OneSeq Target Enrichment

Simultaneous detection of genome-wide copy number changes, cnLOH, indels, and gene mutations

Agilent’s OneSeq panel allows to study both CNVs and mutations for your constitutional studies using one assay. Compared to deep whole genome sequencing, OneSeq provides a more cost-effective and efficient solution for accurate detection of genomic aberrations and variants in a single assay.

– Detect copy number changes at a targeted resolution of 300kb in a genome-wide backbone

– Detect copy number changes at a targeted higher resolution of 25kb– 50kb in disease-associated ClinGen regions

– Detect genome-wide LOH as small as 5Mb

– Detect SNPs and indels

Congenital structural malformation and developmental disorders, including intellectual disability, autism, and attention deficit hyperactivity disorder (ADHD), are neuropsychiatric disorders that manifest in early childhood as deviations from the normal development. In the past 5 years, major advances have been made in the identification of specific genetic causes of these disorders. The methods used in previous studies include mainly karyotyping and fluorescence in situ hybridization (FISH) for fusion genes, aCGH for copy number changes, and direct sequencing and PCR for gene mutations. Although WGS has the potential to offer a single platform solution for determining the full range of abnormalities from single gene mutations to aneuploidy, the current cost and turnaround time of deep coverage WGS prevent it from being implemented in high-throughput clinical research laboratories. With targeted sequencing, only a subset of genes or defined genomic regions are sequenced, allowing time, expenses, and data storage to be focused on the regions of the genome of interest. However, it has not been possible to perform a genome-wide survey of copy number changes with targeted sequencing. Agilent’s OneSeq target enrichment kits are designed so that genome-wide copy number changes, cnLOH, indels, and targeted mutations can be simultaneously determined. myGenomics provide full service sample to analyzed report in 20-30days.

Target enrichment has been great for mutations (indels & SNVs), but not so easy for large chromosomal aberrations

Sample requirements

Genomic DNA (1-5 micrograms) / 2ml whole blood in lavender top tube / Tissue / FFPE sections.

Turnaround time:

Sample-Report: 20-30 days


Raw data (FASTq files) and if analysis requested: VCF (Variant Call File). CNV and cnLOH reports with BWA mapping, GATK variant call, Filter for Variant Allele Frequency (1000 genome), Filter for known pathogenic variants (dbSNP) or suspect variants (Frameshift, Stop gain, Stop loss), SIFT score, Polyphen score. Advanced and custom analyses also available.

Additional deliverables

Initial sample QC, Fragmentation QC, Library prep QC, Target enrichment QC, Sequencing reads QC, Coverage and FastQC plots.