BPER diagnostic sensitivity, specificity, positive and negative predictive values to detect at least 1 mutation by sample were 100% [69-100], 95% [85-99], 83% [52-97], and 100.
cfDNA NGS analyses using BPER were performed on plasma from pancreatic-cancer patients who had 1 plasma sample at initiation of chemotherapy (100 plasma samples), and lung-cancer patients who had serial plasma samples when treatment was initiated and during follow-up (273 plasma samples).
In particular, the BPER method was analytically more sensitive than dPCR at detecting the EGFR exon-19 deletions, which had a very low PER (<0.
The positivity rate of ctDNA was similar in pretreatment plasma samples from patients with KRAS and/or TP53 mutations (16/25, 64%), confirming that the BPER method was suitable for a broad range of mutations.
We developed an R package, which contains functions to analyze BAM files of targeted NGS with the BPER method.
7] Nonstandard abbreviations: ctDNA, circulating tumor DNA; dPCR, digital PCR; NGS, next-generation sequencing; PER, position error rate; AF, allele frequency; BPER, base-PER; SNV, single nucleotide variation; Safe-SeqS, Safe-Sequencing System; INDEL, insertion/deletion; SNP, single nucleotide polymorphism; cfDNA, cell-free DNA; FFPE, formalin-fixed paraffin-embedded; BAM, binary alignment; GATK, Genome Analysis Tool Kit; MAF; minor AF.
3 February 2010 A[cent sign]a'[not sign]a[euro]oe Credit rating agency Fitch has revised the outlook on Italy's Banca Popolare dell'Emilia Romagna (BIT:EMII), or BPER
, to "negative" from "stable", BPER
said in a statement.