Specification of the NGS platelet panel

Targeted sequencing with the Ion Torrent System is able to identify single nucleotide variants, small insertions and small deletions. Variants in repeat sequences, large homopolymers and large insertions/deletions are not or difficult to identify.

The designed Thrombo AmpliSeq Panel (IAD96657_243) consists of 1468 amplicons and is covering 346,5 Kbase for 73 different genes as listed in Table 1. The panel is covering 98,8% of the desired regions (all coding regions (exons), flanking intronic regions, untranslated regions and promotor areas with known mutations).

Table 1: List of genes in Thrombo AmpliSeq panel, version 1.0

Overview genes present in Thrombo AmpliSeq panel

ABCG5	BLOC1S4	FLI1	GNB3	HPS6	NBEAL2	PTGS1	VIPAS39
ABCG8	BLOC1S5	FLNA	GP1BA	ITGA2	P2RY1	RASGRP2	VWF
ACTN1	BLOC1S6	GATA1	GPlBB	ITGA2B	P2RY12	RBM8A	WAS
ADRA2A	BLOC1S7/SNAPIN	GATA2	GP6	ITGB1	PEAR1	RHOA
ANKRD26	CYCS	GFI1B	GP9	ITGB3	PIK3CG	RUNX1
ANO6	DTNBP1	GNA12	HOXA1	LYST	PLAU	TBX1
AP3B1	ETV6	GNA13	HPS1	MASTL	PLCB2	TBXA2R
BLOC1S1	F2R	GNAI1	HPS3	MPL	PLCB3	TBXAS1
BLOC1S2	FCGR2A	GNAQ	HPS4	MYH9	PLCG2	THPO
BLOC1S3	FERMT3	GNAS	HPS5	NBEA	PRKACG	TUBB1

The percentage of target bases that is covered at least 20 times (%Base20x) is at least 99,1% for the recommended Mapped Reads of 2.800.000. This acceptance criteria will result in a coverage 98,8% of the areas of interest.

For 30 different genes a few bases are missed, either in the design or due to practical coverage, as listed in Table 2. Some pathogenic variants listed in the HGMD database are missed as well, as can be seen in Table 2.