Attachment_3_DNA_Sequencing-SOW_Final_3-25-16.pdf

PDF 116 KB Posted May 5, 2016

Attached to: DNA Sequencing Services Federal contract opportunity
Solicitation number: NIEHS2016-0217
Issued by: Department of Health and Human Services National Institutes of Health

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Other files attached to DNA Sequencing Services, newest first.
File	Type	Posted
Attach_4-Add_Bus_Prop_Inst_5-6-2016.pdf	PDF	May 6, 2016
DNA_Sequencing_Services_RFP_NIEHS2016_0217.pdf	PDF	May 6, 2016
Attachment_2_Intent_Form.pdf	PDF	May 5, 2016
Attachment_1_PackandDelivOfProposal.pdf	PDF	May 5, 2016
DNA_Sequencing_Services_RFP_NIEHS2016_0217.pdf	PDF	May 5, 2016
Attachment_5_NIH-RC-2_Invoice_Instr.pdf	PDF	May 5, 2016
Attach4-Add_Bus_Prop_Inst.pdf	PDF	May 5, 2016

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Attachment 1

DNA SEQUENCING SERVICES

Statement	of	Work
for	the	National	Institutes	of

Environmental Health Sciences (NIEHS)

March 21, 2016

A. Introduction

The

National

Institute

Environmental

Health

Sciences

(NIEHS)

(http://www.niehs.nih.gov/index.cfm),

located

Research

Triangle

Park

(RTP),

North

Carolina,

one

research

institutes

and

centers

that

comprise

the

National

Institutes

Health

(NIH)

(http://www.nih.gov/).

The

mission

the

NIEHS

reduce

the

burden

human

illness

and

disability

understanding

how

the

environment

influences

the

development

and

progression

human

disease.

support

this

mission,

NIEHS

seeks

establish

reliable,

rapid

and

cost‐

effective

Sanger

Method

capillary‐based

DNA

sequencing

services

contract

which

supports

investigators

within

the

intramural

research

program

NIEHS.

This

sequencing

information

will

provide

vital

information

ongoing

investigations

regarding

environmental

disease

mechanisms

and

the

genetic

component

involved

causes,

outcomes,

and

progression

environmental

diseases.

This

contract

will

provide

high

quality

DNA

sequencing

individual

samples

and

accompanying

bioinformatics

support.

The

majority

the

biological

samples

will

plasmid

DNA

and

Polymerase

Chain

Reaction

(PCR)

generated

samples

from

variety

species

that

include,

but

are

not

limited

to,

human,

rodent

and

recombinant

DNA

isolated

from

various

tissue

sources

and

cell

lines.

The

contractor

shall

provide

sample

storage

and

preservation

which

are

critical

for

subsequent

nucleic

acid

analysis.

Information

needed

assist

the

contractor

their

ability

perform

the

service

correctly

will

provided

prior

sequencing;

data

analysis

will

performed

NIEHS.

B. Requirements/Specifications

Independently

and

not

agent

the

Federal

Government,

the

contractor

shall

supply

services,

qualified

personnel,

materials,

equipment

and

facilities

not

otherwise

provided

the

contractor

the

Government

under

terms

this

contract,

required

perform

work

set

forth

below:

1. The	contractor	shall	perform	high‐throughput	Sanger	DNA	resequencing
using	robotic	automation	and	sample	barcode	tracking,	sufficient	to

Attachment 1

support

volume

approximately

67,500

sequencing

samples

per

contract

period

with

estimated

range

4,000

–

9,000

per

month

and

average

7,500

per

month.

2. The contractor shall provide sequence data from user‐provided 96 well

plates

PCR

strip

tubes

containing

PCR

amplifiable

material,

which

may

genomic

DNA

plasmid

DNA.

The

requirement

for

PCR

amplification

prior

cycle

sequencing

will

specified,

the

time

sample

submission,

the

sample

submitter

for

each

sample

within

given

plate

tube.

The

contractor

shall

verify

(by

gel

electrophoresis)

success

PCRs

required

produce

the

DNA

template

for

successful

sequencing.

Note:

Samples

requiring

PCR

for

the

production

the

DNA

template

for

sequencing

will

provided

additional

time

for

this

process.

The

contractor

will

not

required

isolate

genomic

DNA

from

cells

tissues.

Successful

PCR

amplifications

require

production

single

DNA

band

the

appropriate

size.

3. Contractor shall normalize DNA template(s) for PCR amplification and sequencing when requested by the submitter.

4. Samples which fail to produce data due to capillary failure or other contractor technical problems are repeated immediately.

Note

‐Successful

sequencing

runs

cover

the

desired

region

length

for

PCR

products,

least

500

bases

for

plasmid

DNA

while

achieving

quality

score

for

each

base

20.

