DNA extraction, Bisulfite treatment, PCR and Next Generation DNA sequencing (NGS)
Reported
2-3 weeks
Additional Information
The binding of alkyl adducts to the O6 position of guanine cause double stranded DNA breaks and mispairing, resulting in apoptosis and cell death. The MGMT gene is ubiquitously expressed and encodes for a DNA repair protein that removes alkyl adducts from alkylated guanines. This process interferes with the alkylating agent temozolomide, which is used to treat glioblastoma. In some glioblastoma tumors, epigenetic methylation of CpG islands in the MGMT promoter, results in silencing or attenuation of MGMT expression, thus increasing the temozolomide induced-cytotoxicity and portending a better prognosis.
The coupling of MGMT promoter methylation with radiotherapy and alkylating chemotherapy drugs such as carmustine or temozolomide, has been shown to increase mean patient survival. Therefore, the MGMT methylation test is used as a prognostic indicator to treatment with alkylating agents.
This assay is based on bisulfite treatment of genomic DNA recovered from the tumor areas of the submitted slides. Next-Gen DNA sequencing of a 191 bp MGMT promoter region consisting of 17 CpG dinucleotides and spanning Sp1 and other transcription factor binding sites, is used to determine the extent of CpG methylation status in this region. The assay has approximately 2% of methylation detection sensitivity.
The result is reported as "POSITIVE: METHYLATED" if one or more CpG sites are methylated.
Reported values consist of:
1) A methylation index, ranging from 0 to 17 that reflects the number of methylated CpG sites.
2) A methylated fraction, ranging from >0 to 1, that provides an estimation of methylation sites in the analyzed specimen (reported only for positive specimens}.
3) An overall methylation score ranging from > 0 to 17 that consists of the multiplication of the methylation index with the methylation fraction (reported only for positive specimens}.
This test was developed and its performance characteristics determined by the Clinical Laboratories at the Medical Center at UC San Francisco. It has not been cleared or approved by the U.S. Food and Drug Administration.
Synonyms
O6 methylguanine DNA methyltransferase
Supplemental Test Request Form Required
Yes
Sample Type
Formalin-fixed, paraffin-embedded 10-micron tissue sections on five (5) unstained, uncharged glass slides. One adjacent H&E stained slide should be included.
Remarks
1- Tissue sections on slides selected for MGMT methylation analysis must optimally be at least 1 cm2.
2- A pathologist should circle the tumor area of an H&E slide.
3- Five (5) unstained additional slides cut serially and adjacent to the H&E slide must also be submitted.
4- Label slides with pathology case number and block identification.
5- All specimens must be accompanied with a pathology report.
Stability (from collection to initiation)
Formalin-fixed, paraffin-embedded tissues are stable indefinitely at room temperature
Unacceptable Conditions
1- Insufficient tumor tissue present on slide as determined by pathologist and/or lab may not yield adequate results and could be reported as QNS.
2- Required number of slides not included.
3- Slides not labeled or not accompanied by completed requisition form (if not ordered directly through Department of Pathology).
Test Code
MGMT
Performing Lab
Medical Genomics - Molecular Diagnostics
Unacceptable Conditions
1- Insufficient tumor tissue present on slide as determined by pathologist and/or lab may not yield adequate results and could be reported as QNS.
2- Required number of slides not included.
3- Slides not labeled or not accompanied by completed requisition form (if not ordered directly through Department of Pathology).
Stability (from collection to initiation)
Formalin-fixed, paraffin-embedded tissues are stable indefinitely at room temperature
Reference Interval
Negative
No methylation
Methylation Index=0
Additional Information
The binding of alkyl adducts to the O6 position of guanine cause double stranded DNA breaks and mispairing, resulting in apoptosis and cell death. The MGMT gene is ubiquitously expressed and encodes for a DNA repair protein that removes alkyl adducts from alkylated guanines. This process interferes with the alkylating agent temozolomide, which is used to treat glioblastoma. In some glioblastoma tumors, epigenetic methylation of CpG islands in the MGMT promoter, results in silencing or attenuation of MGMT expression, thus increasing the temozolomide induced-cytotoxicity and portending a better prognosis.
The coupling of MGMT promoter methylation with radiotherapy and alkylating chemotherapy drugs such as carmustine or temozolomide, has been shown to increase mean patient survival. Therefore, the MGMT methylation test is used as a prognostic indicator to treatment with alkylating agents.
