Sorting Functionality Design Specification: Document Control

Pull List Specifications
Document control
Superseded documents
Document File Version Issue Date with- Replaced by Reason
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Version history
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affected to:
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Sorting Functionality
Design Specification
Section Change Reason for change
Version: 1.1
Outstanding issues and omissions

Section Issue or Ommission
Distribution control
Author:
Shelley Tworoger
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 15 Date: 24/12/2008

Distribution List
Company Entity Recipient Name Action
Shelley Tworoger
Mark Magid
Rakesh Kukatla
Helena Judge-Ellis
Jeanne Sparrow
Eric Rimm
Sue Hankinson

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.............................................................8
1.7 Contacts10
1.7.1 List of comments of final sign off..........................................................10
2. Functional Overview................................................................................11
2.1 Business Objectives
(See separate, expanded flow chart for sorting)............................................11
2.2 .a Functional Diagram..............................................................................11
2.2.b Functional Diagram in more detail......................................................12
“Original Sort List”
instructions to go from pulled order to aliquot order.......................................12
“Sending Sort List”........................................................................................12
2.3 Design Mock-up.......................................................................................13
2.4 Requirements..........................................................................................13
2.4.1 Primary.................................................................................................13
2.5 Non-Functional Requiremets...................................................................13
2.6 Outstanding Issues..................................................................................14

Document Title : [11632880.doc]
1.Introduction
1.1Purpose of document
The Sorting Functionality will continue the process of pulling samples from the freezer
and ultimately sending to a laboratory. This functionality will build on the information
generated in the Pull List Functionality, specifically the location of pulled vials into
Freezer Pull Boxes. The purpose of this document is to outline the specifications for
the Sorting functionality in HealthTrack to create Sort Lists for the NHS, NHS2, PHS,
and HPFS cohorts.
1.2Background
Sort Lists are instructions for placing participant vials from a Freezer Pull Box to an
Original Sort Box or Final Sending Box. This is a critical step before aliquoting large
original vials into smaller subvial aliquots and for sorting subvials into the Final
Sending Boxes. It is important to sort these vials such that cases and their matched
controls can be aliquoted at the same time, when possible, and are next to each other
in the Final Sending Box. The purpose of this project will be to create a Sort List
application as part of HealthTrack that will allow the research assistant to sort from
Freezer Pull Boxes to Original Sort Boxes and Final Sending Boxes and create labels
for the new boxes.
1.3Scope of the specification

The only concern of this application and specification are the sort lists to be used by
the lab or analysts. A completed pull list is a requirement to any work within this
application.
1.4Input
Sort List functionality input data comprises of:
• A Pull List ID number in which all samples have been pulled and the pull list is
updated to reflect any changes that may have occurred during pulling (i.e. the
pull list is finalized);
• User specified parameters such as Original Sort / Aliquot / Sending Box type
and size, Permanent Storage Box type and size, Aliquot preferences such as
Vial type, Volume and Number of Aliquots.
1.5Output
Primary output – Aliquot Sort List
A list of original ID’s (separately for original vial sizes), their location in a Freezer Pull

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Box of a specific Pull List, and their new expected location in the Original Sort Box.
Information should be stored in the database to notate the status of the location and a
history/audit table are highly suggested. The format is described below:
o A primary header denoting Original vial type, the type of report (Aliquot Sort
List), and the Pull List ID
o A secondary header that notes user name, date, pull list id, number of sort
boxes per vial type, sample type, collection, endpoint, lab code(s), lab name(s),
follow-up cycles.
o A table containing the following fields: Participant ID, Current location of vial in
Freezer Pull box, new location in Original Sort Box,
o The sorting of the samples into the Original Sort Box should be as follows:
 Case-control order (sort on the variable MATCHID from sending list),
when possible i.e. when the case and control are both the same vial
type.
 Case-control samples should be randomly ordered within a set
 If the matched case (or matched control) for any ID is of a different vial
type, then sort the single ID into the Aliquot Sort Box.
o The formatting of the Aliquot Sort List should be as follows:

