Severe toxicity to capecitabine due to a new variant at a donor splicing site in the dihydropyrimidine dehydrogenase (DPYD) gene

Figures & data

Table 1 List of primers used for DPYD exon sequencing

Exon number	Forward	Reverse	Fragment size
EXON 1	ACTTGGCTCTCTGGCTGGAGCTT	AAACTTTCCCGCGTCTCTCACTC	234
EXON 2	TTAGCCAGGTGTGGTAGCGTAC	TGCCTTACAATGTGTGGAGTG	410
EXON 3	TGAGACTTCTGTGACAGCTGTA	CCTCAAGGGAAGTCTCTCCAC	442
EXON 4	GGAGTGCCAAAGATGAAACACA	TGGATTTGCTAAGACAAGCTG	362
EXON 5	TCCTATGTGTCAAATACTCTGCT	TGGGTATCAACAGAGCACCA	444
EXON 6	AGGAGGCATGACTCTAGAAAGG	CCATTAAAAGAAATATTCACAGGGCT	719
EXON 7	AGAATGTAGATGTCCTCATGCA	TGCATGACATTTGCTGTTAATC	331
EXON 8	AGCCCTTAATAGAACATGTTCCT	TGAAGGCAGTCATTCTTCTGG	374
EXON 9	TGCTTACAGATGTTTTCCTCT	ACAATGTGCTGCTGAGCTTG	324
EXON 10	TGGAAAACTGCAAGATGCAA	AGCCCTTGAGTATTGACAAAG	312
EXON 11	TGGTGAAAGAAAAAGCTGCAT	GTTCTTTTCAATACTTGCCACT	548
EXON 12	TGTGTTGTTAACTCCAATATTTCGT	TCAAGCATCCTCCCGCTT	621
EXON 13	TTCGGATGCTGTGTTGAAGT	AATGTGTAATGATAGGTCTTGTCAAA	443
EXON 14	GCTTTTCTTTGTCAAAAGGAGAC	AGCTTCACATTGTGTGGGTT	409
EXON 15	TAATTCCAAAGCCCCAAATG	TTTCTCATGGCAGCTCTTTATTT	346
EXON 16	TCAACGGTGAAAGCCTATTG	AGCTTCCCTCATTTTCCACT	318
EXON 17	TTTGTCTTGCACGTCTCCAG	AGGATCTTGTGTTTCCAGATCA	437
EXON 18	TGAGAAAGTAAAGTTGTGGTAATT	GGGATCATAAAGGGCACAAA	423
EXON 19	TCCAGTGACGCTGTCATCA	ACAGGACAGGAAATAAACCTCA	434
EXON 20	AGACGGCTACTGATCCATCA	TCTGAAATAGAAACCAAGGCTGA	375
EXON 21	CCCATTTTTCTCTTCTCTGAGC	ATGCATGCTTGCCAGTGT	423
EXON 22	TCTTTCAGAAGACAAACATCTAAGC	CAGAAAATGCTTTCTGCCGTA	402
EXON 23	ACGCTAAAATGGGGACATTG	ACATAAGACAACTGGCAGTG	517
EXON SKIPPING	TTAAAATCTGATGGCACACCTTG	TGCTTTTCAGATAAAGCAGGGCT

Figure 1 Sequence electropherogram of the 2242+1G>T variant. Blue, dCTP; green, dATP; black, dGTP; red, dTTP.

Abbreviations: dATP, deoxyadenosine triphosphate; dCTP, deoxycytidine triphosphate; dGTP, deoxyguanosine triphosphate; DPYD, dihydropyrimidine dehydrogenase; dTTP, deoxythymidine triphosphate.

Figure 2 Exon skipping sequence.

Notes: Left: Electrophoresis of amplified cDNA from peripheral blood mononuclear cells of a patient carrying the 2242+1G>T variant. Right, upper: Graphic representation of skipping of exon 19. Right, lower: Sequence electropherogram using the primer Ex18F. A double sequence is observed for 85 nucleotides corresponding to overlapping of exons 19 and 20.

Figure 3 Structures of wild-type DPYD and truncated DPYD.

Notes: The interpretation of mutation effect and the molecular modeling were performed by using Deep View Swiss-PDB viewer and Tasser. (A) Modeling of wild-type DPYD; (B) modeling of truncated DPYD.

Table 2 DPYD phenotyping results

UH2 concentration, ng/mL	U concentration, ng/mL	UH2/U concentration ratio	Activitya
89.32	13.47	6.6	Normal
85.16	24.13	3.5	Deficient
47.19	18.45	2.6	Deficient

Notes:

a Criteria for activity deficiency: uracil concentration >16 ng/mL and/or UH2/U ratio <6.

Abbreviations: UH2, dihydrouracil; U, uracil.