omnihub system release 1.0 functional requirements · testing. detailed information will be listed...

OmniHub System

Release 1.0

Functional Requirements

Clinical Report for the OmniSeq Target Test

Document ID: OmniHub_REQ_05

01/29/2014

Version 1.0

Copyright ©2014 Computer Task Group, Inc. All rights reserved.

Uncontrolled copy when printed.

System Name: OmniHub System Document ID: OmniHub_REQ_05

Document Title: Clinical Report for the OmniSeq Target Test Author: Danielle Eberle

Version: 1.0 Revision Date: 01/29/2014

Prepared by CTG for Roswell Park Cancer Institute Corporation of 24

Copyright © 2014 CTG. ALL RIGHTS RESERVED. Confidential materials. DUPLICATION OR DISCLOSURE IS PROHIBITED WITHOUT PERMISSION.

Approvals

Based on my area(s) of expertise, I attest that the document’s content is correct and complete.

Role Name Organization Title Responsibility Signature Date

System Owner Joy Hoffmann CTG Principal Consultant Approve

System Custodian Kumar Madurai CTG Principal Consultant Approve

Computer Systems Quality Assurance

David Garratt CTG Practice Lead Approve

Business Analyst Danielle Eberle

CTG Business Analyst Write

Process/ Data Owner

Dr. Carl Morrison RPCI Clinical Chief, Pathology, Executive Director, Genomics Consortium

Approve

Process/ Data Owner

Christopher Darlak RPCI Director, Research Applications & Informatics

Approve

Process/ Data Owner

Mary Nesline RPCI Director, Genomics Clinical Support Informatics

Approve

User Dr. Grace Dy RPCI Oncologist Review Not Needed NA

User Dr. Nikhil Khushalani

RPCI Oncologist Review Not Needed NA






Revision History

Version Number

Revision Date Summary of change Revised by

0.0 07/31/2013 New Document Danielle Eberle

0.1 12/05/2013 –

12/20/2013

Complete rebuild to include revisions compliant to the new

version of the GO report

Danielle Eberle

0.2 01/09/2014 Additional fields added Danielle Eberle

0.3 01/15/2014 Updates to include new GO report. Danielle Eberle

1.0 01/29/2014 Finalization needed, signatures pending Danielle Eberle






1.0 Clinical Report

1.1 General Requirements

1.1.1 One OmniSeq Target clinical report will be generated for each OmniSeq Target order by GenomOncology.

Note: CTG is not creating the report, but receiving the report as a PDF from GenomOncology.

1.1.2 The OmniSeq Target clinical report will be created and displayed in a PDF format.

1.1.3 The OmniSeq Target clinical report will be sent to RPCI for printing and manual scanning into SRM. (At initial

implementation).

Note: This functionality will be a part of initial implementation and may change in future scope.

1.1.3 The OmniSeq Target clinical report will be secondarily stored in JPEG format to meet clinical retention

requirements.

Note: This functionality will be in a future implementation – not release 1.0

1.1.4 Clinical monitoring is not in scope for report creation.

1.2 Page Header

1.2.0 The first page header of the clinical report will contain:

1) The Personalized Medicine Pathways logo

2) OmniSeq Target ™ Informed Medicine Report for [cancer type] Cancer

3) Report Date in D/M/YYYY format

4) Page Number in Page [#] format

Note: Each field is described in greater detail in following requirement sections

