Pull List Specifications

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Aliquot

Design Specification
Section Change Reason for change

Version: 1.1

Outstanding issues and omissions

Section Issue or Ommission

Distribution control
Owner and approver for
distribution: Shelley Tworoger
Signature: Date:

Brigham and Women’s Hospital, Channing Laboratory

Copyright © 2005. All rights reserved.

Author: Shelly Tworoger Page 1 of 12 Date: 24/12/2008

Pull List Specifications

Distribution List
Company Entity Recipient Name Action

Shelley Tworoger

Mark Magid
Rakesh Kukatla
Helena Judge-Ellis
Jeanne Sparrow
Eric Rimm
Sue Hankinson

Author: Shelly Tworoger Page 2 of 12 Date: 24/12/2008

Pull List Specifications

Contents

1. Introduction 4
1.1 Purpose of document................................................................................4
1.2 Background................................................................................................4
1.3 Scope of the specification.........................................................................4
1.4 Input 4
1.5 Output 4
1.6 Glossary of Terms and Definitions.............................................................6
1.7 Contacts8
1.7.1 List of comments of final sign off............................................................8

2. Functional Overview.................................................................................9
2.1 Business Objectives
(See separate, expanded flow chart for sorting)..............................................9
2.2 Functional Diagram...................................................................................9
2.3 Design Mock-up.......................................................................................10
2.4 Requirements..........................................................................................10
2.4.1 Primary.................................................................................................10
2.5 Non-Functional Requiremets...................................................................11
2.6 Outstanding Issues..................................................................................11

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1.Introduction

1.1Purpose of document
The Aliquot Functionality will continue the process of sorting samples pulled from the
freezer and ultimately sending to a laboratory. This functionality will build on the
information generated in the Pull List Functionality and Sort list functionality,
specifically the location of original vials into Original Sort Boxes. The purpose of this
document is to outline the specifications for the Aliquot functionality in HealthTrack to
create labels and box maps for the NHS, NHS2, PHS, and HPFS cohorts.

1.2Background
Aliquoting original vials into smaller subvials is an integral part of the blood laboratory
operation. To reduce the number of times a sample is thawed (and refrozen), when
an original vial is pulled, it is often aliquoted completely into subvials. The original vial
is not put back in the freezer. Occasionally (e.g. for buffy coat or cheek cells), only
one or two aliquots are made and then the original vial is put back in the freezer and
becomes a remainder vial. The aliquoting process requires the sorting of original
vials into case-control order. RAs will then label potential new subvials, aliquot, and
place subvials that are for a specific lab code into aliquot boxes and subvials to be
stored in the repository into permanent storage boxes. The purpose of this project will
be to create a user interface for the research assistant to enter the number of subvials
to be created, make labels for the new subvials, and to enter locations of new
subvials into the database.

1.3Scope of the specification

The only concern of this application and specification are the aliquot labels and lists to
be used by the lab or analysts. A completed pull and sort list is a requirement to any
work within this application.

1.4Input
• The Aliquot List functionality input data will be included on the Sorting
Functionality form.

1.5Output
Primary output – Aliquotting Labels
Generate labels for the Aliquot sort and store boxes and should have the format
below:

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ALIQUOT SORT (or STORE) BOX

Pull list ID: < ID >
Box: < # > of <total #>
Cohort: < name >
Collection: < name >
Endpoint/project: < name >
Labcode (s): < number >
Lab Name(s) <name>

Generate labels for subvials to be aliquoted and should have the format below:

Participant ID: <ppt ID>

Unique vial ID: <vial ID>
Volume: < volume >

<will include a 2-D barcode

containing these three pieces of
information>
The order of these labels will be: 1. Aliquots for the labcodes in the related pull list,
sorted in priority order and 2. Other aliquots going to permanent storage in volume
order.

Generate labels for boxes to go into permanent storage:

PERMANENT STORAGE BOX

Cohort: < name >
Collection: < name >
Unique box id: <ID>
Subvials
Sample type: <sample type>
<2-D bar code containing unique
box id>

Primary output – Aliquot worksheet

This is a list of IDs, in aliquot order (see Sorting Functionality Specifications), that
are separated by original vial size. See Appendix A for more detail.

Box maps for all of the boxes generated will be created.

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1.6Glossary of Terms and Definitions

