Hatanpaa 2003a.

Study characteristics
Patient Sampling	Inclusion/exclusion criteria Inclusion criteria: tested for 1p/19q codeletion by ≥ 2 of the following 3 reference methods with concordant results: CGH, FISH and PCR‐based microsatellite analysis with comparison to normal DNA from the same participant. Prior testing Tested for 1p/19q codeletion by ≥ 2 of the following 3 reference methods with concordant results: CGH, FISH and PCR‐based microsatellite analysis with comparison to normal DNA from the same participant. Appeared that histopathological grading was redone from the original studies.
Patient characteristics and setting	Number of participants/tumours with results for 1p/19q status by ≥ 2 DNA‐based tests: 10 Country: USA Population source and setting: FFPE glioma specimens with concordant results in Smith 1999 or Burger 2001 (note: we could not match 1 tumour, T117, to tumours described in either study) Age: NR Gender: NR Karnofsky performance status: NR First diagnosis/recurrent disease: NR in this publication. Smith 1999 included both primary and recurrent tumour specimens.
Index tests	4 tests: CGH, FISH, PCR (with comparison to normal DNA) and PCR (without comparison to normal DNA) CGH Tumour sample type: NR Region(s) analysed: NR Cut‐off: Smith 1999 references Mohapatra G, Kim DH, Feuerstein BG. Detection of multiple gains and losses of genetic material in ten glioma cell lines by comparative genomic hybridization. Genes, Chromosomes & Cancer 1995;13;86‐93. In this publication: quote: "Definition of CGH ratio thresholds to define ratios that were indicative of changes in DNA copy number, we performed 21 CGH experiments using normal control DNA. We calculated average ratio changes and standard deviations by using the software program cghprofstats. new (Piper et al., 1994). The average ratio for all 21 hybridizations was 0.99 (range 0.9‐1.1). The average standard deviation was 0.04 (range 0.02‐0.06). Taking these findings into consideration, we chose upper and lower ratio thresholds of 1.2 and 0.8, respectively. Any change in ratio in excess of these thresholds was interpreted as indicative of DNA copy number changes only if found in both forward and reverse experiments. Amplifications were defined both by a ratio >2.0 and by visual inspection". Piper J, Rutovitz D, Sudar D, Kallioniemi A, Kallioniemi O, Waldman FM, et al. Computer image analysis of comparative genomic hybridization. Cytometry 1995;19:10‐26 also cited. FISH Tumour sample type: NR Region(s) analysed: from Smith 1999: 1p36, 1q24, 19p13.1, 19q13.1‐q13.2, 19q13.3 Cut‐off: for Smith 1999 we defined codeletion defined as hemizygous deletion of 1p36, 1q13.1‐q13.2 and 19q13.3. What defined hemizygous deletion NR. Also cited Qian J, Bostwick DG, Takahashi S, Borell TJ, Herath JF, Lieber MM et al. Chromosomal anomalies in prostatic intraepithelial neoplasia and carcinoma detected by fluorescence in situ hybridization. Cancer Research 1995;55:5408‐14. In this paper (quote) "abnormal autosomal loss required ≥55% nuclei with zero or one signal". Unclear if this threshold was used. PCR (with comparison to normal DNA) (referred to as PCR‐based LOH below. Note: the risk of bias and applicability judgements for this PCR variant appear inFigure 7) Tumour sample type: NR Region(s) analysed: 1p: D1S468, D1S1612, D1S1597, D1S199, D1S1665, D1S1728, D1S1588, D1S1675, D1S187; 19q: D19S213, D19S569, D19S422. D19S219, SM, S19S112, S19S412, D19S596, HRC, D19S589, D19S218 Cut‐off: For Smith 1999 we defined codeletion as all markers showing confirmed allelic loss, presumed allelic loss, were homozygous or were indeterminant. Additional details: PCR with comparison to normal DNA PCR (without comparison to normal DNA) Tumour sample type: FFPE Region(s) analysed: chromosome 1: D1S162, D1S226, D1S199, D1S186, D1S312; chromosome 19: D19S112, D19S918, D19S206. Cut‐off: presence of 1 allele or LOH pattern A or B at all loci ("LOH pattern A, consisted of a shorter allele (the allele measuring fewer nucleotides in length) with a relatively high peak and a longer allele with a diminutive peak (Fig. 6). The height of the longer allele was never more than 12% of the height of the shorter allele … LOH pattern B, the intensity of the shorter allele was less than that of the longer allele"). Additional details: PCR‐based LOH (microsatellite) without the need for comparison to normal DNA. Quote: "Multiplex PCR amplification of microsatellite loci followed by high‐resolution PCR product sizing by capillary electrophoresis on formalin‐fixed, paraffin‐embedded tissue".
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?	No
Was a case‐control design avoided?	Yes
Did the study avoid inappropriate exclusions?	No
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?			Low concern
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))
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?	No
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 (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?	Unclear
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 or aCGH (or both))
DOMAIN 2: Index Test (Methylation array)
DOMAIN 2: Index Test (FISH)
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?	Unclear
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)
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?	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 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