Genetic Profiling of Follicular Lymphoma

DNeasy Tissue and Blood Kit (Qiagen, Venlo, Netherlands) were utilized to isolate DNA. Libraries were created via Agilent SureSelect Human All Exon kit V6 (Agilent Technologies, CA, USA) and sequenced on an Illumina NovaSeq 6000 platform with 150 bp paired-end reads. Valid sequencing data were then aligned to the GRCh37/hg19 by BWA (v0.7.12) (28 (link)). Then, SAM tools (29 (link)), Picard (v1.87) and Genome Analysis Toolkit (GATK) (30 (link)) were used to sort BAM files and performing repeated marking, local realignment, and base quality recalibration. Single nucleotide variants (SNVs) were identified using the GATK Unified Genotyper and indels were determined using VarScan. ANNOVAR package (31 (link)) were used for annotation of all substitutions and indels. Recurrent mutated genes in FL reported in previous literature were selected and further analysed (5 (link)).

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Zhang T., Liu H., Gao F., Gong W., Cui Y., He J., Li L., Qiu L., Qian Z., Zhou S., Meng B., Ren X., Zhang H, & Wang X. (2022). m6A-Regulator Expression Signatures Identify a Subset of Follicular Lymphoma Harboring an Exhausted Tumor Microenvironment. Frontiers in Immunology, 13, 922471.

Publication 2022

DNeasy Tissue and Blood Kit Agilent SureSelect Human All Exon kit V6 NovaSeq 6000

Blood Exon Genes Genome Human Indels Nucleotide Tissue

Corresponding Organization : Tianjin Medical University Cancer Institute and Hospital

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Variable analysis

independent variables

Agilent SureSelect Human All Exon kit V6 (Agilent Technologies, CA, USA)
Illumina NovaSeq 6000 platform with 150 bp paired-end reads

dependent variables

Sequencing data
Identified single nucleotide variants (SNVs)
Determined indels

control variables

GRCh37/hg19 reference genome
BWA (v0.7.12) for alignment
SAMtools, Picard, and Genome Analysis Toolkit (GATK) for sorting, marking, realignment, and base quality recalibration
GATK Unified Genotyper for SNV identification
VarScan for indel determination
ANNOVAR package for annotation of substitutions and indels
Recurrent mutated genes in follicular lymphoma (FL) reported in previous literature

Annotations

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