Fast multiclonal clusterization of V(D)J recombinations from high-throughput sequencing

BMC Genomics

Table 2 Two most abundant TR γ clones detected in 100,000 sequences from diagnosis sample (Diag) of a patient with ALL

				Vidjil	IMGT/V-QUEST	IgBlast
Clone #01	TRGV5*01	-5/CC/0	TRGJ1*02	9 204 reads	7 376 reads	11 319 reads
	... GTGCCACCTGGG	CC	TTATTATAAGAA...	(31.9%)	(42.1%)	(36.3%)
Clone #02	TRGV10*02	-5/AGAC/ -3	TRGJP1*01	253 reads	175 reads	353 reads
	... TGTGCTGCGTGG	AGAC	CCACTGGTTGGT...	(0.88%)	(0.80%)	(1.1%)

In this sample, 28 809 reads have been segmented by Vidjil, 29 039 by IMGT/HighV-QUEST (and 21 876 when taking into account IMGT/JunctionAnalysis results) and 31 147 by IgBlast. For each method, the number of associated reads is given. The VJ segmentation proposed by Vidjil was manually checked against the analysis provided by IMGT/V-QUEST and IgBlast. Clone #01 has the recombination TRGV5*01 -5/CC/0 TRGJ1*02, which means that the V gene is TRGV5*01, according to the IMGT nomenclature, and its last five nucleotides have been deleted. The N-diversity region is composed of two inserted Cs, and the J gene is TRGJ1*02, which has no deletion.

ISSN: 1471-2164