Supplementary Materials

Somatic mutation in single human neurons tracks developmental and transcriptional history

Michael A. Lodato, Mollie B. Woodworth, Semin Lee, Gilad D. Evrony, Bhaven K. Mehta, Amir Karger, Soohyun Lee, Thomas W. Chittenden, Alissa M. D’Gama, Xuyu Cai, Lovelace J. Luquette, Eunjung Lee, Peter J. Park, Christopher A. Walsh

Materials/Methods, Supplementary Text, Tables, Figures, and/or References

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  • Figs. S1 to S14
  • Captions for tables S1 to S10
  • Materials and Methods
Table S1
Coverage statistics for bulk tissues and single-cell MDA WGS.
Table S2
Validation of candidate SNVs. "Triple-called" SNVs and SNVs called by GATK and only one somatic caller were validated by Sanger sequencing in single-neuron MDA samples and bulk tissue. In addition, while performing genotyping for shared SNVs across 226 cells from the cortex, three SNVs, present in Brain B Neurons 2 and 77, were validated in Neuron 24 which were not called by MuTect or Varscan. Two of the SNVs were called by GATK only and one SNV which was not called but had supporting reads for the ALT allele.
Table S3
Triple-called SNVs called in each single neuron. Chromosome, hg19 position, reference and alternate alleles, and genotypes of each single neuron and bulk heart are indicated. 0 indicates reference allele, 1 indicated heterozygous allele.
Table S4
Correlation of single-neuron SNV rate and replication time. Spearman correlation and p-value in each chromosome and across the whole genome in neurons from Brains A, B, and C.
Table S5
Analysis of expression level of mutated genes. Mutated genes were tested for enrichment in each of four quartiles for the indicated samples, corrected for gene length. All genes with an SNV in an intron or exon were used.
Table S6
Enrichment of somatic SNVs in epigenetic features. Correlation between 10 Mb bin-based mutation rates (from Brain A, Brain B, Brain, C, and TCGA GBM) and the sizes of Roadmap epigenomic features.
Table S7
Gene ontology analysis of single-neuron SNVs. GO terms which were enriched for single neuron SNVs, raw and corrected p-values, number of genes in each GO category in the genome, and the number of hits in the dataset are shown. SNVs in genes highlighted in Figure 4 are presented. KEGG Pathway analysis of single-neuron SNVs. KEGG Pathways enriched for single neuron SNVs, raw p-values, indication corrected p-value significance, number of genes in each GO category in the genome, and number of hits in the dataset are shown.
Table S8
Protein-altering SNVs. SNVs that induce missense or nonsense changes, hg19 position, the mutated genes, the reference and alternate alleles, and the effect of the SNV on the protein product are shown. Human gene mutation database (HGMD) query results for human diseases associated with mutated genes are shown. Second sheet shows SIFT/PROVEAN prediction of the functional impact of protein altering SNVs. The third sheet contains noncoding SNVs highlighted in Fig. 2F.
Table S9
Shared SNVs genotyped across single neurons. Variant hg19 position and substitution type, single neurons in which the SNVs were validated, and those in which the variants were initially triple called, are indicated. Other WGS evidence for validated non-triple called SNVs is indicated.
Table S10
Analysis of shared SNVs by ultra-deep sequencing of a targeted panel. Shared Brain B SNVs were sequenced across a panel of 25 cortical samples (A-Z), 7 body samples, and 4 unrelated control samples. Spatial location of cortical samples A-Z is shown in the second sheet.