5. The contractor shall employ staff trained in bioinformatics to perform successful primer production for new sequencing projects.

6. Contractor will be required to develop assays necessary to determine the

DNA

sequence

requested

the

COR

Investigator.

This

includes,

but

not

limited

to,

primer

design,

PCR

optimization,

and

sequence

reaction

optimization.

DNA

reference

sequence(s)

accession

number(s)

will

provided.

The

government

retains

all

rights

use

developed

assays

and

must

provided

all

technical

information,

including

but

not

limited

to,

formulations

reagents

used

assay,

instrumentation

type

used

and

all

settings

and

calibrations

instrument

regarding

each

assay

within

hours

written

request

from

the

COR

Principal

Investigator.

7. The contractor shall provide a reliable method of sample transport both to

and	from	NIEHS	campus	and	contractor’s	laboratory/facility.	This	may	be
achieved	by:	in‐house	courier,	local	contracted	courier,	or	through	FedEx	or

UPS.

Attachment 1

8. The	contractor	shall	provide	all	necessary	sample	collection	material	for
the	shipment	of	samples,	including	but	not	limited	to:	sample	collection
plate	or	vial,	refrigerated	sample	storage	method	of	samples	prior	to
sequencing	analysis,	appropriate	pre‐paid	shipping	containers,	and	a
sample	record	tracking	system/method.

9. When submitting samples, the investigator shall provide plate key or tube

label	information	containing	sample	names	with	sample	identifiers	at	the
time	of	submission.	Multiple	sequencing	runs	may	be	requested	per
template	as	specified	by	user.

10. Data shall be returned to the investigator via the Internet or by email as

attachments

within

two

(2)

working

days

receipt

plasmid

DNA

samples

and

within

five

(5)

working

days

receipt

genomic

DNA.

This

will

require

generation

the

DNA

template

PCR,

then

DNA

sequencing

that

product.

Data

shall

generated

using

appropriate

software

compatible

both

and

Apple

formats

for

data

analysis

specified

the

Contracting

Officer’s

Representative

(COR).

Except

explicitly

authorized

NIEHS,

the

contractor

shall

maintain

the

confidentiality

all

sequencing

data

generated

this

contract.

The

Contractor

shall

not

publish

use

the

data

and

results

for

any

purpose

other

than

those

expressly

authorized

the

COR.

NOTE:	Turnaround	time	for	data	is	calculated	according	to	receipt	of
samples	at	contractor’s	facility.	The	contractor	shall	notify	NIEHS	of	receipt
of	materials	on	the	same	day	as	receipt.

11. The contractor shall promptly identify to the COR any concerns or barriers

to	performance	within	24	hours	of	identification	of	problem.	The
contractor	is	responsible	for	production	and	implementation	of	solutions
within	24	hours	of	COR	contact.

12. The contractor shall provide any requested information and respond to the

COR’s comments and suggestions within 24 hours of contact.

13. The contractor shall provide Weekly Status Reports listing the following information:

a) number	of	samples	received,	including	date	received;
b) number	of	samples	successfully	sequenced,	including	date	data	was

sent	to	NIEHS;
c) number	of	samples	unsuccessfully	sequenced,	including	the	cause	of

failure and the date that notification was sent to the NIEHS investigator;

d) number	of	samples	requiring	PCR	amplification;
e) number		of	samples	requiring	DNA	normalization;

Attachment 1

f) status of Quality Control data, including the week’s success and error rate.

14. The contractor shall provide monthly written reports summarizing

sequencing	activities	to	include	number	of	samples	sequenced,	number	of
samples	requiring	PCR	amplification,	number	of	samples	requiring	DNA
normalization,	number	of	assays	developed.

15. All reports and other electronic deliverables must be Section 508 compliant.

16. Contractor shall maintain confidentiality of all data and secure back‐up of

all	essential	data,	including	but	not	limited	to,	all	DNA	sequencing	data
generated,	sample	tracking	and	storage	information,	and	Quality	Control

information.

17. The contractor shall have no access, and shall not attempt access, to any

type	of	personal	identifiers	or	other	form	of	identifying	information	with
the	human	samples	provided.

18. The contractor shall return or destroy, as instructed by the COR, all DNA

from	investigators	no	sooner	than	180	days	after	completing	sequencing	or
as	agreed	upon	and	approved	by	the	COR.	Remaining	unused	primers	will
be	returned	to	the	COR	for	long	term	storage.

NOTE:	This	includes	primers	produced	and	synthesized	by	the	contractor
for	use	in	the	performance	of	this	contract.

File details come from the government source that posted it. Updated Nov 14, 2017.