Learn More (deletion/duplication analysis)

The method used to detect a deletion or duplication varies by the size of the CNV.

Method 1 Size of Deletion or Duplication (in bp, kb, or Mb)
1-10 bp >10-1000 bp >1-10 kb >10-1000 kb ≥1 Mb
Sanger sequencing YesPossible 2NoNoNo
NGS YesPossible 2No 3No 3No 3
MLPA 4NoYesPossibleNoNo
Quantitative PCR 4 NoYesPossibleNoNo
Long-range PCR 4, 5NoNoPossiblePossibleNo
Gene-targeted aCGH 6NoYes 6YesYesYes
CMA NoNoPossibleYesYes
FISH NoNoNoPossibleYes
Karyotype NoNoNoNoPossible starting at ~3 Mb
bp = base pairs; kb = kilobases; Mb = megabases
1. For detailed descriptions see definitions for individual methods.
2. Deletions and duplications with breakpoints falling within PCR amplification primers (Sanger sequencing) or within enrichment targeted regions (NGS) may be detected by these methods.
3. Methods to call copy number changes from NGS data are currently being developed.
4. This method is designed to detect CNVs in targeted regions only, typically deletions or duplications of one or a few exons. The size of large deletion of the region surrounding the targeted region will not be recognized and the breakpoints cannot be defined by this method.
5. This is a targeted assay that can detect known or suspected deletions in the region of interest (see targeted analysis for pathogenic variants).
6. This method is designed to detect single-exon deletions or duplications, but also contains genome-wide backbone probes that can detect larger deletions and duplications.

Posted: 6-14-16

Related terms: chromosomal microarray; deletion; duplication; FISH; next-generation sequencing; PCR; Sanger sequencing; targeted analysis for pathogenic variants

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