Table 1.
Total number of sequences | Sequences with VH, DH, JH gene assignmenta | Length of VH replacement footprint | VH replacement footprint motifs in N1 | VH replacement footprint motifs in N2 | p-Valueb | Frequency of VH replacement products (%)c | |
---|---|---|---|---|---|---|---|
Test IgH sequencesd | 417 | 396 | 3 | 217 | 140 | 0.0001 | 54.7 |
4 | 99 | 64 | 0.0028 | 25.0 | |||
5 | 29 | 15 | 0.0437 | 7.3 | |||
6 | 5 | 3e | NAf | NAf | |||
7 | 2 | 0 | NAf | NAf | |||
NCBI IgH sequencesg | 61,851 | 39,438 | 3 | 23,195 | 20,699 | 0.0001 | 58.8 |
4 | 13,365 | 11,240 | 0.0001 | 33.9 | |||
5 | 4788 | 3499 | 0.0001 | 12.1 | |||
6 | 1490 | 813 | 0.0001 | 4.3 | |||
7 | 382 | 140 | 0.0001 | 1.1 |
aUnique IgH gene sequences with identifiable VH, DH, and JH genes were analyzed. These IgH sequences contain both functional and non-functional IgH rearrangements. N1, VH–DH junction regions; N2, DH–JH junction regions.
bThe frequencies of VH replacement footprint motifs with different length within the N1 or the N2 regions were compared by two-tailed Chi square with Yates’ correction. p < 0.05 is considered statistically significant and p < 0.0001 is considered extremely statistically significant.
cThe frequency of VH replacement products was calculated using the number of sequences with VH replacement motifs with different length in the N1 regions divided by the total number of unique IgH gene sequences.
dThese IgH gene sequences had been analyzed manually for VH replacement products (37).
eAll the three 6-mer footprints within the N2 regions could be due to second DH gene segments.
fNot applicable.
gThe human IgH gene sequence dataset was downloaded from the NCBI database on April 20, 2011.