Patient Preparation

N/A

Collect

5 - 10 unstained slides, 1 H&E stained slide for percent tumor analysis

Specimen Preparation

5 - 10 unstained slides, 1 H&E stained slide for percent tumor analysis

Pediatric Collection

Same as Adult collection.

Unacceptable Conditions

Less than 10% tumor present in the sample is deemed quanity not sufficient.

Storage/Transport Temperature

Room temperature

Stability (from collection to initiation)

Room Temperature

Performed

Samples must be cut and to Molecular Diagnostics by end of business on Thursday for the following week's run. Testing starts on Tuesday; preliminary results available on the following Tuesday. Final results available in 14-21 days from sample receipt.

Remarks

N/A

Ordering Recommendations

This test targets genes with known significance for lung adenocarcinoma and melanoma.

Performed

Samples must be cut and to Molecular Diagnostics by end of business on Thursday for the following week's run. Testing starts on Tuesday; preliminary results available on the following Tuesday. Final results available in 14-21 days from sample receipt.

Methodology

Library preparation followed by Next Generation Sequencing (NGS)

Reported

Barring unforeseen circumstances, Friday of the week following the week testing is started.

Notes

Curls may be submitted instead of slides if the percent tumor has been assessed by the submitting physician or designee and no macrodissection is necessary. This panel includes the following clinically actionable genes: ALK, AKT1, APC, BRAF, CDH1, CTNBB1, EGFR, ERBB2/HER2, FBXW7, FGFR2, FOXL2, GNAQ, GNAS, KIT, KRAS, MAP2K1, MET, MSH6, NRAS, PDGFRA, PIK3CA, PTEN, SMAD4, SRC, STK11, and TP53

Section

Molecular Diagnostics

Group Components

N/A

Medicare Regulated Tests

Yes

Reference Lab Notes

N/A

Reference Interval

Negative

Interpretive Data

NOTES:
This test simultaneously assesses the mutation status of multiple genes that have been shown to be involved in a variety of cancer types. Determining mutation status may assist in rendering diagnoses, provide prognostic information and/or help guide the choice of chemotherapeutic agents. Chemotherapeutic agents that target specific altered proteins are increasingly used in the treatment of patients with cancer. The efficacy of these drugs is highly related to the genetic makeup of individual tumors. The test detects only alterations included in the test design (see below) and a negative result does not exclude the possibility of other mutations even within the same gene. Intronic (non-coding) variants are not reported unless they are known to be clinically significant. Sequence variants that have been identified in general population and known to be benign are not included in the test report unless specifically requested.
 
TEST PERFORMED:
The test was performed after DNA preparation using the Illumina TruSight Oncology 500 preparation kit and next-generation sequencing (NGS) on the Illumina NextSeq instrument. TruSight Oncology Mutation Panel 26 (TSO26) library preparation kit uses hybrid-capture chemistry combined with bioinformatics, and utilizes inclusive of unique molecular indexes (UMIs) for high sensitivity in variant detection.  TSO26 simultaneously identifies point mutations and insertions/deletions in specific regions of 26 genes (listed below). This test routinely detects heterozygous mutations in tissue with 10% or greater tumor content or homozygous mutations in tissue with more than 5% or greater tumor content. Any sequence variants not reported in the result section were deemed non-deleterious (e.g., benign single nucleotide polymorphisms, synonymous variants) or not detected by this assay unless otherwise indicated in the interpretation above. The Emory Healthcare GenomOncology Pathology Workbench was used to annotate this case.
 