1.2.1 Report Date: The date for which the clinical report was generated.

D/M/YYYY

e.g. 2/14/2014

1.2.2 Page #: The current page number of the clinical report.

Page 1

1.3 Page Footer

1.3.1 Client Specimen ID: pathology assigned alphanumeric identification of the specimen used in OmniSeq testing.

[A - ## - ####A# - #] e.g. S-13-0293A1-1

1.3.2 Report Status: the type of report, such as Final, Addendum, or Amendment

***REPORT STATUS*** e.g. ***FINAL REPORT***

1.3.3 Ordering Physician: clinician responsible for ordering or approving the order for the patient.

Ordering Physician: [First Last, title] e.g. Ordering Physician: Helen Hunt, MD

1.4 Patient Section






1.4.0 The first page Patient information subsection of the Information section will contain:

1) Patient Name, in [First Last] format

2) Date of Birth in D/M/YYYY format

3) Medical Record Number in MRN: [######] format

4) Sex in M/F format

1.4.1 Name: EMR generated patient first name and surname.

Name: [First Last] e.g. John Smith

1.4.2 Date of Birth: EMR generated patient date of birth.

DOB: D/M/YYYY e.g. 1/1/1959

1.4.2 Medical Record Number: EMR generated medical record number for patient tracking.

MRN: [######] e.g. 654321

1.4.3 Sex: patient’s recorded sex

Sex: A e.g. M

1.5 Order Information

1.5.0 The first page Order Information section will contain:

1) Order ID in [A - ## - #####] format

2) Ordering Physician

3) Order Indication

4) Ordering Client

1.5.1 Order ID: EMR assigned alphanumeric identification of the test instance

Order ID: [A - ## - #####] e.g. P-14-76541

1.5.2 Ordering Physician: clinician responsible for ordering or approving the order for the patient.

Physician: [First Last, title] e.g. Helen Hunt, MD

1.5.3 Order Indication: the diagnosis, histology, and disease stage as determined by the ordering clinician and verified by

the pathologist.

Indication: [Diagnosis, Histology, Stage] e.g. Lung Cancer, Non‐Small Cell Carcinoma, Stage III

1.5.4 Ordering Client: the facility, institute, or hospital from which the ordering clinician originates from

Client: [Client Name] e.g. Roswell Park Cancer Institute

1.6 Test Specimen

1.6.0 The first page Specimen Information subsection of the Information section will contain:

1) Sample ID in [A-##-####A#-#] format

2) Specimen Source in [Tumor Type] format.

3) Collection Date in D/M/YYYY format

4) Received Date in D/M/YYYY format

1.6.1 Sample ID: pathology assigned alphanumeric identification of the specimen used in OmniSeq testing






Sample ID: [A - ## - ####A# - #] e.g. S-13-02930A1-1

1.6.2 Specimen Source: the description of the tumor’s procurement type

Source: [Tumor Type] e.g. Primary Tumor

1.6.3 Collection Date: the date of specimen procurement from the patient

Collected: D/M/YYYY

1.6.4 Received Date: the date the tumor was received in the OmniHub laboratory

Received: D/M/YYYY

1.7 OmniSeq Target ™ SUMMARY*

1.7.0 Within The OmniSeq Target ™ SUMMARY* section of the OmniSeq Target clinical report, the following

columns will be populated with results data:

1) Target

2) Alteration Type

3) Test Method

4) Alternations Detected

5) Alterations Failed Testing

The post script note contains descriptions of the technology utilized in the OmniSeq Target test: NGS=Next

Generation Sequencing, FISH=Fluorescent In Situ Hybridization, DD= Digital Detection

*Refer to detailed reports for each test method for result and value information for each target.

1.7.1 Target: a distinct sequence of nucleotides, or gene, forming part of a chromosome the order of which determines

some characteristic.

e.g. AKT1

1.7.2 Alteration Type: the category of variation such as Mutation, Translocation, or Copy Number

e.g. Mutation

1.7.3 Test Method: contains descriptions of the technology utilized in the OmniSeq Target test: NGS=Next Generation

Sequencing, FISH=Fluorescent In Situ Hybridization, DD= Digital Detection

e.g. NGS

*Refer to detailed reports for each test method for result and value information for each target.

1.7.4 Alteration Detected: a YES / NO / PENDING answer to notify the health care provider of a variation detected.

Detailed information will be listed in future sections for variations with a YES or a PENDING. YES and

PENDING answers will be in red color.

1.7.5 Alterations Failed Testing: a YES / NO / PENDING answer to notify the health care provider of a target that failed

testing. Detailed information will be listed in future sections for variations with a YES or a PENDING. YES and

PENDING answers will be in red color.

1.7.6 Summary Report Comments: a free text field for capturing additional knowledge

1.7.7 The OmniSeq Target clinical report will contain a General Disclaimer located at the end of each section of the

document:

Summary report electronically signed by Carl Morrison, MD |CLIA Laboratory License: 33D0171366|

M/D/YYYY 0:00AM






Roswell Park Cancer Institute, Elm & Carlton Streets, Buffalo NY 14263| 1 (716) 845-2300

1.7.8

The OmniSeq Target clinical report will contain a General Disclaimer located at the end of the summary section of

the document:

Decisions about patient care and treatment must be based on the independent medical judgment of the treating physician, taking into

consideration all applicable information concerning the patient’s condition, such as patient and family history, physical examinations, information from other diagnostic tests, and patient preferences, in accordance with the standard of care in a given community. A treating physician’s decisions

should not be based on a test such as this, or on the information contained in this report.

