Table A. Nature of base substitutions in VH genes
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Substitutions in controlsSubstitutions in A-T patients
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To:TCAGTotalTo:TCAGTotal
From:From:
T/47172084 T/582034112
C105/2234161C126/2333182
A3743/103183 A4651/111208
G266798/191 G3571119/225
Total168157137157619Total207180162178727
Mutations at G or C sites57%Mutations at G or C sites56%
Transversions43%Transversions43%
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Table B. VH3, D and J gene usage in A-T patients and age-matched controls
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Control clonesA-T clones
No.%No.%
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VH3 genes
VH3-77(16.7%)5(12.5%)
VH3-91(2.4%)1(2.5%)
VH3-112(4.8%)5(12.5%)
VH3-130(0)1(2.5%)
VH3-150(0)2(5%)
VH3-201(2.4%)0(0)
VH3-214(9.5%)3(7.5%)
VH3-237(16.7%)6(15%)
VH3-304(9.5%)2(5%)
VH3-30-31(2.4%)4(10%)
VH3-332(4.8%)6(15%)
VH3-483(7.1%)1(2.5%)
VH3-490(0)1(2.5%)
VH3-532(4.8%)2(5%)
VH3-641(2.4%)0(0)
VH3-661(2.4%)0(0)
VH3-721(2.4%)1(2.5%)
VH3-731(2.4%)0(0)
VH3-744(9.5%)0(0)*a
Total4240
D gene family
D18(17%)4(8%)
D211(23%)16(31%)
D314(30%)20(37%)
D44(9%)1(2%)
D53(6%)5(10%)
D65(11%)5(10%)
D72(4%)1(2%)
Total47b(100%)52(100%)
JH gene family
JH14(8%)1(2%)
JH22(4%)2(4%)
JH37(15%)6(12%)
JH415(31%)36(69%)***
JH57(15%)1(2%)*
JH613(27%)6(12%)
Total48(100%)52(100%)
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a). The statistical analysis was performed using 2 test. The numbers that are significantly
different from the control’s are bolded. * p < 0.05, *** p < 0.001. For VH3 gene usage,
the data from A-T cell lines was included.
b). In one clone, the D segment could not be unambiguously assigned.
Table C. Characteristics of the CDR3 regions in cells from A-T patients and age-matched controls
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Control clonesA-T clones
(n=48)(n=52)
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Length of CDR312.6 + 5.412.1 + 3.9
Length of N nucleotides
N1 (VH-D junction)5.0 + 6.04.0 + 3.8
N2 (D-JH junction)5.0 + 5.24.9 + 6.1
P-nucleotide insertion14/48 (29.2%)18/52 (34.6%)
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Fig. A , G/C mutation (normal)
, A/T mutation (normal)
,G/C mutation (A-T)
, A/T mutation (A-T)
Transitions
-15 -10 -5 0 +5 +10 +15
Transversions
Nature of base substitutions around the switch junctions in normal controls
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To:TCAGTotal
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From:
T/0*336**
C15***/81033***
A30*/58**
G6511*/22
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Total245**221869
Mutations at G or C sites80%***
Transversions55%
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Fig. ANature of base substitutions around the switch junctions in normal individuals. A. Mutations at or close to the switch junctions (+15 bp). The ruler indicates the position of the mutations relative to the switch breakpoints. 0 position was defined as a nucleotide precisely at the breakpoint that was not identical to either of the S regions. Minus and plus numbers indicate positions in the S and S regions respectively. Nucleotide substitutions that resulted from transitions are shown above the ruler and those caused by transversions are shown below the ruler. B. Mutation patterns around the switch junctions. The statistical analysis was performed using 2 test assuming a random distribution of replacement. * p< 0.05, ** p<0.01, ***p<0.001.