A deletion/duplication genetic test checks whether one or more parts of a gene are missing or present in extra copies. It is often ordered with DNA sequencing because the two methods look for different types of pathogenic variants. Sequencing is best at finding letter-level changes and small insertions or deletions, while deletion/duplication analysis measures gene dosage. A person can therefore have a negative sequencing result and still carry a clinically important whole-gene or exon-level copy number change. The test may focus on one gene, a panel of genes, or selected regions identified by another assay. Laboratories use methods such as multiplex ligation-dependent probe amplification, quantitative PCR, digital PCR, targeted microarray, and read-depth analysis from next-generation sequencing. Interpretation depends on which exons are involved, whether the change disrupts the reading frame, whether the duplication’s structure is known, and how well the finding matches the condition being evaluated.
- Deletion/duplication analysis complements sequencing: It detects missing or extra exons and whole genes that standard sequence analysis may not find.
- Coverage must be checked gene by gene: Some assays detect single-exon CNVs, while others reliably detect only larger multi-exon events.
- A positive result may be diagnostic: Pathogenic deletions and duplications can cause inherited neurologic, muscular, cardiac, metabolic, cancer-predisposition, and other disorders.
- Duplications can be harder to interpret than deletions: Their effect may depend on orientation, insertion site, and whether they preserve or disrupt gene structure.
- Family testing can clarify inheritance and recurrence risk: A targeted assay is usually used after the familial CNV is known.
- A negative result does not exclude all variants: Repeat expansions, balanced rearrangements, deep intronic changes, and low-level mosaicism may need separate testing.
Table of Contents
- What Deletion/Duplication Testing Looks For
- How Laboratories Measure Gene Copy Number
- Common Clinical Uses and Gene Examples
- How Deletion Results Are Interpreted
- Why Duplication Results Need Extra Caution
- Negative, Uncertain, and Technical Results
- Inheritance, Family Testing, and Reproductive Risk
- Preparation and Follow-Up
What Deletion/Duplication Testing Looks For
Genes are divided into coding segments called exons, separated by introns. A deletion/duplication test asks whether expected gene segments are present in the usual number of copies. In a typical autosomal gene, two copies of each exon are expected. A heterozygous deletion leaves one copy. A heterozygous duplication usually creates three copies. A homozygous deletion removes both copies, while a biallelic result can also involve different deletions on the two chromosomes.
The term is most often used for gene-targeted testing. It may assess:
- One or more exons within a single gene.
- The entire coding region of one gene.
- All genes on a hereditary disease panel.
- A known familial deletion or duplication.
- A region suggested by exome, genome, or microarray data.
This is different from a genome-wide copy number variant test, although both measure gains and losses. A focused deletion/duplication assay is designed to answer a narrower question with high sensitivity in specified genes. It may detect a one-exon deletion that a broad chromosomal microarray misses because the exon is smaller than the array’s resolution.
Gene dosage changes cause disease through several mechanisms. A deletion can remove a gene entirely, eliminate critical exons, shift the reading frame, or remove a promoter needed for expression. A duplication can interrupt a gene, add extra functional dosage, or create an abnormal transcript. In recessive disease, a deletion on one chromosome may combine with a sequence variant on the other. In X-linked disease, a deletion may have different effects depending on chromosomal sex and X-inactivation.
A laboratory order that says “sequencing with deletion/duplication analysis” is broader than sequencing alone. Patients should verify that both components were completed, especially when the result is negative. Some genes have a substantial proportion of pathogenic variants caused by copy-number changes, so omitting dosage analysis can materially lower diagnostic sensitivity.
How Laboratories Measure Gene Copy Number
Several technologies can produce a deletion/duplication result. The report should state which method was used and its validated resolution.
Multiplex ligation-dependent probe amplification
MLPA uses probe pairs that bind next to each other on selected DNA targets. Only correctly bound probes are ligated and amplified. The amount of product from each probe is compared with control samples. A reduced peak suggests a deletion; an increased peak suggests a duplication.
MLPA can test dozens of exons in one reaction and is widely used for DMD, BRCA1, BRCA2, MSH2, MLH1, PMS2, SMN1, and many other genes. Its strength is robust targeted dosage measurement. Its main limitation is that it evaluates only the sites represented by probes. A small sequence change under a probe-binding site can occasionally reduce binding and mimic a deletion, which is one reason confirmation or sequencing review may be needed for a single-probe result.