1.8 Mutations Section

1.8.0 Starting on page 2, a detailed section for each variation type will be published. The Mutations section will contain

the following subsections:

1) Clinically Actionable

2) Not Clinically Actionable

3) Mutation Test Comments

4) Mutation Electronic Signature

1.8.1 Clinically Actionable

1) Target

2) Result

3) AA Change

4) Variant

5) Position

6) Alteration Type

7) Frequency

8) Disease

9) Therapy Knowledge Source

1.8.1.1 Target: a distinct sequence of nucleotides, or gene, forming part of a chromosome the order of which determines


e.g. BRAF

1.8.1.2 Result: the analysis result of the target. Failed Testing, Pathogenic, Wild Type, Pending Confirmation, and

Unknown

e.g. Pathogenic

1.8.1.3 AA Change: amino acid change; sequence of nucleotides which determines protein creation coupled to some

characteristic

e.g. V600E

1.8.1.4 Variant: the specific substitution of amino acid that creates the mutation of the target.

e.g. 1799T>A

1.8.1.5 Position: the exact placement of the target variant mutation, written in chromosomal and amino acid numeric.

[CH#:######-######] e.g. 7:140453136-140453136

1.8.1.6 Alteration Type: the mutation classification. Complex –insertion inframe / Substitution-Missense,

e.g. Substitution-Missense






1.8.1.7

Frequency: The ratio of variant cells to somatic cells.

e.g. Freq 0.28

1.8.1.8 Disease: The current cancer diagnosis at the time the order for the test is placed. From the ordering list that contains

mycancergenome disease data.

e.g. Lung Cancer

1.8.1.9 Therapy Knowledge Source: Report contains link to source of knowledge. Currently in scope the therapy source is

mycancergenome for phase I.

e.g. MyCancerGenome.org

1.8.2 Clinically Actionable

1) Target

2) Result

3) AA Change

4) Variant

5) Position

6) Alteration Type

7) Frequency

8) Prevalence

9) dbSNP ID



e.g. BRAF

1.8.2.2 Result: the analysis result of the target; Failed Testing, Pathogenic, Wild Type, and Unknown

e.g. Pathogenic

1.8.2.3 AA Change: amino acid change, sequence of nucleotides which determines some characteristic

e.g. V600E


e.g. 1799T>A

1.8.2.5 Position: the exact placement of the target variant mutation, written in chromosomal and amino acid numeric.

[CH#:######-######] e.g. 7:140453136-140453136

1.8.2.6 Alteration Type: the mutation classification. Complex –insertion inframe / Substitution-Missense,

e.g. Substitution-Missense

1.8.2.7

Frequency: The ratio of variant cells to somatic cells.

e.g. Freq 0.28

1.8.2.8 Prevalence: The total number of cases of a given disease in a specified population at a designated time.

e.g. 0.37






1.8.2.9 dbSNP ID: contains the identification number corresponding to the Single Nucleotide Polymorphism Database

(dbSNP): a free public archive for genetic variation within and across different species developed and hosted by the

National Center for Biotechnology Information (NCBI) in collaboration with the National Human Genome

Research Institute (NHGRI). The field contains a link to the knowledge source at NIH.

e.g. rs121913265

http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=121913265

1.8.3 Mutation Test Comments: additional text box containing comments regarding the testing process. Each comment

includes a date stamp and name of author.

e.g. Confirmation for PIK3CA is pending completion [J. Conroy, Lab Manager 2/6/14]

1.8.3.1 Mutation Test Review Box:

e.g. Pathogenic=xxxxxxxxxx, Wild Type=xxxxxxxxxxx, Failed Testing=xxxxxxxxxxxx,

Pending Confirmation = xxxxxxxxxxxxxxxxxxx, Unknown =xxxxxxxxxxxxx

1.8.4 Mutation Electronic Signature:

Mutation report electronically signed by Carl Morrison, MD |CLIA Laboratory License: 33D0171366| 2/8/2014 8:39AM


1.9 Translocations Section

1.9.0 A detailed section for each variation type will be published. The Translocations section will contain the following

subsections:


2) Non-Actionable

3) Translocation Test Comments

4) Translocation Electronic Signature

1.9.1 The translocation section will contain the following columns if results have been identified (i.e. failed or observed):

1) Target

2) Analytical Interpretation

3) Clinical Interpretation

4) Probes

5) Image Analysis Method

6) Results interpreted

7) ISCN

8) Tumor Cells

9) Observers




e.g. ALK

1.9.1.2 Analytical Interpretation: either negative or positive rearrangement noted from the results.

e.g. Rearrangement Positive

1.9.1.3 Clinical Interpretation: text including description of the genetic implications of the results.

e.g. The results showed breakapart signals in at least 50% of the neoplastic cells. These results are consistent with

http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=121913265






ALK gene translocation, but do not identify the translocation partner.

