Precision in details
Contributes to the detection of SNVs, small indels and depth signals used in the evaluation of deletions and duplications.
Hybrid genomic sequencing
NeoGenoma Omni: higher resolution to investigate the most difficult regions.
By combining short and long readings from the same sample, it offers the greatest diagnostic power in the portfolio when both technologies are relevant. It expands the resolution of structural variants, repeats and pseudogenes, without guaranteeing that the cause will be found.
- Method
- Short + long reads
- Scope
- Nuclear and mitochondrial genome
- Sample
- Blood or mouth swab
- Post-report
- Infinity VUS included
Flexible hiring
Start with NeoGenoma. Add long reading only if necessary.
The investigation can start with NeoGenoma. If the result does not resolve the case, the team can evaluate the long-read add-on to form the hybrid analysis.
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01 · First stage
Request NeoGenoma.
Perform whole-genome sequencing with short reads first and evaluate long-read complement as per clinical need.
Get to know NeoGenoma -
02 · Enlargement on demand
Complete only if necessary.
If the case remains undiagnosed, the team can add the additional long reading step without repeating the short reading. The new evidence is integrated with the NeoGenoma data.
Request the add-on
Sample Eligibility: the subsequent complement depends on the quantity, quality and storage conditions of the original sample. The team confirms technical feasibility before hiring; a new sample collection may be necessary.
How it works
Each technology solves a different part of the problem.
Short readings provide depth and baseline accuracy. Long reads cut through repetitive passages and help reconstruct the context of complex regions. Pipeline Hybrid NeoGenomica integrates both pieces of evidence into a single analysis.
Structural context
It traverses repeats, pseudogenes and breakpoints, expanding the resolution of complex insertions and rearrangements.
A clinical interpretation
The evidence is processed together and related to the phenotype, without generating a sequence of independent reports.
What Long Reading Adds
More context for complex variant classes.
The gain depends on the region, the type of change, the quality of the sample and the validated scope of each module.
01
Structural variants
Inversions, translocations, large deletions, duplications, insertions and complex rearrangements.
02
Repetition Expansions
Repetitive regions that isolated short reads may not scale or map properly.
03
Pseudogenes and homology
Loci such as PMS2, SMN1/SMN2, CYP21A2 and GBA, in which the origin of the sequence may be ambiguous.
04
Methylation and allelic phase
5mC signals in selected clinical regions and relationship between variants on the same haplotype.
Clinical indication
When can NeoGenoma Omni add more?
Especially when a difficult region, a repeat, a rearrangement or a previous inconclusive result supports the need to expand the investigation.
Neurology
Ataxias and expansion diseases
Conditions with progressive ataxia, neuropathy, vestibulopathy or suspected recurrent expansion.
Neuromuscular
FSHD and recurrent dystrophies
Situations where repeat size, haplotype and methylation may be relevant.
Endocrinology
Congenital adrenal hyperplasia
Investigation of CYP21A2, gene conversions and rearrangements of the RCCX locus.
Difficult genes
Pseudogenes and high homology
When short reads can map to more than one locus and make classification difficult.
Clinical genetics
Neurodevelopment and malformations
Complex cases in which CNVs, insertions, inversions or translocations can explain the phenotype.
Oncogenetics
Lynch and complex rearrangements
Families with strong clinical suspicion and inconclusive tests, according to specialized assessment.
Internal technical validation
Performance measured on benchmark data.
The pipeline was compared on the GIAB HG002 sample with official truth sets. The results below describe this benchmark and do not equate to clinical sensitivity in all cases.
21% → 74%
Structural variants
Detection in the short read benchmark versus hybrid analysis.
13% → 72%
Inserts
Gain observed mainly on longer insertions.
≈29% → 88%
Difficult clinical genes
Structural variants in regions of the GIAB CMRG set.
>99%
SNVs and indels
Accuracy observed for small variants in the evaluated set.
GIAB HG002 sample; truth sets of v5.0q structural variants, v4.2.1 small variants, and CMRG regions. Internal technical validation NeoGenomica.
Integrated scope
A broad set of variant classes.
The pipeline integrates SNVs, indels, CNVs, insertions, structural variants, repeats, regions of high homology and selected methylation modules, according to technical criteria.
Technical transparency
When the main suspicion is mosaicism.
NeoGenoma Omni is not intended for the investigation of somatic mosaicism at low allelic fraction. When this is the main clinical suspicion, the NeoExoma Mosaico offers high depth and confirmation of relevant candidates within the technical criteria. In CNVs and structural variants, there may be uncertainty in the delimitation of coordinates.
Post-report follow-up
Science evolves. The interpretation of a variant may also evolve.
All NeoGenomica tests include Infinity VUS for variants of uncertain significance that are reported.
Your result monitored over time
A variant of uncertain significance, or VUS, is a finding for which the available evidence does not yet allow us to conclude whether it is related to the disease. Infinity VUS monitors classification updates even after the report is issued.
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01 · Monitor
Periodically compares reported VUS with new evidence and classifications.
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02 · Review
A material change is forwarded for expert review before any communication.
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03 · Update
When the reclassification is confirmed and applicable to the case, the responsible team is notified and the report can be updated.
Test day
From indication to integrated report.
A single flow to combine short reads, long reads, and clinical context.
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01
Medical request
The diagnostic hypothesis, phenotype and previous tests guide the analysis modules.
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02
Sample collection
Blood or mouth swab, depending on the technical requirements of the case.
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03
Two sequences
The same sample is processed with short reads and long reads.
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04
Hybrid analysis
The evidence is integrated and reviewed by the specialized team.
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05
Report and follow-up
The result relates the findings to the clinical context and includes Infinity VUS.
Frequently asked questions
Before ordering.
What is the difference to NeoGenoma?+
The two analyze the genome. Omni adds long reads to increase the resolution of insertions, structural variants, repeats, selected methylation, and regions of high homology.
Do I need to hire the complete NeoGenoma Omni from the beginning?+
No. It is possible to start with NeoGenoma and request the long read add-on if the case remains undiagnosed, without repeating the short read step. Reusing the original sample depends on technical evaluation and a new sample collection may be necessary.
Does the test investigate mosaicism?+
Mosaicism at low allelic fraction is beyond the scope of this methodology. For this hypothesis, consider the NeoExoma Mosaico.
Which sample is used?+
Blood or mouth swab, according to technical requirements and team guidance. The same sample is used to generate both reading modalities.
Does the test need a medical request?+
Yes. Clinical hypothesis and previous tests are essential to select modules, prioritize variants and interpret results.
Complex cases
Discuss where long reading can add.
Our team helps match the phenotype, previous testing, and suspected variant class to the best analysis design.
Catalog information
Technical data of NeoGenoma Omni
Additional readings for difficult regions, available from the beginning or as a second step after NeoGenoma.
- Applications
- Rare and hereditary diseases, Genome-wide investigation
- Accepted samples
- peripheral blood (preferred), Mouth swab, DNA extraído
- Estimated deadline
- Deadline subject to confirmation by the technical team.
- Methodology
- Hybrid genomic sequencing with short and long reads from the same sample.
- Analytical scope
- Nuclear and mitochondrial genome, with complementary resolution for structural variants, repeats, pseudogenes, selected methylation and allelic phase.
- Medical request
- Required
Requirements
Medical request with diagnostic hypothesis, phenotype and previous tests. The subsequent complement depends on the quantity, quality and storage of the original sample.
Limitations
Mosaicism at low allelic fraction is beyond the scope of this methodology. The gain depends on the region, the type of change, the quality of the sample and the validated scope of each module.
