodendrogliomas and oligoastrocytomas included. Prior testing Histopathological diagnosis according to WHO 2007 classification.
Patient characteristics and setting	Number of participants/tumours with results for 1p/19q status by ≥ 2 DNA‐based tests: 52 Country: Spain Population source and setting: Virgen de la Salud Hospital (Toledo, Spain), Clinic Hospital (Barcelona, Spain), and Xeral‐Cies Hospital (Vigo, Spain). Time period NR Age: mean: 45.8 years, standard deviation: 12.5 years Gender: 55.8% male Karnofsky performance status: NR First diagnosis/recurrent disease: NR
Index tests	4 tests: aCGH, FISH, MLPA and PCR aCGH Tumour sample type: fresh‐frozen Region(s) analysed: whole genome Cut‐off: quote: "Genomic imbalances were determined on the basis of the log2 of the Cy3/Cy5 ratios of the average of 3 clone replicates, and regions were considered to have a gain or loss of DNA if at least 2 consecutive clones exceeded the +/‐0.25 threshold". Additional details: used a (quote) "whole human genome CGH array developed in collaboration with Dr. Klaas Kok at the University Medical Centre Groningen (Department of Genetics, Groningen, The Netherlands)". FISH Tumour sample type: FFPE Region(s) analysed: 1p36/1q25, 19p13/19q13 (Vysis Inc., Downers Grove, Illinois, USA) Cut‐off: quote: "Tumors were considered as having loss when an unbalanced 1p/1q (1 vs 2 signals) or 19p/19q (2 vs 1 signal) was identified in more than 25% of tumor cells. In addition, loss with ploidy was noted when an unbalanced pattern 1p/1q of 2 versus 4 signals or an unbalanced 19p/19q of 4 versus 2 signals was detected". MLPA Tumour sample type: unclear, either FFPE or frozen Region(s) analysed: NR. Salsa kit P088, MRC‐Holland, Amsterdam, the Netherlands Cut‐off: losses scored when ≥ 3 test probes exhibited a ratio < 0.7. Additional details: Salsa kit P088, MRC‐Holland, Amsterdam, the Netherlands PCR Tumour sample type: fresh‐frozen or FFPE Region(s) analysed: 1p: D1S199, D1S186, D1S162, D1S312, D1S226; 19q: D19S918, D19S112, D19S206 Cut‐off: LOH pattern, when the shorter allele presented a relatively high peak and the longer allele a low peak (never > 12% of the height of the shorter allele), or when the intensity of the shorter allele was less than that of the longer allele. When all markers were homozygous, LOH was scored as positive. Additional details: PCR‐based LOH (microsatellite) without the need for comparison to normal DNA. References Hatanpaa 2003a.
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?	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)
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)
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))
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?	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 (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