Comparing different methods of determining whether gliomas are missing arms 1p and 19q of the chromosomes

Why is improving the detection of 1p/19q codeletion in glioma important?

Gliomas are a type of brain tumour (cancer). There are different types of glioma, with different changes in their genetic material. One of the possible genetic changes is the loss of parts of two of our 23 chromosomes. When both a specific part of chromosome 1 and a specific part of chromosome 19 are missing, it is known as '1p/19q codeletion'. 1p/19q codeletion is used to diagnose a glioma known as an oligodendroglioma. Presence of 1p/19q codeletion can also tell us how long a patient with a glioma may survive and which is the best medicine to treat that patient.

What is the aim of this review?

We wanted to find out which is the most accurate and cost-effective way to identify 1p/19q codeletion in gliomas.

What is studied in the review?

The review examined and compared all methods to detect 1p/19q codeletion that are based on the deoxyribonucleic acid (DNA, which contains the information for an organism to develop, survive and reproduce) of the tumour. These include tests known as FISH and CISH, which are performed directly on tumour tissue and a number of other tests that are based on DNA extracted from the tumour tissue including: PCR-based LOH, real-time PCR, MLPA, SNP array, CGH array and NGS. None of these tests is perfect, so there is no 'gold standard' against which to compare them. The two most commonly used tests (FISH and PCR-based LOH) were used as the best available reference tests against which to examine the others.

What are the main results of the review?

We found 53 studies. Most tests were good at identifying instances of 1p/19q codeletion (meaning they were tests with good 'sensitivity') that had been identified by either of the two common tests. However, there were some differences in how well the tests were able to rule out 1p/19q codeletion when it did not seem to be present (the 'specificity' of the test). NGS and SNP arrays were better at this (i.e. having fewer 'false-positives' results) when considered against FISH as the reference test. The cost per correct diagnosis was lowest for MLPA, although this was not a firm finding because the amount of evidence was small.

How reliable are results of the studies in this review?

Our certainty in the evidence was low or very low, because there were few studies for most of the tests and there were limitations to almost all the studies. Similarly, the economic analysis must be interpreted with caution due to the relatively small number of studies.

To whom do the results of this review apply?

The ways in which the tests were performed were thought to be representative of how they would be performed in practice. However, many of the studies included people with specific types of gliomas, so the results might not be representative of all people with gliomas.

What are the implications of this review?

The limited evidence suggests that currently used techniques show good sensitivity for detection of 1p/19q codeletion. NGS and SNP arrays may have higher specificity when FISH is the reference standard, but this comes at greater cost per test.

How up-to-date is this review?

The latest search for studies took place in August 2019.

Authors' conclusions: 

In our review, most techniques (except G-banding) appeared to have good sensitivity (few false negatives) for detection of 1p/19q codeletions in glioma against both FISH and PCR-based LOH as a reference standard. However, we judged the certainty of the evidence low or very low for all the tests. There are possible differences in specificity, with both NGS and SNP array having high specificity (fewer false positives) for 1p/19q codeletion when considered against FISH as the reference standard. The economic analysis should be interpreted with caution due to the small number of studies.

Read the full abstract...

Complete deletion of both the short arm of chromosome 1 (1p) and the long arm of chromosome 19 (19q), known as 1p/19q codeletion, is a mutation that can occur in gliomas. It occurs in a type of glioma known as oligodendroglioma and its higher grade counterpart known as anaplastic oligodendroglioma. Detection of 1p/19q codeletion in gliomas is important because, together with another mutation in an enzyme known as isocitrate dehydrogenase, it is needed to make the diagnosis of an oligodendroglioma. Presence of 1p/19q codeletion also informs patient prognosis and prediction of the best drug treatment. The main two tests in use are fluorescent in situ hybridisation (FISH) and polymerase chain reaction (PCR)-based loss of heterozygosity (LOH) assays (also known as PCR-based short tandem repeat or microsatellite analysis). Many other tests are available. None of the tests is perfect, although PCR-based LOH is expected to have very high sensitivity.


To estimate the sensitivity and specificity and cost-effectiveness of different deoxyribonucleic acid (DNA)-based techniques for determining 1p/19q codeletion status in glioma.

