D'Haene 2019.

Study characteristics
Patient Sampling	Inclusion/exclusion criteria Inclusion criteria: quote: "samples were selected according to the availability of NGS results obtained by the Ion AmpliSeq CHP (v2, Thermo Fisher Scientific, Carlsbad, CA, United States) and the availability of the 1p/19q codeletion status, as determined by FISH". Exclusion criteria: NGS results were excluded if they were low quality. Prior testing Presumably histopathological diagnosis (WHO 2016 classification for glioma samples), although not explicitly reported. Had to have NGS and FISH results.
Patient characteristics and setting	Number of participants/tumours with results for 1p/19q status by ≥ 2 DNA‐based tests: 50 Country: Belgium Population source and setting: Department of Pathology, Erasme Hospital, Brussels, Belgium. Time period NR Age: NR Gender: NR Karnofsky performance status: NR First diagnosis/recurrent disease: NR
Index tests	2 tests: FISH and NGS FISH Tumour sample type: FFPE Region(s) analysed: 1p36/1q25 and 19p13/19q13 (Vysis Inc., Downers Grove, Illinois, USA) Cut‐off: quote: "The codeletion was considered to be positive in cases where the ratio of red (1p or 19q) versus green (1q or 19p) signals were lower than 0.8 after scoring at least 50 nuclei". NGS Tumour sample type: FFPE Region(s) analysed: 55 SNPs along the full length of chromosomes 1 and 19 (30 on chromosome 1 and 25 on chromosome 19). Quote: "These SNPs were selected based on the high polymorphic value of their minor allele frequency, as reported on the National Center for Biotechnology Information (NCBI) dbSNP database, as well as from previous reports [24,28]. The average distance between SNPs is 5.2 Mb in 1p, 8.0 Mb in 1q, 1.9 Mb in 19p, and 2.1 Mb in 19q". SNPs: 1p: rs7663, rs169957, rs309481, rs159525, rs157208, rs6425953, rs7315, rs7903, rs504816, rs7374, rs87061, rs11811946, rs5680, rs191142, rs54396, rs106075, rs1132, rs8888, rs6604120, rs8128; 1q: rs2275073, rs347303, rs4575136, rs898114, rs1342566, rs12744553, rs2802849, rs1770214, rs6692892, rs16848862, rs2275073, rs347303, rs4575136, rs898114, rs1342566; 19p: rs13345388, rs7256720, rs36115836, rs164020, rs57167556, rs2114724, rs7246440, rs10419689, rs8107776, rs4808732; 19q: rs7283, rs2542297, rs33841, rs12852, rs1291, rs17628, rs166539, rs3817, rs10113, rs8355, rs11573, rs193040, rs3814, rs10217, rs10448. Cut‐off: quote: "To detect 1p/19q LOH, we firstly applied a quality criterion based on the SNP coverage. The test was considered optimal, suboptimal, or non‐informative, according to the number of SNPs that were covered by fewer than 250 reads (Table 3). Secondly, the allelic frequencies (AF) for each SNP (with more than 250×) were annotated. Homozygous SNPs with the same nucleotide as that of the reference genome will have an AF of approximately 100%, while homozygous SNPs with a nucleotide that differs from the reference genome will have an AF of approximately 0%. Heterozygous SNPs will have an AF of approximately 50%. However, because NGS provides a semi‐quantitative measure based on the number of reads [19], we established the following confidence intervals: 90–100% or 0–10% for homozygous markers, and 40–60% for heterozygous markers. These confidence intervals were defined based on the analysis of 12 nontumor samples. Imbalances of 1p and 19q markers due to LOH were scored when their AFs were outside the established ranges for homozygosity or heterozygosity (i.e., 10–40% or 60–90%) (Figure 1). We defined the criterion for the 1p/19q codeletion as the absence of any heterozygous markers in these chromosomal arms, together with the presence of at least one heterozygous marker in the opposite arm. No codeletion was scored if at least one heterozygous marker was present in 1p or 19q. A whole chromosome arm LOH is observed when there are no heterozygous markers present in either arm". Additional details: custom‐designed glioma NGS‐targeted panel. Sequenced using an Ion Torrent Personal Genome Machine (Thermo Fisher).
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?	No
Was a case‐control design avoided?	Yes
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?			Low concern
DOMAIN 2: Index Test (NanoString)
DOMAIN 2: Index Test (aCGH)
DOMAIN 2: Index Test (NGS)
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 (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?	Yes
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?		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)
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