This assay is based on bisulfite treatment of genomic DNA recovered from the tumor areas of the submitted slides. Next-Gen DNA sequencing of a 191 bp MGMT promoter region consisting of 17 CpG dinucleotides and spanning Sp1 and other transcription factor binding sites, is used to determine the extent of CpG methylation status in this region. The assay has approximately 2% of methylation detection sensitivity.
The result is reported as "POSITIVE: METHYLATED" if one or more CpG sites are methylated.
Reported values consist of:
1) A methylation index, ranging from 0 to 17 that reflects the number of methylated CpG sites.
2) A methylated fraction, ranging from >0 to 1, that provides an estimation of methylation sites in the analyzed specimen (reported only for positive specimens}.
3) An overall methylation score ranging from > 0 to 17 that consists of the multiplication of the methylation index with the methylation fraction (reported only for positive specimens}.
This test was developed and its performance characteristics determined by the Clinical Laboratories at the Medical Center at UC San Francisco. It has not been cleared or approved by the U.S. Food and Drug Administration.
CPT Codes
81287
LDT or Modified FDA
Yes
Available Stat
No
Test Code
MGMT
Performing Lab
Medical Genomics - Molecular Diagnostics
Performed
Run 1X per week, or as needed
Methodology
DNA extraction, Bisulfite treatment, PCR and Next Generation DNA sequencing (NGS)
Remarks
1- Tissue sections on slides selected for MGMT methylation analysis must optimally be at least 1 cm2.
2- A pathologist should circle the tumor area of an H&E slide.
3- Five (5) unstained additional slides cut serially and adjacent to the H&E slide must also be submitted.
4- Label slides with pathology case number and block identification.
5- All specimens must be accompanied with a pathology report.
Sample Type
Formalin-fixed, paraffin-embedded 10-micron tissue sections on five (5) unstained, uncharged glass slides. One adjacent H&E stained slide should be included.
Unacceptable Conditions
1- Insufficient tumor tissue present on slide as determined by pathologist and/or lab may not yield adequate results and could be reported as QNS.
2- Required number of slides not included.
3- Slides not labeled or not accompanied by completed requisition form (if not ordered directly through Department of Pathology).
Reference Interval
Negative
No methylation
Methylation Index=0
Synonyms
O6 methylguanine DNA methyltransferase
Stability (from collection to initiation)
Formalin-fixed, paraffin-embedded tissues are stable indefinitely at room temperature
Reported
2-3 weeks
Additional Information
The binding of alkyl adducts to the O6 position of guanine cause double stranded DNA breaks and mispairing, resulting in apoptosis and cell death. The MGMT gene is ubiquitously expressed and encodes for a DNA repair protein that removes alkyl adducts from alkylated guanines. This process interferes with the alkylating agent temozolomide, which is used to treat glioblastoma. In some glioblastoma tumors, epigenetic methylation of CpG islands in the MGMT promoter, results in silencing or attenuation of MGMT expression, thus increasing the temozolomide induced-cytotoxicity and portending a better prognosis.
The coupling of MGMT promoter methylation with radiotherapy and alkylating chemotherapy drugs such as carmustine or temozolomide, has been shown to increase mean patient survival. Therefore, the MGMT methylation test is used as a prognostic indicator to treatment with alkylating agents.
This assay is based on bisulfite treatment of genomic DNA recovered from the tumor areas of the submitted slides. Next-Gen DNA sequencing of a 191 bp MGMT promoter region consisting of 17 CpG dinucleotides and spanning Sp1 and other transcription factor binding sites, is used to determine the extent of CpG methylation status in this region. The assay has approximately 2% of methylation detection sensitivity.
The result is reported as "POSITIVE: METHYLATED" if one or more CpG sites are methylated.
Reported values consist of:
1) A methylation index, ranging from 0 to 17 that reflects the number of methylated CpG sites.
2) A methylated fraction, ranging from >0 to 1, that provides an estimation of methylation sites in the analyzed specimen (reported only for positive specimens}.
3) An overall methylation score ranging from > 0 to 17 that consists of the multiplication of the methylation index with the methylation fraction (reported only for positive specimens}.
This test was developed and its performance characteristics determined by the Clinical Laboratories at the Medical Center at UC San Francisco. It has not been cleared or approved by the U.S. Food and Drug Administration.