Search strategy: 

We searched MEDLINE, Embase and BIOSIS up to July 2019. There were no restrictions based on language or date of publication. We sought economic evaluation studies from the results of this search and using the National Health Service Economic Evaluation Database.

Selection criteria: 

We included cross-sectional studies in adults with glioma or any subtype of glioma, presenting raw data or cross-tabulations of two or more DNA-based tests for 1p/19q codeletion. We also sought economic evaluations of these tests.

Data collection and analysis: 

We followed procedures outlined in the Cochrane Handbook for Diagnostic Test Accuracy Reviews. Two review authors independently screened titles/abstracts/full texts, performed data extraction, and undertook applicability and risk of bias assessments using QUADAS-2. Meta-analyses used the hierarchical summary ROC model to estimate and compare test accuracy. We used FISH and PCR-based LOH as alternate reference standards to examine how tests compared with those in common use, and conducted a latent class analysis comparing FISH and PCR-based LOH. We constructed an economic model to evaluate cost-effectiveness.

Main results: 

We included 53 studies examining: PCR-based LOH, FISH, single nucleotide polymorphism (SNP) array, next-generation sequencing (NGS), comparative genomic hybridisation (CGH), array comparative genomic hybridisation (aCGH), multiplex-ligation-dependent probe amplification (MLPA), real-time PCR, chromogenic in situ hybridisation (CISH), mass spectrometry (MS), restriction fragment length polymorphism (RFLP) analysis, G-banding, methylation array and NanoString. Risk of bias was low for only one study; most gave us concerns about how patients were selected or about missing data. We had applicability concerns about many of the studies because only patients with specific subtypes of glioma were included. 1520 participants contributed to analyses using FISH as the reference, 1304 participants to analyses involving PCR-based LOH as the reference and 262 participants to analyses of comparisons between methods from studies not including FISH or PCR-based LOH.

Most evidence was available for comparison of FISH with PCR-based LOH (15 studies, 915 participants): PCR-based LOH detected 94% of FISH-determined codeletions (95% credible interval (CrI) 83% to 98%) and FISH detected 91% of codeletions determined by PCR-based LOH (CrI 78% to 97%). Of tumours determined not to have a deletion by FISH, 94% (CrI 87% to 98%) had a deletion detected by PCR-based LOH, and of those determined not to have a deletion by PCR-based LOH, 96% (CrI 90% to 99%) had a deletion detected by FISH. The latent class analysis suggested that PCR-based LOH may be slightly more accurate than FISH. Most other techniques appeared to have high sensitivity (i.e. produced few false-negative results) for detection of 1p/19q codeletion when either FISH or PCR-based LOH was considered as the reference standard, although there was limited evidence. There was some indication of differences in specificity (false-positive rate) with some techniques. Both NGS and SNP array had high specificity when considered against FISH as the reference standard (NGS: 6 studies, 243 participants; SNP: 6 studies, 111 participants), although we rated certainty in the evidence as low or very low. NGS and SNP array also had high specificity when PCR-based LOH was considered the reference standard, although with much more uncertainty as these results were based on fewer studies (just one study with 49 participants for NGS and two studies with 33 participants for SNP array).

G-banding had low sensitivity and specificity when PCR-based LOH was the reference standard. Although MS had very high sensitivity and specificity when both FISH and PCR-based LOH were considered the reference standard, these results were based on only one study with a small number of participants. Real-time PCR also showed high specificity with FISH as a reference standard, although there were only two studies including 40 participants.

We found no relevant economic evaluations. Our economic model using FISH as the reference standard suggested that the resource-optimising test depends on which measure of diagnostic accuracy is most important. With FISH as the reference standard, MLPA is likely to be cost-effective if society was willing to pay GBP 1000 or less for a true positive detected. However, as the value placed on a true positive increased, CISH was most cost-effective. Findings differed when the outcome measure changed to either true negative detected or correct diagnosis. When PCR-based LOH was used as the reference standard, MLPA was likely to be cost-effective for all measures of diagnostic accuracy at lower threshold values for willingness to pay. However, as the threshold values increased, none of the tests were clearly more likely to be considered cost-effective.