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: short and long reads.
Combines short and long reads to investigate structural variants, repeats and complex regions. It can be ordered from the start or added to NeoGenoma, depending on the case.
- Accepted samples
- Peripheral blood (preferred), Buccal swab, Extracted DNA
- Turnaround time and when it starts
- 4 to 8 weeks, after acceptance of the sample
- Medical order
- Required. View requirements and limitations.
Flexible ordering
Start with NeoGenoma. Add long-read sequencing 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-read sequencing step without repeating the short-read sequencing. 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 ordering; a new sample collection may be necessary.
How it works
Each technology solves a different part of the problem.
Short reads provide depth and base accuracy. Long reads span repetitive regions and help reconstruct the context of complex regions. Pipeline Hybrid NeoGenomica integrates both sources of evidence in 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 reads add
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 short reads alone may not size or map accurately.
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.
Cancer genetics
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.
Follow-up after your results
Infinity VUS
All NeoGenomica tests include Infinity VUS to follow reported variants of uncertain significance. When a relevant reclassification is confirmed after specialist review, the doctor is notified and the report may be updated.
Understand results and Infinity VUSTesting process
From indication to integrated report.
A single flow to combine short reads, long reads, and clinical context.
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01
Medical order
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 order 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 a buccal swab, according to the technical requirements and the team’s guidance. The same sample is used to generate both types of reads.
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-read sequencing can add.
Our team helps match the phenotype, previous testing, and suspected variant class to the best analysis design.
Test information
Technical details for NeoGenoma Omni
Method, scope, requirements and limitations
Additional reads 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), Buccal swab, Extracted DNA
- Estimated turnaround time
- 4 to 8 weeks, after acceptance of the sample
- 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 order
- 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.
Additional information
Subsequent reuse of the sample depends on technical evaluation; a new sample collection may be necessary. Infinity VUS included.