1.9.1.4 Probes: identification method used to detect rearrangements involving genes, specific to disease

e.g. Probes: Vysis LSI ALK, 2p23, spectrumorange/spectrumgreen (break apart)

1.9.1.5 Image Analysis Method

e.g. Manual

1.9.1.6 Results Interpreted: yes or no answer concerning if the results have been reviewed by the proper personnel

e.g. Yes

1.9.1.7 ISCN: International System for Human Cytogenetic Nomenclature (2013) reference volume containing the

recommendations of the International Standing Committee on Human Cytogenetic Nomenclature

e.g. Other nuc ish(ALKx4)(5'ALK sep 3'ALKx1){200}

1.9.1.8 Tumor Cells: the number of tumor cells counted in the biospecimen

e.g. 200

1.9.1.9 Observers: number of pathology observers

e.g. 2

1.9.1.10 Therapy Knowledge Source: Report contains link to source of knowledge. Currently the therapy source is



1.9.2 Translocation Test Comments: additional text box containing comments regarding the translocation testing process.

Each comment includes a date stamp and name of author.

e.g. RET Failed Testing – specimen was inadequate for testing [J. Conroy, Lab Manager 2/6/14]

1.9.3 Translocation Electronic Signature:

Translocation report electronically signed by Petr Starostik, MD |CLIA Laboratory License: 33D0171366| 2/8/2014 8:39AM


1.10 Copy Number Variants section

1.10.0 Copy Number Variants: a detailed section for each variation type will be published.

A detailed section for each variation type will be published. The Translocations section will contain the following

subsections:


2) Not Clinically Actionable

3) Copy Number Variants Test Comments

4) Copy Number Variants Electronic Signature

1.10.1 The copy number variants section will contain the following columns if results have been identified (i.e. failed or

observed):

1) Target

2) Variant

3) Result

4) Log2Ratio






5) Copy Number

6) Disease




e.g. FGFR1


e.g. Amplification

1.10.1.3 Result: the analysis result of the target; Failed Testing, Pathogenic, Wild Type, and Unknown

e.g. Gain or Loss

1.10.1.4 Log2Ratio: The process of analyzing data produced by a test for DNA copy number variation in patient's sample.

e.g. 2.21

1.10.1.5 Copy Number: the numeral of the copy number associated with the mutation of the variant

e.g. 8

1.10.1.6 Disease: The current cancer diagnosis at the time the order for the test is placed. From the ordering list that contains

mycancergenome disease data.

e.g. Lung Cancer

1.10.1.7 Therapy Knowledge Source: Report contains link to source of knowledge. Currently in scope the therapy source is



1.10.2 Copy Number Variant Test Comments: additional text box containing comments regarding the testing process.

Each comment includes a date stamp and name of author.

e.g. Failed Testing – specimen was inadequate for testing [J. Conroy, Lab Manager 2/6/14]

1.10.3 Copy Number Variant Electronic Signature:

Copy number variant report signed by Petr Starostik, MD |CLIA Laboratory License: 33D0171366| 2/8/2014 8:39AM


1.11 Surgical Pathology Review Summary

1.11.0 1) Submitted Pathology Report

2) Reviewed Pathology Tissue Site

3) Reviewed Pathology Diagnosis

4) Source

5) Necrosis

6) Tumor Nuclei

7) Cellularity

8) Directed Tissue Dissection Required

9) Summary of Received Samples for Testing

10) Surgical Pathology Review Summary Comments

11) Surgical Pathology Electronic Signature






1.11.1 Submitted Pathology Report: alphanumeric identification associated with the pathology report

e.g. S-13-02930A1

1.11.2 Reviewed Pathology Tissue Site: the description of the origin of the sample’s tumor site

e.g. Lung left upper lobe of, NOS

1.11.3 Reviewed Pathology Diagnosis: A statement that identifies the disease type classification. Includes American Joint

Committee on Cancer (AJCC) staging, or progression identification, of the disease.

