This October, we’re highlighting three customer publications that demonstrate how genomic analysis can support discoveries in rare genetic disorders, neurological conditions, and cancer research. From identifying a novel BORCS8 variant associated with fetal holoprosencephaly, to investigating an ATP1A3 variant linked to an adult-onset PLS-like syndrome, and exploring the genetic mechanisms of chemoresistance in canine mammary carcinoma cells, these studies showcase the diverse applications of genomic tools in uncovering genetic variation and advancing scientific understanding.
Novel Homozygous Consensus Splice Site Variant in the BORCS8 Gene Associated with Fetal Semi-Lobar Holoprosencephaly
Background: Holoprosencephaly (HPE) is a congenital brain malformation caused by the incomplete separation of the forebrain into two hemispheres during embryonic development, with severity ranging from mild to severe and potentially causing facial abnormalities, developmental delays, seizures, and hormonal dysfunction. HPE can result from environmental factors, chromosomal abnormalities, or genetic mutations, and this case report describes a novel association between fetal semi-lobar HPE and a homozygous pathogenic splice-site variant in the BORCS8 gene, identified through exome sequencing.
Objective: This case broadens the known features of BORCS8-related disease and suggests BORCS8 as a potential HPE-associated gene, although further cases are needed to confirm its role and establish possible disease mechanisms.
Subjects and Methods: A 26-week fetal ultrasound in a consanguineous couple revealed semilobar holoprosencephaly and cerebellar abnormalities suggestive of rhombencephalosynapsis, with no significant variants identified in known HPE-associated genes. Further testing confirmed a homozygous pathogenic BORCS8 splice-site variant (c.150+1G>T) in the fetus, with both asymptomatic parents identified as heterozygous carriers, and the same brain malformation recurred in a second pregnancy, supporting a potential association between BORCS8 and HPE.
Results: The researchers identified a novel homozygous BORCS8 splice-site variant associated with recurrent fetal semi-lobar holoprosencephaly, suggesting BORCS8 as a candidate HPE gene and highlighting the need for further research to confirm its role and improve genetic counseling and prenatal screening.
Conclusions: It was hypothesized that the severe presentation of holoprosencephaly (HPE) resulted from a BORCS8 variant causing complete loss of gene function. The researchers propose that BORCS8 dysfunction may contribute to HPE by disrupting Sonic Hedgehog (SHH) signaling, impairing neuronal migration and axonal growth, or interfering with primary cilia formation, all of which are important for normal brain development. However, further cases and functional studies are needed to confirm these mechanisms, as the study was limited by the lack of detailed fetal autopsies and molecular analyses of the variant’s effects.
How VarSeq Was Used: “Genomic view of the binary alignment map file after exome sequencing analysis using Varseq software (Golden Helix Inc., Bozeman, MT, USA) showing a homozygous variant in the BORCS8 gene”
Citation: Tamhankar P M, Tamhankar V, Shah D, et al. (September 26, 2026) Novel Homozygous Consensus Splice Site Variant in the BORCS8 Gene Associated with Fetal Semi-lobar Holoprosencephaly. Cureus 18(9): e116976. https://doi.org/10.7759/cureus.116976.
A De Novo ATP1A3 p.Arg995His Variant in a Patient with an Adult-Onset Primary Lateral Sclerosis-Like Syndrome
Background: ATP1A3-related disorders are a spectrum of rare neurological diseases caused by pathogenic variants in ATP1A3, which encodes the neuronal α3 subunit of the Na⁺/K⁺-ATPase, disrupting ion homeostasis and leading to diverse clinical manifestations, including alternating hemiplegia of childhood, CAPOS syndrome, rapid-onset dystonia-parkinsonism, epilepsy, cerebellar ataxia, and neuropsychiatric symptoms.
Objective: This study reports the first known case of adult-onset primary lateral sclerosis associated with a de novo ATP1A3 variant, expanding the phenotypic spectrum of ATP1A3-related disorders.
Subjects and Methods: Clinical data were retrospectively reviewed over four years, while targeted exome sequencing, variant interpretation, and parental segregation and parentage analyses were performed to identify and characterize the ATP1A3 variant.
Results: The study identified a de novo heterozygous ATP1A3 p.Arg995His variant, classified as a variant of uncertain significance, in a patient with adult-onset progressive primary lateral sclerosis (PLS), while extensive diagnostic testing revealed no alternative etiology.
Conclusions: The study concludes that ATP1A3-related disease may present with an adult-onset PLS-like upper motor neuron syndrome, expanding its potential phenotypic spectrum and supporting consideration of ATP1A3 in unexplained adult-onset spasticity, although the clinical significance of the identified p.Arg995His variant remains uncertain.
