Table 2.

In silico size-based filtering of insert size for ctDNA detection

Publication	Methods	Cancer (sample size)	Baseline detection characteristics	Results
Mouliere et al., 2018 [68]	sWGS to calculate tMAD scores Size selection for inserts with lengths of 90–150 bp	“High ctDNA” cancers from melanoma, ovarian, lung, colorectal, cholangiocarcinoma, and other (N = 189) Healthy controls (N = 65)	AUC = 0.69	After size selection, AUC increase to 0.90
	WES for point mutations Size selection for inserts with lengths of 90–150 bp	HGSOC (N = 6; pre-treatment)	821 mutations identified in 6 patients, with mean MAF of 12.0% (median of 9.5%, range 0.53–100%)	Mean increase in MAF of 2.2-fold (median 2.25-fold increase) In 6 of 6 patients, size selection identified an additional 188 mutations, with mean MAF of 21.5% (median of 16.9%, range 3.0–88.9%)
		HGSOC (N = 6; post-treatment)	202 mutations identified in 6 patients, with mean MAF of 8.1% (median of 6.5%, range 1.2–47.6%)	In 6 of 6 patients, size selection identified an additional 122 mutations, with mean MAF of 30.3% (median of 25.0%, range 7.3–85.7%)
		Colorectal, cholangiocarcinoma pancreatic, and prostate (N = 16)	2133 mutations in plasma with matched mutations in tumour DNA (MAF range ~1% to ~70%)	Size selection increased mean MAF by 1.7-fold in 97% of mutations In 13 of 16 patients, size selection identified additional mutations
Smith et al., 2020 [115]	sWGS to detect SCNAs based on tMAD score Size selection for inserts with lengths of 90–150 bp	Renal tumours (benign to metastatic; N = 48)	SCNA detected in 4 of 48 (6.3%) samples	After size selection, 41 of 48 samples met criteria for tMAD analysis (> 2 million reads) Average tMAD score increased 2.2-fold (range 1.25–4.83) SCNA-based ctDNA detected in 8 additional patients (11/48, 22.9%)
		RCC, N = 43, 41 patients with metastatic disease, 35 patients with primary tumour removed	SCNA detected in 8 of 43 samples (18.6%), with median MAF of 7% (range 4–17%)	SCNA detection increased to 14 of 43 samples (32.6%) MAF increased by a mean of 2.2-fold (range 0.9–5.7) to a median of 8% (range 4–23%)
Nygard et al., 2020 [168]	sWGS to detect SCNAs based on tMAD score Size selection for inserts with lengths of 90–150 bp	Inoperable, stage III NSCLC (N = 6; 23 samples)	SCNA detection in 5 (22%) samples from 3 of 6 patients	SCNA detection increased to 16 of 23 samples (70%) from 6 of 6 patients

AUC area under the curve, ctDNA circulating tumour DNA, HGSOC high-grade serous ovarian carcinoma, MAF mutant allele frequency, NSCLC non-small cell lung cancer, RCC renal cell carcinoma, SCNA somatic copy number alteration, sWGS shallow whole genome sequencing, tMAD trimmed median absolute deviation from copy number neutrality, WES whole exome sequencing