Gene  Transcript (chr#): exon covered (transcribed coverage %/coding coverage %)
AKT1 - NM_001014432.1 (chr14): exon-1 (0/NA); exon-2 (0/NA); exon-3 (38/100); exon-4-exon-14 (100/100); exon-15 (7/100)
ALK - NM_004304.5 (chr2): exon-1 (42/100); exon-2-exon-28 (100/100); exon-29 (60/100)
APC - NM_000038.6 (chr5): ): exon-1 (100/NA); exon-2-exon-15 (100/100); exon-16 (75/100)
BRAF - NM_004333.6 (chr7): ): exon-1 (38/100); exon-2-exon-17 (100/100); exon-18 (4/100)
CDH1 - NM_004360.5 (chr16): exon-1 (28/100); exon-2-exon-15 (100/100); exon-16 (9/100) 
CTNNB1 - NM_001904.4 (chr3): exon-1 (0/NA); exon-2 (24/100); exon-3-exon-14 (100/100); exon-15 (16/100)
EGFR - NM_005228.5 (chr7): exon-1 (25/100); exon-2-exon-27 (100/100); exon-28 (5/100)
ERBB2 - NM_004448.3 (chr17): exon-1-exon-26 (100/100); exon-27 (51/100)
FBXW7 - NM_033632.3 (chr4): exon-1 (0/NA); exon-2 (88/100); exon-3-exon-11 (100/100); exon-12 (14/100)
FGFR2 - NM_022970.3 (chr10): exon-1 (0/NA); exon-2 (51/100); exon-3-exon-17 (100/100); exon-18 (26/100)
FOXL2 - NM_023067.4 (chr3): exon-1 (38/100)
GNAQ - NM_002072.5 (chr9): exon-1 (19/100); exon-2 - exon-6 (100/100); exon-7 (0/0)
GNAS - NM_000516.6 (chr20): exon-1 (92/100); exon-2 - exon-12 (100/100); exon-13 (29/100)
KIT - NM_000222.2 (chr4): exon-1 (44/100); exon-2-exon-15 (100/100); exon-16 (99/99); exon-17-exon-20 (100/100); exon-21 (12/100)
KRAS - NM_004985.5 (chr12): exon-1 (0/NA); exon-2 (92/100); exon-3-exon-4 (100/100); exon-5 (8/100)
MAP2K1 - NM_002755.3 (chr15): exon-1 (14/100); exon-2-exon-4 (100/100); exon-5 (0/0); exon-6-exon-10 (100/100); exon-11 (11/100)
MET - NM_001127500.3 (chr7): exon-1 (0/NA); exon-2 (98/100); exon-3-exon-20 (100/100); exon-21 (9/100)
MSH6 - NM_000179.2 (chr2): exon-1 (63/100); exon-2-exon-9 (100/100); exon-10 (48/100)
NRAS - NM_002524.5 (chr1): exon-1 (0/NA); exon-2 (88/100); exon-3-exon-4 (100/100); exon-5 (97/100); exon-6 (0/NA); exon-7 (18/NA)
PDGFRA -      NM_006206.6 (chr4): exon-1 (0/NA); exon-2 (82/100); exon-3-exon-22 (100/100); exon-23 (9/100)
PIK3CA - NM_006218.4 (chr3): exon-1 (33/NA); exon-2 (82/100); exon-3-exon-20 (100/100); exon-21 (4/100)
PTEN - NM_000314.8 (chr10): exon-1 (8/100); exon-2-exon-8 (100/100); exon-9 (4/100)
SMAD4 - NM_005359.6 (chr18): exon-1 (0/NA); exon-2 (66/100); exon-3-exon-11 (100/100); exon-12 (3/100) 
SRC - NM_005417.4 (chr20): exon-1 (0/NA); exon-2 (0/NA); exon-3 (0/NA); exon-4 (98/100); exon-5-exon-13 (100/100); exon-14 (9/100)
STK11 - NM_000455.5 (chr19): exon-1 (20/100); exon-2-exon-8 (100/100); exon-9 (93/100); exon-10 (0/NA)
TP53 - NM_000546.5 (chr17): exon-1 (40/NA); exon-2 (74/100); exon-3-exon-10 (100/100); exon-11 (38/100)
 
BIOINFORMATICS PROCESS:
Illumina TSO500 Local Application version tso500-ruo-2.1.0.60
 
