Resolving the dark matter of ABCA4 for 1054 Stargardt disease probands through integrated genomics and transcriptomics

KHAN, MUBEEN; WHELAN, LAURA; BULTS, FEMKE; DE BAERE, ELFRIDE; BAUWENS, MIRIAM; VAN DEN BORN, L. INGEBORGH; DOCKERY, ADRIAN; FARRAR, G. JANE; GILISSEN, CHRISTIAN; GREENBERG, JACQUIE; HOISCHEN, ALEXANDER; JÄGLE, HERBERT; KELLNER, ULRICH; LAMEY, TINA M.; MCLAREN, TERRI L.; MILLER, RIANNE; OLDAK, MONIKA; PUECH, BERNARD; SALAMEH, MANAR; SIMONELLI, FRANCESCA; SZAFLIK, JACEK P.; TRACEWSKA, ANNA M.; ZANLONGHI, XAVIER; ROACH, JOHN N. DE; WEBER, BERNHARD H. F.; CORNELIS, STÉPHANIE S.; RUNHART, ESMEE H.; ALSWAITI, YAHYA; BANFI, SANDRO; BEN-YOSEF, TAMAR; DEFOORT, SABINE; DUDAKOVA, LUBICA; SALLUM, JULIANA MARIA FERRAZ; GLAVA?, DAMJAN; HAYASHI, TAKAAKI; HOYNG, CAREL B.; KAMAKARI, SMARAGDA; KLAVER, CAROLINE C. W.; MACDONALD, IAN M.; MENA, MARCELA D.; NEWMAN, HADAS; PIETERSE, MARC; RAMESAR, RAJ; SALLES, MARIANA VALLIM; SPITAL, GEORG; THOMPSON, JENNIFER A.; VAN ZWEEDEN, MARTINE; LISKOVA, PETRA; AYUSO, CARMEN; DHAENENS, CLAIRE?MARIE; POZO-VALERO, MARTA DEL; MISHRA, KETAN; ALTALBISHI, ALAA; BANIN, EYAL; BOON, CAMIEL J. F.; DEVO

GENETICS IN MEDICINE

LIPPINCOTT WILLIAMS & WILKINS

Año: 2020 vol. 22 p. 1235 - 1246

1098-3600

Purpose: Missing heritability in human diseases represents a major challenge, and this is particularly true for ABCA4-associated Stargardt disease (STGD1). We aimed to elucidate the genomic and transcriptomic variation in 1054 unsolved STGD and STGD-like probands. Methods: Sequencing of the complete 128-kb ABCA4 gene was performed using single-molecule molecular inversion probes (smMIPs), based on a semiautomated and cost-effective method. Structural variants (SVs) were identified using relative read coverage analyses and putative splice defects were studied using in vitro assays. Results: In 448 biallelic probands 14 known and 13 novel deep-intronic variants were found, resulting in pseudoexon (PE) insertions or exon elongations in 105 alleles. Intriguingly, intron 13 variants c.1938-621G>A and c.1938-514G>A resulted in dual PE insertions consisting of the same upstream, but different downstream PEs. The intron 44 variant c.6148-84A>T resulted in two PE insertions and flanking exon deletions. Eleven distinct large deletions were found, two of which contained small inverted segments. Uniparental isodisomy of chromosome 1 was identified in one proband. Conclusion: Deep sequencing of ABCA4 and midigene-based splice assays allowed the identification of SVs and causal deep-intronic variants in 25% of biallelic STGD1 cases, which represents a model study that can be applied to other inherited diseases.