Research on ”dark matter” in genomic analysis on ABCA4 gene for Stargardt disease identifies 25% of biallelic cases.

Researchers based in the Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands, including a broad international effort of 75 experts, have reported the results of an analysis on 1,054 Stargardt disease probands within the ABCA4 gene.  The study used deep sequencing of the ABCA4 gene to identify structural variants and deep-intronic variants in 25% of biallelic Stargardt disease (STGD1).  The expectation from this study is that this model may be useful for the application of several other inherited diseases.


Stargardt disease (STGD1) has an estimated prevalence of 1/10,000 and is caused by variants in the ABCA4 gene, an autosomal recessive retinal dystrophy characterized by central retinal degeneration. According to the literature, there are more than 900+ unique variants reported in ABCA4-related retinopathies, of which 50% variants are missense mutations. While the majority of cases is caused by biallelic variants in the ABCA4 gene, there can be up to 30% of the cases being unresolved and this missing heritability provides a significant challenge to understand the molecular genetics in the disorder.  “Dark-matter”, as identified in cosmology, is referenced in the title of the paper in question as analogous to the “dark-genome”, or so-called “junk DNA”, whereby almost ~98.5% of the intronic or house-keeping components of a gene are historically considered to be “non-functional” (subject how to defining protein coding sequences vs. non-coding DNA).  However, over the last 30 years of research, there has been a universe of rich biological matter in the literature ranging from early transposable elements to anti-sense, RNA interference and the recent CRISPR technologies for gene therapy.  As highlighted in the authors’ report, two pathogenic alleles have recently confirmed clinical diagnosis for Stargardt diseasewith several promising clinical trials in progress based on RNA modulation with antisense oligonucleotides (see Genet Med. 2019; 21:1761–1771; Genet Med. 2019; 21:1751–1760, and; Am J Hum Genet. 2018; 102:517–527).


In the current study, the research reported on the use of 483 single-molecule molecular inversion probes (“smMIPs”) to sequence the 50 exons and 12 intronic regions carrying 11 pathogenic “deep-intronic” (DI) variants of 412 genetically unsolved STGD1 cases. The study design used a semi-automated, high-throughput and cost-effective comprehensive sequence analysis of the entire ABCA4 gene.   The results of the study found 14 known and 13 novel deep-intronic variants within 448 biallelic probands. In their discussion, the research team commented that, “we not only identified nine novel NCSS (non-canonical splice sites) variants and 13 novel DI (deep intronic) variants, but also 11 novel heterozygous SVs (structural variants). The large setup of this study allowed us to provide a “landscape” overview of the different variant types underlying STGD1”. In addition, the study showed that their model and approach to probe the intronic regions in one or several genes could likely uncover multiple variants in many other disease genes.