Table 3.
Base frequencies at the coordinates of interest in NB samples analyzed by deep sequencing (Illumina HiSeq 2500)
| Chr position/patient ID | Reads | T | G | C | A | ||||
|---|---|---|---|---|---|---|---|---|---|
| % | P-value | % | P-value | % | P value | % | P value | ||
| F1174L 3520 T>C, chr2:29220831 | |||||||||
| Controls | 79,7051 | 99.987 | NA | 0 | NA | 0.01 | NA | 0.003 | NA |
| PT1 | 32,757 | 92.805 | 0.00E+00 | 0 | NA | 7.192 | 0.00E+00 | 0.003 | NA |
| PT3 | 30,624 | 9999 | NA | 0 | NA | 0.01 | NA | 0 | NA |
| PT4 | 32,998 | 99.979 | NA | 0.003 | NA | 0.009 | NA | 0.009 | NA |
| PT5 | 35,142 | 99.98 | NA | 0 | NA | 0.017 | NA | 0.003 | NA |
| PT6 | 34,977 | 99.977 | NA | 0.003 | NA | 0.011 | NA | 0.009 | NA |
| PT7 | 37,846 | 99.976 | NA | 0 | NA | 0.021 | NA | 0.003 | NA |
| PT8 | 37,000 | 99.986 | NA | 0 | NA | 0.011 | NA | 0.003 | NA |
| PT10 | 31,101 | 99.987 | NA | 0.003 | NA | 0.006 | NA | 0.003 | NA |
| PT11 | 18,320 | 99.989 | NA | 0,005 | NA | 0.005 | NA | 0 | NA |
| PT14 | 31,871 | 99.991 | NA | 0.003 | NA | 0.006 | NA | 0 | NA |
| PT15 | 44,349 | 99.982 | NA | 0.002 | NA | 0.014 | NA | 0.002 | NA |
| PT16 | 35,523 | 99.989 | NA | 0.003 | NA | 0.006 | NA | 0.003 | NA |
| PT17 | 31,232 | 99.99 | NA | 0 | NA | 0.01 | NA | 0 | NA |
| PT18 | 34,764 | 99.974 | NA | 0 | NA | 0.023 | NA | 0.003 | NA |
| PT19 | 36,172 | 99.981 | NA | 0 | NA | 0.014 | NA | 0.006 | NA |
| PT21 | 35,015 | 99.991 | NA | 0 | NA | 0.009 | NA | 0 | NA |
| PT21 | 22,403 | 99.987 | NA | 0 | NA | 0.004 | NA | 0.009 | NA |
| PT22 | 42,150 | 99.988 | NA | 0 | NA | 0.009 | NA | 0.002 | NA |
| PT23 | 36,548 | 99.984 | NA | 0 | NA | 0.014 | NA | 0.003 | NA |
| PT23 | 37,033 | 99.989 | NA | 0 | NA | 0.005 | NA | 0.005 | NA |
| PT24 | 31,343 | 99.987 | NA | 0 | NA | 0.01 | NA | 0.003 | NA |
| F1174L 3522, C>A, chr2:29220829 | |||||||||
| Controls | 796,257 | 0.009 | NA | 0.003 | NA | 99.976 | NA | 0.011 | NA |
| PT1 | 32,732 | 0.009 | NA | 0.003 | NA | 99.985 | NA | 0.003 | NA |
| PT3 | 30,566 | 0.003 | NA | 0 | NA | 99.977 | NA | 0.02 | NA |
| PT4 | 32,908 | 0.015 | NA | 0.006 | NA | 53.27 | 0.00E+00 | 46.709 | 0.00E+00 |
| PT5 | 35,113 | 0.014 | NA | 0 | NA | 99.974 | NA | 0.011 | NA |
| PT6 | 34,885 | 0.011 | NA | 15.055 | 0.00E+00 | 64.718 | 0.00E+00 | 20.212 | 0.00E+00 |
| PT7 | 37,824 | 0.003 | NA | 0 | NA | 99.989 | NA | 0.008 | NA |
| PT8 | 36,884 | 0.005 | NA | 0.005 | NA | 61.463 | 0.00E+00 | 38.521 | 0.00E+00 |
| PT10 | 31,071 | 0.003 | NA | 0 | NA | 99.99 | NA | 0.006 | NA |
| PT11 | 18,266 | 0.011 | NA | 0 | NA | 97.64 | 0.00E+00 | 2.349 | 0.00E+00 |
| PT14 | 31,840 | 0.009 | NA | 0 | NA | 99.846 | 3.37E-16 | 0.144 | 1.66E-25 |
