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

KHAN, MUBEEN; CORNELIS, STÉPHANIE S.; POZO-VALERO, MARTA DEL; WHELAN, LAURA; RUNHART, ESMEE H.; MISHRA, KETAN; BULTS, FEMKE; ALSWAITI, YAHYA; ALTALBISHI, ALAA; DE BAERE, ELFRIDE; BANFI, SANDRO; BANIN, EYAL; BAUWENS, MIRIAM; BEN-YOSEF, TAMAR; BOON, CAMIEL J. F.; VAN DEN BORN, L. INGEBORGH; DEFOORT, SABINE; DEVOS, AURORE; DOCKERY, ADRIAN; DUDAKOVA, LUBICA; FAKIN, ANA; FARRAR, G. JANE; SALLUM, JULIANA MARIA FERRAZ; FUJINAMI, KAORU; GILISSEN, CHRISTIAN; GLAVA?, DAMJAN; GORIN, MICHAEL B.; GREENBERG, JACQUIE; HAYASHI, TAKAAKI; HETTINGA, YMKJE M.; HOISCHEN, ALEXANDER; HOYNG, CAREL B.; HUFENDIEK, KARSTEN; JÄGLE, HERBERT; KAMAKARI, SMARAGDA; KARALI, MARIANTHI; KELLNER, ULRICH; KLAVER, CAROLINE C. W.; KOUSAL, BOHDAN; LAMEY, TINA M.; MACDONALD, IAN M.; MATYNIA, ANNA; MCLAREN, TERRI L.; MENA, MARCELA D.; MEUNIER, ISABELLE; MILLER, RIANNE; NEWMAN, HADAS; NTOZINI, BUHLE; OLDAK, MONIKA; PIETERSE, MARC; PODHAJCER, OSVALDO L.; PUECH, BERNARD; RAMESAR, RAJ; RÜTHER, KLAUS; SALAMEH, MANAR; SALLES, MARIANA VALLIM; SHARON, DROR; S

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.