In recent years, the adoption of advanced bioinformatics platforms has enabled clinicians and researchers to identify novel variants, characterize complex inheritance patterns, and better understand the clinical impact of genetic disorders. Below are publications from customers in September 2025, showcasing the work built upon the trusted capabilities of our VarSeq and VS-CNV software to annotate, filter, and interpret genomic variants with confidence. We are deeply grateful to see our solutions trusted in these impactful publications, where researchers and clinicians have helped drive discoveries that directly inform precision medicine.
Detection of a Novel Homozygous PEX5 Stop-Loss Variant Associated with Zellweger Syndrome in a Highly Endogamic Family
Zellweger syndrome (ZS) is a heterogeneous group of clinical conditions that commonly manifest with neurodevelopmental delay, multiple neurological abnormalities, visual and auditory impairments, and adrenocortical dysfunction. ZS is an autosomal recessive peroxisomal disorder resulting from mutations in one of over 13 identified genes. We report the case of a male child with episodic seizures starting at 18 days of life, followed by neurodevelopmental delay and neuroimaging findings of asymmetric polymicrogyria and cortical abnormalities. His healthy parents were consanguineous, and notably, a brother, who passed away at the age of 5 years-old, had epilepsy and adrenoleukodystrophy. Exome sequencing allowed the identification of a novel stop-loss homozygous variant in the PEX5 gene in the index case. The phenotype associated to this gene, Zellweger syndrome, as well as the inheritance mechanism, is consistent with that observed in both the patient and his brother.
“The DNA of the patient and both parents was extracted from a whole-blood sample using the Quick-DNA 96 plus kit (Zymo Research). After assessing the quality and quantity of the DNA, a genomic library was prepared using MGIEasy FS DNA Library Prep Kit and fragments ranging from 200 to 400pb were obtained. The regions of interest were captured through the Exome Capture V5 probe and streptavidin beads. The final PCR reaction was enriched and employed specific primers. Sequencing and library preparation were performed using MGI DNBSEQ-G50 platform for Gencell Pharma (Bogotá, Colombia). The reads obtained were mapped and aligned to the reference genome (hg19) and variant calling was performed using the GATK v4.0.5.1 tool.11 Analyses of coverage and depth were conducted using the BAMBA tool, and 50X was the acceptable threshold. The variants obtained in VCF format (variant call format) were imported into VarSeq software (Golden Hélix v2.2.3) for annotation and filtering according to different criteria. Filtered candidate variants were assessed using the American College of Medical Genetics and Genomics guidelines (ACMG). Bioinformatics procedures were performed in the laboratory of the Genetics and Genomics Research Center of the Universidad del Rosario (CIGGUR), Bogotá (Colombia).”
Double Pathogenic or Likely Pathogenic Variants in Cancer Predisposition Genes in Hungarian Cancer Patients
Identification of two or more pathogenic/likely pathogenic (P/LP) variants in cancer susceptibility genes carried by the same patient have important consequences for patient management. We have limited information about the effect of double heterozygosity (DH) in cancer susceptibility genes. The prevalence of DH among Hungarian cancer patients referred to oncogenetic counselling, and comparison of their phenotypes to single variant carriers were performed. In total, 2050 patients were analysed by multigene panel sequencing. Variants of 48 established cancer predisposition genes by ACMG guidelines were evaluated. In overall, P/LP variants were found in 19.8% of cases. DH was observed in 16 cases, amount to 0.8% of all patients, and to 4.0% of positive cases. Appearance of multiple primary tumours was not associated with DH compared to non-P/LP and single P/LP carriers (p = 0.71 and p = 0.54, respectively). Within a cohort of patients referred with suspected HBOC syndrome, earlier tumour formation was observed when DH cases were compared to non-P/LP carriers (p = 0.01), but difference between single and DH carriers was not statistically significant (p = 0.19; Bonferroni corrected alpha = 0.017). Our observations provide information about the incidence of DH status among Hungarian hereditary cancer patients and suggest that DH did not increase the risk of cancer compared to individuals with single P/LP mutation.
“In addition to the DRAGEN pipeline, we also used the VarSeq CNV algorithm (v2.6.2 Golden Helix, Bozeman, Montana, USA) for CNV calling. Calls were retained when p < 0.05 and the Z-score ≤ −3 or Z-score ≥ 3, and normalised read depth < 0.7 or >1.2 for heterozygous deletions and duplications, respectively. Variants were annotated by BaseSpace Variant Interpreter (Illumina, San Diego, CA, USA) and VarSeq (Golden Helix, Bozeman, MT, USA).”
Clinical profile, atrophy and inheritance patterns of pathogenic MAPT gene mutations in Frontotemporal dementia detected using whole exome sequencing: a single-center first report from India
Background/Objectives
Frontotemporal Dementia (FTD) is one of the common causes of early-onset degenerative dementia and is a clinically and pathologically heterogeneous group of neurodegenerative disorders. Globally, Microtubule Associated Protein Tau (MAPT), progranulin (GRN), and Chromosome 9 open reading frame 72(C9orf72) are the common FTD genetic mutations. However, they have not been reported from India, and only one progranulin (PGRN) mutation has been reported so far. This study aims to describe the clinical features and radiological patterns of seven patients of FTD harbouring pathogenic MAPT mutations from an Indian cohort of Frontotemporal dementia, using whole-exome sequencing (WES) for the first time.
Methods
Subjects with dementia fulfilling the criteria for frontotemporal dementia were recruited from a teaching university hospital in South India. All of them underwent detailed clinical evaluation, neuroimaging, and genetic analysis by Whole Exome Sequencing (WES).
Results
Among 86 patients with FTD who underwent WES, seven had MAPT mutations. Notably, two are novel variants.
Conclusion
In the Indian context, pathogenic MAPT in FTD is being reported for the first time and notably from a single center by WES. Identifying pathogenic MAPT genes is important in planning mutation-specific clinical trials and understanding ethical and cultural differences in genetic FTD inheritance.
“Subjects with FTD who consented to blood sampling underwent genetic testing by Next Generation Sequencing. Whole-exome sequencing libraries were prepared using 37 Mb capture probe sets (including protein-coding genes and the mitochondrial genome by Twist Biosciences kit, USA, and were sequenced on the Illumina NextSeq 550 platform using 2×150 bp read chemistry (Illumina: San Diego, CA, USA). Reads from the sequence output were aligned to the human reference genome (GRCh38) using Burrows-Wheeler Aligner (BWA). Variants to the reference were called using the Genomic Analysis Tool Kit (GATK; http://www.broadinstitute.org/gatk) to produce variant files in VCF format. Highly confident variants with depth and Phred score were selected for annotation, and further analysis was performed using VarSeq (Golden Helix, Inc., USA) to obtain potential and clinically relevant variants. Pathogenicity of the variants was assessed based on American College of Medical Genetics (ACMG) guidelines. [36]. This study protocol was reviewed and approved by the Institutional Ethical Committee No/NIMHANS/(BS & NS Division)/24th meeting/2020 dated June 11, 2020. Repeat Prime PCR was not performed.”
These studies from September 2025 highlight the importance of genomic analysis in rare diseases, cancer, and neurodegeneration. Our reliable and robust software supports these efforts to progress precision medicine. We proudly provide tools that empower clinicians and researchers worldwide to accelerate variant interpretation, improve diagnostic accuracy, and advance patient care. We remain committed to supporting the global genomics community with innovative, user-friendly, and rigorous solutions.