Pancreatic Adenocarcinoma Cancer Genomic Findings

Illustrates Domains

GF

Illustrates Variables

SPDEVID
GFREFID
GFTSTDTL
GFRESCAT
GFINHERT
GFSYM
 GFSYMTYP
GFSPCCND
 GFMETHOD
GFASYDTC


Content

This example shows the representation of genetic findings from a multigene panel test in a pancreatic cancer study. The sponsor ran the test on tumor tissue from the primary and secondary tumors, when available. Details on the specimen handling and characteristics are provided in the Biospecimen (BE/BS) domains previously shown. GFREFID is the specimen reference number assigned in the BS/BE domain. The multigene panel test the sponsor used provided a detailed report. In this report, results were classified into categories (e.g., clinically actionable, pathogenic, pharmacogenetic variant, variant of unknown significance). These result classifications were represented using the GFRESCAT variable. This report also included the total number of mutations present in a tumor specimen (tumor mutation burden (TMB) or mutation load).

GFDTC is the date that the specimen was collected. However, as it was of interest to the sponsor, the NSV GFASYDTC was used to represent the date of the actual testing on the sample.

gf.xpt
Rows 1-7:

Show the various findings from the multigene panel test (identified by the sponsor-defined SPDEVID) performed. GFTESTCD and GFTEST are used to represent the type of variation investigated. GFSPCCND was used to represent whether results were obtained from a paraffin-embedded sample or from frozen tissue. The use of --SPCCND is currently under discussion (see Section 1.3, Known Issues).

Row 8:Shows TMB that was obtained using DNA with "TARGETED GENOME SEQUENCING".
Row 9:Shows TMB that was obtained from circulating tumor DNA (ctDNA) with "WHOLE EXOME SEQUENCING" (WES).

gf.xpt

RowSTUDYIDDOMAINUSUBJIDSPDEVIDGFSEQGFREFIDGFTESTCDGFTESTGFTSTDTLGFCATGFORRESGFORRESUGFSTRESCGFSTRESNGFSTRESUGFRESCATGFINHERTGFSYMGFSYMTYPGFNAMGFSPECGFSPCCNDGFMETHODVISITNUMGFDTC

GFASYDTC
1PACA017GF1700ACME GENE PANEL XXX-600G1300067SHRTVARShort variationPREDICTED CODING SEQUENCE CHANGEPRECISION MEDICINE TESTING225delC

225delC



CLINICALLY ACTIONABLE

SOMATIC VARIATION

CDKN2APROTEIN CODINGXXXDNAPARAFFIN EMBEDDEDTARGETED GENOME SEQUENCING12008-05-05

2009-05-06
2PACA017GF1700ACME GENE PANEL XXX-600G2300067SHRTVARShort variation

PREDICTED AMINO ACID CHANGE

PRECISION MEDICINE TESTING

A76fs

A76fs



CLINICALLY ACTIONABLESOMATIC VARIATIONCDKN2APROTEIN CODINGXXXDNAPARAFFIN EMBEDDEDTARGETED GENOME SEQUENCING12008-05-05

2009-05-06
3PACA017GF1700ACME GENE PANEL XXX-600G3300067

CPNUMVAR

Copy Number Variation

NUMBER OF COPIES

PRECISION MEDICINE TESTINGCOPY NUMBER LOSS

COPY NUMBER LOSS



CLINICALLY ACTIONABLESOMATIC VARIATIONBRAC2



DNAPARAFFIN EMBEDDEDTARGETED GENOME SEQUENCING12008-05-05

2009-05-06
4PACA017GF1700ACME GENE PANEL XXX-600G4400081SHRTVARShort variationPREDICTED CODING SEQUENCE CHANGEPRECISION MEDICINE TESTING1832C>A

1832C>A



PATHOGENICGERMLINE VARIATIONBRAC2PROTEIN CODING

DNA

FROZEN

TARGETED GENOME SEQUENCING12009-04-30

2009-05-06
5PACA017GF1700ACME GENE PANEL XXX-600G5400081SHRTVARShort variationPREDICTED CODING SEQUENCE CHANGEPRECISION MEDICINE TESTING35G>T

35G>T



CLINICALLY ACTIONABLESOMATIC VARIATIONKRASPROTEIN CODING

DNAFROZENTARGETED GENOME SEQUENCING12009-04-30

2009-05-06
6PACA017GF1700ACME GENE PANEL XXX-600G6400081SHRTVARShort variationPREDICTED CODING SEQUENCE CHANGEPRECISION MEDICINE TESTING238G>C

238G>C



PHARMACOGENETIC VARIANTGERMLINE VARIATIONTPMTPROTEIN CODING

DNAFROZENTARGETED GENOME SEQUENCING12009-04-30

2009-05-06
7PACA017GF1700ACME GENE PANEL XXX-600G7400081SHRTVARShort variationPREDICTED CODING SEQUENCE CHANGEPRECISION MEDICINE TESTINGc.1441G>T

c.1441G>T



VARIANT OF UNKNOWN SIGNIFICANCESOMATIC VARIATIONARHGAP5PROTEIN CODING

DNAFROZENTARGETED GENOME SEQUENCING

1

2009-04-30

2009-05-06
8PACA017GF1700ACME GENE PANEL ZZZ-130G8300067-1TMB

Tumor Mutation Burden

VARIANT SEQUENCE BURDEN INTERPRETATION

PRECISION MEDICINE TESTINGINTERMEDIATE



INTERMEDIATE





SOMATIC VARIATION





DNA

TARGETED GENOME SEQUENCING12008-05-05

2009-05-06
9PACA017GF1700ACME GENE PANEL ZZZ-130G9400082TMBTumor Mutation Burden

NUMBER OF SEQUENCE VARIANTS

PRECISION MEDICINE TESTING14

/MBP



14

/MBP



SOMATIC VARIATION





ctDNA



WHOLE EXOME SEQUENCING12008-05-05

2009-05-06

GF NSV Metadata