Cell-free DNA liquid biopsy for early detection of gastrointestinal cancers: A systematic review

Table 4 Details of extraction and sequencing methods used in each of the included studies

Ref.	Source of cfDNA	Focus in cfDNA	Extraction method (used kit)	Sequencing method	Sequencing method details
Li et al[13]	Plasma	Methylated markers	QIAamp Circulating Nucleic Acid Kit (Qiagen, 55114)	NGS	Illumina HiSeq 2000 platform
Chen et al[14]	Plasma	Cancer-specific methylation signatures	QIAamp Circulating Nucleic Acid kit (Qiagen, 55114)	NGS	APA Library Quantification Kit for Illumina (KK4844) and sequenced on an Illumina NextSeq 500
Guler et al[18]	Plasma	5hmC modifications	QIAamp Circulating Nucleic Acid Kit (QIAGEN, Germantown, MD)	NGS	NextSeq550 instrument with version 2 reagent chemistry (Illumina, San Diego, CA).
Junca et al[12]	Plasma	KRAS and BRAF mutational status	QIAamp Circulating Nucleic Acid kit (Qiagen, Hilden, Germany)	RT-PCR	Q24 PyroMark system (Qiagen, Hilden, Germany)
Tao et al[15]	Plasma	Somatic copy number aberration	QIAamp CirculatingNucleic Acid Kit (Qiagen)	NGS	Next generation sequencing (Illumina)
Cristiano et al[19]	Plasma	Fragmentation size	Qiagen Circulating Nucleic Acids Kit (Qiagen GmbH)	NGS	NEBNext DNA Library Prep Kit for Illumina
Li et al[17]	Plasma	Aberrant DNA hypermethylation of CpGislands	DNeasy Blood & TissueKit (Qiagen)	NGS	Methylated CpG tandem ampli-fication and sequencing
Qu et al[16]	Plasma	Specific mutations	ARCHITECT i2000SR Chemical luminescence immunity analyzer	NGS	Next generation sequencing
Cai et al[11]	Plasma	5hmC modifications	NA	NGS	5hmC-Seal
Wan et al[9]	Plasma	cfDNA mutations patterns	MagMAX cfDNA Isolation Kit	NGS	Illumina NovaSeq 6000 Sequencing System
Jensen et al[20]	Plasma	Tumour-specific DNA methylation	Gentra Puregene Tissue Kit (Qiagen)	DD-PCR	Bisulfite sequencing and methylation-specific droplet digital PCR
Nunes et al[21]	Plasma	Aberrant DNA methylation	QIAamp MinElute ccfDNA (Qiagen, Hilden, Germany)	qMSP	qMSP
Perrone et al[22]	Plasma	KRAS mutated cfDNA	Qiamp DNA Blood Extraction Kit (Qiagen)	RT-PCR	RT-PCR

NGS: Next-generation sequencing; RT-PCR: Real-time polymerase chain reaction; qMSP: Multiplex methylation-specific polymerase chain reaction.