CPT Codes
81287
LDT or Modified FDA
Yes
Supplemental Test Request Form Required
Yes
Ordering
Available Stat
No
Performing Lab
Medical Genomics - Molecular Diagnostics
Performed
Run 1X per week, or as needed
Methodology
DNA extraction, Bisulfite treatment, PCR and Next Generation DNA sequencing (NGS)
Reported
2-3 weeks
Additional Information
The binding of alkyl adducts to the O6 position of guanine cause double stranded DNA breaks and mispairing, resulting in apoptosis and cell death. The MGMT gene is ubiquitously expressed and encodes for a DNA repair protein that removes alkyl adducts from alkylated guanines. This process interferes with the alkylating agent temozolomide, which is used to treat glioblastoma. In some glioblastoma tumors, epigenetic methylation of CpG islands in the MGMT promoter, results in silencing or attenuation of MGMT expression, thus increasing the temozolomide induced-cytotoxicity and portending a better prognosis.
The coupling of MGMT promoter methylation with radiotherapy and alkylating chemotherapy drugs such as carmustine or temozolomide, has been shown to increase mean patient survival. Therefore, the MGMT methylation test is used as a prognostic indicator to treatment with alkylating agents.
This assay is based on bisulfite treatment of genomic DNA recovered from the tumor areas of the submitted slides. Next-Gen DNA sequencing of a 191 bp MGMT promoter region consisting of 17 CpG dinucleotides and spanning Sp1 and other transcription factor binding sites, is used to determine the extent of CpG methylation status in this region. The assay has approximately 2% of methylation detection sensitivity.
The result is reported as "POSITIVE: METHYLATED" if one or more CpG sites are methylated.
Reported values consist of:
1) A methylation index, ranging from 0 to 17 that reflects the number of methylated CpG sites.
2) A methylated fraction, ranging from >0 to 1, that provides an estimation of methylation sites in the analyzed specimen (reported only for positive specimens}.
3) An overall methylation score ranging from > 0 to 17 that consists of the multiplication of the methylation index with the methylation fraction (reported only for positive specimens}.
This test was developed and its performance characteristics determined by the Clinical Laboratories at the Medical Center at UC San Francisco. It has not been cleared or approved by the U.S. Food and Drug Administration.
Synonyms
O6 methylguanine DNA methyltransferase
Supplemental Test Request Form Required
Yes
Collection
Sample Type
Formalin-fixed, paraffin-embedded 10-micron tissue sections on five (5) unstained, uncharged glass slides. One adjacent H&E stained slide should be included.
Remarks
1- Tissue sections on slides selected for MGMT methylation analysis must optimally be at least 1 cm2.
2- A pathologist should circle the tumor area of an H&E slide.
3- Five (5) unstained additional slides cut serially and adjacent to the H&E slide must also be submitted.
4- Label slides with pathology case number and block identification.
5- All specimens must be accompanied with a pathology report.
Stability (from collection to initiation)
Formalin-fixed, paraffin-embedded tissues are stable indefinitely at room temperature
Unacceptable Conditions
1- Insufficient tumor tissue present on slide as determined by pathologist and/or lab may not yield adequate results and could be reported as QNS.
2- Required number of slides not included.
3- Slides not labeled or not accompanied by completed requisition form (if not ordered directly through Department of Pathology).
Processing
Test Code
MGMT
Performing Lab
Medical Genomics - Molecular Diagnostics
Unacceptable Conditions
1- Insufficient tumor tissue present on slide as determined by pathologist and/or lab may not yield adequate results and could be reported as QNS.
2- Required number of slides not included.
3- Slides not labeled or not accompanied by completed requisition form (if not ordered directly through Department of Pathology).
Stability (from collection to initiation)
Formalin-fixed, paraffin-embedded tissues are stable indefinitely at room temperature
Result Interpretation
Reference Interval
Negative
No methylation
Methylation Index=0
Additional Information
The binding of alkyl adducts to the O6 position of guanine cause double stranded DNA breaks and mispairing, resulting in apoptosis and cell death. The MGMT gene is ubiquitously expressed and encodes for a DNA repair protein that removes alkyl adducts from alkylated guanines. This process interferes with the alkylating agent temozolomide, which is used to treat glioblastoma. In some glioblastoma tumors, epigenetic methylation of CpG islands in the MGMT promoter, results in silencing or attenuation of MGMT expression, thus increasing the temozolomide induced-cytotoxicity and portending a better prognosis.
The coupling of MGMT promoter methylation with radiotherapy and alkylating chemotherapy drugs such as carmustine or temozolomide, has been shown to increase mean patient survival. Therefore, the MGMT methylation test is used as a prognostic indicator to treatment with alkylating agents.