 First column is Participant ID in the intended order (caco order) the in
Aliquot Sort Box
 Second column in the current location in the Freezer Pull Box
 Third column is expected location in the Aliquot Sort Box
o A footer that notes date, pull list ID, vial type

o See Appendix A for an example.
Generate labels for the Original Sort boxes and should have the format below:
ORIGINAL SORT BOX
Pull list ID: < ID >
Box: < # > of <total #>
Cohort: < name >
Collection: < name >
Endpoint/project: < name >
Volume: < volume >
Labcode (s): < number >
Lab Name(s) <name>
Aliquotting Takes Place-See separate Specs
2. Primary output – Aliquot Ship Sort List/ Aliquot Store Sort List
A list of original ID’s (separately for original vial sizes), their location in a Original Sort
Box of a specific Pull List, and their derivative ID's expected location in the Aliquot
Ship Box or Aliquot Store Box. Information should be stored on the database to
notate the status of the location and a history/audit table are highly suggested. The

format is described below:

o A primary header denoting Original vial type, the type of report (Aliquot Ship
Sort List or Aliquot Store Sort List), and the Pull List ID
o A secondary header that notes user name, date, pull list id, number of Aliquot
Ship Boxes or Aliquot Store Boxes per vial type, sample type, collection,
endpoint, lab code(s), lab name(s), follow-up cycles.
Original Sort box, new location of derivative vials in Aliquot Ship Sort Box or
Aliquot Store Box
o The sorting of the samples into the Aliquot Ship Box and Aliquot Store Box are
the same as the original vial sort box with sorting as further identified in the
Aliquot Specifications.
o The formatting of the Aliquot Ship Sort List and Aliquot Store list should be as
follows:
 First column is Participant ID in the intended order (caco order) the in
Aliquot Ship Box or Aliquot Store box.
 Second column in the current location in the Original Sort Box
 Third column is expected location in the Aliquot Ship Box or Aliquot
Store Box (see Aliquot Specs)

Generate labels for the Ship-Aliquot Sort Box and Stor-Aliquot Sort Box should
have the format below:
ALIQUOT SHIP BOX
Cohort: < name >
Lab Name(s) <name>
ALIQUOT STORE BOX

Cohort: < name >
SEE SEPARATE SPECS FOR MORE DETAIL ON ALIQUOTING
Primary output – Final Sending Sort List

A list of Subvial ID’s for a specific labcode, their location in a Aliquot Sort Box OR a
Freezer Pull Box, and their new expected location in the Final Sending Box.

Information should be stored in the database to notate the status of the location and a
history/audit table are highly suggested. The format is described below:
o A primary header denoting current subvial location (Aliquot Sort Box or Freezer
Pull Box), the type of report (Sending Sort List), and the Pull List ID
o A secondary header that notes user name, date, pull list id, number of Final
Sending Boxes, sample type, collection, endpoint, lab code, follow-up cycle,
and volume. NOTE ONLY ONE LABCODE PER FINAL SENDING SORT LIST.
Aliquot Box or Freezer Pull Box, and new expected location in Final Sending
Box
o The sorting of the samples INTO THE FINAL SENDING BOX should be as
follows:
 Case-control order (sort on the variable MATCHID from sending list)
 Case-control samples should be randomly ordered within a set (Note:
this can be the same order as in the Original Sort Box and Aliquot Sort
Box)
 Case-control sets should be randomly ordered

Generate labels for the Final Sending boxes and should have the format below:
FINAL SENDING BOX
Cohort: < name >
Volume: < volume >

1.6Glossary of Terms and Definitions

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
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

2.Functional Overview
2.1Business Objectives
(See separate, expanded flow chart for sorting)
2.2.a Functional Diagram

Enter Assay Request Enter Assay Request Enter Assay Request
*if replace/delete participants

**if need to change parameters
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)

***if a vial is Generate Pull Box Labels
missing in
freezer, pull (Blood Lab RA Pulls Tubes***)
alternate vial if
one exists, if Generate Sub-Sending List by Assay Request
not remove from to note which ID’s will actually be set.
list + any matched
controls if a case Sorting Lists Information Defined (e.g. Box size, aliquot volumes)
Sort Lists Generated
-Aliquot sort list, separated Final sort list, separate by assay

by original vial volume request , notes where subvials are
-Generates labels for newly placed into sending boxes. Make
aliquoted tubes QC labels
Actual aliquots recorded Add QCS w/ labels that have fake ID’s
in healthtrack Put subvials into
sending box
New aliquots into Computer generates a box list/ASCII file

sending box Double check, give sub-sending list to programmer

2.2.b Functional Diagram in more detail

Sorting
“Freezer Pull Box” “Freezer Pull Box”
Originals Subvials
“Original Sort List”

instructions to go from pulled
order to aliquot order
“Original Sort Box”

Originals sorted into aliquot order,
(CaCo order) within vial type,
before aliquotting
“Sending Sort List”

Instructions to go from aliquot order
“Aliquot “Aliquot
Store Box” Send Box” (originals) or from pulled order (subs) to
Subvials, Subvials,
aliquotted aliquotted sending order
from originals from originals
for permanent for lab codes. “Final Sending Box”
storage. Requires
Requires Aliquot Sheet All subs to send out sorted into
Aliquot Sheet
QC vials added to
Storing Final Sending Boxes
“Permanent Storage Box” Double check:

