Genomic Variations in Plasma Cell Free DNA Differentiate Early Stage Lung Cancers from Normal Controls

Lung Cancer Journal



Drs. Shu Xia and others recently determined that early stage lung cancer can be detected in patients, using noninvasive, blood-based genomic and genetic assays which sensitively distinguish early stage disease when combined with other existing screening strategies, including low-dose CT scanning.

To evaluate copy number variations (CNV) and identify potential mutations, they performed low-pass whole-genome sequencing and targeted sequencing of 50 cancer genes. The NEXTflex™ Cell Free DNA-Seq Kit was used to construct libraries from cfDNAs and tumor tissue DNAs isolated from lung adenocarcinoma patients, and from cfDNAs isolated from normal controls for low-pass whole-genome Illumina sequencing. Targeted sequencing was performed using the Ion AmpliSeq™ Cancer Hotspot Panel V2.

To accurately reflect the tumor-associated genomic abnormality burden in plasma, Xia et al. developed a new scoring algorithm, plasma genomic abnormality (PGA) score, by summarizing absolute log2 ratios in most variable genomic regions. Digital PCR and allele-specific PCR was performed to validate mutations detected by targeted sequencing.

Xia, S. et al. (2015) Genomic variations in plasma cell free DNA differentiate early stage lung cancers from normal controls. Lung Cancer. doi: 10.1016/j.lungcan.2015.07.002.

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