At Golden Helix, we’re proud to see how researchers worldwide continue using our software to accelerate discovery and improve clinical decision-making. These October 2025 publications highlight how VarSeq is advancing genetic research across cancer, hereditary disease, and molecular diagnostics. From identifying new variant mechanisms to expanding our understanding of genotype–phenotype relationships, these studies demonstrate how Golden Helix tools empower teams to analyze data efficiently, automate workflows, and translate sequencing results into meaningful clinical insight.
Title: Non-truncating BMPR1A variants associated with familial colorectal cancer and adenomatous polyps
Background: Pathogenic variants in BMPR1A classically cause juvenile polyposis syndrome, but emerging evidence links non-truncating variants to colorectal cancer without hamartomatous polyps, suggesting broader genotype-phenotype variability.
Objectives: To investigate how non-truncating BMPR1A variants contribute to familial colorectal cancer and adenomatous polyps through clinical, genetic, and molecular characterization.
Subjects and Methods: Four Finnish families with microsatellite-stable colorectal tumors were studied using exome sequencing, BMPR1A variant modeling, haplotype and genealogical analyses, and tumor assessments for loss of heterozygosity, somatic mutations, and mutational signatures in VarSeq.
Results:
- Identified non-truncating BMPR1A variants across four families: c.264_266del (one family), c.506_507insTCC (two families with a shared ancestor), and c.766G>A (one family).
- Multiple lines of evidence supported causality: co-segregation with CRC/polyps, in-silico deleterious modeling, “two-hit” inactivation via LOH or somatic mutation in tumors, and absence of alternative predisposition variants on exome sequencing.
- Most polyps in carriers were adenomatous; only three polyps with hamartomatous features were observed across two carriers from two families.
- Tumor mutational profiles of colorectal adenomas/carcinomas mirrored mismatch-repair–proficient CRC in general.
Conclusions: Our findings support the notion that the clinical phenotype of BMPR1A variants may extend beyond classical JPS. Genotype-phenotype correlations are complex, since molecular comparison of constitutional and tumor features of our families to those published from JPS families in the literature show a significant overlap. The variety of clinical phenotypes warrants recognition in the clinical management of BMPR1A carriers and their family members.
“VarSeq® (Golden Helix Inc., Bozeman, MT) was used for tertiary analysis. We applied several filters to exclude common variants and select significant variants. Sample based computed filter for variants was first set to be PASS. Variants with total minor allele frequencies (MAF) ≥ 0.001 according to GnomAD v4.0 were removed. RefSeq Genes 110, NCBI database was used to extract indel, misssense and nonsense variants from only protein coding area, excluding intronic and intergenic variants but including splice site-related intronic variants. Then dbNSPF Functional Prediction Voting was used to predict missense variants’ pathogenicity. There are five different prediction programs in VarSeq: SIFT Pred, Mutation Taster Pred, MutationAssessor Pred, FATHMM Pred, and FATHMM MKL Coding Pred. We only considered missense type variants predicted pathogenic by 5 of 5 prediction programs. Variants in low complexity regions were excluded by using Low Complexity Regions and Universal Mask-GHI filters.”
Nieminen, T.T., Kuismin, O., Laine, R. et al. Non-truncating BMPR1A variants associated with familial colorectal cancer and adenomatous polyps. BMC Cancer 25, 1435 (2025). https://doi.org/10.1186/s12885-025-14865-8
Title: A deep intronic PHEX variant in a large Danish family with hereditary hypophosphatemia and a milder skeletal, but more severe dental phenotype
Background: X-linked hypophosphatemia (XLH) results from PHEX variants causing renal phosphate wasting, but phenotype severity varies and deep intronic variants are rarely reported.
Objectives: To identify the genetic cause of hereditary hypophosphatemia in a large Danish family with a mild skeletal but severe dental phenotype.
Subjects and Methods: Nineteen family members were clinically evaluated; whole-genome sequencing, splice prediction, and exon-trapping assays using VarSeq and nanopore sequencing were performed to characterize PHEX intronic variants and confirm functional effects.
Results:
- Discovered a novel deep intronic PHEX variant (c.1080-687A>G) creating an alternative exon and premature stop codon, verified by exon-trapping and RNA-seq.
- Variant segregated with disease across 14 informative meioses and was classified as pathogenic (ACMG class 5).
- Transcripts with the alternative exon accounted for 96.4% of total expression, supporting loss of functional PHEX protein.
- Affected individuals showed a mild skeletal phenotype but more severe dental manifestations compared to typical PHEX-positive XLH cases.
Conclusions: This study identifies a novel deep intronic PHEX splice variant as the cause of mild X-linked hypophosphatemia in a large Danish family, expanding the known mutational spectrum of PHEX. The findings underscore that whole-genome and intron analyses are essential for accurate diagnosis, particularly in patients with atypically mild phenotypes.
“DNA from whole blood from the index patient was extracted using Tecan automatic system (Promega) and sequencing performed using DNA PCR Free Library Prep (Illumina) and NovaSeq 6000 (Illumina) to an average sequencing depth of 30×. Data analysis was performed by a GATK-pipeline, and a subsequent focused analysis of PHEX using VarSeq 2.2.1 (reference genome hg19). The intronic variants were sorted based on their frequency in gnomAD 2.1, and all rare variants (<1 % frequency in gnomAD 2.1) in the intronic sequences of PHEX were subjected to manual investigation for splice effect using the software AlamutVisualPlus, with the splice prediction tools MaxEntScan, NNsplice and GeneSplicer. After this manual search of each variant in AlamutVisualPlus, the variant c.1080-687 A > G was the only variant where the splice prediction tools indicated that the introduction of this variant to the DNA sequence of PHEX could lead to altered splicing and thereby altered expression of the PHEX protein. The detected variant in PHEX was verified by Sanger sequencing. Segregation analysis in the family was also performed by Sanger sequencing.”
