Since 2014, GeneDx has been detecting copy number variants (CNVs) directly from exome sequencing data.

Our methods can reliably detect most deletions and duplications involving three or more coding exons; smaller deletions or duplications may not be reliably identified. All reported CNVs are confirmed by an orthogonal method such as array CGH, MLPA, or PCR. Parental confirmations for reportable CNVs are reported without additional charges when a trio is submitted. CNV analysis may not be possible in a subset of specimens. All Xome-based reports will include whether CNV detection was possible. At this time, exome based technology is not a replacement for the sensitivity of exon level aCGH.

Our CNV analysis via XomeDx^® can identify:

• Large multi-gene chromosomal aberrations
• Small, partial gene, and intragenic CNVs; deletions and duplications of three exons or larger are reliably identified
• CNVs of one to two exons in size may be identified
• Chromosomal aneuploidy
• Uniparental disomy (UPD)

CNV analysis is limited or may not be possible in regions with reduced coverage, extreme GC- or AT-content, or significant homology to pseudogenes or segmental duplications. Our method may not always detect balanced aberrations, mosaicism, deletions/duplications involving only part of an exon, or CNVs in non-coding regions of the genome.