Comprehensive serial molecular profiling of an “N of 1” exceptional non-responder with metastatic prostate cancer progressing to small cell carcinoma on treatment

Table 1 Sequencing statistics for the diagnostic prostate biopsy sample containing conventional adenocarcinoma (PR-259) and subsequent liver metastasis with small cell/neuroendocrine carcinoma (PR-258)

Parameter	PR259	PR258
DNA sequencing
Mapped reads (n)	25,670,652	2,937,737
On target reads (%)	98.1 %	99.0 %
Total aligned base reads	2,672,758,224	322,308,287
Total base reads on target	2,562,288,371	310,618,776
Average base coverage depth	1,517	184
Uniformity of base coverage	51.2 %	90.9 %
Target base coverage at 20×	89.9 %	94.2 %
Target base coverage at 100×	71.7 %	72.4 %
Target bases with no strand bias	93.5 %	93.3 %
Total called variants^a	2,556	1,177
Variants passing filtering^b	5	6
Somatic variants^c	3	4
Prioritized somatic variants^d	1	2
RNA sequencing
Total reads (n)	66,564	247,655
Uniquely mapped to genome (%)	38 %	79 %
Identified gene fusions (n)	0	0

^aVariants called by automated low stringency variant calling
^bVariants passing filtering of technical artifacts, poorly supported variants, germline SNPs and synonymous/non-coding variants
^cVariants confirmed as somatic through exome sequencing of germline DNA
^dSomatic variants prioritized as likely driving oncogenic or tumor suppressive mutations as described in the eMethods