Lhotska 2015.
| Study characteristics | |||
| Patient Sampling |
Inclusion/exclusion criteria Inclusion criteria: low grade (WHO grade II) oligodendroglioma and oligoastrocytoma Prior testing Not explicitly reported but presumably histopathological diagnosis |
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| Patient characteristics and setting |
Number of participants/tumours with results for 1p/19q status by ≥ 2 DNA‐based tests: 20 Country: Czech Republic Population source and setting: Department of Neurosurgery, Central Military Hospital and 1st Faculty of Medicine, Charles University, Prague, Czech Republic and the Department of Neurosurgery, Regional Hospital, Liberec, Czech Republic. 2005–2014 Agea: 56.5% aged ≤ 50 years (median age 34.5 years); 43.5% aged > 50 years (median age 57 years) Genderb: 55.6% male Karnofsky performance status: NR First diagnosis/recurrent disease: NR aFor whole population: the study included 23 participants with oligodendroglioma or oligoastrocytoma, results for both tests available for 20. bFor whole population: this result included participants with astrocytoma (1p/19q status not investigated). 23 participants with oligodendroglioma or oligoastrocytoma. Results for both tests available for 20. |
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| Index tests |
2 tests: FISH and SNP array FISH Tumour sample type: fresh Region(s) analysed: 1p36/1q25, 19q13/19p13 (Vysis probes; Abbott Molecular, Des Plaines, Illinois, USA) Cut‐off: 5% for deletion SNP array Tumour sample type: fresh Region(s) analysed: genome wide Cut‐off: NR and participants not classified. We set the criteria for codeletion as 1 copy of (or homozygous for) 1p36.33p11.2 or 1p31.1p12 or 1p31.3p31.1 AND 1 copy of (or homozygous for) 19q12q13.43 or 19q13.2q13.43 or 19q13.32q13.43. Additional details: human CytoSNP‐12 BeadChip (Illumina, San Diego, California) |
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| 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 | All tests performed with tumour tissues taken during routine neurosurgical procedures and peripheral blood taken after the procedures. | ||
| 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? | Yes | ||
| 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) | |||
| DOMAIN 2: Index Test (FISH (variant 4)) | |||
| DOMAIN 2: Index Test (SNP array) | |||
| 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? | Low risk | ||
| Are there concerns that the index test, its conduct, or interpretation differ from the review question? | Low concern | ||
| 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? | 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 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 | ||