Supplementary Data 1 from Somatic Exonic Deletions in RUNX1 Constitutes a Novel Recurrent Genomic Abnormality in Acute Myeloid Leukemia
Year: 2025
Type: supplementary-materials
Abstract: Somatic exonic deletions in RUNX1: a novel recurrent genomic abnormality in acute myeloid leukemia Clinical informationThe WHO performance status of the cohort was as follows: Grade 0, n=25 (30%); Grade 1, n=39 (47%); Grade 2, n=12 (14%); Grade 3, n=4 (5%); and Grade=4, n=3 (4%).Sixty-nine patients (83%) were treated with intensive chemotherapy while 4 (5%) and 10 (12%) were treated with Hypomethylating agents or with palliative care respectively. NGS library preparation and sequencing using TruSight Myeloid panel:Genomic DNA was extracted from bone marrow or whole blood using the EZ1 DNA Blood Kit.Extracted DNA was quantified with the Qubit dsDNA BR Assay kit and Qubit 2.0 fluorometer (Thermo Fisher Scientific).Sequencing libraries were prepared from 50 ng input DNA using the Trusight Myeloid Sequencing Panel (Illumina, San Diego, California) according to manufacturer's instructions.This panel consists of 568 unique amplicons (~ 250 base-pairs) covering either hotspots or full coding region of 54 genes that are frequently mutated in myeloid neoplasms.For list of genes see https://www.illumina.com/products/by-type/clinical-research-products/trusight-myeloid.html.After PCR clean-up each library was quantified using the Qubit dsDNA HS Assay kit and their fragment size distribution was assessed by an Agilent 2200 Tapestation system (Agilent, Technologies) with the high sensitivity D1000 Screen Tape.Equimolar libraries (6 per run) were then pooled and denatured.Pair-end sequencing was performed on the Illumina Miseq platform using a reagent kit v3 to generate 2x150 bp read lengths as specified by the manufacturer.Amplicon mapping to human genome reference GRCh37/hg19, demultiplexing, soft clipping of primer sequences, alignment and variant calling was performed using the TruSeq Amplicon analysis as implemented in the MiSeq Reporter software v2.6 (Illumina, San Diego, California).Reads were not stitched.The Illumina pipeline was complemented with pindel 0.2.5b8 to search for larger insertions, deletions, and internal tandem duplications.Regions with low coverage (<100x) were reported using in house algorithms to identify any regions where the analysis failed to produce data.Variants present in more than 15% of 1287 clinical routine samples were A B C D Array analysis not performed, no data available Study ID: P7
Authors: Anna Eriksson, Marie Engvall, Lucy Mathot, Albin Österroos, Martin Rippin, Lucia Cavelier, Claes Ladenvall, Panagiotis Baliakas
Language: English
Subfield: Hematology
Field: Medicine
Domain: Health Sciences
Open Access status: gold
OpenAlex ID: W4416670648