Non-Small Cell Carcinoma, Stage IIIA

1.11.4 Source: the description of the specimen type

e.g. Primary Tumor

1.11.5 Necrosis: the percentage of dead or destroyed cells relative to other cells

e.g. 10%

1.11.6 Tumor Nuclei: the percentage of cells with a mutated or cancerous nuclei relative to healthy cells

e.g. 60%

1.11.7 Cellularity: the state of a tissue or other mass as regards the number of constituent cells

e.g. 2%

1.11.8 Directed Tissue Dissection Required

e.g. yes / no

1.11.9 Summary of Received Samples for Testing:

1) Received

2) Client Sample ID

3) Type

4) Quantity

5) Unit

6) Source

7) Purpose

8) Comments

1.11.9.1 Received date: The date for which the specimen was received by the performing lab.

D/M/YYYY

1.11.9.2 Client Sample ID: alphanumeric identification associated with the pathology report

e.g. S-13-02930A1-1

1.11.9.3 Type: The sample categorization

e.g. Stained FFPE Slide

1.11.9.4 Quantity: Number of received samples for testing

e.g. 1






1.11.9.5 Unit: How the sample was stored

e.g. Slide

1.11.9.6 Source: How the sample was preserved and transported such as formalin-fixed, paraffin-embedded

e.g. FFPE

1.11.9.7 Purpose: the reason the sample was delivered to the performing lab

e.g. QC

1.11.10 Surgical Pathology Review Summary Comments: additional text box containing comments regarding the pathology

process. Each comment includes a date stamp and name of author.

e.g. Failed Testing – specimen was inadequate for testing [J. Conroy, Lab Manager 2/6/14]

1.11.11

Surgical Pathology Electronic Signature:

Surgical Pathology Review Summary electronically signed by Kazunori Kanehira, MD |CLIA Laboratory License: 33D0171366| 2/8/2014 8:39AM


1.12 Disclaimers

1.12.1 About OmniSeq Target ™

OmniSeq Target ™ is a comprehensive molecular test to detect tumor DNA alterations in the genes AKT1, ALK,

BRAF, CTNNB1, DDR2, EGFR, ERBB2 (HER2), FGFR1, GNA11, GNAQ, JAK2, KIT, KRAS, MAP2K

(MEK1), MET, NRAS, PDGFRA, PIK3CA, PTEN, RET, ROS1, SMAD4 and SMO. The results can be used to

determine the likelihood of response or resistance to targeted agents and other cancer therapies. OmniSeq Target ™

analyzes primary or metastatic tumors using up to three test modes, by Next Generation Sequencing (NGS)

technologies for Mutations (20 Gene NGS1), Fluorescent In Situ Hybridization (FISH) for Translocations (3 Gene

CTX1) and Digital Detection (DD) technologies for Copy Number Variants (3 Gene CNV1). OmniSeq Target ™

was developed and its performance characteristics determined by the Department of Pathology, Roswell Park

Cancer Institute. It has not been cleared or approved by the U.S. Food and Drug Administration (FDA). The FDA

has determined that such clearance or approval is not necessary. The test is used for clinical purposes. It should not

be regarded as investigational or for research. The laboratory is certified under the Clinical Laboratory

Improvement Amended of 1988 (CLIA-88) as qualified to perform high complexity clinical laboratory testing.

There is no guarantee that OmniSeq Target ™ will be reimbursed by any healthcare provider, insurer or third party

payer and patients are responsible for the cost of the test.

A gene-level result summary is provided in the Summary section of the OmniSeq Target ™ report. A separate

report for each completed test mode in OmniSeq Target ™ is completed by a board certified pathologist and

provides results details at the variant level. Details about each technology and the limitations of each test mode

methodology are provided in the “About” sections of the report for each completed test mode. The expected

turnaround time for OmniSeq Target ™ is 5-10 days once a sample is received in the testing laboratory. Any gene

with some or all results pending beyond 10 days is reported in the results Summary as Pending Confirmation. Any

gene for which one or more variants fail testing in one or more of the three test modes is reported in the Summary

Section as an alteration failed testing.

