Thomas 2017.

Study characteristics
Patient Sampling	Inclusion/exclusion criteria Nested in a phase II study. Inclusion criteria: diagnosis of anaplastic oligodendroglioma or anaplastic oligoastrocytoma according to the WHO 2000 classification (mixed tumours should have a minimum of 25% oligodendroglial elements); aged ≥18 years; Karnofsky performance status ≥ 60; adequate organ and bone marrow function including a granulocyte count ≥ 1.5 × 109/L, platelet count of ≥ 100 × 109/L, aspartate aminotransferase ≤ 2× UNL, serum creatinine ≤1.5 × UNL and bilirubin ≤ 1.5 × UNL. Exclusion criteria: systemic or non‐contiguous leptomeningeal metastases; prior cranial RT or systemic chemotherapy; other concurrent malignancy with the exception of cervical carcinoma in situ or basal cell carcinoma of the skin; serious illness that would interfere with the prescribed treatment; pregnancy or lactation; refusal to use effective contraception. Prior testing Histopathological diagnosis according to the WHO 2000. Quote: "Within 2 weeks of starting treatment, all patients were evaluated with a complete history, physical and neurological examination, contrast enhanced MRI [magnetic resonance imaging], a biochemistry panel, and complete blood count and underwent screening for hepatitis B and C and HIV".
Patient characteristics and setting	Number of participants/tumours with results for 1p/19q status by ≥ 2 DNA‐based tests: 19 Country: USA Population source and setting: phase II study Agea: median: 44 years, interquartile range: NR; range: 30–66 years Gender: 65.9% male Karnofsky performance status: median 90, range 70–100 First diagnosis/recurrent disease: unclear. Quote: "Patients with newly diagnosed AO [anaplastic oligodendroglioma] or AOA [anaplastic oligoastrocytoma] were eligible to participate in this prospective multicenter phase II study". aFor whole population: 41 people in the phase II study, only 19 had available tissue with adequate DNA quality and quantity for NGS.
Index tests	2 tests: FISH and NGS FISH Tumour sample type: NR Region(s) analysed: NR Cut‐off: NR NGS Tumour sample type: NR Region(s) analysed: genome wide Cut‐off: NR Additional details: MSK‐IMPACT: a hybridisation capture‐based sequencing assay utilising an Illumina HiSeq 2500 platform.
Target condition and reference standard(s)	Target condition was absolute 1p/19q deletion. FISH 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?	Yes
Was a case‐control design avoided?	Yes
Did the study avoid inappropriate exclusions?	Yes
Could the selection of patients have introduced bias?		Low 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)
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?	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?			High
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)
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 (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