This assay is based on bisulfite treatment of genomic DNA recovered from the tumor areas of the submitted slides. Next-Gen DNA sequencing of a 191 bp MGMT promoter region consisting of 17 CpG dinucleotides and spanning Sp1 and other transcription factor binding sites, is used to determine the extent of CpG methylation status in this region. The assay has approximately 2% of methylation detection sensitivity.
The result is reported as "POSITIVE: METHYLATED" if one or more CpG sites are methylated.
Reported values consist of:
1) A methylation index, ranging from 0 to 17 that reflects the number of methylated CpG sites.
2) A methylated fraction, ranging from >0 to 1, that provides an estimation of methylation sites in the analyzed specimen (reported only for positive specimens}.
3) An overall methylation score ranging from > 0 to 17 that consists of the multiplication of the methylation index with the methylation fraction (reported only for positive specimens}.
This test was developed and its performance characteristics determined by the Clinical Laboratories at the Medical Center at UC San Francisco. It has not been cleared or approved by the U.S. Food and Drug Administration.
Administrative
CPT Codes
81287
LDT or Modified FDA
Yes
Complete View
Available Stat
No
Test Code
MGMT
Performing Lab
Medical Genomics - Molecular Diagnostics
Performed
Run 1X per week, or as needed
Methodology
DNA extraction, Bisulfite treatment, PCR and Next Generation DNA sequencing (NGS)
Remarks
1- Tissue sections on slides selected for MGMT methylation analysis must optimally be at least 1 cm2.
2- A pathologist should circle the tumor area of an H&E slide.
3- Five (5) unstained additional slides cut serially and adjacent to the H&E slide must also be submitted.
4- Label slides with pathology case number and block identification.
5- All specimens must be accompanied with a pathology report.
Sample Type
Formalin-fixed, paraffin-embedded 10-micron tissue sections on five (5) unstained, uncharged glass slides. One adjacent H&E stained slide should be included.
Unacceptable Conditions
1- Insufficient tumor tissue present on slide as determined by pathologist and/or lab may not yield adequate results and could be reported as QNS.
2- Required number of slides not included.
3- Slides not labeled or not accompanied by completed requisition form (if not ordered directly through Department of Pathology).
Reference Interval
Negative
No methylation
Methylation Index=0
Synonyms
O6 methylguanine DNA methyltransferase
Stability (from collection to initiation)
Formalin-fixed, paraffin-embedded tissues are stable indefinitely at room temperature
Reported
2-3 weeks
Additional Information
The binding of alkyl adducts to the O6 position of guanine cause double stranded DNA breaks and mispairing, resulting in apoptosis and cell death. The MGMT gene is ubiquitously expressed and encodes for a DNA repair protein that removes alkyl adducts from alkylated guanines. This process interferes with the alkylating agent temozolomide, which is used to treat glioblastoma. In some glioblastoma tumors, epigenetic methylation of CpG islands in the MGMT promoter, results in silencing or attenuation of MGMT expression, thus increasing the temozolomide induced-cytotoxicity and portending a better prognosis.
The coupling of MGMT promoter methylation with radiotherapy and alkylating chemotherapy drugs such as carmustine or temozolomide, has been shown to increase mean patient survival. Therefore, the MGMT methylation test is used as a prognostic indicator to treatment with alkylating agents.
This assay is based on bisulfite treatment of genomic DNA recovered from the tumor areas of the submitted slides. Next-Gen DNA sequencing of a 191 bp MGMT promoter region consisting of 17 CpG dinucleotides and spanning Sp1 and other transcription factor binding sites, is used to determine the extent of CpG methylation status in this region. The assay has approximately 2% of methylation detection sensitivity.
The result is reported as "POSITIVE: METHYLATED" if one or more CpG sites are methylated.
Reported values consist of:
1) A methylation index, ranging from 0 to 17 that reflects the number of methylated CpG sites.
2) A methylated fraction, ranging from >0 to 1, that provides an estimation of methylation sites in the analyzed specimen (reported only for positive specimens}.
3) An overall methylation score ranging from > 0 to 17 that consists of the multiplication of the methylation index with the methylation fraction (reported only for positive specimens}.
This test was developed and its performance characteristics determined by the Clinical Laboratories at the Medical Center at UC San Francisco. It has not been cleared or approved by the U.S. Food and Drug Administration.