The OmniSeq Target ™ test reports actionable alterations in the tumor type tested and for other tumor types as

described by the My Cancer Genome expert knowledgebase website (www.MyCancerGenome.org), hosted by

Vanderbilt University, Nashville, Tennessee. Each variant in the OmniSeq Target test is associated with a cancer-

variant specific web page on the My Cancer Genome website. Each My Cancer Genome cancer-variant page

describes the gene and its pathway, a summary of the gene’s variants for the specific cancer and variant level

information including implications for targeted therapeutics and relevant active clinical trials. The association of

each OmniSeq Target ™ test variant with the My Cancer Genome website is managed by Roswell Park Cancer

Institute, Buffalo, NY. While the information in My Cancer Genome has been reviewed by oncology experts,

decisions about patient care and treatment must be based on the independent medical judgment of the treating






physician, taking into consideration all applicable information concerning the patient’s condition, such as patient

and family history, physical examinations, information from other diagnostic tests, and patient preferences, in

accordance with the standard of care in a given community. There is no guarantee that detection of any variant by

this test will result in therapeutic efficacy or lack of efficacy. The absence of detected variants by this test does not

confer a lack of therapeutic efficacy for any drug or therapy known to target any gene included in this test. It is

possible that therapeutic implications associated with variants detected by this test are not suitable for a specific

patient.

1.12.2 NGS Mutation Testing

About 20 Gene NGS1: 20 Gene NGS1 uses next generation sequencing (NGS) to analyze all exons for the genes

AKT1, ALK, BRAF, CTNNB1, DDR2, EGFR, ERBB2 (HER2), GNA11, GNAQ, JAK2, KIT, KRAS, MAP2K

(MEK1), NRAS, PDGFRA, PIK3CA, PTEN, RET, SMAD4 and SMO. Specifically, 20 Gene NGS1 detects single

nucleotide variants and insertions/deletions in tumor DNA using two parallel NGS technologies - the Ion Torrent

Personal Genome Machine (PGM) and the Illumina MiSeq, using a methodology that optimizes sensitivity and

minimizes false positive calls. 20 Gene NGS1 either reflexively confirms variants that are detected independently

by both the PGM and MiSeq technologies in parallel, or variants are first detected by a single NGS platform (PGM

or MiSeq), and sequentially confirmed by Sanger sequencing. This method assures 20 Gene NGS1 meets the

standards of New York State Department of Health and that results are of the highest quality.

For single nucleotide variants, 20 Gene NGS1 has an assay sensitivity and PPV of 99.8% and 97.5%, respectively

in frozen specimens and 98.3% and 96.7%, respectively, for FFPE specimens. For insertions and deletions 20 Gene

NGS1 has an assay sensitivity and PPV of 100% and 91%, respectively, for both frozen and FFPE specimens. 20

Gene NGS1 detects single nucleotide variants, insertions and deletions with 95% sensitivity at a minimum VAF of

2.87% and 2.90%, respectively, for frozen specimens, and 3.56% and 3.60% respectively, for FFPE specimens. The

SMO A68V variant, as well as most insertions and deletions in 20 Gene NGS1, are only detectable by the MiSeq

platform.

20 Gene NGS1 variant results are presented as either Clinically Actionable or Not Clinically Actionable. Clinically

actionable variants for the tumor type tested are presented first, followed by clinically actionable variants for any

other tumor type(s). The tumor type tested is represented as the diagnosis reported by the treating physician at the

time the test is ordered and corresponds to the pathology report and quality control of the specimen provided for

testing. Results for clinically actionable variants are presented alphabetically by gene. Results for variants that are

not clinically actionable are presented in order of known population prevalence.

In the 20 Gene NGS1 Mutation report for variants that are Clinically Actionable, the Result for each variant is

classified as Pathogenic, Wild Type, Failed Testing, or Pending Confirmation. Pathogenic indicates the variant is

an actionable mutation. Wild Type indicates there are significant therapeutic implications associated with a specific

gene when no actionable mutations are detected. Failed Testing indicates there are no results available for a specific

variant because it did not pass technical quality control measures in testing. Pending Confirmation is reported for

variants that require additional time to complete testing beyond 10 business days. Results of confirmation testing

are provided as report addendums at a later date. AA Change (Amino Acid Change) reports variant impact at the

protein level. Variant represents the nucleotide(s) at the DNA level using Human Genome Variation Society

(HGVS) standards for coding DNA reference sequence. Position refers to the variant location at the DNA level per

hg19 build and provides the start and stop positions for the variant. Alteration Type provides a functional

description of the mutation at the DNA level using standards developed from the Catalog of Somatic Mutations

(COSMIC) (http://cancer.sanger.ac.uk/cancergenome/projects/cosmic). Freq represents the variant allelic frequency

(VAF) for the specific variant. Disease is used to group actionable variants as being associated with the tumor type

tested or other tumor types based on the My Cancer Genome web knowledgebase. In electronic copies of the

report, Therapy Knowledge Source provides the link to the variant-specific webpage on the My Cancer Genome

site. Otherwise, it displays the general website address only for lookup purposes (www.MyCancerGenome.org).

