Figure 2.

Somatic and Germline Mutations are Bi-allelic

Integrative Genomics Viewer (IGV) visualization of two samples showing both methods of establishing phase. Each panel shows reads from the initial discovery sequencing and the reads used to establish phase.

(A) Somatic and germline mutations in 6003-1 are both A>T point mutations and highlighted by the blue and green regions respectively. Because the distance between these mutations is relatively small (357bp), phase was established using Illumina short-reads (also used for validation). Black lines between reads denote read pairs, showing that both reads originate from a single molecule of DNA. Each molecule with the somatic mutation contains the wild-type (WT) allele at the germline mutation position; this proves that the mutations are bi-allelic.

(B) Somatic and germline mutations in sample 6001-3, both small deletions. The genomic distance between these mutations is 4377bp. In long reads that span the two mutations, each read with the somatic mutation contains the WT allele at the position of the germline mutation.