Best practices for variant calling in clinical sequencing

Table 1 Sequencing strategies for NGS and empirical variant detection sensitivity. The Otoscope hearing loss panel v5 [18], which targets 89 genes and microRNAs, illustrates a typical gene panel. The approximate size of the total target space is given in megabase pairs (Mbp). Typical exome kits target ~ 50 Mbp of genome bases comprising coding sequences, splice sites, alternative exons, and some non-coding RNAs, though this space varies among manufacturers

Strategy	Panel	Exome	Genome
Size of target space (Mbp)	~ 0.5	~ 50	~ 3200
Average read depth	500–100×	100–150×	~ 30–60×
Relative cost	$	$$	$$$
SNV/indel detection	++	++	++
CNV detection	+	+	++
SV detection	–	–	+
Low VAF	++	+	+

Dollar signs represent approximate relative costs, though it should be noted that the cost of panel sequencing depends on the size of the panel. The empirical performance of each strategy for detecting variants of different classes is indicated as good (+), outstanding (++), or poor/absent (−)

ISSN: 1756-994X