Ultra-deep Illumina paired-end sequencing of cfDNA from cell lines

Accurate identification of genomic variations in cfDNA/ctDNA samples remains a challenge. This is mainly due to low allele frequency of some variants in the cfDNA/ctDNA mixture. In this project, we perform ultra-deep sequencing of DNA reference material obtained from SeraCare and Horizon Discovery using a custom 18-gene panel. The samples are as follows:- SeraCare:--- AF5: 5% variant allele frequency--- AF12: 1.2% variant allele frequency--- AF06: 0.6% variant allele frequency--- AF01: 0.1% variant allele frequency--- AFWT: Wild type with 0% variant allele frequency-Horizon Discovery:--- HD786: 5% variant allele frequency--- HD753: Wild type with 0% variant allele frequencyEach sample was sequenced twice using Illumina NextSeq500 sequencer (PE 2 x 150 bp).The number of reads per sample ranges between 33,000,000 and 79,000,000 paired-end reads. The sequencing read coverage ranges between 80,000x and 150,000x.