ITD assembler: an algorithm for internal tandem duplication discovery from short-read sequencing data

ABySS: a parallel assembler for short read sequence data.

Widespread adoption of massively parallel deoxyribonucleic acid (DNA) sequencing instruments has prompted the recent development of de novo short read assembly algorithms. A common shortcoming of the available tools is their inability to efficiently assemble vast amounts of data generated from large-scale sequencing projects, such as the sequencing of individual human genomes to catalog natural...

FMS-related tyrosine kinase 3 internal tandem duplication (FLT3-ITD): a villain among others

cute myeloid leukemia (AML) is the most frequent acute eukemia of adult patients with an estimated 10,070 new cases n Brazil in 2016. Most of the cases are de novo, without a efined etiology, and around two thirds of the patients will die f the disease, according to the Instituto Nacional de Câncer INCA).1 Genetic aberrations may help to differentiate patients ho have a good from those with a d...

A neoepitope generated by an FLT3 internal tandem duplication (FLT3-ITD) is recognized by leukemia-reactive autologous CD8+ T cells.

The FLT3 receptor tyrosine kinase is expressed in more than 90% of acute myelogeneous leukemias (AMLs), up to 30% of which carry an internal tandem duplication (ITD) within the FLT3 gene. Although varying duplication sites exist, most FLT3-ITDs affect a single protein domain. We analyzed the FLT3-ITD of an AML patient for encoding HLA class I-restricted immunogenic peptides. One of the tested p...

Bias from removing read duplication in ultra-deep sequencing experiments

MOTIVATION Identifying subclonal mutations and their implications requires accurate estimation of mutant allele fractions from possibly duplicated sequencing reads. Removing duplicate reads assumes that polymerase chain reaction amplification from library constructions is the primary source. The alternative-sampling coincidence from DNA fragmentation-has not been systematically investigated. ...

Cooperation between the partial tandem duplication of Mll (Mll PTD) and internal tandem duplication of FLT3 (FLT3 ITD) in the pathogenesis of acute myeloid leukemia (AML)