Subs not sent out, put in new o vials against boxlist
locations, recorded in Htrack o ID list (ascii file) against boxlist

2.3Design Mock-up
2.4Requirements
2.4.1Primary
Below are the fields that should be included on the Sort List Request user-interface:
Pull List ID - single selection pull down list based on previous inputs
The following criteria apply:

a) corresponding to specified Cohort, End Point and Specimen Type;
b) NOT ASSOCIATED WITH THE OTHER SORT LISTS;
c) Only pull lists in the Finalized stage;
The following fields will be shown: Cohort, End point, Specimen Type,
and other criteria selected in the pull list.
Original Sort Box type- single selection simple table (with columns Box Type Name, Box ID
Prefix, Box Type Description, Width, Height) is used to specify type of
the temporary boxes where vials will be placed for aliquoting. Only box
types with the attribute “Can be a Sort box” = “Yes” are retrieved from
DB and displayed in the table. NOTE: This box type applies to the
following subsequent boxes: Aliquot sort box, aliquot store box, and final
sending box.
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.
Permanent Storage Box type - single selection simple table (with columns Box Type Name,
Box ID Prefix, Box Type Description, Width, Height) is used to specify
type of the temporary boxes where vials will be placed for final sending
to the laboratory. Only box types with the attribute “Can be a Permanent
Storage box” = “Yes” are retrieved from DB and displayed in the table.
Comments - up to 1000 characters.
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
None

Appendix A
Sort List Helena Ellis August 7, 2006
Pull List ID 567843 13 Aliquot Boxes Plasma, NHS1.1
Breast Cancer 90-98 Assay Requests 1422, 1423, 1424 Rifai, Hollis, Shu
Vial Type 1.8ml
Paticipant ID # Location in Freezer Pull Box Location in Aliquot Box
1234567 2,82 1,1

2345789 1,2
6,55
3456789 3,24 1,3
4567891 1,76 1,4
5678912 12,55 1,5
6789123 13,62 1,6


Sorting Functionality Design Specification: Document Control

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Pull List Specifications

Changes since last version

Outstanding issues and omissions

Brigham and Women’s Hospital, Channing Laboratory

Author: Shelly Tworoger Page 1 of 15 Date: 24/12/2008

Author: Shelly Tworoger Page 2 of 15 Date: 24/12/2008

Author: Shelly Tworoger Page 3 of 15 Date: 24/12/2008

1.3Scope of the specification

Author: Shelly Tworoger Page 4 of 15 Date: 24/12/2008

o The formatting of the Aliquot Sort List should be as follows:

o A footer that notes date, pull list ID, vial type

Aliquotting Takes Place-See separate Specs

Author: Shelly Tworoger Page 5 of 15 Date: 24/12/2008

format is described below:

o A footer that notes date, pull list ID, vial type

ALIQUOT STORE BOX

SEE SEPARATE SPECS FOR MORE DETAIL ON ALIQUOTING

Primary output – Final Sending Sort List

Author: Shelly Tworoger Page 6 of 15 Date: 24/12/2008

o A footer that notes date, pull list ID, vial type

Author: Shelly Tworoger Page 7 of 15 Date: 24/12/2008

1.6Glossary of Terms and Definitions

Author: Shelly Tworoger Page 8 of 15 Date: 24/12/2008

1.7.1List of comments of final sign off

Author: Shelly Tworoger Page 10 of 15 Date: 24/12/2008

2.2.a Functional Diagram

*if replace/delete participants

Create Pull List Request

See Intermediate Results (Put “hold” on potential vials)

Generate Freezer Pull List(s)

Sort Lists Generated

-Aliquot sort list, separated Final sort list, separate by assay

New aliquots into Computer generates a box list/ASCII file

Author: Shelly Tworoger Page 11 of 15 Date: 24/12/2008

2.2.b Functional Diagram in more detail

“Original Sort List”

“Original Sort Box”

“Sending Sort List”

“Permanent Storage Box” Double check:

Author: Shelly Tworoger Page 12 of 15 Date: 24/12/2008

The following criteria apply:

Comments - up to 1000 characters.

Author: Shelly Tworoger Page 13 of 15 Date: 24/12/2008

Author: Shelly Tworoger Page 14 of 15 Date: 24/12/2008

Sort List Helena Ellis August 7, 2006

Pull List ID 567843 13 Aliquot Boxes Plasma, NHS1.1

Vial Type 1.8ml

Paticipant ID # Location in Freezer Pull Box Location in Aliquot Box

1234567 2,82 1,1

4567891 1,76 1,4

5678912 12,55 1,5

6789123 13,62 1,6

Author: Shelly Tworoger Page 15 of 15 Date: 24/12/2008

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