REFERENCES:
1.          Na K,et al. JNeurooncol. 2019 May;142(3):445-454. PMID: 30710203.
2.     GiardinaT,et al. Pathology. 2018 Jun;50(4):389-401. PMID: 29752127.
3.     PestingerV,et al. MolDiagnTher. 2020 Jun;24(3):339-349. Erratum in:MolDiagnTher. 2020 Aug;24(4):505. PMID: 32306292.
4.          Prieto-PotinI,et al. PeerJ. 2020 Oct 6;8:e10069. PMID: 33083132.
5.          Fisher KE,et al. JMolDiagn. 2016 Mar;18(2):299-315. PMID: 26801070.
6.     SequistLV,et al. AnnOncol. 2011 Dec;22(12):2616-2624. PMID: 22071650.
7.     Li T,et al. JClinOncol. 2013 Mar 10;31(8):1039-49. PMID: 23401433.
8.     Lindeman NI,et al. ArchPatholLab Med. 2013 Jun;137(6):828-60. Erratum in: ArchPatholLab Med. 2013 Sep;137(9):1174. PMID: 23551194.
9.     MazièresJ,et al. JClinOncol. 2013 Jun 1;31(16):1997-2003. PMID: 23610105.
10.     SonobeM,et al. 2006 Jul;8(3):351-6. PMID: 16825508.
11.     Oxnard GR,et al. JClinOncol. 2013 Mar 10;31(8):1097-104. PMID: 23401445.
12.     My Cancer Genome website:http://www.mycancergenome.org/
13.     Ensemblgenome browser:http://www.ensembl.org/index.html
14.     UCSC genome browser:http://genome.ucsc.edu/
 
LEGEND:
Chr: chromosome
Ex: exon
COSMIC: Mutation ID in the Catalogue Of Somatic Mutations in Cancer (http://cancer.sanger.ac.uk/)
dbSNP: RS number of alteration in dbSNP database (http://www.ncbi.nlm.nih.gov/SNP/)
 
 
This test was performed at Emory University Hospital, 1364 Clifton Road, Atlanta, Georgia 30322
 
The results of this test should not be used alone as the sole basis for diagnosis and/or treatment. These results may, however, prove useful when used in conjunction with other diagnostic procedures and clinical evaluations. Use of these results, in this manner, can be considered to fall within the scope of the practice of medicine. This test was developed and its performance characteristics determined by Emory Medical Laboratory. It has not been cleared or approved by the United States Food and Drug Administration.
 

CPT Codes

81445, G0452

LOINC

  • 48017-8

Performing Lab

Molecular Diagnostics
Collection

Patient Preparation

N/A

Collect

5 - 10 unstained slides, 1 H&E stained slide for percent tumor analysis

Specimen Preparation

5 - 10 unstained slides, 1 H&E stained slide for percent tumor analysis

Pediatric Collection

Same as Adult collection.

Unacceptable Conditions

Less than 10% tumor present in the sample is deemed quanity not sufficient.

Storage/Transport Temperature

Room temperature

Stability (from collection to initiation)

Room Temperature

Performed

Samples must be cut and to Molecular Diagnostics by end of business on Thursday for the following week's run. Testing starts on Tuesday; preliminary results available on the following Tuesday. Final results available in 14-21 days from sample receipt.

Remarks

N/A
Ordering

Ordering Recommendations

This test targets genes with known significance for lung adenocarcinoma and melanoma.

Performed

Samples must be cut and to Molecular Diagnostics by end of business on Thursday for the following week's run. Testing starts on Tuesday; preliminary results available on the following Tuesday. Final results available in 14-21 days from sample receipt.

Methodology

Library preparation followed by Next Generation Sequencing (NGS)

Reported

Barring unforeseen circumstances, Friday of the week following the week testing is started.

Notes

Curls may be submitted instead of slides if the percent tumor has been assessed by the submitting physician or designee and no macrodissection is necessary. This panel includes the following clinically actionable genes: ALK, AKT1, APC, BRAF, CDH1, CTNBB1, EGFR, ERBB2/HER2, FBXW7, FGFR2, FOXL2, GNAQ, GNAS, KIT, KRAS, MAP2K1, MET, MSH6, NRAS, PDGFRA, PIK3CA, PTEN, SMAD4, SRC, STK11, and TP53

Section

Molecular Diagnostics

Group Components

N/A

Medicare Regulated Tests

Yes

Reference Lab Notes

N/A
Result Interpretation

Reference Interval

Negative

Interpretive Data

NOTES:
This test simultaneously assesses the mutation status of multiple genes that have been shown to be involved in a variety of cancer types. Determining mutation status may assist in rendering diagnoses, provide prognostic information and/or help guide the choice of chemotherapeutic agents. Chemotherapeutic agents that target specific altered proteins are increasingly used in the treatment of patients with cancer. The efficacy of these drugs is highly related to the genetic makeup of individual tumors. The test detects only alterations included in the test design (see below) and a negative result does not exclude the possibility of other mutations even within the same gene. Intronic (non-coding) variants are not reported unless they are known to be clinically significant. Sequence variants that have been identified in general population and known to be benign are not included in the test report unless specifically requested.
 
