Cowell 2004.

Study characteristics
Patient Sampling	Inclusion/exclusion criteria NR. However, (quote) "To assess the usefulness of CGHa for the identification of LOH events in low‐grade brain tumors, we used DNA from a series of 3 different tumor subtypes whose LOH status had previously been determined using microsatellite markers (23). The tumors had been grouped according to histopathological diagnosis and divided into low‐grade oligodendrogliomas (LGO), anaplastic oligodendrogliomas (AO), and mixed oligoastrocytomas (MOA). From the original series of tumors classified using microsatellite markers, we analyzed representative samples that consisted of 6 LGOs, 5 AOs, and 3 MOAs. In each of these groups were examples of tumors where there was clear presence or absence of LOH for at least one of the microsatellite markers on each of the 1p and 19q chromosome arms". Prior testing Presumably histopathological diagnosis, although not explicitly reported. To be included in this study LOH status had to have previously been determined using microsatellite markers (PCR‐based LOH).
Patient characteristics and setting	Number of participants/tumours with results for 1p/19q status by ≥ 2 DNA‐based tests: 14 Country: USA Population source and setting: Cleveland Clinic Foundation Department of Neurosurgery. Time period NR Age: NR Gender: NR Karnofsky performance status: NR First diagnosis/recurrent disease: NR
Index tests	2 tests: aCGH and PCR aCGH Tumour sample type: frozen Region(s) analysed: genome wide. Quote: "A genome‐wide resource of ~6,000 FISH‐mapped, gene/marker content‐verified, sequenced BAC clones (22) from the RPCI‐11 human BAC library are represented as immobilized DNA targets on glass slides for array‐based CGH analysis, as previously described (20). Each clone is spotted in triplicate at 280 µm intervals (see http://genomics.roswellpark.org for a complete list of clones)". Cut‐off: quote: "In general, background variation was considered to extend between ratios of 1.2 and 0.8 for diploid tumors on the linear scale and hybridization ratios outside of these values were considered losses or gains of genetic material". PCR Tumour sample type: frozen Region(s) analysed: 1p36 (D1S552, D1S1612, D1S468), 1p31 (D1S551, D1S430), 19q13.4 (D19S254, D19S572) Cut‐off: NR
Target condition and reference standard(s)	Target condition was absolute 1p/19q deletion. 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?	Unclear
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)
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 (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?	Unclear
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?		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)
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?	Yes
Could the patient flow have introduced bias?		Low risk