How VarSeq Was Used: “Genetic testing was performed using a targeted exome-based approach comprising 262 genes associated with hereditary ataxia, including ATP1A3. Genomic DNA was extracted from peripheral blood, and exonic regions were captured using the xGen Exome Panel v2.0 (Integrated DNA Technologies, Coralville, IA, USA). Paired-end sequencing (2 × 100 bp) was performed on a NovaSeq 6000 platform (Illumina, San Diego, CA, USA). Bioinformatic analysis was performed using the Data Genomics Exome Pipeline (v19.1), including single-nucleotide variant and insertion/deletion analysis. Copy-number variants were assessed using VarSeq (Golden Helix). The ATP1A3 coding region achieved 100% coverage at > 20×, with a mean sequencing depth of 136.9×.”
Citation: P. Hernandez-Vitorique, M. García de Burgos, A. Campos Villegas, M. J. Gómez Heredia, and P. Carbonell Corvillo, “ A De Novo ATP1A3 p.Arg995His Variant in a Patient With an Adult-Onset Primary Lateral Sclerosis-Like Syndrome,” Clinical Genetics (2026): 1–5, https://doi.org/10.1111/cge.70254.
Integrated Gene Expression and Mutation Profiling of Chemoresistance in Canine Mammary Carcinoma Cells
Background: Canine mammary gland tumors are common, often malignant neoplasms that frequently exhibit chemoresistance, potentially mediated by ABC transporters such as MDR1 and MRP1, highlighting the need to understand resistance mechanisms to develop more effective targeted therapies.
Objective: This study aimed to establish chemo-resistant canine mammary carcinoma cells and investigate the expression of ABC transporter genes (MDR1, MRP1, MRP2, MRP3, and BCRP) to better understand the molecular mechanisms underlying chemoresistance in canine mammary tumors.
Subjects and Methods: The study investigated doxorubicin-induced chemoresistance in five canine mammary carcinoma cell lines, including two newly established and characterized cell lines. Cells were gradually exposed to increasing concentrations of doxorubicin, and resistance was assessed using MTT cell viability assays. RT-qPCR was used to measure the expression of five ABC transporter genes (MDR1, MRP1, MRP2, MRP3, and BCRP) before and after treatment. Additionally, SNP genotyping and copy number variation analysis were performed to identify potential genomic changes associated with chemoresistance.
Results: The results showed that UNESP-CMR1 cells had the highest baseline expression of MDR1, BCRP, MRP1, and MRP3, while doxorubicin exposure altered ABC transporter gene expression across cell lines. Only three of the five cell lines developed increased resistance, associated primarily with increased MDR1 and/or MRP1 expression, whereas two became more sensitive to doxorubicin. SNP/CNV analysis also identified 35 genetic differences between treated and untreated cells, including variants in the ALK and RALGAPA2 genes, suggesting potential genomic changes associated with treatment.
Conclusions: The study found that ABC transporter genes (MDR1, MRP1, MRP2, MRP3, and BCRP) may contribute to differences in doxorubicin sensitivity and chemoresistance among canine mammary tumor cell lines, with MRP2 potentially playing a key role. While three cell lines developed increased resistance, two became more sensitive after treatment, highlighting the complexity of chemoresistance and the need for individualized treatment protocols. Genetic variations in genes such as ALK and RALGAPA2 may also influence treatment response, but larger studies and functional validation are needed to confirm these findings.
How SVS Was Used: “All cell line genotypes were obtained using the Illumina CanineHD BeadChip (≈230 K SNPs). The SNP dataset used for cell line comparison was generated with SNP & Variation Suite (SVS) v8.9 (Golden Helix Inc., Bozeman, MT, USA). Before the analysis, SNP positions were remapped from the CanFam3.1 assembly to the ROS_Cfam_1.0 reference genome using the rs identifiers assigned to each variant. These rs identifiers were then used as input for the Ensembl Variant Effect Predictor (VEP) tool (https://www.ensembl.org/info/docs/tools/vep/index.html) to retrieve the updated genomic coordinates in the ROS_Cfam_1.0 assembly and determine the position of each SNP relative to annotated genes.”
Citation: P.F. Lainetti, A.F. Leis-Filho, M.S. Franzoni, L.G.D. Benevenuto, V. Grieco, M.G. Strillacci, R. Laufer-Amorim, C.E. Fonseca-Alves, Integrated gene expression and mutation profiling of chemoresistance in canine mammary carcinoma cells, Research in Veterinary Science, 2026, https://doi.org/10.1016/j.rvsc.2026.106431.
