Laboratory Concepts: Array Management

 

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Fundamental Concepts

 
              

 

Fundamental Concepts

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Laboratory Concept LabVantage Concept Example
Define Physical Properties of a Plate - Plate Dimensions and Total Well Volume Array Management allows you to test and analyze a large number of Samples together as a single group as in Plates or Gels. In LabVantage these are called Arrays.

Array Types define the physical attributes of the array you plan to use, such as a 96 well Plate. Within LabVantage, wells of the plate are referenced as Array Items.

 I plan to perform PCR Analysis using a 96-well Plate, so I create an Array Type "96 Well PCR Plate" with 8 rows and 12 columns.
Setup the Plate - Define the positions of Standards, Blanks, Unknowns, Controls etc. along with Replicate Count & Dilution

Array Layouts determine how content (Unknown Samples or Controls) is loaded into the Array. It includes:

• Zones to identify the positions of Unknown Samples or Controls.
• Arrangement Rules to define multiple repeats and dilutions applicable to content of each zone.
I then create "PCR Layout" as follows:
Yellow = Controls
Blue = Unknowns
1 2 3 4 5 6 7 8 9 10 11 12
A P1 U1 U2 U3 U4 U5 U6 U7 U8 U9 U10 N1
B P2 U11 U12 U13 U14 U15 U16 U17 U18 U19 U20 N2
C P3 U21 U22 U23 U24 U25 U26 U27 U28 U29 U30 N3
D P4 U31 U32 U33 U34 U35 U36 U37 U38 U39 U40 N4
E P5 U41 U42 U43 U44 U45 U46 U47 U48 U49 U50 N5
F P6 U51 U52 U53 U54 U55 U56 U57 U58 U59 U60 N6
G P7 U61 U62 U63 U64 U65 U66 U67 U68 U69 U70 N7
H P8 U71 U72 U73 U74 U75 U76 U77 U78 U79 U80 N8

I create two Control Zones, yellow for the Positive Control and blue for the Negative Control. The Unknown Zone is green and will hold the Unknown Samples. The Arrangement for the Unknown Zone is Content only, 1 Array Item per distinct Sample. Array Items are loaded left to right.
Indicate the type of Control or Sample used for analysis

Define the Method for Analyzing Plate Results

Array Methods define behavior of how the array is used for the laboratory technique. This includes both how the Array is to be loaded, as well as how it will be analyzed and on which instrument. It contains:

• Loading Methods todetermine what type of Content is presented during Loading.
• Analysis Methods to define the result Parameters for the instrument raw data and aggregate calculations.
I then define Method "PCR Method" with both Array Loading and Array Analysis details.

When loading the Unknown Samples into the Array I would like to see all Samples of Sample Type "DNA". The Positive Control will be Consumable lots of Consumable type "DNA Standard" and the Negative Control Consumable lots of type "NTC".

I define the result parameters and the limits as shown below:

Value Limit
Ct > 40
Fluorescence > 5
Standard Deviation for Negative and Positive Control < 2


Average for the Controls 		Positive Negative
Ct > 40

Fluorescence Inclusive
between 5 and 25

 Ct < 45

Fluorescence < 5

I need to calculate a Standard Deviation for both the Positive and Negative Controls. I include the following in the Array Analysis Method:

stdev([ArrayItem:Zone=#|#|Ct;Standard])

stdev([ArrayItem:Zone=#|#|Flourescence;Standard])

I would also like the average for both Controls:

avg([ArrayItem:Zone=#|#|Ct;Standard])

avg([ArrayItem:Zone=#|#|Flourescence;Standard])
Load Plate with Samples and Controls LabVantage provides a drag and drop visual editor that provides an ability to load an array with samples, Consumables, treatments etc. First I create a new Array, "Array 1", onto which I will apply Method "PCR Method".

I choose to "Load" the Unknown Samples first. I am presented with a list of 100 Samples of type "DNA". I select 80 Samples (the number of available Array Items in the Unknown Zone). When I "Load" the Samples they fill the Unknown Zone starting in the upper left, moving right, one after the other. After the first row is filled, loading moves to the first Array Item (in the Unknown Zone) of the next row (according to the Arrangement Rule).