| PT15 | 44,301 | 0.007 | NA | 0 | NA | 99.989 | NA | 0.002 | NA |
| PT16 | 35,485 | 0.014 | NA | 0.003 | NA | 99.969 | NA | 0.011 | NA |
| PT17 | 31,207 | 0 | NA | 0.003 | NA | 99.99 | NA | 0.006 | NA |
| PT18 | 34,734 | 0.014 | NA | 0.003 | NA | 99.977 | NA | 0.006 | NA |
| PT19 | 36,146 | 0.019 | NA | 0.011 | NA | 99.967 | NA | 0.003 | NA |
| PT21 | 34,986 | 0.009 | NA | 0.003 | NA | 90.896 | 0.00E+00 | 9.089 | 0.00E+00 |
| PT21 | 22,338 | 0.004 | NA | 0 | NA | 99.624 | 1.04E-56 | 0.367 | 1.16E-74 |
| PT22 | 42,101 | 0.012 | NA | 0.002 | NA | 99.929 | 2.70E-01 | 0.05 | 3.41E-02 |
| PT23 | 36,413 | 0.014 | NA | 0.003 | NA | 62.722 | 0.00E+00 | 37.259 | 0.00E+00 |
| PT23 | 36,925 | 0.008 | NA | 0 | NA | 75.355 | 0.00E+00 | 24.636 | 0.00E+00 |
| PT24 | 31319 | 0.003 | NA | 0 | NA | 99.987 | NA | 0.006 | NA |
| R1275Q 3824 G>A, chr2:29209798 | |||||||||
| Controls | 1,005,867 | 0.016 | NA | 99.956 | NA | 0.001 | NA | 0.027 | NA |
| PT1 | 49,218 | 0.008 | NA | 99.974 | NA | 0 | NA | 0.018 | NA |
| PT3 | 53,946 | 0.011 | NA | 99.972 | NA | 0.002 | NA | 0.015 | NA |
| PT4 | 51,659 | 0.006 | NA | 99.783 | 1.41E-31 | 0 | NA | 0.211 | 3.33E-46 |
| PT5 | 73,384 | 0.022 | NA | 99.95 | NA | 0.001 | NA | 0.027 | NA |
| PT6 | 68,439 | 0.013 | NA | 98.004 | 0.00E+00 | 0.001 | NA | 1.981 | 0.00E+00 |
| PT7 | 49,685 | 0.002 | NA | 99.964 | NA | 0.002 | NA | 0.032 | NA |
| PT8 | 52,130 | 0.006 | NA | 99.969 | NA | 0 | NA | 0.025 | NA |
| PT10 | 50,187 | 0.01 | NA | 53.265 | 0.00E+00 | 0.004 | NA | 46.715 | 0.00E+00 |
| PT11 | 46,445 | 2.119 | 0.00E+00 | 88.937 | 0.00E+00 | 0 | NA | 8.942 | 0.00E+00 |
| PT14 | 27,110 | 0 | NA | 75.393 | 0.00E+00 | 0.007 | NA | 24.592 | 0.00E+00 |
| PT15 | 34,878 | 0.011 | NA | 73.195 | 0.00E+00 | 0.003 | NA | 26.788 | 0.00E+00 |
| PT16 | 47,751 | 0.013 | NA | 52.667 | 0.00E+00 | 0.004 | NA | 47.31 | 0.00E+00 |
| PT17 | 56,685 | 0.023 | NA | 76.465 | 0.00E+00 | 0 | NA | 23.512 | 0.00E+00 |
| PT18 | 52,198 | 0 | NA | 65.732 | 0.00E+00 | 0.004 | NA | 34.262 | 0.00E+00 |
| PT19 | 55,451 | 0.005 | NA | 50.333 | 0.00E+00 | 0.002 | NA | 49.651 | 0.00E+00 |
| PT21 | 51,696 | 0.006 | NA | 97.373 | 0.00E+00 | 0 | NA | 2.621 | 0.00E+00 |
| PT21 | 44,126 | 0.005 | NA | 76.069 | 0.00E+00 | 0 | NA | 23.925 | 0.00E+00 |
| PT22 | 48,821 | 0.006 | NA | 53.327 | 0.00E+00 | 0 | NA | 46.662 | 0.00E+00 |
| PT23 | 52,852 | 0.011 | NA | 99.97 | NA | 0 | NA | 0.019 | NA |
| PT23 | 59,037 | 0.007 | NA | 99.978 | NA | 0 | NA | 0.015 | NA |
| PT24 | 51,971 | 0.01 | NA | 99.835 | 1.59E-16 | 0 | NA | 0.156 | 9.57E-26 |
The mutations detected by deep sequencing and ddPCR are indicated in bold.