Quantitative and digital PCR
Quantitative PCR compares target amplification with a reference gene. Digital PCR partitions DNA into many small reactions and counts positive partitions, allowing precise relative or absolute copy measurement. These methods are useful for confirming a suspected CNV, testing relatives, or measuring a small number of exons. They are not efficient for broad discovery across hundreds of genes.
Targeted microarray
A gene-focused array contains dense probes over selected genes. It can detect exon-level or multi-exon gains and losses when probe coverage is sufficient. Like other hybridization methods, it may not reveal the exact breakpoint or orientation of a duplication.
NGS read-depth analysis
Modern gene panels and exome tests often infer copy number from the number of sequencing reads aligned to each exon. Patient coverage is normalized against other samples and technical expectations. Consistently low depth across adjacent exons suggests deletion; high depth suggests duplication.
Read-depth methods allow sequence and dosage analysis from the same data, but performance depends on uniform capture, reference samples, GC content, batch size, and bioinformatic validation. Single-exon calls are generally harder than multi-exon calls. Homologous genes and pseudogenes can create mapping problems.
| Method | Best use | Can test many targets? | Common limitation |
|---|---|---|---|
| MLPA | Exon-level dosage in selected genes | Moderate | Only probe sites are measured |
| qPCR | Targeted confirmation or family testing | Low | Relative quantification and few targets |
| Digital PCR | Precise targeted copy counting | Low | Requires predefined targets |
| Targeted array | Dense coverage across selected genes | High | Breakpoint structure is usually unresolved |
| NGS CNV calling | Combined sequence and dosage panel | High | Uneven coverage and pseudogenes |
No method’s name guarantees sensitivity. The laboratory’s validation—such as whether it reliably detects a single exon, a partial exon, mosaic events, or duplications in a specific gene—is more important than the platform label.
Common Clinical Uses and Gene Examples
Deletion/duplication analysis is used across many inherited disease areas because gene-level CNVs are a recurrent pathogenic mechanism.
Neuromuscular disorders
The DMD gene is a classic example. Large exon deletions and duplications cause many cases of Duchenne and Becker muscular dystrophy. The exact exon pattern can affect whether the reading frame is disrupted and may influence eligibility for exon-skipping treatment. SMN1 copy-number testing is central to spinal muscular atrophy diagnosis and carrier screening, although the assay must also address silent-carrier configurations and SMN2 copy number when relevant.
PMP22 duplication causes most Charcot-Marie-Tooth disease type 1A, while PMP22 deletion causes hereditary neuropathy with liability to pressure palsies. These reciprocal changes illustrate how extra and missing dosage of the same gene can produce different disorders.
Hereditary cancer
Whole-exon and whole-gene deletions or duplications occur in BRCA1, BRCA2, MSH2, MLH1, PMS2, EPCAM, APC, TP53, and other cancer-predisposition genes. A hereditary cancer panel that performs sequence analysis but lacks validated CNV detection is incomplete for many indications. EPCAM deletions are especially important because certain 3′ deletions can silence the neighboring MSH2 gene through methylation and cause Lynch syndrome.
Cardiac, renal, and connective-tissue disease
Exon-level CNVs can occur in genes associated with cardiomyopathy, arrhythmia, aortopathy, polycystic kidney disease, Alport syndrome, and connective-tissue disorders. Some regions are difficult because of pseudogenes or homologous sequences. PKD1 and PMS2, for example, require specialized approaches to distinguish the functional gene from highly similar genomic copies.
Metabolic and recessive conditions
A deletion in one allele may be missed when only sequence variants are reported. If the remaining allele carries a pathogenic small variant, the combination can establish a recessive diagnosis. Laboratories may suspect this when a sequence variant appears homozygous but only one parent carries it, or when read depth suggests one allele is absent.
Known familial testing
Once a family-specific deletion or duplication is established, relatives usually receive a targeted assay rather than a full panel. Targeted testing is more direct, reduces uncertain findings, and clearly answers whether the familial variant is present. A familial variant test may use MLPA, PCR, or another method chosen for that exact CNV.
How Deletion Results Are Interpreted
A deletion result should state which exons or genomic coordinates are missing, whether one or both copies are affected, the assay used, and the clinical classification.
Whole-gene deletions
A whole-gene heterozygous deletion is often pathogenic when loss of one copy is a known disease mechanism. However, interpretation can extend beyond the named gene. The deletion may include neighboring genes and produce a contiguous-gene syndrome with additional features. A targeted assay may not define how far the deletion extends, so chromosomal microarray or genome sequencing may be recommended.
