Table 1.

Summary of genomic analyses.

Sequencing analysis
Number of amplicons attempted 219,229 (100%)
Number of amplicons passing quality control* 208,311 (95%)
Fraction of bases in passing amplicons with PHRED > 20 98.3%
Number of genes analyzed 20,661
Number of transcripts analyzed 23,219
Number of exons analyzed 175,471
Total number of nucleotides successfully sequenced 689,071,123
Number of somatic mutations identified (n = 22 samples) 2,325
Number of somatic mutations (excluding Br27P) 993
    Missense 622
    Nonsense 43
    Insertion 3
    Deletion 46
    Duplication 7
    Splice site or UTR 27
    Synonymous 245
Average number of sequence alterations per sample 47.3
Copy number analysis
Total number of SNP loci assessed for copy number changes 1,069,688
Number of copy number alterations identified (n = 22 samples) 281
    Amplifications 147
    Homozygous deletions 134
Average number of amplifications per sample 6.7
Average number of homozygous deletions per sample 6.1
  • * Passing amplicons were defined as having PHRED20 scores or better over 90% of the target sequence in 75% of samples analyzed [see (12) for additional information].