Additional file 2 of Genome-wide survey of tandem repeats by nanopore sequencing shows that disease-associated repeats are more polymorphic in the general population
Creators: name: Mitsuhashi, Satomi
name: Frith, Martin C.
name: Naomichi Matsumoto
Publisher: name: figshare
Year: 2021
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: FOS: Biological sciences

description: Additional file 2. Figure S1. Variation of tandem repeat length (copy number) in long reads from 21 individuals. x-axis: copy number change relative to the human reference (hg38). y-axis: read number. Three different repeat types ((A) exonic CAG, (B) exonic GGC and (C) intronic AAAAT) are shown. Disease repeats: 12 CAG repeats, 14 GGC repeats, and 7 intronic AAAAT repeats. Other repeats: exonic CAG: n = 1840, exonic GGC: n = 3073, intronic AAAAT: n = 19,744. For each repeat type, we show ten sets of “other repeats” for comparison. Each set of “other repeats” is a random selection of the same number of repeats as the number of disease repeats. Figure S2. Repeat length mean and spread of each triplet repeat type. There are 10 kinds of triplet repeat, AAC, CAC, CCT, CTT, GAT, GTA, GTC, TAA CAG and GGC. The numbers of repeats are; 650 (AAC), 632 (CAC), 1862 (CCT), 737 (CTT), 430 (GAT), 47 (GTA), 73 (GTC), 682 (TAA), 1839 (CAG) and 2907 (GGC). The variation of the repeat length in 21 individuals are shown. x-axis: interquartile range (IQR), y-axis: mean repeat length (bp). In merged boxplots, ranges are the 25th and 75th percentiles, dots are outliers and lines in boxes are median. Figure S3. Variability of exonic repeats. Number of exonic tandem repeats (A) and IQR (B) of each unit are shown. Shorter-unit repeats have more variation. Dots represent outliers. Boxplot ranges are the 25th and 75th percentiles. Lines in boxes are median. Most of the IQRs from repeats whose length are more than six are zero. Figure S4. Comparison of tantan and TRF annotated tandem repeats (A) There are more tantan annotated tandem-repeats than TRF-annotated repeats, however, the distribution of the number of the loci has similar tendency. x-axis: length of repeat unit, y-axis: number of loci. (B) Proportions of triplet repeat sequences are similar between tantan and TRF annotation. Figure S5. Variability of CAG repeats using TRF-annotated repeats.Variation (IQR) and length of repeats with disease-associated sequences. Coding CAG repeats (A), and non-coding exonic CAG repeats (B). x-axis: IQR, y-axis: mean repeat length (bp). n provides the numbers of repeat loci. In merged boxplots on the right and upper, ranges are the 25th and 75th percentiles, dots are outliers and lines in boxes are median. Figure S6. Variability of GGC repeats using TRF-annotated repeats.Variation (IQR) and length of repeats with disease-associated sequences. Coding GGC repeats (A), and non-coding exonic GGC repeats (B). x-axis: IQR, y-axis: mean repeat length (bp). n provides the numbers of repeat loci. In merged boxplots on the right and upper, ranges are the 25th and 75th percentiles, dots are outliers and lines in boxes are median. Figure S7. Variability of AAAAT repeats using TRF-annotated repeats.Variation (IQR) and length of repeats with disease-associated intronic AAAAT sequences. x-axis: IQR, y-axis: mean repeat length (bp). n provides the numbers of repeat loci. In merged boxplots on the right and upper, ranges are the 25th and 75th percentiles, dots are outliers and lines in boxes are median. Figure S8. Repeat length correlates with near-by SNPs. (A) Distribution of tandem repeat length (copy number) in combined long reads of GLS and ATXN3 disease-associated repeats from 21 individuals. x-axis: copy number change relative to the human reference (hg38). y-axis: read count. (B) Three GWAS reported SNPs were near the GLS and ATXN3 repeats. Repeat lengths of each genotype were compared using unpaired t test. P values are shown. Figure S9. Gaucher disease severity modifying SNPs correlate with repeat length.(A) Distribution of tandem repeat length (copy number) in combined long reads of CLN8 from 21 individuals. Note that there is bimodal distribution, with peaks around zero and − 13 copy number changes. x-axis: copy number change relative to the human reference (hg38). y-axis: read count. (B) One GWAS reported SNP rs11986414 is inside and another SNP rs4875960 is near this repeat. In both SNPs, genotype A tends to have larger repeat length.