What does it do?
Reads many DNA fragments simultaneously and generates digital data.
Genetic Technology · Sequencing and Copy-Number Analysis
NGS – Next-Generation Sequencing
NGS refers to next-generation sequencing platforms that can read many DNA regions in parallel and may be used in some PGT applications for chromosome copy-number or targeted gene analysis.
- The analysis is limited to the scope of the requested test
- Platform output requires laboratory validation and bioinformatic interpretation
- Use of an NGS platform does not guarantee live birth or a healthy child
Understand the topic in one minute
NGS: Quick Summary
Use in PGT
May support assessment of chromosome copy number, segmental changes or targeted gene analysis.
Required stages
DNA amplification, sequencing, bioinformatic analysis and report verification.
Key limitation
Not every NGS test has the same scope, resolution or clinical meaning.
Key information
What Is NGS – Next-Generation Sequencing?
NGS is a family of technologies capable of reading DNA sequences in high-throughput parallel workflows.
In brief:
The limited DNA obtained from an embryo biopsy is first amplified, then read on a sequencing instrument and analysed using software. What NGS can show depends on the panel, library preparation and bioinformatic algorithm used.
In PGT-A, NGS may assess signals of missing or extra chromosome copies by comparing relative amounts of DNA. In PGT-M, different NGS-based methods may be used for direct variant analysis or linkage markers.
The fact that an NGS instrument produces large amounts of data does not mean that the entire genome is interpreted clinically. The test reports only regions within its validated analytical scope and changes above its defined resolution.
Laboratories may differ in DNA-amplification methods, sequencing depth, mosaic thresholds, segmental-reporting policies and quality-control rules. Results should be judged according to validation data and the clinical question, not the platform name alone.
- Whether the test is being used for PGT-A, PGT-M or another purpose is clarified
- Analytical resolution and findings that will not be reported are explained
- Mosaic and segmental-result thresholds are discussed
- A plan for clinical confirmation and counselling of results is defined
Differences between tests
Are NGS and PGT the Same Thing?
PGT is a group of clinical tests; NGS is one of the analysis technologies that may be used for those tests.
PGT-A / PGT-M / PGT-SR
Defines the genetic question being assessed in the embryo.
- Requires an indication and counselling
- Forms part of the biopsy and IVF pathway
- Results are linked to transfer decision-making
NGS
Reads biopsy DNA and generates copy-number or targeted-sequence data.
- Can be used for different tests
- Is not a clinical indication by itself
- Depends on laboratory algorithms and quality control
Is NGS always superior to other platforms?
No. Current professional assessments do not demonstrate that one PGT-A platform is superior in every setting. Test reliability depends on the entire laboratory workflow.
Who should be assessed?
In Which Genetic Applications Can NGS Be Used?
Its use depends on laboratory validation and the genetic question being asked.
PGT-A
Screening copy number across all 24 chromosomes and, depending on the method, some segmental findings.
PGT-M
Targeted variants, linkage markers or combined-analysis protocols.
PGT-SR
Assessment of unbalanced chromosome regions associated with structural rearrangements.
Carrier screening
Parallel analysis of many genes in defined gene panels.
Diagnostic genetics
Panels, exome sequencing or selected other analyses in a medical genetics laboratory.
Research and quality
Controlled use in research on new algorithms, mosaicism and embryo genetics.
Does NGS detect every genetic condition?
No. Variants outside the panel, resolution or reporting scope may not be detected. Embryo-biopsy testing also has the limitation that sampled cells may not fully represent the whole embryo.
Preparation before testing
What Is Defined Before NGS Analysis?
Technology should be selected to answer the clinical question; the clinical question should not be created simply because a technology is available.
Clinical indication
The PGT-A, PGT-M or PGT-SR objective is defined.
Sample type
Embryo biopsy, blood or another DNA source is specified.
Test scope
Whole-chromosome, targeted-gene, panel or linkage analysis is selected.
Analytical limits
Sequencing depth, mosaic threshold, segment size and no-result criteria are explained.
Control samples
Family DNA or reference samples may be required for tests such as PGT-M.
Consent and data
Policies for incidental findings, data storage and report sharing are explained.
Step-by-step process
How Is NGS Analysis Performed?
NGS analysis of an embryo-biopsy sample involves several laboratory stages.
Sample acceptance and identity
The biopsy tube is verified against the embryo code.
DNA amplification
DNA from the small number of cells is amplified using whole-genome amplification.
Library preparation
DNA fragments are prepared with appropriate labels for the sequencing instrument.
Sequencing
Many DNA fragments are read in parallel.
Bioinformatic analysis
Raw data are processed for quality, copy number or targeted variants.
Quality control
Read count, coverage and control samples are assessed.
Report generation
Results are converted into the reporting categories of the clinical test.
Embryo matching
The report is transferred to the clinical record using the correct embryo code.
Timeline
How Long Does an NGS Result Take?
Timing depends on sample number, test type and the laboratory workflow.
Biopsy and dispatch
The sample is prepared for the laboratory after embryo biopsy.
DNA and library
Amplification and sequencing preparation are performed.
Sequencing run
Samples may be processed together according to instrument capacity.
Bioinformatics
Data are analysed and passed through quality filters.
Report approval
Specialist review and the final result category are completed.
Transfer
Embryos are used in a separate FET cycle after results.
How many days do I need to stay in Cyprus?
