High accuracy mutation detection in leukemia on a selected panel of cancer genes.
With the advent of whole-genome and whole-exome sequencing, high-quality catalogs of recurrently mutated cancer genes are becoming available for many cancer types. Increasing access to sequencing technology, including bench-top sequencers, provide the opportunity to re-sequence a limited set of cancer genes across a patient cohort with limited processing time. Here, we re-sequenced a set of cancer genes in T-cell acute lymphoblastic leukemia (T-ALL) using Nimblegen sequence capture coupled with Roche/454 technology. First, we investigated how a maximal sensitivity and specificity of mutation detection can be achieved through a benchmark study. We tested nine combinations of different mapping and variant-calling methods, varied the variant calling parameters, and compared the predicted mutations with a large independent validation set obtained by capillary re-sequencing. We found that the combination of two mapping algorithms, namely BWA-SW and SSAHA2, coupled with the variant calling algorithm Atlas-SNP2 yields the highest sensitivity (95%) and the highest specificity (93%). Next, we applied this analysis pipeline to identify mutations in a set of 58 cancer genes, in a panel of 18 T-ALL cell lines and 15 T-ALL patient samples. We confirmed mutations in known T-ALL drivers, including PHF6, NF1, FBXW7, NOTCH1, KRAS, NRAS, PIK3CA, and PTEN. Interestingly, we also found mutations in several cancer genes that had not been linked to T-ALL before, including JAK3. Finally, we re-sequenced a small set of 39 candidate genes and identified recurrent mutations in TET1, SPRY3 and SPRY4. In conclusion, we established an optimized analysis pipeline for Roche/454 data that can be applied to accurately detect gene mutations in cancer, which led to the identification of several new candidate T-ALL driver mutations.
Center for Human Genetics, KU Leuven, Leuven, Belgium.
Zeynep
Z
Kalender Atak
Kim
K
De Keersmaecker
Valentina
V
Gianfelici
Ellen
E
Geerdens
Roel
R
Vandepoel
Daphnie
D
Pauwels
Michaël
M
Porcu
Idoya
I
Lahortiga
Vanessa
V
Brys
Willy G
WG
Dirks
Hilmar
H
Quentmeier
Jacqueline
J
Cloos
Harry
H
Cuppens
Anne
A
Uyttebroeck
Peter
P
Vandenberghe
Jan
J
Cools
Stein
S
Aerts
D001483:Base Sequence; D045744:Cell Line, Tumor; D002999:Clone Cells; D004252:DNA Mutational Analysis / Q000379:methods*; D052138:Genes, Neoplasm / Q000235:genetics*; D006801:Humans; D008969:Molecular Sequence Data; D009154:Mutation / Q000235:genetics*; D009363:Neoplasm Proteins / Q000235:genetics; D054218:Precursor T-Cell Lymphoblastic Leukemia-Lymphoma / Q000235:genetics*; D013997:Time Factors; D025521:Tumor Suppressor Proteins / Q000235:genetics
D009363:Neoplasm Proteins; D025521:Tumor Suppressor Proteins