TEST PERFORMED:
The test was performed after DNA preparation using the Illumina TruSight Oncology 500 preparation kit and next-generation sequencing (NGS) on the Illumina NextSeq instrument. TruSight Oncology Mutation Panel 26 (TSO26) library preparation kit uses hybrid-capture chemistry combined with bioinformatics, and utilizes inclusive of unique molecular indexes (UMIs) for high sensitivity in variant detection.  TSO26 simultaneously identifies point mutations and insertions/deletions in specific regions of 26 genes (listed below). This test routinely detects heterozygous mutations in tissue with 10% or greater tumor content or homozygous mutations in tissue with more than 5% or greater tumor content. Any sequence variants not reported in the result section were deemed non-deleterious (e.g., benign single nucleotide polymorphisms, synonymous variants) or not detected by this assay unless otherwise indicated in the interpretation above. The Emory Healthcare GenomOncology Pathology Workbench was used to annotate this case.
 
Gene  Transcript (chr#): exon covered (transcribed coverage %/coding coverage %)
AKT1 - NM_001014432.1 (chr14): exon-1 (0/NA); exon-2 (0/NA); exon-3 (38/100); exon-4-exon-14 (100/100); exon-15 (7/100)
ALK - NM_004304.5 (chr2): exon-1 (42/100); exon-2-exon-28 (100/100); exon-29 (60/100)
APC - NM_000038.6 (chr5): ): exon-1 (100/NA); exon-2-exon-15 (100/100); exon-16 (75/100)
BRAF - NM_004333.6 (chr7): ): exon-1 (38/100); exon-2-exon-17 (100/100); exon-18 (4/100)
CDH1 - NM_004360.5 (chr16): exon-1 (28/100); exon-2-exon-15 (100/100); exon-16 (9/100) 
CTNNB1 - NM_001904.4 (chr3): exon-1 (0/NA); exon-2 (24/100); exon-3-exon-14 (100/100); exon-15 (16/100)
EGFR - NM_005228.5 (chr7): exon-1 (25/100); exon-2-exon-27 (100/100); exon-28 (5/100)
ERBB2 - NM_004448.3 (chr17): exon-1-exon-26 (100/100); exon-27 (51/100)
FBXW7 - NM_033632.3 (chr4): exon-1 (0/NA); exon-2 (88/100); exon-3-exon-11 (100/100); exon-12 (14/100)
FGFR2 - NM_022970.3 (chr10): exon-1 (0/NA); exon-2 (51/100); exon-3-exon-17 (100/100); exon-18 (26/100)
FOXL2 - NM_023067.4 (chr3): exon-1 (38/100)
GNAQ - NM_002072.5 (chr9): exon-1 (19/100); exon-2 - exon-6 (100/100); exon-7 (0/0)
GNAS - NM_000516.6 (chr20): exon-1 (92/100); exon-2 - exon-12 (100/100); exon-13 (29/100)
KIT - NM_000222.2 (chr4): exon-1 (44/100); exon-2-exon-15 (100/100); exon-16 (99/99); exon-17-exon-20 (100/100); exon-21 (12/100)
KRAS - NM_004985.5 (chr12): exon-1 (0/NA); exon-2 (92/100); exon-3-exon-4 (100/100); exon-5 (8/100)
MAP2K1 - NM_002755.3 (chr15): exon-1 (14/100); exon-2-exon-4 (100/100); exon-5 (0/0); exon-6-exon-10 (100/100); exon-11 (11/100)
MET - NM_001127500.3 (chr7): exon-1 (0/NA); exon-2 (98/100); exon-3-exon-20 (100/100); exon-21 (9/100)
MSH6 - NM_000179.2 (chr2): exon-1 (63/100); exon-2-exon-9 (100/100); exon-10 (48/100)
NRAS - NM_002524.5 (chr1): exon-1 (0/NA); exon-2 (88/100); exon-3-exon-4 (100/100); exon-5 (97/100); exon-6 (0/NA); exon-7 (18/NA)
PDGFRA -      NM_006206.6 (chr4): exon-1 (0/NA); exon-2 (82/100); exon-3-exon-22 (100/100); exon-23 (9/100)
PIK3CA - NM_006218.4 (chr3): exon-1 (33/NA); exon-2 (82/100); exon-3-exon-20 (100/100); exon-21 (4/100)
PTEN - NM_000314.8 (chr10): exon-1 (8/100); exon-2-exon-8 (100/100); exon-9 (4/100)
SMAD4 - NM_005359.6 (chr18): exon-1 (0/NA); exon-2 (66/100); exon-3-exon-11 (100/100); exon-12 (3/100) 
SRC - NM_005417.4 (chr20): exon-1 (0/NA); exon-2 (0/NA); exon-3 (0/NA); exon-4 (98/100); exon-5-exon-13 (100/100); exon-14 (9/100)
STK11 - NM_000455.5 (chr19): exon-1 (20/100); exon-2-exon-8 (100/100); exon-9 (93/100); exon-10 (0/NA)
TP53 - NM_000546.5 (chr17): exon-1 (40/NA); exon-2 (74/100); exon-3-exon-10 (100/100); exon-11 (38/100)
 