There is no need to remain in Cyprus while NGS laboratory analysis is underway. The IVF and biopsy schedule is followed, and the report can be explained remotely.
Factors affecting outcomes
What Affects the Quality of NGS Analysis?
The entire pre-analytical, analytical and bioinformatic pathway matters more than the instrument alone.
Number of biopsy cells
Too few or damaged cells can affect the amount of DNA available.
DNA amplification
Amplification bias can distort copy-number signals.
Sequencing depth
Influences data resolution and reliability.
Bioinformatic algorithm
Thresholds for mosaicism and segmental changes may vary between laboratories.
Controls and validation
Local validation and quality-control materials are essential.
Clinical interpretation
The analytical result should be interpreted by a specialist in the context of the embryo and patient.
Important distinction:
High technical sequencing quality does not guarantee embryo implantation or live birth. Analytical performance and clinical outcome are different concepts.
Personalised cost planning
NGS – Next-Generation Sequencing Costs
Cost varies according to analysis scope, sample number and the PGT laboratory service.
Test type
PGT-A, PGT-M, PGT-SR or a combined analysis.
Number of samples
Number of embryos or family samples tested.
Library preparation and sequencing
Reagents, instrument use and sequencing-run costs.
Bioinformatics
Data analysis, algorithms and specialist interpretation.
Test development
Targeted-variant and linkage work for PGT-M.
IVF and biopsy
Treatment, embryo culture and biopsy are separate from the NGS analysis itself.
Find out what your individual plan may include
Clarifying why NGS is being used and exactly what will be reported can help avoid unnecessary analysis and cost.
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Validation, Data Security and Traceability in an NGS Laboratory
An NGS result should be supported by a documented chain covering sample identity, instrument run, software version and specialist approval.
Barcode and sample identity
Each biopsy tube and library is tracked using a unique identifier.
Positive/negative controls
Controls are used to assess contamination and technical error.
Instrument quality metrics
Read count, base quality and coverage are monitored.
Software version
Algorithm and reference-genome changes are documented.
Data security
Access to raw data, reports and patient information is restricted to authorised users.
Report revision
If new information or a quality issue arises, changes are version-controlled and documented.
Multidisciplinary approach
NGS, Embryology and Genetics Analysis Team
Applying NGS to the right clinical question and integrating results into embryo planning require multidisciplinary management.
Obstetrics, Gynaecology and IVF Specialist
Op. Dr. Beril Yüksel
Assesses how the NGS result may be used clinically within the IVF and transfer plan.
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Scientific Director
Prof. Dr. Münevver Serdaroğulları
Coordinates test scope, scientific validation, consent and data management.
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Embryology Laboratory Director
Zafer Atayurt
Manages biopsy, tubing, freezing and the result-to-embryo matching chain.
View profile →Medical genetics assessment
Clinical interpretation of genetic risk and test results should involve an appropriately qualified medical geneticist or genetic counsellor. The IVF and embryology team manages integration of testing into reproductive treatment.
Balanced information
What Are the Risks and Limitations of NGS?
If high data capacity is misunderstood, it can create unnecessary confidence or anxiety.
Scope misconception
Using NGS does not mean that the entire genome or every disease has been tested.
Amplification error
DNA amplification bias can occur in samples containing very few cells.
Mosaic interpretation
Intermediate signals may be reported differently depending on laboratory thresholds.
Segmental resolution
Small changes may fall below the detection limit.
Software dependence
Algorithms and software versions can influence the result.
Uncertain clinical benefit
More detailed technical data do not necessarily mean a higher live-birth rate.
Common questions
Frequently Asked Questions About NGS – Next-Generation Sequencing
Answers about the role of NGS in PGT, test scope and technical limitations.
What is NGS?
A family of next-generation sequencing technologies that read many DNA fragments in parallel to generate digital genetic data.
Is NGS a treatment?
No. It is an analysis platform used in genetic testing.
Are NGS and PGT the same thing?
No. PGT is a group of clinical tests; NGS is one of the platforms that may be used for those tests.
Does NGS detect every genetic condition?
No. It can detect only findings within the test scope, resolution and reporting rules.
What does NGS assess in PGT-A?
It assesses relative chromosome copy number and, depending on the platform, some segmental or mosaic signals.
Can NGS be used for PGT-M?
Yes. It may be used in laboratory-validated methods for targeted variants and linkage markers.
Is NGS more accurate than other tests?
One platform has not been shown to be superior in every setting; the whole workflow and laboratory validation are important.
Can NGS identify mosaic embryos?
Some intermediate signals may be reported as mosaic; thresholds and clinical interpretation vary between laboratories.
Can an NGS result be wrong?
Incorrect or no-result analyses can occur because of sample, amplification, sequencing or algorithm-related factors.
How long does an NGS result take?
It may take several days or longer depending on the test and laboratory workflow.
Does NGS require an embryo biopsy?
For embryo PGT, blastocyst biopsy is generally required.
Is prenatal testing needed after NGS-based PGT?
PGT does not exclude all fetal genetic conditions; prenatal screening and diagnostic options should be offered.
Do I need to stay in Cyprus while waiting for the NGS result?
No. Embryos are frozen during analysis and the result can be discussed remotely.
What affects the cost of NGS?
Test type, number of samples or embryos, test development, sequencing and the scope of bioinformatic analysis.