Next-generation sequencing-based multigene mutational screening for acute myeloid leukemia using MiSeq: applicability for diagnostics and disease monitoring

Correlation of mutation profile and response in patients with myelofibrosis treated with ruxolitinib

“…7 The entire coding sequences of 28 genes (ABL1, ASXL1, BRAF, DNMT3A, EGFR, EZH2, FLT3, GATA1, GATA2, HRAS, IDH1, IDH2, KIT, KRAS, MDM2, IKZF2, JAK2, MLL, MPL, MYD88, NOTCH1, NPM1, NRAS, PTPN11, RUNX1, TET2, TP53, and WT1) were sequenced using a next generation sequencing (NGS)-based custom-designed assay using the Illumina MiSeq platform as previously described. 6 Testing for insertion and deletion mutations in CALR was performed as previously described. 8 Testing for SRSF2 mutations was not performed.…”

“…In recent years, with the explosion of whole genome sequencing efforts, a number of rare, but recurrent, mutations have been identified in myeloproliferative neoplasms (MPNs), suggesting that there may be several paths to the development of MPNs, which have heterogeneous clinical presentations and treatment responses. [3][4][5] To detect genes that may be correlated with response to ruxolitinib and other clinicopathologic features, we performed a comprehensive mutation profile of 29 genes recurrently mutated in primarily myeloid malignancies 6 in a cohort of 95 patients with MF who were treated with ruxolitinib in a phase 1/2 study. 7 …”

The potential for liquid biopsies in the precision medical treatment of breast cancer

“…NGS has been developed to target the genome at various scales (whole genome 205 , whole exome 206 , and targeted panels [207][208][209] ) and are a key component toward realizing personalized care in oncology. A genome-wide screen for copy number changes has the advantage that it is an untargeted approach, which does not require any prior knowledge about characteristics of the primary tumor genome or its metastatic deposits.…”

“…Murtaza et al 206 presented an extensive comparison of biopsy and plasma samples collected from a MBC patient over a 3-year clinical course, in which whole exome sequencing (WES) and deep sequencing of plasma DNA and tumor biopsies revealed resistance to targeted agents such as lapatinib, a tyrosine kinase inhibitor of EGFR (epidermal growth factor receptor) and HER2. Thus deep sequencing of plasma DNA, applied to selected samples with high tumor burden in blood, may help identify the mutations associated with drug resistance 193,219 .…”

Characterization of gene mutations and copy number changes in acute myeloid leukemia using a rapid target enrichment protocol

“…Capture, mapping and quantification of FLT3-ITD alleles is a major challenge that will likely require bespoke targeting and bioinformatic approaches, especially for longer ITDs that were missed in our study. 29,32 On the other hand, we suggest that deep sequencing can provide increased sensitivity for short and subclonal ITDs that may be easily missed by conventional PCR, leading to incorrect prognostic characterization of the patient. Indeed, in our study we identified 3 subclonal NPM1 and FLT3 indels that could not be confirmed by PCR followed by agarose gel electrophoresis or capillary sequencing.…”