Article Figures & Data
Figures
- Figure 1.
Substantial discordance between variant level functional prediction methods. From 1220 variants in 21 SRNS genes identified in the 1000G, the top 25% scored as most deleterious (n=255) by each of Polyphen2, SIFT, and MutationTaster were studied for concordance of prediction. Requiring one of three methods to classify variants as damaging implicates 493 variants as causal. Two of three implicate 210 variants as causal. Requiring all three programs to be in concordance reduced the number of causal variants to 62.
- Figure 2.
Transcript-specific filtering influences the accuracy of monogenic diagnosis. The horizontal axis represents the base position in the coding sequence of the INF2 gene on the basis of the longest transcript. The vertical axis is the combined annotated–dependent depletion (CADD) score of each potential variant. All possible missense and nonsense variants in this region are plotted in gray. Blue indicates variants observed in the 1000G, and orange indicates variants observed in 311 subjects with NS. Yellow indicates known pathogenic variants reported in ClinVar 138. The green interval represents the exons for the most selected transcript with the highest TIMS score (ENST00000398337). It is apparent that rare variants found in patients with NS are enriched in this transcript, whereas rare variants found in the 1000G are not. CDS, coding DNA sequence.
- Figure 3.
Increasing the number of genes sequenced increased the prevalence of incorrectly identified variants. The horizontal axis is the number of candidate genes sequenced assuming median gene length (1271 bp), and the vertical axis is the proportion of individuals classified with a monogenic diagnosis. Under assumptions of a fixed background prevalence and false negative rate, curves represent the total proportions of monogenic diagnosis, those expected to be correct, and those expected to be incorrect.
- Figure 4.
Effect of prevalence of true monogenic NS on the relative risk of a variant found in the 21–gene SRNS gene set being in a patient who is monogenic versus population control. The horizontal axis is the prevalence of monogenic NS in a population. As the prevalence of monogenic NS increases, the relative risk of the variant being in a patient versus a subject in the 1000G increases as well.
- Figure 5.
Achievement of complete remission does not significantly differ by monogenic status. Unadjusted Kaplan–Meier plot of the proportion of CR in patients with NS stratified by monogenic status. Plot is truncated at day 1000. P value was determined with an unadjusted Cox proportional hazards model of CR and monogenic status. HR, hazard ratio.
- Figure 6.
Genome–wide background prevalence of rare and deleterious variants. All coding variants observed in the 1000G were classified as pathogenic or benign on the basis of stringent filtering criteria (maximum ancestry–specific EVS MAF<0.1%, 1000G MAF<5%, and loss of function or nonsynonymous and passing the two of three functional filter). Then, for each gene, the resulting background prevalence of predicted pathogenic mutations is calculated. A background prevalence of 1% for a given gene indicates that 1% of subjects in the 1000G carry a rare and deleterious variant in this gene. Subsets of genes (Concise Methods) and inheritance models considered are represented on the horizontal axis. Bars depict the proportions of genes within a gene set having background prevalence of predicted pathogenic variation within specific ranges. hOMIM, hand curated Online Mendelian Inheritance in Man; MAF, minor allele frequency.
Tables
Name Value or Distribution Median age, yr 34 Age range, yr 2–84 Histologic diagnosis FSGS (30%), minimal change (22%), membranous (15%), IgA nephropathy (10%), others (23%; Supplemental Table 1) Fraction of pediatric patients 30% Continental ancestry European (48%), African (29%), admixed American (15%), East Asian (9%) Inheritance Mode Genes Dominant ACTN4, CD2AP, CFH, INF2, LMX1B, TRPC6, WT1 Recessive COQ2, COQ6, CUBN, ITGA3, LAMB2, MYO1E, NEIL1, NPHS1, NPHS2, PDSS2, PLCE1, PTPRO, SCARB2, SMARCAL1 - Table 3.
Characteristics of the default filter devised to classify variants as causal for NS
Parameter Default No. of genes 21 AF threshold in sequenced samples <5% AF threshold in the EVS <0.5% (dominant gene); <1% (recessive gene) AF threshold in the 1000G Not used Functional prediction threshold Predicted damaging by two of three of PolyPhen2, SIFT, and MutationTaster (A or D) Transcript specificity Longest transcript Conservation score (GERP) Not used GERP, genome evolutionary rate profiling.
- Table 4.
Characteristics of the stringent filter devised to classify variants as causal for NS
Parameter Default No. of genes 21 AF threshold in sequenced samples <5% AF threshold in the EVS <0.1% (dominant gene); <0.1% (recessive gene) AF threshold in the 1000G <1% in any of 26 populations Functional prediction threshold Predicted damaging by two of three of PolyPhen2, SIFT, and MutationTaster Transcript specificity Most negatively selected Conservation score (GERP) >4 GERP, genome evolutionary rate profiling.
Subject Ancestry Histology Gene Genotype Amino Acid Change HGMD Pediatric Remission Immunosuppressive Agent RAAS Agent 1 AFR MCD NPHS1 HOM_ALT p.A765V No Yes Complete None Yes 2 AMR FSGS TRPC6 HET p.N765S No Yes Complete Steroid Yes 3 AFR MCD CD2AP HET p.M496I Yes Yes Complete Steroid No 4 EUR IgM nephropathy WT1 HET p.C350R No Yes Complete Steroid, tacrolimus, MMF No 5 EUR ICGN INF2 HET p.E220K Yes Yes None None Yes 6 EUR FSGS NPHS2 HOM_ALT p.A284V Yes Yes None None Yes 7 EUR MCD INF2 HET p.A13T Yes No Complete Steroid Yes 8 EUR FSGS TRPC6 HET p.D798H No No Partial None Yes LMX1B HET p.D374N No 9 AMR FSGS INF2 HET p.P35R No No Partial Steroid, CNI Yes AFR, African 1000G continental ancestry; AMR, American 1000G continental ancestry; EUR, European continental ancestry; MCD, minimal change disease; ICGN, immune complex GN; HOM_ALT, homozygous for the alternative allele; HET, heterozygous variant; MMF, mycophenolate mofetil; CNI, calcineurin inhibitor; RAAS, renin-angiotensin-aldosterone system.
Description of Subsets Classified Monogenic (%; Fraction) Overall 2.9 (9/312) Pediatric 6.3 (6/95) Pediatric + FSGS 6.7 (2/30) Pediatric + FSGS + no CR 6.3 (1/16) Pediatric + FSGS + CR 7.1 (1/14) Pediatric + FSGS or MCD 5.5 (4/73) Pediatric + no CR 5.6 (2/36) Pediatric + CR 6.8 (4/59) Adult 1.4 (3/217) Adult + FSGS 2.7 (2/75) Adult + FSGS + no CR 3.8 (2/53) Adult + FSGS + CR 0.0 (0/22) Adult + FSGS or MCD 3.2 (3/95) Adult + no CR 1.5 (2/133) Adult + CR 1.2 (1/84) All + FSGS 3.8 (4/105) All + FSGS + no CR 4.3 (3/69) All + FSGS + CR 2.8 (1/36) All + FSGS or MCD 4.2 (7/168) All + not FSGS 2.4 (5/207) All + no CR 2.4 (4/169 All + CR 3.5 (5/143) MCD, minimal change disease.
Supplemental Data
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