Targeted Callers
Generated on 2026-05-07
Targeted Callers
Repetitive regions in the human genome pose a challenge for general variant calling approaches which typically cannot make use of potentially misplaced MAPQ0 reads. Furthermore, high sequence homology of some genes with a pseudogene paralog can lead to a wide variety of common structural variants (SVs) in the population, requiring specialized targeted calling approaches. DRAGEN supports targeted calling for a number of genes/targets as described in subsequent target-specific sections. For more information, refer to the DRAGEN user guide.
DRAGEN: DRAGEN 4.5.4 | Assay: WGS
Performance summary
Targeted caller concordance summary (WGS)
CYP2D6
211
212
99.5%
SMN1
247
250
98.8%
SMN2
244
250
97.6%
GBA
24
24
100.0%
CYP2B6 (GeT-RM)
70
76
92.1%
CYP2B6 (PacBio HiFi)
123
125
98.4%
CYP21A2
82
84
97.6%
HBA1/2
244
247
98.8%
RHD/RHCE
41
42
97.6%
CYP2D6
Concordant across 211 out of 212 (99.5%) WGS samples with calls from GeT-RM and long read sequencing data.
CYP2D6 concordance by star allele type
without SV
90
89 (98.9%)
deletion
15
15 (100%)
duplication
12
12 (100%)
fusion/conversion
26
26 (100%)
Total
143
142 (99.3%)
References: DRAGEN Product Guide | Cyrius: accurate CYP2D6 genotyping using WGS data
SMN1/2
Concordant across 247/250 (98.8%) WGS samples for SMN1 and 244/250 (97.6%) WGS samples for SMN2, compared against digital PCR and MLPA.
SMN1 concordance by copy number
0
42
42 (100%)
1
23
23 (100%)
2
96
94 (97.9%)
3
68
68 (100%)
4
20
20 (100%)
6
1
0 (0%)
Total
250
247 (98.8%)
SMN2 concordance by copy number
0
26
26 (100%)
1
73
71 (97.3%)
2
92
89 (96.7%)
3
54
54 (100%)
4
5
4 (80%)
Total
250
244 (97.6%)
References: DRAGEN Product Guide | SMA carrier screening from WGS data
GBA
Concordant across 24/24 (100%) WGS samples compared against digital PCR and long read sequencing data.
GBA concordance by variant type
Gain
None
10
10 (100%)
Loss
None
2
2 (100%)
Loss
RecNciI
1
1 (100%)
Loss
A495P
1
1 (100%)
Neutral
L483P
7
7 (100%)
Neutral
c.1263del
1
1 (100%)
Neutral
c.1263del+RecTL
2
2 (100%)
Total
24
24 (100%)
References: DRAGEN Product Guide | GBA gene for Gaucher and Parkinson disease research
CYP2B6
Concordance against calls from GeT-RM and long read sequencing data. Concordance is based on metabolizer status when multiple genotypes are reported. Two discordant samples in the PacBio comparison are due to a novel star allele (*U1) resulting in multiple possible genotypes.
CYP2B6 concordance by reference source
GeT-RM
76
70 (92.1%)
PacBio HiFi reads
125
123 (98.4%)
References: DRAGEN Product Guide
CYP21A2
Concordant across 82/84 (97.6%) WGS samples across three benchmark sets with calls from long-range PCR, MLPA and long read sequencing.
CYP21A2 concordance by benchmark set
Internal
14
13 (92.9%)
1KGP
66
65 (98.5%)
Coriell
4
4 (100%)
Total
84
82 (97.6%)
References: DRAGEN Product Guide | CYP21A2 blog
HBA1/2
Concordant across 244/247 (98.8%) WGS samples compared against long read sequencing data.
HBA1/2 WGS concordance by genotype
aa/aa
202
199 (98.5%)
-α3.7/aa
31
31 (100%)
--/aa
4
4 (100%)
-α3.7/-α3.7
4
4 (100%)
αααα3.7/aa
3
3 (100%)
-α4.2/aa
2
2 (100%)
αααα4.2/aa
1
1 (100%)
Total
247
244 (98.8%)
References: DRAGEN Product Guide | HBA targeted caller
LPA
LPA copy number is assessed via allele-specific KIV-2 repeat quantification. Accuracy was evaluated by trio/duo-based inheritance analysis and comparison against Bionano optical mapping.
Figure: (A) Trio-based phased KIV-2 copy number comparison in 120 offspring vs best-matching parental call. (B) Duo-based comparison in 153 offspring. (C) Total copy number vs Bionano optical mapping (n=145). (D) Allelic copy number vs Bionano optical mapping (n=145). Pearson's r and P-value shown per panel.
References: DRAGEN Product Guide | KIV-2 copy number variants for cardiovascular disease risk
RHD/RHCE
Concordant across 41/42 (97.6%) WGS samples compared against long read sequencing data.
RHD/RHCE concordance by gene conversion status
Not present
24
24 (100%)
Heterozygous
10
9 (90%)
Homozygous
8
8 (100%)
Total
42
41 (97.6%)
References: DRAGEN Product Guide
Star Allele Caller
The Star Allele Caller identifies the genotypes and metabolism status of the following PGx genes that are included in FDA's PGx recommendations or have CPIC Level A designation: CACNA1S, CFTR, CYP2C19, CYP2C9, CYP3A4, CYP3A5, CYP4F2, IFNL3, RYR1, NUDT15, SLCO1B1, TPMT, UGT1A1, VKORC1, DPYD, G6PD, MT-RNR1, BCHE, ABCG2, NAT2, F5 and UGT2B17. For more information, refer to the DRAGEN user guide.
1K genomes project
3201
PharmCAT (from DRAGEN gVCF)
DPYD, CACNA1S, UGT1A1, TPMT, CYP3A5, CFTR, CYP2C19, CYP2C9, SLCO1B1, NUDT15, VKORC1, CYP4F2, RYR1, IFNL3
100%
Coriell
96
PharmCAT (from DRAGEN gVCF)
DPYD, CACNA1S, UGT1A1, TPMT, CYP3A5, CFTR, CYP2C19, CYP2C9, SLCO1B1, NUDT15, VKORC1, CYP4F2, RYR1, IFNL3
100%
Coriell
96
GeT-RM (using orthogonal methods)
CYP2C19, CYP2C9, CYP3A5, CYP4F2, TPMT
94%*
1K genomes project
100
Aldy (from BWA/GATK BAM)
G6PD, CFTR, IFNL3, TPMT, VKORC1
100%
* Truth set from 2016; 6% calls from outdated star allele definition.
Last updated
Was this helpful?