Table 1.
Clinical characteristics of enrolled familial hypercholesterolemia patients.
Fig 1.
Exome sequencing analysis of familial hypercholesterolemia (FH).
The steps for identifying FH-causing variants in three genes are shown, in addition to the subsequent genetic analyses of whole-exome sequencing data that led to the identification of pathogenicity.
Table 2.
Known pathogenic mutations in three FH-linked genes (n = 69).
Fig 2.
Pedigree analysis of a patient with LDLR p.D834Rfs/- mutation.
(A) A simplified pedigree of the P05 family. The upper right arrow indicates the proband; squares indicate males, and circles indicate females. Open and filled symbols indicate unaffected and affected individuals, respectively. Asterisks indicate family members who underwent clinical examinations and molecular analyses. WT refers wild-type. (B) Clinical examination data and sequencing chromatograms. Vertical arrows indicate the mutation site. (C) Integrative Genomics Viewer screenshot of p.D834Rfs/-. Sequencing reads show that a single nucleotide substitution (G>C) and frameshift deletion (AT/-) occurred at the cis position.
Table 3.
Novel pathogenic mutations in three FH-linked genes (n = 69).
Fig 3.
Copy number variation (CNV) detection in LDLR.
SVD-ZRPKM values were used to detect CNVs by the CoNIFER algorithm and were calculated by transforming reads per kilobase per million values into standardized z-scores, based on the mean and standard deviation across all analyzed exomes. (A) The SVD-ZRPKM regional plot of the P25 patient with a large copy number deletion in LDLR. (B) The SVD-ZRPKM regional plot of the P17 patient and family member (P17-F01) with an inherited copy number deletion in LDLR. Green and blue indicate SVD-ZRPKM values of P17 and P17-F01, respectively. Values are plotted based on P17. (C) Pedigree of the P17 patient with CNV. The upper right arrow indicates the proband; squares indicate males, and circles indicate females. Open and filled symbols indicate unaffected and affected individuals, respectively. Asterisks indicate family members who underwent clinical examinations and CNV analyses. (D) TaqMan Copy Number Assay for P25, P17, and family members of P17. Red indicates the assay for P25 by probe #1 within intron 5; blue indicates the assay for P17 and other members by probe #2 (overlapped from intron 10 to exon 11). The assay was performed in duplicate and repeated. Results were plotted by CopyCaller software v.2.0.