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Pipeline publication

[…] els, but due to the low number of cases, a correlation between the level of decrease in M-protein and the overall response was not statistically established., Targeted sequencing was completed using Nextera Custom Enrichment library (Illumina). The custom targeted panel consisted of capture probes for genes known to be relevant in MDS, acute myeloid leukemia (AML) and other hematologic malignancies (both somatic and germline targets, N=169). The list of genes targeted can be found in Online Supplementary Table S4. The enriched targets were subjected to massive sequencing using Illumina MiSeq sequencer, with an average target depth of 260x., The generation of BAM (.bam) files (alignment with Burrows-Wheeler Aligner [BWA] 0.7.9a) with its preprocessing and detection of somatic point mutations/insertions and deletions was carried out in accordance with the Genome Analysis Toolkit (GATK) best practices. Only variants with high-quality reads and a minimum depth of at least 20 and six positives were considered for further analysis. Sequencing results were annotated using ANNOVAR. Variants were considered somatic if they were not reported within the Exome Aggregation Consortium (ExAC) germline database (ExAC, Cambridge, MA, USA). Novel splicing, stop-gain and insertions-deletions variants were prioritized and studied further., The R package forest plot was used to plot odds ratios (OR) computed using Fisher’s exact test and response rates, the 95% confidence intervals of which were computed using logistic regression, i.e., the R function generalized linear model (glm) was used with y ~ 1 as the model and the statistical distribution family set to binomial., From January 2000 to December 2016, we saw and treated 62 patients with PRCA who fulfilled the diagnost […]

Pipeline specifications

Software tools BWA, GATK, ANNOVAR
Diseases Blood Protein Disorders, Lymphoproliferative Disorders, Agammaglobulinemia, Lymphoproliferative Disorders, Lymphoma, Parvoviridae Infections, Anemia, Thoracic Neoplasms, Neoplasms, Complex and Mixed, Thymus Neoplasms, Lymphoproliferative Disorders, Lymphoma, Leukemia, Lymphoproliferative Disorders