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Agilent Launches SureCall Software for Clinical Research Customers of its Target Enrichment Panels


This title of this article has been updated to clarify that clinical researchers are the target customers for SureCall.

Agilent Technologies has launched a free bioinformatics tool called SureCall that is intended to provide analysis capabilities for clinical customers of its target-enrichment portfolio of products.

Anniek De Witte, Agilent's product manager for comparative genomic hybridization and next-generation sequencing software, told BioInform that SureCall, which performs variant calling and classification, was designed to make it easier for clinical researchers to use NGS-based target enrichment.

It complements two other components in Agilent's portfolio: its custom HaloPlex target-enrichment panels, which are used to sequence small panels of genes for studies focused on inherited disorders, cancer, or infectious disease; and SureDesign, a free web-based portal that lets customers design their own targeted enrichment panels, she explained.

SureCall, according to De Witte, was developed to make the data analysis step of the target-enrichment process easier for clinical customers that are just now starting to use NGS-based panels. These clients, she said, usually want automated tools that are simple to run without requiring specialized knowledge, parameters, or infrastructure.

"There are good tools out there to do alignment and variant calling that … are very overwhelming with a lot of knobs to turn," which makes it difficult for clinical researchers who lack bioinformatics expertise to "know what to do and which settings to use," she said.

SureCall's "default workflow," on the other hand, is easy to run, she said. Users input the raw data from Illumina or Ion Torrent sequencers, describe the sample, and then run the analysis, which takes less than an hour on standard desktops and laptops, she said. More experienced users have the option to customize the workflows.

Agilent's SureCall is comprised of a combination of open source and proprietary algorithms, she explained. It uses the Burrows Wheeler aligner and the Torrent Mapping Alignment Program, TMAP, to align Illumina and Ion Torrent sequence reads, respectively; runs an adaptor removal step that is designed specifically for Agilent panels; and then uses SamTools to call variants, she said.

It also calculates SIFT and PolyPhen scores for each identified mutation and links to PubMed, the Catalogue of Somatic Mutations in Cancer, the National Center for Biotechnology Information, and locus-specific databases to pull in additional information about the genes and mutations from publicly available literature, she said.

Finally, SureCall uses a proprietary algorithm to categorize or rank mutations. Users can also review supporting evidence such as raw data and confidence measures as well as information from resources such as the Online Mendelian Inheritance in Man database and the database of genomic structural variation.

With SureCall, users can also select and later change the categories that are used to classify the mutations found in their samples, De Witte said. This mutation categorization step is performed automatically, which differentiates SureCall from similar software packages where users are required to categorize mutations manually, she said.

Other differentiators, according to De Witte, include different levels of user control and sample tracking. Multiple users can also log in and use the same system, she said.

Since SureCall was launched at the Advances in Genome Biology and Technology conference last month, De Witte said that so far Agilent has received "positive" feedback from customers who have downloaded it. However, she said that it's still too early to tell how useful the tool is to customers.

The current version of SureCall only works with Agilent's custom HaloPlex gene panels but the next release — which will come out in the second half of this year —will be able to analyze data from Agilent's HaloPlex exome kits, which the company also launched at AGBT.

De Witte also said that the company plans to release updated versions of its GeneSpring and CytoGenomics software later this year.

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