Background
Methods
Patients
Patient | Sex/Age | FISH | IgVH status | Stage (Binet) | Total 2D reads count |
TP53 mapped reads |
---|---|---|---|---|---|---|
CLL#1 | F/62 | del(17)(p13), del(13)(q14) | Unmutated | A | 329 | 217 |
CLL#2 | M/59 | del(17)(p13), del(13)(q14) | Unmutated | B | 307 | 173 |
CLL#3 | M/59 | del(17)(p13), del(13)(q14) | Unmutated | A | 210 | 104 |
CLL#4 | M/63 | del(17)(p13), del(13)(q14) | Unmutated | A | 288 | 194 |
CLL#5 | F/65 | del(17)(p13), del(13)(q14) | Mutated | A | 212 | 188 |
CLL#6 | M/72 | del(17)(p13) | Mutated | A | 342 | 173 |
CLL#7 | F/30 | del(13)(q14) | Unmutated | A | 220 | 208 |
CLL#8 | M/64 | del(17)(p13), del(13)(q14) | Unmutated | B | 154 | 135 |
CLL#9 | M/56 | del(17)(p13), del(13)(q14), del(11)(q22), +12 | Unmutated | B | 147 | 135 |
CLL#10 | F/72 | del(17)(p13), del(13)(q14) | Unmutated | B | 197 | 90 |
CLL#11 | F/45 | del(17)(p13), del(13)(q14) | Unmutated | B | 147 | 120 |
CLL#12 | F/65 | del(17)(p13), del(13)(q14) | Mutated | A | 119 | 113 |
Sanger sequencing
TP53 Amplification and barcoding
Minion library preparation and sequencing
Data analysis
Results
TP53 mutation analysis by Sanger sequencing
TP53 mutation analysis by MinION sequencing
Read type | Number of reads | Minimum length (bp) | Max length (bp) | Mean length (bp) | |
---|---|---|---|---|---|
Pass | 1D Template | 3619 | 186 | 7607 | 4209 |
1D complement | 3619 | 173 | 7821 | 4047 | |
2D consensus | 3619 | 176 | 7209 | 4170 | |
Fail | 1D Template | 18319 | 5 | 199114 | 3407 |
1D complement | 7926 | 9 | 123134 | 3552 | |
2D consensus | 4195 | 115 | 73841 | 3991 |
Data analysis and error correction
Variant calling and annotation
Variant filtering
Patient | Genomic description | Protein description | Exon/Intron | Functional Domain | Mutation frequencya
| Raw Readsb
| ALECc
| Nanocorrectc
|
---|---|---|---|---|---|---|---|---|
CLL#2 | g.7577144A > G | p.Leu265Pro | 8-exon | DNA binding | 34 % | 38.6 % | 39.13 % | 78.72 % |
CLL#8 | g.7577548C > T | p.Gly245Ser | 7-exon | DNA binding | 31 % | 26.9 % | 30.28 % | ND |
CLL#10 | g.7577121_7577122GC > TT | p.Arg273Ser | 8-exon | DNA binding | 58 % | 41.5 % | 61.29 % | 93.55 % |
CLL#11 | g.7577501del | p.Ser261Valfsb84 | 7-exon | DNA binding | 46 % | 39.7 % | 44.21 % | 35.48 % |
CLL#12 | g.7578406C > T | p.Arg175His | 5-exon | DNA binding | ND | 18.3 % | 16.67 % | ND |