Long-Read Sequencing
Research-grade Nanopore long-read (LR) whole genome sequencing to clarify reported variants.
Turnaround time is 4-6 weeks.
Who is this test for?
Patients for whom long-read sequencing assessment would help to clarify the classification of the VUS such as:
- CNVs (duplications, inversions, insertions, deletions, balanced translocations, etc)
- Triplet repeat expansion definition
- Uniparental disomy (UPD)
- Low level mosaicism
- FMR1 premutation expansion risk
- Methylation status of FMR1 full mutation
This test will focus on the variant in question and no unrelated sequence data will be reported.
Sequencing & Interpretation
Our LR genome sequencing test is performed on the Oxford Nanopore Technologies PromethION platform. This sequencing assay has the capacity to identify single nucleotide variants (SNVs) and small insertions and deletions (indels) in regions of the genome inaccessible by short-read technologies. It also provides complete profiling of short tandem repeat expansions, structural variants (SVs) such as insertions, inversions, and translocations, and copy number variants (CNVs).
Basecalling, mapping, variant calling, and phasing are performed using the EPI2ME pipeline developed by Oxford Nanopore Technologies. This pipeline leverages the latest production-level bioinformatics tools to generate a comprehensive set of genomic variants. Details of the analysis pipeline can be found at https://github.com/epi2me-labs/wf-human-variation.
Test Limitations
- Absence of a change in the variant classification does not exclude a genetic basis for clinical findings
- The sensitivity for detecting different types of variation by Nanopore long-read genome sequencing is not yet well established, and therefore, the causal variant may not be detected
- The sensitivity for detecting indels is known to be low and these variants may not be detected by this assay
- Interpretation of genetic variation is based on current biological and clinical knowledge of gene-disease associations and on current understanding of the association with phenotype and family history
Samples & Ordering
Requirements
- 1 tube (3.0ml-5.0mL; min 1.0ml) of whole blood drawn in an EDTA tube
- This tube/kit can be ordered through our kit order page
- Samples should be shipped at ambient temperature (18-25℃) or refrigerated (2-8℃)
- Whole blood is stable for 5 days at ambient temperature (18-25℃) or 7 days refrigerated (2-8℃). Do not freeze.
Shipping Address
Alamya Health
℅ Breakthrough Genomics
2 Hughes, #100
Irvine, CA 92618