Ransom 1992a.

Study characteristics
Patient Sampling	Inclusion/exclusion criteria Inclusion criteria: participants with oligodendroglioma, pilocytic astrocytoma, or ependymoma Prior testing Tumours were classified morphologically according to the WHO 1993 classification and were graded by the St Anne/Mayo method (Daumas‐Duport 1988).
Patient characteristics and setting	Number of participants/tumours with results for 1p/19q status by ≥ 2 DNA‐based tests: 5 Country: USA Population source and setting: location NR. May 1988 to June 1990 Age: mean: 45.0 years, standard deviation: 17.0 years Gender: 80% male Karnofsky performance status: NR First diagnosis/recurrent disease: 80% (4/5) first diagnosis, 20% (1/5) recurrent disease
Index tests	2 tests: G‐banding and RFLP G‐banding Tumour sample type: NR Region(s) analysed: genome wide Cut‐off: N/A Additional details: from Ransom 1992b: "cytogenetically analyzed using previously described methods (Jenkins et al., 1989)". RFLP Tumour sample type: frozen Region(s) analysed: 1p: DIZ2 (1p36.3), AMY (1p21), NGFB (1p22.1); 19q D19S8 (19q13.2), S19S7 (19cen‐q12) Cut‐off: NR Additional details: from Ransom 1992b: "Paired blood and tumor DNA specimens were digested with various restriction enzymes and electrophoresed on agarose gels. Southern blotting was performed, and nylon membranes were hybridized under high stringency to a series of probes detecting RFLPs on all human chromosomes (Feinberg and Vogelstein, 1984; Southern, 1975). The resulting autoradiographs were then examined for signal intensity. Quantitative densitometry was applied to autoradiographs in cases were subjective interpretation was not immediately obvious. A normal range for relative tumor/leukocyte DNA allele intensity was established using the 3'HVR probe, which detects multiple alleles on chromosome 16 and is frequently heterozygous. The probe 3'HVR was chosen because of its high PIC score and because chromosome 16 is rarely lost in gliomas (James et al., 1988; this report). Quantitative results were then objectively classified into the categories of loss, no loss, or indeterminate, as determined by comparison to normal range values".
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	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)
DOMAIN 2: Index Test (NGS)
DOMAIN 2: Index Test (G‐banding)
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 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)
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 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))
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