BIOINFORMATICS PROCESS:
Illumina TSO500 Local Application version tso500-ruo-2.1.0.60
 
REFERENCES:
1.          Na K,et al. JNeurooncol. 2019 May;142(3):445-454. PMID: 30710203.
2.     GiardinaT,et al. Pathology. 2018 Jun;50(4):389-401. PMID: 29752127.
3.     PestingerV,et al. MolDiagnTher. 2020 Jun;24(3):339-349. Erratum in:MolDiagnTher. 2020 Aug;24(4):505. PMID: 32306292.
4.          Prieto-PotinI,et al. PeerJ. 2020 Oct 6;8:e10069. PMID: 33083132.
5.          Fisher KE,et al. JMolDiagn. 2016 Mar;18(2):299-315. PMID: 26801070.
6.     SequistLV,et al. AnnOncol. 2011 Dec;22(12):2616-2624. PMID: 22071650.
7.     Li T,et al. JClinOncol. 2013 Mar 10;31(8):1039-49. PMID: 23401433.
8.     Lindeman NI,et al. ArchPatholLab Med. 2013 Jun;137(6):828-60. Erratum in: ArchPatholLab Med. 2013 Sep;137(9):1174. PMID: 23551194.
9.     MazièresJ,et al. JClinOncol. 2013 Jun 1;31(16):1997-2003. PMID: 23610105.
10.     SonobeM,et al. 2006 Jul;8(3):351-6. PMID: 16825508.
11.     Oxnard GR,et al. JClinOncol. 2013 Mar 10;31(8):1097-104. PMID: 23401445.
12.     My Cancer Genome website:http://www.mycancergenome.org/
13.     Ensemblgenome browser:http://www.ensembl.org/index.html
14.     UCSC genome browser:http://genome.ucsc.edu/
 
LEGEND:
Chr: chromosome
Ex: exon
COSMIC: Mutation ID in the Catalogue Of Somatic Mutations in Cancer (http://cancer.sanger.ac.uk/)
dbSNP: RS number of alteration in dbSNP database (http://www.ncbi.nlm.nih.gov/SNP/)
 
 
This test was performed at Emory University Hospital, 1364 Clifton Road, Atlanta, Georgia 30322
 
The results of this test should not be used alone as the sole basis for diagnosis and/or treatment. These results may, however, prove useful when used in conjunction with other diagnostic procedures and clinical evaluations. Use of these results, in this manner, can be considered to fall within the scope of the practice of medicine. This test was developed and its performance characteristics determined by Emory Medical Laboratory. It has not been cleared or approved by the United States Food and Drug Administration.
 
Administrative

CPT Codes

81445, G0452

LOINC

  • 48017-8

Performing Lab

Molecular Diagnostics

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