Deletions of recessive disease genes: CNV contribution to carrier states and disease-causing alleles

Abstract

Over 1200 recessive disease genes have been described in humans. The prevalence, allelic architecture, and per-genome load of pathogenic alleles in these genes remain to be fully elucidated, as does the contribution of DNA copy-number variants (CNVs) to carrier status and recessive disease. We mined CNV data from 21,470 individuals obtained by array-comparative genomic hybridization in a clinical diagnostic setting to identify deletions encompassing or disrupting recessive disease genes. We identified 3212 heterozygous potential carrier deletions affecting 419 unique recessive disease genes. Deletion frequency of these genes ranged from one occurrence to 1.5%. When compared with recessive disease genes never deleted in our cohort, the 419 recessive disease genes affected by at least one carrier deletion were longer and located farther from known dominant disease genes, suggesting that the formation and/or prevalence of carrier CNVs may be affected by both local and adjacent genomic features and by selection. Some subjects had multiple carrier CNVs (307 subjects) and/or carrier deletions encompassing more than one recessive disease gene (206 deletions). Heterozygous deletions spanning multiple recessive disease genes may confer carrier status for multiple single-gene disorders, for complex syndromes resulting from the combination of two or more recessive conditions, or may potentially cause clinical phenotypes due to a multiply heterozygous state. In addition to carrier mutations, we identified homozygous and hemizygous deletions potentially causative for recessive disease. We provide further evidence that CNVs contribute to the allelic architecture of both carrier and recessive disease-causing mutations. Thus, a complete recessive carrier screening method or diagnostic test should detect CNV alleles.

Figure 1.

Attributes of the 3212 Tier 1 heterozygous deletions (potential carrier CNVs). Data are divided by array version (V7, blue; V8, plum) and based on the minimum deleted interval of each CNV. (A–C) The distributions of (A) deletion size, (B) number of RefSeq genes contained within each deletion, and (C) recessive disease genes per deletion. The spectrum of deletions identified by the V8 (exon-focused) array contains proportionally more small, single-gene events. (D) Distribution of heterozygous Tier 1 deletions per subject. A total of 18,641 subjects had no heterozygous Tier 1 deletion and are not shown. (E) Distribution of total recessive disease genes deleted per individual. This is an estimate of the distribution of per-person recessive carrier load attributable to copy-number variation. Individuals with no heterozygous Tier 1 deletion are omitted.

Figure 2.

Allele frequency spectrum and assortment of heterozygous Tier 1 deletions (potential carrier CNVs). (A) Histogram of the prevalence with which each of 419 recessive disease genes is deleted by heterozygous Tier 1 CNVs, demonstrating a predominance of rarely affected genes and a few more commonly deleted genes. (B) Chronological ascertainment of unique recessive disease genes affected by heterozygous Tier 1 deletions. As more individuals with Tier 1 heterozygous deletions are analyzed (x-axis), additional recessive disease genes are identified that were not previously found to be deleted in our cohort, up to a total of 419 of 1228 known recessive disease genes (34%). The ascertainment of unique, deleted recessive disease genes continues to rise even after assessing 2829 subjects with a Tier 1 heterozygous deletion. (C) To determine whether Tier 1 heterozygous CNVs are distributed randomly among subjects, we compared the number of V8 individuals with two or three Tier 1 heterozygous CNVs deleting a single recessive disease gene (279 subjects; red line) to that expected by chance (black probability distribution; see text and Supplemental Methods). There was no statistically significant enrichment of individuals with multiple potential carrier deletions (P = 0.312), suggesting that carrier CNVs, numerically, are distributed randomly among our cohort. (D) Co-occurrence (or absence of co-occurrence) of heterozygous deletions in all pairs of 374 recessive disease genes among V8 cases displayed as a correlation matrix. Genes are plotted along each axis consecutively by genomic position. (Blue) Relative enrichment of codeletion; (red) relative paucity of codeletion.

Figure 3.

Comparison of deletion carrier frequency in our cohort to point mutation carrier frequency reported by Lazarin et al. (2013). Values are derived from Supplemental Table S10. SNV and deletion carrier frequencies for a given gene are poorly correlated (Spearman correlation coefficient = 0.122; P[estimated] = 0.399). Genes for which deletion carrier frequency is higher than SNV carrier frequency are labeled and in green.

Figure 4.

Two hundred ninety-four chromosomal regions contain “consecutive” recessive disease genes. A homozygous or hemizygous deletion containing two or more recessive disease genes not interrupted by a dominant or rec/dom disease gene could lead to a complex recessive phenotype (i.e., a recessive contiguous gene syndrome); heterozygous deletion of the same region may render an individual a carrier for two or more recessive conditions. Such “consecutive” recessive disease genes are indicated by the purple bars above each chromosome, which span from the start of the first recessive disease gene in the series to the end of the last one. Selected chromosomal bands are numbered for locational reference.

Figure 5.

Features of recessive disease genes deleted in our cohort. The 419 recessive disease genes deleted at least once by a Tier 1 heterozygous CNV were compared with all other recessive disease genes. Those deleted in our cohort are (A) farther from the nearest dominant disease gene (P = 3.3 × 10⁻¹⁵); (B) larger, genomically (P = 9.3 × 10⁻¹⁶); and (C) had a lower fractional Alu content (P = 2.3 × 10⁻¹¹) than the remaining recessive disease genes. All P-values result from the Wilcoxon rank sum test with continuity correction.

Figure 6.

Homozygous Tier 1 deletions. Each illustrates a unique feature of homozygous deletions. (A) The hypotonia-cystinuria syndrome (HCS) region (top) is homozygously deleted in subject 163 (middle, light gray shading on probe log₂ plot). Twelve heterozygous Tier 1 deletions affect SLC3A1 (bottom) in our cohort, demonstrating diverse sizes and locations of carrier alleles. Each is plotted by minimum (thick line) and maximum (thin line) boundaries. No Tier 1 CNV affected solely PREPL. (B) NPHP1, the disease gene for juvenile nephronophthisis 1 and other conditions, is homozygously deleted as part of a compound heterozygous deletion, likely mediated by the complex repeat architecture of this region (colored bars above RefSeq genes track). Arrow indicates heterozygously deleted region. (C) Six homozygous deletions of a noncoding alternative exon 1 of LEPREL1. This CNV is mostly likely not pathogenic (see text). Database of Genomic Variant CNVs are shown (“table browser query on dgv”).

Figure 7.

Model explaining the potential impact of adjacent genomic features on gene-specific deletion carrier frequency. (A) Recessive disease gene without a nearby dominant disease gene (e.g., NPHP1). Most deletions encompassing this recessive disease gene do not also delete a dominant disease gene and are thus solely carrier deletions. (B) Recessive disease gene near to a haploinsufficient dominant disease gene (e.g., MYO15A and RAI1, respectively). Many deletions of the recessive disease gene also delete the dominant disease gene, rendering the individual a carrier and affected with dominant disease. This mutation is selected out of the population.