W81K0216T0130_0002_Next_Gen_Testing_Madigan_Army_Medical_Center.pdf

W40M PACIFIC RGNL CNTRG OFC

US MEDCOM HCAA JBLM HCC

POC: JOSE DOMINGO

673 WOODLAND SQUARE LOOP SE, SUITE 101

LACEY WA 98503-1066

0010846606

AMENDMENT OF SOLICITATION/MODIFICATION OF CONTRACT

Except as provided herein, all terms and conditions of the document referenced in Item 9A or 10A, as heretofore changed, remains unchanged and in full force and effect.

15A. NAME AND TITLE OF SIGNER (Type or print)

30-105-04EXCEPTION TO SF 30

APPROVED BY OIRM 11-84

STANDARD FORM 30 (Rev. 10-83) Prescribed by GSA

FAR (48 CFR) 53.243

A. The purpose of this amendment is to complete the follow ing actions:

1. Provide Questions and JBLM-HCC Responses (Q&A). NOTE: All questions received to date are included.

2. Provide Attachment - CAP Laboratory Standards for Next-Generation Sequencing Clinical Tests

3. See Summary of Changes for details.

1. CONTRACT ID CODE PAGE OF PAGES

J 1 2

16A. NAME AND TITLE OF CONTRACTING OFFICER (Type or print)

16C. DATE SIGNED

BY 24-Aug-2016

16B. UNITED STATES OF AMERICA15C. DATE SIGNED15B. CONTRACTOR/OFFEROR

(Signature of Contracting Officer)(Signature of person authorized to sign)

8. NAME AND ADDRESS OF CONTRACTOR (No., Street, County, State and Zip Code) X W81K02-16-T-0130

X 9B. DATED (SEE ITEM 11)

09-Aug-2016

10B. DATED (SEE ITEM 13)

9A. AMENDMENT OF SOLICITATION NO.

11. THIS ITEM ONLY APPLIES TO AMENDMENTS OF SOLICITATIONS

X The above numbered solicitation is amended as set forth in Item 14. The hour and date specified for receipt of Offer is extended, X is not extended.

Offer must acknowledge receipt of this amendment prior to the hour and date specified in the solicitation or as amended by one of the following methods:

(a) By completing Items 8 and 15, and returning copies of the amendment; (b) By acknowledging receipt of this amendment on each copy of the offer submitted;

or (c) By separate letter or telegram which includes a reference to the solicitation and amendment numbers. FAILURE OF YOUR ACKNOWLEDGMENT TO BE RECEIVED AT THE PLACE DESIGNATED FOR THE RECEIPT OF OFFERS PRIOR TO THE HOUR AND DATE SPECIFIED MAY RESULT IN

REJECTION OF YOUR OFFER. If by virtue of this amendment you desire to change an offer already submitted, such change may be made by telegram or letter, provided each telegram or letter makes reference to the solicitation and this amendment, and is received prior to the opening hour and date specified.

12. ACCOUNTING AND APPROPRIATION DATA (If required)

13. THIS ITEM APPLIES ONLY TO MODIFICATIONS OF CONTRACTS/ORDERS.

IT MODIFIES THE CONTRACT/ORDER NO. AS DESCRIBED IN ITEM 14.

A. THIS CHANGE ORDER IS ISSUED PURSUANT TO: (Specify authority) THE CHANGES SET FORTH IN ITEM 14 ARE MADE IN THE

CONTRACT ORDER NO. IN ITEM 10A.

B. THE ABOVE NUMBERED CONTRACT/ORDER IS MODIFIED TO REFLECT THE ADMINISTRATIVE CHANGES (such as changes in paying office, appropriation date, etc.) SET FORTH IN ITEM 14, PURSUANT TO THE AUTHORITY OF FAR 43.103(B).

C. THIS SUPPLEMENTAL AGREEMENT IS ENTERED INTO PURSUANT TO AUTHORITY OF:

D. OTHER (Specify type of modification and authority)

E. IMPORTANT: Contractor is not, is required to sign this document and return copies to the issuing office.

14. DESCRIPTION OF AMENDMENT/MODIFICATION (Organized by UCF section headings, including solicitation/contract subject matter where feasible.)

10A. MOD. OF CONTRACT/ORDER NO.

2. AMENDMENT/MODIFICATION NO. 5. PROJECT NO.(If applicable)

6. ISSUED BY

3. EFFECTIVE DATE

24-Aug-2016

CODE

W40M PACIFIC RGNL CNTRG OFC

USA MEDCOM HCAA

160 KRUKOWSKI RD BLDG 160

HONOLULU HI 96819-1552

W81K02 7. ADMINISTERED BY (If other than item 6)

4. REQUISITION/PURCHASE REQ. NO.

CODE W81K02

FACILITY CODECODE

EMAIL:TEL:

W81K02-16-T-0130

SECTION SF 30 BLOCK 14 CONTINUATION PAGE

SUMMARY OF CHANGES

SECTION SF 1449 - CONTINUATION SHEET

The following have been added by full text:

AMENDMENT 0002 Q&A

QUESTIONS and JBLM-HCC RESPONSES

RFP – W91YU0-16-T-0130

24 Aug 16 – Amendment 0002

Question 1. For each of the panels described, what are the minimum QC metrics (based upon using a next generation sequencing platform)? Please specify, passing criteria for quality, minimum depth of coverage, percent region of interest coverage, etc.

JBLM-HCC Response- QC metrics are not well-defined at this time. I am attaching the current standards (2015) from the College of American Pathologists, our accreditation organization. The expectation is that performance and interpretation are within the standard defined by CAP.

Question 2. Please define the regions of interest. Therefore, exonic +/- 10 bp (or greater) intron, deep intronic variants, promoter and UTR regions, hotspot/known variants only?

JBLM-HCC Response- Exonic +/- 10bp intronic sequence would suffice.

Question 3. What is the deliverable? BAM files, VCF files, all variants detected, all variants annotated/screened, variants of unclear significance included, only clinically (or likely) relevant variants reported.

JBLM-HCC Response- All variants detected with interpretation of clinical relevance of variants based on published literature. If variants of uncertain significance (VUS) are detected they should be annotated as such.

Question 4. Is copy number variation (CNV) detection required?

JBLM-HCC Response- Not required, but encouraged.

Question 5. Is a confirmatory method required (arrays for CNV or Sanger for sequencing)?

JBLM-HCC Response-Confirmatory testing is not required unless it is intrinsic to the validation of the NGS assay performed.

NOTE: To clarify the solicitation is not for NGS, which is a technique, but rather panel-based testing for disease assayed by NGS technology. That explains why we are looking primarily for clinically relevant interpretation rather than raw data that we would interpret ourselves.

(End of Summary of Changes)