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Term Definition
Assay Any type of measurement done on a biological sample
A oracle view that combines fields from a normalized structure of
Translation Table many fields to create one long but shallow table of permutations that
can be used in the UI for user’s ease
Vial A tube filled with biological specimen to be used in an assay request
or as part of a pull list.
General term for the functionality that generates the all the vial lists
Pull List including freezer locations, used to pull biospecimens from freezers
for a set of labcodes.
STAGES OF PULL LIST
Entering the initial data for a pull list, choosing labcodes, setting
Initialization parameters. Includes making decisions about appropriate parameter
settings and changing those parameters to get the best list. Vials are
temporarily reserved until the parameters are changed or approved.
Approved and finalized the pull list, all final parameter settings
selected. Vials are reserved in the database. Pull list has been
Active (Activate) generated and blood lab personnel are actively pulling samples out
of the freezer. Includes updating the freezer file when an incorrect
tube is found, getting new locations of alternate vials, and noting
what new subvials have been created.
Completed and After all vials have been pulled for a particular pull list, updates are
Updated made to the freezer file, including marking of original vials (and
subvials) as removed. Also includes final update to the sub-sending
list that notes which vials were sent for which assay requests.
TYPES OF LISTS IN PULL LIST FUNCTIONALITY
Original vial list List of original vials, separated by vial type (i.e. vial size), with
locations in the freezer and other information (see appendix) to be
used for pulling vials for a Pull List. Generated by the pull list
functionality.
Subvial list List of subvials, separated by assay request, with locations in the
freezer and other information (see appendix) to be used for pulling
vials for a Pull List. Generated by the pull list functionality.
Index number A sequential set of numbers, beginning at 1, assigned to each vial in
a pull list overall all original and sub-vial lists. In other words, no
number is repeated and this acts as a unique identifier within pull
list.
Unique Vial ID ID number assigned by oracle for every vial handled in a pull list or
other project
Participant ID The ID number assigned to a participant when he or she entered the
study
Pull list ID ID number assigned by oracle for each Pull List generated for a set
of assay requests.
Sub-sending list A list of all potential IDs/vials in an assay request. Notes what vial
was sent for that individual, whether a vial was sent for that
individual, and if not sent then why.
Original Sort List A set of instructions, with list of original vials (separated by vial
type/size), their locations in the Freezer Pull Box and their new
expected locations in the Original Sort Box to prepare for aliquoting
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1.7Contacts
Name Job Title/ Position/ Signoff Telephone E-mail
Role
Shelley Project Lead 5-2087 nhsst@channing.ha
Tworoger rvard.edu
Mark Magid Project 5-0074 mgmagi@hotmail.c
Development om
Rakesh Project 5-2575 rkukatla@hsph.harv
Kukalta Development ard.edu
Helena Lab Manager 617-732-5781 nhhje@channing.ha
Judge Ellis rvard.edu
End User
Jeanne Data Manager 5-4220 nhjms@channing.h
Sparrow arvard.edu

1.7.1List of comments of final sign off

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2.Functional Overview
2.1Business Objectives
(See separate, expanded flow chart for sorting)
2.2Functional Diagram
Enter Assay Request
*if replace/delete participants
**if need to change parameters
***if a vial is
missing in
freezer, pull
alternate vial if
one exists, if Generate Sub-Sending List by Assay Request
not remove from
list + any matched
controls if a case
-Aliquot sort list, separated
by original vial volume
-Generates labels for newly
aliquoted tubes
Actual aliquots recorded
in healthtrack
New aliquots into
sending box
Author: Shelly Tworoger
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Enter Assay Request Enter Assay Request
Conduct tally to find cases/controls
that may need to be removed,
update sending lists.
Create Pull List Request
* **
See Intermediate Results (Put “hold” on potential vials)
Finalize Pull List
Generate Freezer Pull List(s)
Generate Pull Box Labels
(Blood Lab RA Pulls Tubes***)
to note which ID’s will actually be set.
Sorting Lists Information Defined (e.g. Box size, aliquot volumes)
Sort Lists Generated
Final sort list, separate by assay
request , notes where subvials are
placed into sending boxes. Make
QC labels
Add QCS w/ labels that have fake ID’s
Put subvials into
sending box
Computer generates a box list/ASCII file
Double check, give sub-sending list to programmer
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2.3Design Mock-up

2.4Requirements

2.4.1Primary
The user will access the aliquot functionality from within the sort list functionality as these two
are inextricably linked. Below is the field that is included in the Sort functionality that is
particularly relevant to the Aliquot user-interface:

Aliquot Preferences - multiple selection simple table (with columns Vial Type, Volume,
Number) is used to specify the number of aliquots (of a specific volume)
that need to be made for each vial type.
**Htrack will automatically enter aliquots that are specifically for the lab codes in the related
pull list. The order of these aliquots will be in the priority order of the lab codes noted in the pull
list. The RA will enter extra possible vials at various volumes to account for variability in the
original vial volumes.

OTHER SPECIFICATIONS:
1. Placement of aliquoted subvials for specific lab codes into the aliquot send boxes
The location of subvials slated for a particularly lab code will be noted by Htrack on the
Aliquot Worksheet. They will be placed in the box consecutively (in order of lab code priority)
with no spaces between IDs (note: vials for multiple lab codes will be in one box). These vials
will be scanned as they are made to make an accurate box list of the aliquot send box (if a
certain vial cannot be made this will be recognized in Htrack). This information, along with the
subvials pulled from the freezer will be integrated to allow both vials types to be sorted directly
into the final sending boxes. (See sorting specifications for more detail on this last aspect).

3. Placement of aliquoted subvials for permanent storage

The location for remaining subvials cannot be automatically assigned as each ID may
have a different number of subvials, depending on the volume of the original vial. Vials will be
placed in temporary aliquot store boxes. Then the vials will be scanned as they are placed
from the aliquot store boxes into the permanent storage box. The RA will scan the box label
(which contains the unique box ID) and then will scan each vial as it is placed into the box in
order. The vial bar code contains all the information needed to store it in the database,
participant ID, unique vial ID, and volume. When the box is filled (or all subvials are placed),
the RA will enter the data into the database. When the boxes are put into their permanent
freezer locations using existing functionalities

4. Placement of remainder original vials back into permanent storage

Remainder vials (originals that have had at least one freeze-thaw cycle) are to be
placed back in their original locations. While the vial is thawed, a new label, containing a
barcode, will be placed on the label so ease its placement back into the freezer. Using the
original pull list of original vials the RA will scan the vials individually and place them back into
the freezer. The database will be updated to reflect that the vial is returned, add an additional
freeze-thaw cycle and update the expected volume. Vials that are not scanned will be
considered as empty and permanently removed.

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2.5Non-Functional Requiremets
Research Assistants and Lab Technicians are not typically technically advanced. The
user interface of this and any part of Htrack needs to accommodate for their skill set
and ensure usability by making the product as easy to use for non-technical people
as possible.

2.6Outstanding Issues

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