Bone marrow failure NGS 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 BMF Panel (IAD156379_243) consists of 3140 amplicons and is covering 861,9 Kbase. 99,1% of desired areas (exons, flanking intronic regions, untranslated regions and promotor areas) are covered from the following 180 genes:

Overview genes present in BMF-panel
ABCAl1	BLOC1S3	CXCR4	FANCE	HPS1	MAP2K2	PMS2	RPL35A	SAMD9L	THP0
ABCB7	BLOC1S6	CYCS	FANCF	HPS3	MASTL	PRF1	RPL36	SBDS	TINF2
ABCG5	BRCA1	DDX41	FANCG	HPS4	MKL1	PTPN11	RPL5	SBF2	TP53
ABCG8	BRCA2	DHFR	FANCI	HPS5	MLPH	RAB27A	RPS10	SEC23B	TPM4
ACBD5	BRIP1	DKC1	FANCL	HPS6	MPL	RAC2	RPS14	SH2D1A	TPP1
ACD	C15orf41	DNAJC21	FANCM	IKZF1	MTHFD1	RAD51	RPS15	SLC37A4	UBE2T
ACTB	C6orf25	DTNBP1	FAS	IL2RG	MYO5A	RAD51C	RPS15A	SLFN14	UNC13D
ADA	CBL	ELANE	FASLG	ITK	NBEAL2	RBM8A	RPS17	SLX4	USB1
ADA2	CDAN1	EPCAM	FlI2	JAGN1	NBN	RIT1	RPS19	SMARCD2	VIPAS39
AK2	CDC42	ERCC4	FYB	JAK2	NF1	RMRP	RPS24	SOS1	VPS33B
ALAS2	CEBPA	ERCC6l2	G6PC3	KLF1	NOLA2	RNF168	RPS26	SRC	VPS45
ANKRD26	CEBPE	ETV6	GATA1	KRAS	NOLA3	RPL10	RPS27	SRP72	WAS
AP3B1	CLPB	EVl1	GATA2	LAMTOR2	NRAS	RPL11	RPS28	STX11	WDR1
AP3D1	COX4-1	FADD	GFl1	LIG4	PALB2	RPL15	RPS29	STXBP2	WIPF1
ASXL1	CSF2RA	FANCA	GFl1B	LYST	PARN	RPL26	RPS7	TAZ	WRAP53
ATM	CSF3R	FANCB	GINS1	MAD2L2	PGM3	RPL27	RTEL1	TCIRG1	XIAP
ATRX	CTCl	FANCC	HAX1	MAGT1	PLAU	RPL27A	RUNX1	TERC	XRCC2
BLM	CTSC	FANCD2	HOXA11	MAP2K1	PLCB2	RPL31	SAMD9	TERT	YARS2

Genes present in BMF-panel
The percentage of target bases that is covered at least 20 times (%Base20x) is at least 99,0% for the recommended Mapped Reads of 4.000.000. For 69 different genes a few bases are missed, either in the design or due to practical coverage, as listed in Part 1 of the table below. Some pathogenic variants listed in the HGMD database are missed as well, as can be seen in part 2 of this table.