Multi-exon deletions
A deletion of consecutive exons can disrupt the reading frame, remove essential protein domains, or occasionally preserve the frame. For some genes, an in-frame deletion may retain partial function and produce a milder phenotype. The reading-frame rule is useful but not universal; the biological role of the removed exons and transcript matters.
Single-exon deletions
Single-exon calls require close quality review. A rare sequence variant at the probe or primer site can cause allele dropout and mimic deletion. Confirmation with a second method or breakpoint analysis may be necessary. When confirmed, a single-exon deletion can be fully pathogenic if it disrupts the transcript.
Homozygous or biallelic deletions
Loss of both copies often has a stronger effect and may cause severe recessive disease. In tumor testing, the term homozygous deletion may instead describe loss of both tumor copies of a suppressor gene, sometimes diluted by normal cells. Constitutional and tumor results should not be interpreted under the same framework.
Deletion plus a sequence variant
When one allele is deleted and the other carries a pathogenic sequence change, the variants must be shown to be in trans—on opposite chromosomes—when the disorder is recessive. Parental testing may establish phase. A report that lists two findings without phase may not yet prove a biallelic diagnosis.
A deletion can also remove regulatory elements rather than coding exons. Some gene-targeted assays include promoters or known noncoding hotspots, while others do not. The coverage table should specify these regions.
Why Duplication Results Need Extra Caution
A duplication means extra DNA was measured, but dosage alone may not reveal how the extra segment is arranged. This uncertainty can affect pathogenicity.
A tandem duplication sits next to the original sequence. It may create an abnormal transcript if it duplicates internal exons in a way that disrupts the reading frame. A duplication inserted elsewhere may not affect the original gene in the same way. An inverted duplication may have another consequence. Standard MLPA or read-depth analysis often cannot distinguish these structures.
Whole-gene duplications may cause disease when increased gene dosage is established. In other genes, an extra intact copy has no proven effect. For this reason, a whole-gene duplication should not be called pathogenic simply because a deletion of the same gene causes disease. Haploinsufficiency and triplosensitivity are separate biological properties.
Internal exon duplications may be evaluated by predicted transcript effect. If duplicated exons are expected to be repeated in the messenger RNA and shift the reading frame, pathogenicity may be likely. Yet genomic position and orientation must be considered. RNA studies, long-range PCR, genome sequencing, or breakpoint analysis can sometimes resolve the structure.
Duplications can also be part of a complex rearrangement with a nearby deletion or inversion. A focused assay may report the dosage change but miss the complete architecture. When the phenotype is more severe or different than expected, a broader structural-variant test may be appropriate.
In hereditary cancer genes, laboratories generally confirm clinically significant duplications and assess whether they are expected to disrupt gene function. Treatment or preventive surgery should not be based on an unconfirmed, poorly characterized gain.
Negative, Uncertain, and Technical Results
A negative deletion/duplication result means the laboratory found no reportable copy-number change within the validated regions and limits of that assay. It does not mean that the gene or genome is free of pathogenic variation.
The result may not exclude:
- Single-nucleotide variants and small insertions or deletions if sequencing was not performed.
- Partial-exon changes smaller than the assay’s probe spacing.
- Deep intronic or regulatory variants.
- Balanced inversions or translocations.
- Repeat expansions.
- Low-level mosaic deletions or duplications.
- CNVs in genes not included on the test.
- Complex rearrangements that produce a normal net copy number.
- Tissue-limited changes absent from blood.
A VUS may involve an exon or gene with limited dosage evidence, an atypical duplication structure, or a change inherited from a relative with uncertain features. Clinical management should not assume that a VUS caused the disorder. Segregation studies, RNA analysis, breakpoint characterization, and future reclassification may help.
Technical or indeterminate results occur when sample quality, DNA quantity, coverage, or normalization is inadequate. A single low-quality exon may be marked as not evaluable even when the rest of the gene is negative. The laboratory may recommend recollection or an alternative method.
Reports can also contain an apparent discrepancy between sequencing and dosage data. For example, a heterozygous sequence variant may appear at an unusually high allele fraction because the other allele is deleted. Conversely, a duplicated allele can alter variant fractions. Integrating sequence and copy-number evidence often reveals the true genotype.