Therapy Knowledge Source is periodically updated by the authors at Vanderbilt University to reflect the most

current knowledge about variant-specific therapeutic associations. This information, including the list of clinical

trials, may be incomplete in some areas.

For variants that are Not Clinically Actionable, Prevalence represents the reported frequency of that variant

according to dbSNP (www.ncbi.nlm.nih.gov/SNP/). In electronic copies of the report, dbSNP ID provides the link

to the variant-specific webpage on the dbSNP database website. Variants that are not clinically actionable and are

not in dbSNP are listed first because they are more likely to be somatic variants of unknown significance. When

two or more variants represented in dbSNP are detected, they appear on the report in order of ascending variant






allelic frequency (VAF).

1.12.3 ALK FISH Translocation Testing

The OmniSeq Target Translocation Test for ALK was submitted to the New York State Department of Health for

approval under the name "FISH ALK". The LSI ALK (Anaplastic Lymphoma Kinase) Dual Color, Break Apart

Rearrangement Probe contains two differently labeled probes on opposite sides of the breakpoint of the ALK gene.

An approximately 250 kb probe for the telomeric side of the ALK breakpoint is labeled with SpectrumOrangeTM.

The centromeric probe is approximately 300 kb and labeled with SpectrumGreenTM. This region is involved in the

vast majority of breakpoints for known 2p23 rearrange-ments that occur in t(2;5) and its variants. The t(2;5) has

been shown to fuse the nucleophosmin (NPM) gene located on omosome 5q35 with the gene on omosome 2p23.2.

This NPM/ALK gene fusion gives rise to a chimeric protein that is overexpressed. When hybridized with the LSI

ALK Dual Color, Break Apart Rearrangement Probe, the 2p23 ALK region in its native state will be seen as two

immediately adjacent or fused orange/green (yellow) signals (2F). However, if a t(2;5) or other omosome

rearrangement at the 2p23 ALK breakpoint region has occurred, one orange and one green signal will be seen,

while the native ALK region will remain as an orange/green fusion signal (1O1G1F). The translocation

(2;5)(p23;q35) is identified in approximately 50% of cases of anaplastic large cell lymphoma. The absence of the

translocation (2;5)(p23;q35) does not exclude the diagnosis of anaplastic large cell lymphoma. Using a panel of

normal tissues and well-defined lymphomas not expected to harbor an ALK translocation, split signals were

identified in less than 5% of cells in this control study.

1.12.4 RET FISH Translocation Testing

The OmniSeq Target Translocation test for RET was submitted to the New York State Department of Health for

approval under the test name "RET". The LSI RET () Dual Color, Break Apart Rearrangement Probe contains two

differently labeled probes on opposite sides of the breakpoint of the RET gene...xxxxxxxxxxxxxxxxxxxxxx

1.12.5 ROS1 FISH Translocation Testing

The OmniSeq Target Translocation test for ROS1 was submitted to the New York State Department of Health for

approval under the test name "ROS1". The LSI ROS1 Dual Color, Break Apart Rearrangement Probe contains two

differently labeled probes on opposite sides of the breakpoint of the ROS1 gene. An approximately 300 kb probe

for the telomeric side of the ROS1 breakpoint is labeled with SpectrumOrangeTM. The centromeric probe is

approximately 550 kb and labeled with SpectrumGreenTM. This region is involved in the vast majority of

breakpoints for known 6q22 rearrangements. Several studies have shown that lung adenocarcinomas with ROS1

rearrangement respond to ALK inhibitors, including crizotinib.

1.12.6 Digital Detection (DD) Copy Number Variant Testing

The OmniSeq Target™ Digital Detection test for copy number variants was submitted for approval to the New

York State Department of Health under the test name "CNV-DD"...






Appendix A – Mockup of Clinical Report

omnihub system release 1.0 functional requirements · testing. detailed information will be listed...

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