Advancements in genomic analysis tools have significantly enhanced the identification and characterization of genetic variants associated with complex diseases. VarSeq, our flagship powerful variant annotation and filtration software, plays a crucial role in streamlining whole-exome sequencing (WES) data analysis, enabling researchers to detect pathogenic mutations efficiently. By utilizing VarSeq’s comprehensive annotation capabilities, researchers were able to filter and prioritize variants, facilitating the identification of this mutation and its potential pathogenic impact. Read about some recent customer applications of VarSeq below.
Identification and functional characterisation of a novel DNASE1L3 variant (c.572A>G, p.Asn191Ser) in three Emirati families with systemic lupus erythematosus and hypocomplementaemic urticarial vasculitis
Objectives To evaluate the functional impact of a novel DNASE1L3 variant (c.572A>G, p.Asn191Ser) in three families with SLE and hypocomplementaemic urticarial vasculitis (HUV) from the United Arab Emirates.
Methods Whole-exome sequencing was performed on affected patients and findings were confirmed using Sanger sequencing in family members. DNASE1L3 protein expression, secretion and enzymatic activity were assessed in HEK293 cell lines. Plasma smear assay for neutrophil extracellular traps (NETs) was evaluated in patients, family members and healthy control.
Results A total of seven patients diagnosed with both SLE and HUV were identified from three unrelated families. All affected individuals were found to carry a homozygous c.572A>G, p.Asn191Ser (191S) variant in DNASE1L3. The variant 191S was shown to impact the secretion and activity of DNASE1L3. Patients homozygous for 191S variant had significantly higher burden (p=0.0409) of NET structure in comparison to heterozygous and healthy control.
Conclusions We functionally evaluated the effect of a novel DNASE1L3 (c.572A>G, p.Asn191Ser) in familial SLE with a consistent pattern of HUV across seven patients. This variant resulted in impaired secretion and enzymatic activity of DNASE1L3 along with increased NETosis in patients with homozygous genotype.
“Genomic DNA (gDNA) was extracted using the QIAcube automated DNA extraction system with the QIAamp DNA Mini Kit (QIAGEN) from peripheral blood samples collected in EDTA tubes. The gDNA quality was assessed using spectrophotometric (NanoDrop, Thermo Fisher Scientific, Waltham, Massachusetts, USA), and the DNA quantity was evaluated via fluorometric quantitation method (Qubit 4.0 fluorometer, Thermo Fisher Scientific). DNA fragmentation was performed using a Covaris LE-220 plus ultrasonication system (Covaris, Woburn, Massachusetts, USA). Whole-exome sequencing (WES) library preparation and Exome capture were performed by the TruSeq DNA Exome (Illumina, San Diego, California, USA.) following the manufacturer’s protocol. Sequencing was performed using S2 flow cell with paired-end reads (2×150 bp) on NovaSeq 6000 system (Illumina). A combination of in-house-developed pipelines and the Illumina DRAGEN Bio-IT Platform (Illumina) was used for read mapping, alignment and variant calling. VarSeq V.2.2.4 software (Golden Helix, USA) was used for variant annotation and filtration.“
Quality-of-Life Assessment in Patients Undergoing Mastectomy and Breast Reconstruction for Moderate-Penetrance Gene-Related Breast Cancer
Background. Breast cancer remains a leading cause of cancer-related death among women, with genetic mutations playing a key role. While high-penetrance mutations are well-studied, moderate-to-low-penetrance mutations, which present challenges in clinical decision-making and patient outcomes, are less understood. This study explores the quality of life of breast cancer patients with moderate-penetrance mutations, focusing on the psychosocial and physical consequences of mastectomy and reconstruction to improve patient-centered care. Materials and Methods. A cohort of 620 breast cancer patients treated at Regina Maria Private Health Network, Bucharest, between January 2022 and July 2024 was identified. From this group, 61 patients were selected based on the following criteria: (1) meeting NCCN genetic testing guidelines, (2) carrying moderate-to-low-penetrance mutations, (3) undergoing bilateral mastectomy with double reconstruction, and (4) agreeing to complete a modified version of the BREAST-Q questionnaire. Genetic testing was performed using a 125-gene next-generation sequencing panel. Statistical analyses included non-parametric tests to examine group differences and correlations. Results. Significant correlations were found between several factors. Emotional distress was positively correlated with concerns for family, while couple relationships and financial burden showed a strong positive association. Negative correlations were found between couple relationships and self-concept. Distress levels varied, with “Interference with personal relationships” causing more distress than “Impact on employment”, and financial burden causing more distressing than impact on sexuality. Conclusions. Prophylactic mastectomy significantly reduces cancer risk for women with moderate-penetrance mutations. This study highlights the relationship between surgical choices and quality-of-life factors, advancing personalized prevention strategies and emphasizing patient-centered care.
“Variants were analyzed using gnomAD and ClinVar databases, along with specialized software tools. Variant calling was performed using GATK (version 4.3.0.0, Broad Institute, Cambridge, MA, USA), while annotation and interpretation were conducted with VarSeq (version 2.4.0, Golden Helix, Bozeman, MT, USA) and Alamut Visual (version 1.11, SOPHiA GENETICS, Rolle, Switzerland). Copy number variations (CNVs) were detected using ExomeDepth (version 1.1.15, University of Cambridge, Cambridge, UK). Pathogenicity was evaluated by a clinical team following ACMG guidelines, and significant findings were confirmed using Sanger sequencing with the ProDye® Terminator Sequencing System (Promega Corporation, Madison, WI, USA) and through Sanger sequencing services provided by Eurofins Genomics (Ebersberg, Germany).“
VarSeq underscores the importance of advanced bioinformatics solutions in genomic medicine, aiding in the discovery of clinically significant variants and enhancing our understanding of disease mechanisms. If you are interested in learning how VarSeq and Golden Helix can be your NGS partner, please email us at [email protected].