Automation of IDT Probe-Based Targeted Enrichment Workflow Using xGen Lockdown Probes in a High-Throughput Lab

Jessica Gearhart, Beth Marosy, Brian Craig, Kim Doheny

Research output: Contribution to journalArticle


The Center for Inherited Disease Research (CIDR) provides high quality next-generation sequencing (NGS), genotyping and statistical genetics consultation to investigators working to discover genes that contribute to disease. CIDR began production level automated genotyping in 1996 with Human STRP linkage panels and continues to automate its production workflows as technologies advance. Automated protocols now exist for Illumina GWAS arrays and whole exome and targeted sequencing in research and clinical settings. CIDR is continually seeking new laboratory and informatics ways to improve its workflow and reduce human error while maintaining the highest quality of data production. Here we have created an automated workflow to process IDT (Integrated DNA Technologies) probe based target enrichment for NGS using the Perkin Elmer Janus to normalize and pool samples prior to capture, and the Agilent Bravo for hybridization, capture, wash, and amplification master mix distribution. HapMap and FFPE generated libraries were enriched for the IDT PanCancer Panel using both manual and automated processing and subsequently were sequenced using the Illumina MiSeq platform. Flowcell data was processed using the CIDRSeqSuite analysis pipeline to generate QC metrics for both processing types to confirm that the addition of automated steps maintained or increased the quality of the sample data. QC data analysis showed that automated processing of samples increased the percent selection of both HapMap and FFPE sample types by over 5%. The reproducibility rate between automated and manual processing was 99.5% for HapMap samples.

Original languageEnglish (US)
Pages (from-to)S7
JournalJournal of biomolecular techniques : JBT
StatePublished - Dec 1 2019

ASJC Scopus subject areas

  • Molecular Biology

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