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Percent of medically relevant genes (defined by GeneTests) covered at ≥20x depth by different technologies. GeneTests is one of several databases containing medically relevant content targeted by the SeqCap EZ MedExome Probes. This figure demonstrates the depth and uniform coverage of the SeqCap EZ MedExome Probes, which covers 100% of coding bases (CDS) at a depth of ≥20x for 57.1% of medically relevant genes compared to only 6.2% of medically relevant genes covered completely using the exome from Competitor A. Mitochondrial genes were excluded for this comparison. The percent of coding bases covered at ≥20x for each consolidated target was determined using GATK (DepthOfCoverage), summarized by gene. Sample prep and capture followed the SeqCap EZ Library SR User’s Guide v5.1. Competitor A kit data was generated by a 3rd party service provider following vendor’s pre-capture multiplexing protocol. All reads were subsampled to 60 million for assessment. Performance was determined following the same bioinformatics pipeline for analysis of both products.

Coverage of medically-relevant regions targeted by the SeqCap EZ MedExome Probes. The kit is designed to provide sequencing coverage for regions defined as medically relevant, including GENE Tests CDS (excluding mitochondrial genes), ClinVar, coding sequence from the set of ~4600 genes identified by the consortium of the Emory Genetics Lab, Harvard Laboratory of Molecular Medicine, and Children's Hospital of Philadelphia (CHOP) and additional regions deemed as medically relevant based on customer input. Sample prep and capture followed the SeqCap EZ SR User's Guide v5.1. A total of 54-individual libraries were tested and sequencing was performed on an Illumina HiSeq 2500 System with v3 chemistry in rapid run mode. Reads are 2x101bp in length. Sequencing reads were randomly subsampled to 60 million reads for performance assessment.

Comparison of target coverage distribution. The SeqCap EZ MedExome Probes demonstrated sustained and high depth of coverage compared to the Competitor A kit. The Fold 80 Base Penalty calculation shows more uniform capture for the SeqCap EZ MedExome Kit. The graph is representative of one sample from one 6-plex capture per product. For both products, the targets are unpadded. The SeqCap EZ MedExome Probes targets reflect empirical targets across all metrics. All reads were randomly subsampled to 60 million for assessment. Sample prep and capture followed the SeqCap EZ Library SR User’s Guide v5.1. Competitor A kit data was generated by a 3rd party service provider following vendor’s pre-capture multiplexing protocol. All reads were subsampled to 60 million for assessment. Performance was determined following the same bioinformatics pipeline for analysis of both products.

Comparison of on-target rate, coverage, and percent SNP sensitivity and specificity. Performance of the SeqCap EZ MedExome Probes was compared against the Competitor A kit. The SeqCap EZ MedExome Probes exhibited greater percent on-target rate, higher coverage of coding exons and better SNP sensitivity/specificity rate. For the Competitor A product, the +100bp padded target was used for on-target read assessment and the unpadded target was used for all other metrics. For the SeqCap EZ MedExome Probes the empirical target was used across all metrics. All reads were randomly subsampled to 60 million for assessment. Sample prep and capture followed the SeqCap EZ Library SR User’s Guide v5.1. Competitor A kit data was generated by a 3rd party service provider following vendor’s pre-capture multiplexing protocol. All reads were subsampled to 60 million for assessment. Performance was determined following the same bioinformatics pipeline for analysis of both products.