A custom capture sequence approach for oculocutaneous albinism identifies structural variant alleles at the OCA2 locus

Stacie K. Loftus, Linnea Lundh, Dawn E. Watkins-Chow, Laura L. Baxter, Erola Pairo-Castineira, C. Nisc, Ian J. Jackson, William S. Oetting, William J. Pavan, David R. Adams

Research output: Contribution to journalArticlepeer-review

4 Scopus citations


Oculocutaneous albinism (OCA) is a heritable disorder of pigment production that manifests as hypopigmentation and altered eye development. Exon sequencing of known OCA genes is unsuccessful in producing a complete molecular diagnosis for a significant number of affected individuals. We sequenced the DNA of individuals with OCA using short-read custom capture sequencing that targeted coding, intronic, and noncoding regulatory regions of known OCA genes, and genome-wide association study-associated pigmentation loci. We identified an OCA2 complex structural variant (CxSV), defined by a 143 kb inverted segment reintroduced in intron 1, upstream of the native location. The corresponding CxSV junctions were observed in 11/390 probands screened. The 143 kb CxSV presents in one family as a copy number variant duplication for the 143 kb region. In the remaining 10/11 families, the 143 kb CxSV acquired an additional 184 kb deletion across the same region, restoring exons 3–19 of OCA2 to a copy-number neutral state. Allele-associated haplotype analysis found rare SNVs rs374519281 and rs139696407 are linked with the 143 kb CxSV in both OCA2 alleles. For individuals in which customary molecular evaluation does not reveal a biallelic OCA diagnosis, we recommend preliminary screening for these haplotype-associated rare variants, followed by junction-specific validation for the OCA2 143 kb CxSV.

Original languageEnglish (US)
Pages (from-to)1239-1253
Number of pages15
JournalHuman mutation
Issue number10
StatePublished - Oct 2021

Bibliographical note

Funding Information:
The authors would like to thank the families with oculocutaneous albinism who have contributed to this study. This study was supported by the Intramural Research Program of the National Institutes of Health and was funded by the National Human Genome Research Institute (NHGRI: 1ZIAHG000136‐21 and NHGRI: 1ZIAHG000215‐18).

Publisher Copyright:
Published 2021. This article is a U.S. Government work and is in the public domain in the USA.


  • OCA2
  • albinism
  • copy number neutral
  • inversion
  • melanosome
  • pigmentation


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