Table 1.
Open in new tab

Overview of Techniques and Their Uses as Described in this Review

Sanger SequencingFISHLOH AnalysisNext- Generation Sequencing (DNA)SNP ArrayMLPAWGS/WESNanopore Sequencing(Nested) MSPRT-MSPMS-MLPAPyrosequencingMethylation Profiling
Costs per assay---~~-+~-~-~+
Sensitivity~~~++~+-+~+++
Point mutations (eg, IDH1/2, ATRX, TP53)•∆••ø••
Codeletion 1p/19qøø•∆••••
Other CNVs (eg, EGFR amplification)•ø•∆•••
Translocations/fusions (eg, KIAA1549-BRAF)ƥ
Methylation (eg, MGMT promoter/profile)••∆•∆
Sanger SequencingFISHLOH AnalysisNext- Generation Sequencing (DNA)SNP ArrayMLPAWGS/WESNanopore Sequencing(Nested) MSPRT-MSPMS-MLPAPyrosequencingMethylation Profiling
Costs per assay---~~-+~-~-~+
Sensitivity~~~++~+-+~+++
Point mutations (eg, IDH1/2, ATRX, TP53)•∆••ø••
Codeletion 1p/19qøø•∆••••
Other CNVs (eg, EGFR amplification)•ø•∆•••
Translocations/fusions (eg, KIAA1549-BRAF)ƥ
Methylation (eg, MGMT promoter/profile)••∆•∆

Abbreviations: ATRX, α-thalassemia/mental retardation syndrome X-linked; BRAF, v-RAF murine sarcoma viral oncogene homolog B; CNV, copy number variation; EGFR, epidermal growth factor receptor; FISH, fluorescent in situ hybridization; IDH1/2, isocitrate dehydrogenase; LOH, loss of heterozygosity; MGMT, methyl guanine methyl transferase; MLPA, multiplex ligation-dependent probe amplification; MS, methylation specific; PCR, polymerase chain reaction; RT-MSP, reverse-transcriptase–methylation-specific polymerase chain reaction; TP53, tumor protein 53; WES, whole-exome sequencing; WGS, whole-genome sequencing.

LEGEND of symbols used: +: High; ~: Medium; -: Low; Δ: Preferred method; •: Possible alternative; ø: Least recommended.

Terms such as “preferred method,” “possible alternative,” and “least recommended” are based on the knowledge and experience of the authors; other laboratories may have a different point of view.

Table 1.
Open in new tab

Overview of Techniques and Their Uses as Described in this Review

Sanger SequencingFISHLOH AnalysisNext- Generation Sequencing (DNA)SNP ArrayMLPAWGS/WESNanopore Sequencing(Nested) MSPRT-MSPMS-MLPAPyrosequencingMethylation Profiling
Costs per assay---~~-+~-~-~+
Sensitivity~~~++~+-+~+++
Point mutations (eg, IDH1/2, ATRX, TP53)•∆••ø••
Codeletion 1p/19qøø•∆••••
Other CNVs (eg, EGFR amplification)•ø•∆•••
Translocations/fusions (eg, KIAA1549-BRAF)ƥ
Methylation (eg, MGMT promoter/profile)••∆•∆
Sanger SequencingFISHLOH AnalysisNext- Generation Sequencing (DNA)SNP ArrayMLPAWGS/WESNanopore Sequencing(Nested) MSPRT-MSPMS-MLPAPyrosequencingMethylation Profiling
Costs per assay---~~-+~-~-~+
Sensitivity~~~++~+-+~+++
Point mutations (eg, IDH1/2, ATRX, TP53)•∆••ø••
Codeletion 1p/19qøø•∆••••
Other CNVs (eg, EGFR amplification)•ø•∆•••
Translocations/fusions (eg, KIAA1549-BRAF)ƥ
Methylation (eg, MGMT promoter/profile)••∆•∆

Abbreviations: ATRX, α-thalassemia/mental retardation syndrome X-linked; BRAF, v-RAF murine sarcoma viral oncogene homolog B; CNV, copy number variation; EGFR, epidermal growth factor receptor; FISH, fluorescent in situ hybridization; IDH1/2, isocitrate dehydrogenase; LOH, loss of heterozygosity; MGMT, methyl guanine methyl transferase; MLPA, multiplex ligation-dependent probe amplification; MS, methylation specific; PCR, polymerase chain reaction; RT-MSP, reverse-transcriptase–methylation-specific polymerase chain reaction; TP53, tumor protein 53; WES, whole-exome sequencing; WGS, whole-genome sequencing.

LEGEND of symbols used: +: High; ~: Medium; -: Low; Δ: Preferred method; •: Possible alternative; ø: Least recommended.

Terms such as “preferred method,” “possible alternative,” and “least recommended” are based on the knowledge and experience of the authors; other laboratories may have a different point of view.

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