Nexome vs. Traditional Workflows

Cell3™ Target: Nexome streamlines the diagnostic process by eliminating the need for multiple analyses such as Chromosomal Microarray (CMA), Multiplex Ligation-dependent Probe Amplification (MLPA), and Fluorescence In Situ Hybridization (FISH).

This results in the following advantages:

Comprehensive Coverage of Clinically Significant Genes

Cell3™ Target: Nexome covers a broader range than many exome products, targeting not only the protein-coding regions of the human genome but also clinically significant non-coding regions. Enhanced probes enable CNV detection in areas where known gene and exon-level reconstructions have been confirmed. It offers excellent coverage against the CCDS, GENCODE, RefSeq, and ACMG73 databases, strengthening probes to accommodate clinically significant genes and CNV detection (Figure 1).

Clinically Enhanced Regions

• Exon-level deletions and duplications targeted by commercially available kits (e.g., MLPA).
• Genes associated with fetal abnormalities for prenatal diagnosis.
• Transcripts and extra exons associated with Early Infant Epileptic Encephalopathy (EIEE) for enhanced epilepsy diagnosis.
• RefSeq transcripts, promoter regions, 5′ and 3′ UTR sequences corresponding to OMIM morbid set of 4,090 genes.
• Non-coding, disease-causing variants.
• Pharmacogenomics (PGx) markers for predicting drug responses.

Precision and Recall of SNVs and INDELs

Cell3™ Target: Nexome detects more “true variants” present in the HG001 human genome standard reference compared to other exome products. Additionally, it maintains excellent accuracy while ensuring comparable recall rates for both SNVs and INDELs (Figure 2a, 2b, 2c, 2d).

SNV

INDELS

• Targets over 51 Mb of the human genome.
• Designed to call up to 30% more variants compared to other commercially available exome products, with a wide range for CNV detection.
• On account of Cell3™ Target: Nexome excellent probe design and performance compared to commercially available exome products, it requires a similar/less amount of sequencing to achieve a mean coverage of 100× with 6.63 Gb (Table 1).

Reliable CNV Calling

Copy number variants (CNVs) account for approximately 10% of disease-associated variants and have been identified in about 10-20% of individuals with neurodevelopmental disorders.

• Designed for superior CNV detection at loci known to have both gene and exon level rearrangements.
• Capable of detecting CNVs with sizes spanning from just a few exons up to multiple contiguous genes (~100 bp–40 Mb).
• Evaluated using samples with known CNV events tested by either MLPA or CMA and confidently recalled CNV mutations from 50 bp (a single exon) up to 42 Mb.
• Detection of clinically relevant events is achieved with superior precision and recall and provides an exome alternative to CMA and MLPA based CNV analysis (Table 2a and 2b).

Table 2a Detection of MLPA-confirmed CNVs.

Table 2b Detection of CMA-confirmed multi-gene CNVs.

Benefits from Straightforward, Automatable Protocols

• The Cell3™ Target: Nexome kit includes all the necessary reagents for library preparation, hybridization, and capture.
• Designed for simplicity, the Cell3™ Target: Nexome workflow requires less than 10 hours in total time, with less than 2 hours of hands-on time.
• Only 1 ng of DNA is required.
• Multiple stop points are incorporated to provide flexibility within laboratory processing.
• Library preparation can be performed manually or automated, processing up to 96 samples in a single batch.
• Indexes are available for up to 384 samples, facilitating flexible batch sizes in high-throughput laboratories and providing scalability for all Illumina sequencers.

References

1.McKusick V. Online Mendelian Inheritance in Man, OMIM™. McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University (Baltimore, MD) and National Center for Biotechnology Information, National Library of Medicine (Bethesda, MD), 2000. Accessed October 10, 2023. https://omim. org. 2009. Full article

2.Smedley D, Schubach M, Jacobsen JO, Köhler S, Zemojtel T, Spielmann M, et al. A whole-genome analysis framework for effective identification of pathogenic regulatory variants in Mendelian disease. The American Journal of Human Genetics. 2016; 99(3):595-606. Full article

3. Landrum MJ, Lee JM, Benson M, Brown GR, Chao C, Chitipiralla S, et al. ClinVar: improving access to variant interpretations and supporting evidence. Nucleic Acids Research. 2018;46(D1):D1062-7.. Full article