Long‐read whole genome sequencing reveals HOXD13 alterations in synpolydactyly. Issue 2 (16th December 2021)

• Record Type: Journal Article
• Authors: Melas, Marilena; Kautto, Esko A.; Franklin, Samuel J.; Mori, Mari; McBride, Kim L.; Mosher, Theresa Mihalic; Pfau, Ruthann B.; Hernandez‐Gonzalez, Maria Elena; McGrath, Sean D.; Magrini, Vincent J.; White, Peter; Samora, Julie Balch; Koboldt, Daniel C.; Wilson, Richard K.
• Is Part Of: Human mutation. Volume 43:Issue 2(2022)
• Page Start: 189
• Page End: 199
• Publication Date: 2021-12-16
• Subjects: genetic disorders -- HOXD13 -- pediatric genetics -- polysyndactyly -- single‐molecule sequencing -- whole genome sequencing; Human chromosome abnormalities -- Periodicals; Mutation (Biology) -- Periodicals; 616.04205
• DOI: 10.1002/humu.24304
• Languages: English
• ISSNs: 1059-7794

Abstract

Abstract: Synpolydactyly 1, also called syndactyly type II (SDTY2), is a genetic limb malformation characterized by polydactyly with syndactyly involving the webbing of the third and fourth fingers, and the fourth and fifth toes. It is caused by heterozygous alterations in HOXD13 with incomplete penetrance and phenotypic variability. In our study, a five‐generation family with an SPD phenotype was enrolled in our Rare Disease Genomics Protocol. A comprehensive examination of three generations using Illumina short‐read whole‐genome sequencing (WGS) did not identify any causative variants. Subsequent WGS using Pacific Biosciences (PacBio) long‐read HiFi Circular Consensus Sequencing (CCS) revealed a heterozygous 27‐bp duplication in the polyalanine tract of HOXD13 . Sanger sequencing of all available family members confirmed that the variant segregates with affected individuals. Reanalysis of an unrelated family with a similar SPD phenotype uncovered a 21‐bp (7‐alanine) duplication in the same region of HOXD13 . Although ExpansionHunter identified these events in most individuals in a retrospective analysis, low sequence coverage due to high GC content in the HOXD13 polyalanine tract makes detection of these events challenging. Our findings highlight the value of long‐read WGS in elucidating the molecular etiology of congenital limb malformation disorders. Abstract : Here we report two pathogenic HOXD13 tandem duplication events—detected via Pacific Biosciences long‐read whole‐genome sequencing (WGS) and validated with Sanger sequencing—that co‐segregate with a synpolydactyly phenotype in two unrelated families. Importantly, these variants were missed by standard Illumina short‐read WGS and presumably are missed by many next‐generation sequencing‐based gene panels. Our findings support the phenotype–genotype correlation in HOXD13 polyalanine expansions and highlight the shortcomings of standard short‐read next‐generation sequencing technologies to detect some classes of pathogenic variants.