Next I load the Control Zones. Since all Array Items in the Zone will receive the same Consumable I can first load the "DNA Standard" into the Positive Control, then "NTC" into the Negative Control.

The Array is loaded and ready for results.
Enter Results Results from the instrument can be either entered manually or can be uploaded directly from the instrument. I am using a "ThermoCycler". My first step is to send the details of the Array I just created to the instrument. When the results are ready, I upload the results back to the Array.
Review Results QC Review is the process of evaluating the overall Array testing process. The Array Method defined evaluation limits for both aggregate Zone parameters, and parameters in the individual Array Items. Based on criteria established in the Array Method, results are rendered in red or green depending on whether or not they meet evaluation limits.

An option to Approve or Reject all or part of the Array is included. After Results have been Reviewed and Approved, you can choose to post final analyzed results back to the Samples.

QC Review shows the following aggregate results:
Zone Parameter Type Value
Negative Control Ct Average 46.2
Negative Control Fluorescence Average 3.125
Positive Control Ct Standard
Deviation		 0.590
Positive Control Fluorescence Standard
Deviation		 1.767
Positive Control Ct Average 45.86
Positive Control Fluorescence Average 9.08

Results are displayed in the Array. Following is an example (only a section of the entire Array with results is shown):

1 2 3 4
A Ct(Standard)
47
Fluorescence
(Standard):5		 S-0415-003
Vol:10ul
Conc:5mg/ml
Ct(Standard):
45
Fluorescence
(Standard):5.6		 S-0415-004
Vol:10ul
Conc:5mg/ml
Ct(Standard):
38
Fluorescence
(Standard):5.9		 S-0415-005
Vol:10ul
Conc:5mg/ml
Ct(Standard):
44
Fluorescence
(Standard):5.9
B Ct(Standard)
46
Fluorescence
(Standard):5.7		 S-0415-0012
Vol:10ul
Conc:5mg/ml
Ct(Standard):
47
Fluorescence
(Standard):9.2		 S-0415-0013
Vol:10ul
Conc:5mg/ml
Ct(Standard):
43
Fluorescence
(Standard):9.9		 S-0415-0014
Vol:10ul
Conc:5mg/ml
Ct(Standard):
44
Fluorescence
(Standard):7.1

I filter out the Array Items that are not within the limits (red). I choose to reject those cells individually and approve the remainder of the Array.
Perform Plate Operations Array Transfer is the process of moving content from one array to another. Common array operations including replication, condensing, splitting, aliquot & derivative plate creation are also supported.

Transfer Methods are predefined rules that determine specifically where, after the transfer, Array Items are placed. It defines the mapping of the source array item to target array item. For example, if you are Condensing 4 smaller Arrays into one larger Array, how do you want the Source Array Items placed in the Target Array, in four quadrants, in columns, rows or interspersed.

 I need to transfer content from "Array 1" whose Ct results were between 36 and 40 for additional testing. I plan to transfer results from several Source Arrays so I decide to use Cherry Picking.
Cherry Picking Cherry Picking allows you to selectively decide which specific Array Items to transfer from the Source Array to the Target Array. During Cherry Picking, I select "Array 1" as the Source Array. I filter the results to find (and select) all Samples whose Ct results were rejected. With all the Array Items I want to transfer selected, I drag them to the Target. The Array Item into which you drop the Samples becomes the first Array Item (for relative positioning). The other Samples are then loaded according to the Array Layout referenced on the Target Array (or in selection order if selected individually).
Generate Instructions for Liquid Handling Robot (LHR) LabVantage provides the ability to generate instructions for LHRbased on Transferred or Cherry Picked Arrays. The LHR Report includes instructions for moving liquid from one Array Item to another. These instructions may be in the form of a spreadsheet and are sent directly to the robot. When I have finished Cherry Picking, I generate an LHR Report that includes all the details.
Store or Dispose Arrays When you are finished with an Array you can either Dispose it or place it into Storage. I choose to dispose "Array1", it is no longer needed.