Bone marrow failure NGS panel

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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 179 genes*:

Overview genes present in BMF-panel

ABCAl

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

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.

Some additional regions might be missed in a sample, due to low coverage or uniformity (part 3, below).

* 20 June 2025: Contrary to what was previously stated on this website, the ADA2 gene is not and has not been part of the bone marrow failure panel. For Sanger sequence analysis of the ADA2 gene, please contact the dept of clinical genetics at the AmsterdamUMC ([email protected], +31 (0)20 - 566 5281).

Background information