XAbTracker® & SeqAgent®: Integrated LIMS and Sequence Analysis Tools for

Antibody Phage Display

February 20, 2017Mark Evans

Best Practices in Personalized and Translational Medicine Short Course

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Established in 1981

Located in Berkeley, CA

Small, publicly traded biotech company

Experts in antibody discovery, optimization, cell line and process development

Currently supporting ongoing Phase 2 clinical trials • XOMA 358: congenital hyperinsulinism & Post-bariatric surgery hyperinsulinism• XOMA 213: Various hyperprolactinemias

About Xoma

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Antibody Phage Display technologies are well established after more than 10 years of use in the Pharmaceutical industry as important drug discovery tools.

Scientific Background

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What has not kept up is adequate data analysis and data management systems.

Screening, DNA sequence analysis and candidate selection can still be very time consuming.

We found that the data analysis aspect was a major bottleneck

Limits the number of drug development projects the pipeline could handle

Problem

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Developed two integrated software applications

SeqAgent™ - integrated DNA sequence analysis package specifically designed for use with antibody V-regions (Fv)• Semi-automated pipeline• Input is zipped DNA sequence files • Converted to protein sequence• Identifies framework and CDR structural features• Produces protein sequence alignment• Highly annotated and ready for final analysis.

Solution

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Developed two integrated software applications

SeqAgent™ - integrated DNA sequence analysis package specifically designed for use with antibody V-regions (Fv)

XAbTracker™ - a clone / assay data management system.• Tracks clones throughout discovery process• Tracks and evaluates associated assay results• Integrated sequence identification via SeqAgent™• Provides flexible workflow and data management for antibody discovery

Solution

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Heterotetramers

8 Constant and 4 variable regions

16 light chain families

7 heavy chain families

Variable region• 4 conserved framework regions• 3 hyper-variable regions

Specific Challenges: Problem of data complexity

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SeqAgent™ analysis workflow

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SeqAgent™ Results Display

1) View management. Add / remove additional sequences or copy view.

2) View controls. 3) Sequence selection box 4) Unique coded sequence identifiers. 5) Heavy and Light chain bin identifiers. Closely

related chain sequences have the same bin identifier.

6) Unique light and heavy chain sequence identifiers.

7) Representative box. Select sequence to

represent a bin. 8) Example of additional tags, signals, etc that

are automatically identified. 9) Framework and CDR regions are identified

and color coded. Alignment gaps are indicated by a dash.

10) Poor DNA sequence quality glyph. 11) Grouped rows that have the same color

background indicate identical chain sequence

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Low quality sequence as well as stop codons, potential post translation modification sites are indicated on the sequences

SeqAgent™ Results Display

1) Showing Query-anchored view, the first row is the anchor for the bin and the second row is identical.

2) Additional glyphs indicating post translational modification site and an amber stop codon.

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SeqAgent™ Results Display

• Individual sequences can be inspected • Sequences of light and heavy chains are tracked as paired sets which

represent functional antibodies

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SeqAgent™ Results Display• Details about individual

chains may still be accessed

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Tracking large numbers of clones, replicates, assays, rearrays, etc. is no trivial task

100s to 1000s of individual bacterial colonies are picked into 96 well plates for screening.

In addition to sequencing, clones are assayed via ELISA, FACS or SPR methods.

In most cases, the original raw data file is parsed directly into XAbTracker™, with the exceptions coming in as tab-text after preprocessing elsewhere, and is associated with the correct clone.

XabTracker™ Data Management System

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Which libraries are used What the target is Which antigens are being screened in each assay Organizational concepts such as Projects, Studies, Study

Rounds, Screens and Assays Several unique naming conventions

• Individual heavy and light chain sequences• Antibodies and their format (IgG, Fab, scFv)• Individual clones, reformatted clones, engineered clones

XabTracker™ keeps track of…

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1.Set thresholds for all plates dynamically to data set min and max values

2.Button locks the results of this analysis in the database

3.Total hit indicator for each plate 4.Data quality (histogram/ scatter

plot). 5.Per plate thresholds can

override the master threshold. 6.Threshold line indicated in

blue, hits in red. Graph values dynamically linked to the plate view, hit colors automatically reflected in the assay plate.

7.Wells in the plate view are colored in shades of blue across 11 scaled bins to indicate data diversity range. When they are a hit, they are colored on a red scale to indicate magnitude of the hit.

XabTracker™

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Multiple antigens and/or multiple analysis criteria can be part of an assay

Two different antigens and a total of three different analyses are summarized.

Red, orange and green in the pie chart legend indicate which pie slice will show the analysis result for that assay.

Hits are indicated in yellow and blue is a non-hit

XabTracker™ Analysis Summary View

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XabTracker™ Improvements Interactive decision making using Venn

diagrams

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Integrated 3D structure prediction pipeline and display

XabTracker™ Improvements

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MacPro server Django / Apache / PostgreSQL / Python /Jquery / D3 stack Dependencies

• Phred / Phrap• Hmmer 3• Emboss• ClustalW• BLAST

Technical details

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Developed in-house• Derived from open-source resources• Less than a year by a team of three

Number of samples that can be analyzed increased >10x Analysis time: days / weeks minutes / hours Standardized analysis methods allow consistent data

interpretation Prosecution of drug targets per year has increased 3x A significant ROI on the manpower costs and minimal cost

• (< $12K) of commercial license fees needed for access to certain open source libraries.

ROI

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Laboratory software is often plagued by antiquated interfaces

We have developed a relatively lightweight, nimble data management and sequence analysis application suite that is specifically designed for antibody discovery

• As thin client systems, they are able to run in web browsers.

• Since they utilize responsive web UI components, the applications work equally well on PC, tablet and even smart phone platforms, providing the users with maximum flexibility.

We believe that these applications provide a good illustration of what the future of laboratory software will look like

Conclusions

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For inquiries contact Zander Strange • zander.strange@xoma.com

Thanks to• Yevheniy (Eugene) Chuba• Matthew Batterton• Lauren Schwimmer• The Discovery Research group at Xoma

• BioIT World and CHI for providing this opportunity

Finally…