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The hidden genomic landscape of acute myeloid leukemia: subclonal structure revealed by undetected mutations
| Content Provider | Scilit |
|---|---|
| Author | Bodini, Margherita Ronchini, Chiara Giacò, Luciano Russo, Anna Melloni, Giorgio E. M. Luzi, Lucilla Sardella, Domenico Volorio, Sara Hasan, Syed K. Ottone, Tiziana Lavorgna, Serena Lo-Coco, Francesco Candoni, Anna Fanin, Renato Toffoletti, Eleonora Iacobucci, Ilaria Martinelli, Giovanni Cignetti, Alessandro Tarella, Corrado Bernard, Loris Pelicci, Pier Giuseppe Riva, Laura |
| Copyright Year | 2015 |
| Description | The analyses carried out using 2 different bioinformatics pipelines (SomaticSniper and MuTect) on the same set of genomic data from 133 acute myeloid leukemia (AML) patients, sequenced inside the Cancer Genome Atlas project, gave discrepant results. We subsequently tested these 2 variant-calling pipelines on 20 leukemia samples from our series (19 primary AMLs and 1 secondary AML). By validating many of the predicted somatic variants (variant allele frequencies ranging from 100% to 5%), we observed significantly different calling efficiencies. In particular, despite relatively high specificity, sensitivity was poor in both pipelines resulting in a high rate of false negatives. Our findings raise the possibility that landscapes of AML genomes might be more complex than previously reported and characterized by the presence of hundreds of genes mutated at low variant allele frequency, suggesting that the application of genome sequencing to the clinic requires a careful and critical evaluation. We think that improvements in technology and workflow standardization, through the generation of clear experimental and bioinformatics guidelines, are fundamental to translate the use of next-generation sequencing from research to the clinic and to transform genomic information into better diagnosis and outcomes for the patient. |
| Related Links | http://www.bloodjournal.org/content/bloodjournal/125/4/600.full.pdf |
| Ending Page | 605 |
| Page Count | 6 |
| Starting Page | 600 |
| DOI | 10.1182/blood-2014-05-576157 |
| Journal | Blood |
| Issue Number | 4 |
| Volume Number | 125 |
| Language | English |
| Publisher | American Society of Hematology |
| Publisher Date | 2015-01-22 |
| Access Restriction | Open |
| Subject Keyword | Biochemistry and Molecular Biology Acute Myeloid Leukemia Next Generation Sequencing Aml Allele Research To the Clinic Subclonal Cancer Somaticsniper Pipelines Journal: Blood (Vol- 79, Issue- 4) |
| Content Type | Text |
| Resource Type | Article |