Before accepting a negative panel as comprehensive, review the test’s gene-specific limitations. Some laboratories publish a coverage table showing exons excluded from CNV calling or genes analyzed by another method. This detail is particularly important for clinically high-risk conditions where a missed diagnosis would change surveillance or treatment.
Inheritance, Family Testing, and Reproductive Risk
A pathogenic deletion or duplication may be inherited from a parent or arise de novo. The inheritance pattern of the affected gene determines family risk.
For an autosomal dominant condition, a carrier usually has a 50% chance of passing the CNV in each pregnancy. The actual chance of symptoms may be lower when penetrance is incomplete. For an autosomal recessive condition, a person with one pathogenic deletion is usually a carrier unless a pathogenic variant is present on the other allele. If both partners carry pathogenic variants in the same gene, each pregnancy may have a 25% chance of the condition.
For X-linked conditions, risk depends on who carries the variant, fetal chromosomal sex, and whether the disorder affects carrier females. Mitochondrial inheritance does not follow these copy-number rules because standard deletion/duplication analysis generally targets nuclear genes.
A de novo result lowers but does not reduce recurrence risk to zero. Germline mosaicism can allow a parent to have more than one affected child even when the CNV is absent from blood. The estimated residual risk depends on the gene, rearrangement mechanism, and family history.
Parental testing can also reveal that a child’s deletion is part of an unbalanced product from a parent’s balanced chromosome rearrangement. A gene-targeted test in the parent may be normal or may only show the same dosage state without revealing chromosome structure. Karyotyping or genome-based analysis may be needed when the deletion extends beyond one gene or a recurrent rearrangement is suspected.
Reproductive options may include natural conception with prenatal diagnostic testing, in vitro fertilization with preimplantation genetic testing for a known familial variant, donor gametes, or adoption. These choices are personal and require accurate characterization of the CNV before a laboratory can design targeted prenatal or embryo testing.
Healthy relatives should generally be offered targeted testing only after the familial result is classified as pathogenic or likely pathogenic and the implications are understood. Testing a VUS in unaffected relatives may be useful for laboratory segregation analysis but should be coordinated through genetics professionals.
Preparation and Follow-Up
Most deletion/duplication tests use blood, saliva, or a cheek-swab specimen and require no fasting. Blood often provides consistent DNA quality. Saliva can contain microbial DNA or yield variable amounts, but it is suitable for many validated assays. Prenatal testing uses chorionic villi or amniotic fluid, and tumor testing may use tissue, marrow, or blood.
Before testing, gather the clinical diagnosis under consideration, prior genetic reports, pathology records when relevant, and a three-generation family history. The laboratory needs exact familial variant notation for targeted testing. A statement such as “my mother had a BRCA deletion” may not identify the gene interval or method well enough to order the correct assay.
After results, ask:
- Were both sequencing and deletion/duplication analysis performed?
- Which exons, promoters, or noncoding regions were covered?
- Can the method detect one-exon changes and low-level mosaicism?
- Was the finding confirmed with another method?
- Are duplication orientation and breakpoints known?
- Does the CNV include neighboring genes?
- Should parents or relatives receive targeted testing?
- Is another assay needed to define structure or search for a second variant?
A pathogenic result may lead to disease-specific surveillance, treatment, cascade testing, or reproductive planning. A negative result may support broader sequencing or a method aimed at repeat expansions, methylation, structural variants, or another tissue. A VUS should be tracked for reclassification rather than treated as a confirmed cause.
Keep the complete laboratory report indefinitely. Exact exon numbers can differ among transcripts, so the report’s transcript accession and version are important. Future laboratories need the genomic coordinates, method, classification, and confirmation details to compare results accurately. A short portal note that says “deletion detected” is not sufficient for family testing or reproductive planning.
References
- The Application of the NGS and MLPA Methods in Molecular Diagnosis of Hereditary Breast and Ovarian Cancer 2025 (Study)
- Copy number variant analysis improves diagnostic yield in a diverse clinical cohort referred for exome sequencing 2025 (Study)
- Diagnostic yield of exome sequencing-based copy number variant analysis in patients with suspected Mendelian disorders 2024 (Study)
- Sequencing approaches in hereditary cancer testing 2026 (Review)
- Multiplex ligation-dependent probe amplification (MLPA) 2025 (Official Educational Resource)
Disclaimer
Deletion/duplication results depend on the exact genes, exons, specimen, and laboratory validation. This article is educational and does not replace genetic counseling, disease-specific medical advice, prenatal consultation, or confirmation of a clinically important result.
