Extended Data Fig. 2: Patient genotyping and population-genetic data.
From: Aberrant phase separation and nucleolar dysfunction in rare genetic diseases
(a) Variant detection and filtering scheme of the whole genome (I1 and I5) and exome sequencing data (I4). (b) gDNA Sanger sequencing data of HMGB1 in I1. (c) gDNA Sanger sequencing data of HMGB1 in I2, and I3, note identical de novo frameshift also found in I2 c.551_554delAGAA, de novo occurrence in I3. (d) Exome sequencing data of HMGB1 in I4. Note identical frameshift as in I2 in I3, and de novo occurrence. (e) Sequencing of HMGB1 cDNA in I3 and an unaffected control. Note the detection of both the wildtype and mutant cDNA in I3. (f) Allele counts of non-synonymous variants in HMGB1’s acidic tail in the gnomAD database (v.2.1.1). Note that especially non-acidic substitutions are rare, and no frameshifts of HMGB1 are listed in gnomAD. (g) Position of nonsynonymous variants in HMGB1’s acidic tail. Note that most variants do not significantly shorten the uninterrupted succession of aspartic acid (D) and glutamic acid (E). The 4 non-acidic substitutions comprise merely 5 of 1123 non-synonymous alleles of the acidic tail listed in gnomAD. (h) Pedigree of family 6. Squares denote male, circles denote female individuals. Individuals diagnosed with BPTAS are highlighted with solid black boxes, and the genotypes are displayed below the boxes. WT = wildtype. (i) Microdeletion in 13q12.3 in I5. CMA data showing loss of HMGB1 in I6. (j) qPCR showing de novo occurrence and revealing deletion of all exons, colored primers are positioned between the last non-deleted and first deleted oligo of the CMA, black primer X chromosomal control. Data are from one biological replicate.