Blechingberg, J., Skipper, K. A., Beck-Nielsen, S. S., & Gregersen, P. A. (2025). A deep intronic PHEX variant in a large Danish family with hereditary hypophosphatemia and a milder skeletal, but more severe dental phenotype. Bone, 188, 117666. https://doi.org/10.1016/j.bone.2025.117666
Title: Diagnostic sequencing identifies high-risk markers and mechanisms of resistance to guide immunotherapy selection.
Background: Molecular diagnostics for multiple myeloma (MM) have traditionally relied on FISH, which can miss key mutations and evolving resistance mechanisms, especially in patients treated with immunotherapies. Targeted next-generation sequencing (NGS) provides a more comprehensive approach, capable of detecting high-risk genomic markers and mechanisms of resistance, including antigen escape, to inform personalized treatment decisions.
Objectives: This study aimed to implement a targeted NGS panel in a clinical setting to identify both high-risk cytogenetic and sequence-based markers as well as mechanisms of treatment resistance. It also sought to evaluate how CD138+ tumor cell purity impacts the detection of key abnormalities, including IGH translocations, mutations, and copy number changes.
Subjects and Methods: A single-center study analyzed 134 CD138-selected bone marrow aspirates from patients with smoldering multiple myeloma (n=11), newly diagnosed MM (n=38), and relapsed/refractory MM (n=79), with matched germline samples from saliva or blood. Libraries were prepared using the Myeloma Genome Project (MGP) v22 targeted panel and sequenced on an Illumina platform. Variants and CNAs were reviewed using VarSeq and IGV, with copy number profiled by iChorCNA, and results discussed in a multidisciplinary myeloma tumor board.
Results:
- Samples with >40% CD138+ purity demonstrated significantly improved detection of genomic abnormalities, with IGH translocations identified in 43–56% of cases compared to 18–28% in lower-purity samples, and CNAs in 80–95% versus 28–33%.
- IMS/IMWG-defined high-risk markers were detected in 15.8% of newly diagnosed cases, with 1q gain or amplification increasing from 21% at diagnosis to 49.4% in relapsed disease, while IMiD resistance pathway alterations (CRBN, CUL4, DDB1, COP9) appeared in approximately 24% of IMiD-treated relapsed patients.
- Among immunotherapy-treated cohorts, 15–16% of anti-CD38–exposed patients showed 4p/CD38 deletions, and 25% of post-BCMA–treated patients harbored TNFRSF17 (BCMA) mutations or deletions, including cases with biallelic loss; one such patient achieved remission after switching to anti-GPRC5D therapy.
- Clinically actionable findings included t(11;14) in 19% of samples, associated with venetoclax response, MAPK pathway mutations (KRAS, NRAS, BRAF) in ~34%, and pathogenic germline variants in 4.5% (ATM, BRCA2, FANCA, FANCM), including one case consistent with biallelic ATM loss.
Conclusions: Targeted NGS provides a more comprehensive and clinically actionable approach than traditional FISH, identifying both high-risk and resistance-associated genomic features that guide real-time treatment decisions. Ensuring adequate CD138+ cell purity is essential for accurate detection and effective integration of sequencing into multiple myeloma care.
“121 We implemented a workflow to introduce targeted sequencing of CD138+ cells from 122 patients with plasma cell disorders to improve molecular diagnostics (Figure 1 and 123 Supplementary Methods). Bone marrow aspirates and saliva samples were acquired 124 from patients. The saliva samples were sent directly to the Diagnostic Genomics 125 laboratory for extraction of germline DNA. In total, 168 bone marrow aspirates were sent 126 to the HematoPathology laboratory where they were assessed for plasma cell 127 involvement by flow cytometry and sorted using anti-CD138 magnetic beads. The 128 CD138+ fraction was re-assessed for purity by flow cytometry and number of cells. At 129 this point, 34 samples (20.2%) failed quality control due to insufficient cells. The 130 remaining 134 samples underwent library preparation and hybridization to the Myeloma 131 Genome Project targeted sequencing panel (v22), followed by paired-end sequencing 132 (Illumina). Data were analyzed, as previously described, somatic variants visually 133 checked in VarSeq (Golden Helix) and the Integrated Genome Viewer (IGV), and a 134 clinical report generated. The report was periodically discussed in the Multiple Myeloma 135 Tumor Board meeting consisting of clinicians, scientists, pathologists, and imaging 136 specialists.”
Sudha, P., Pham, P., Niu, W., Liu, E., Wang, L., Truong, G., Ligocki, C., Al-Azzawi, R., Surapenini, M., Bray, S. M., Vetrini, F., Czader, M., Tayeh, M. K., Lee, K., Abonour, R., Suvannasankha, A., & Walker, B. A. (2025). Diagnostic sequencing identifies high-risk markers and mechanisms of resistance to guide immunotherapy selection. Blood Advances. Advance online publication. https://doi.org/10.1182/bloodadvances.2025017721
The studies published in October 2025 reflect how Golden Helix software continues to drive innovation across precision medicine and translational research. With VarSeq supporting annotation, filtering, and visualization, and VSPipeline automating reproducible workflows from raw data to report, researchers are achieving deeper insight with greater efficiency. Each discovery underscores our mission: to equip the global genomics community with tools that transform complex data into knowledge, advancing science and improving lives.