For July, we’re highlighting three studies that demonstrate the power of genomic analysis across diverse applications: improving liquid biopsy approaches for monitoring cancer through circulating tumor DNA, uncovering genetic diversity among important grape varieties to support viticulture and breeding, and exploring how genetic variation in APOE influences inflammatory responses linked to Alzheimer’s disease risk. Together, these studies illustrate how robust genomic analysis tools can help researchers extract meaningful biological insights from complex sequencing data and accelerate discoveries across multiple fields.
Off-Target-Based Tumor Fraction Estimation from Targeted Sequencing Shows Concordance with Orthogonal Methods Across Advanced Solid Tumors
Background: Circulating tumor DNA (ctDNA) is tumor-derived DNA found in body fluids that can provide a real-time, minimally invasive measure of cancer burden because it reflects tumor-specific genetic changes and has a very short half-life. Changes in ctDNA levels, particularly circulating tumor fraction (ctFraction), have emerged as valuable biomarkers for monitoring treatment response often earlier than conventional imaging.
Objective: This study compared several methods for estimating ctFraction, including ichorCNA, Fragle (using both low-pass whole-genome sequencing and targeted sequencing off-target reads), and the proprietary OTTER algorithm, in 33 patients with advanced solid tumors. The researchers also evaluated paired baseline and post-treatment samples from 20 patients to determine whether changes in ctFraction and variant allele frequency (VAF) after two treatment cycles could serve as measures of molecular response and treatment effectiveness.
Subjects and Methods: This study analyzed blood samples from 42 patients with advanced solid tumors to compare four methods for estimating circulating tumor fraction (ctFraction) from ctDNA. In a subset of 20 patients with paired baseline and post-treatment samples, changes in ctFraction and variant allele frequency (VAF) were evaluated as biomarkers of molecular response to therapy.
Results: In 33 patients with advanced solid tumors, Fragle, ichorCNA, and OTTER showed strong agreement in estimating circulating tumor fraction (ctFraction), with Fragle off-target demonstrating the highest concordance with Fragle LP-WGS while using only targeted sequencing data. In a longitudinal cohort of 20 patients, changes in ctFraction closely tracked changes in variant allele frequency (VAF) and aligned with radiologic responses after two treatment cycles, supporting ctFraction as a promising biomarker for monitoring treatment response.
Conclusions: Fragle showed strong agreement with established ctDNA quantification methods and offers the advantage of estimating ctFraction directly from targeted sequencing data without additional sequencing. However, larger prospective studies are needed to validate its clinical utility.
How VarSeq Was Used: “Somatic variants were detected with the FCCC ctDNA assay in 29 of 33 patients (87.9%); no variants were detected in Pt.10, Pt.12, Pt.22, and Pt.24 (Supplementary Table S2). Out of 156 total detected variants, 77 were classified as oncogenic, likely oncogenic, Tier 1, or Tier 2 according to Cancer KB (Golden Helix) (Supplementary Table S2). As expected, TP53 was the most frequent mutated gene, with 15 patients (45%) harboring oncogenic mutations (Figure 2). Six patients (18%) harbored BRAF variants, which were classified as Tier 1 in four melanoma patients (Pt.14, Pt.15, Pt.16, and Pt.17). Additionally, oncogenic or likely oncogenic PTEN variants were detected in five patients (15%; two lung squamous cell carcinoma, two melanoma, and one breast cancer), TERT variants in five melanoma patients (15%), and Tier 1 KRAS variants in four patients (12%; three lung adenocarcinoma and one colon adenocarcinoma). KRAS Gly12Ala, Gly12Asp, and Gly12Val are classified as Tier 1 variants, as these alterations are associated with poorer survival [35]. In lung adenocarcinoma patients, Pt.9 harbored an EGFR variant located in the exon 19 tyrosine kinase domain conferring sensitivity to EGFR tyrosine kinase inhibitors (TKIs) (Supplementary Table S2). Finally, oncogenic PIK3CA variants were identified in three breast cancer patients (Figure 2).”
Citation: Hasenleithner, S. O., Rao, S., Yu, J. Q., Tan, Y., Sheriff, F., Winn, J. S., Borghaei, H., Edelman, M. J., Giri, A., Astsaturov, I., Wasik, M., Jost, P. J., & Fernandez, S. V. (2026). Off-Target-Based Tumor Fraction Estimation from Targeted Sequencing Shows Concordance with Orthogonal Methods Across Advanced Solid Tumors. International Journal of Molecular Sciences, 27(13), 6078. https://doi.org/10.3390/ijms27136078
Case Report: A Rare Stop-Gained MYZAP Mutation is Associated with Atrioventricular septal defects in an Arabian Family
Background: Atrioventricular septal defect (AVSD) is a group of congenital heart defects caused by abnormal development of the endocardial cushions during embryonic heart formation and is strongly associated with Down syndrome.
Objective: This case study describes a family without Down syndrome or other dysmorphic features in which the father and two daughters each had different forms of AVSD, highlighting the variable presentation of this inherited cardiac defect.
Subjects and Methods: Researchers evaluated an Arabian family with inherited congenital heart defects using clinical cardiac assessments, karyotyping to rule out Down syndrome, whole-exome sequencing, and Sanger sequencing. Variant analysis identified and confirmed a rare MYZAP mutation that segregated with affected family members, supporting its role as the likely genetic cause of the family’s atrioventricular septal defect (AVSD) spectrum.
Results: A family with a range of atrioventricular septal defect (AVSD) abnormalities was found to carry a rare MYZAP loss-of-function variant identified through whole-exome sequencing and confirmed by Sanger sequencing. The affected family members showed variable heart defects, including complete and partial AVSD, mitral valve abnormalities, and conduction problems, suggesting that the MYZAP mutation may contribute to AVSD development but with variable expression influenced by other genetic or environmental factors.
Conclusions: This study suggests that MYZAP may play a role in cardiac septation, though further functional studies are needed to confirm its contribution to congenital heart disease.
How VarSeq Was Used: “Variants were filtered based on the following criteria: (i) exonic or splice-site location; (ii) minor allele frequency (MAF) <0.01 in population databases; (iii) predicted functional impact including missense, nonsense, frameshift, or splice-site variants; and (iv) consistency with the suspected inheritance pattern. Candidate variants were prioritized according to gene function, known disease associations, segregation within the family, phenotypic relevance, and ACMG/AMP guidelines. Variant annotation and filtration were performed within the Golden Helix VarSeq environment, which incorporates the American College of Medical Genetics and Genomics (ACMG) guideline-based classification. Multiple population, clinical, and functional databases, including gnomAD, 1000 Genomes, ClinVar, OMIM, dbSNP, RefSeq, and ExAC, and gene constraint metrics were used to assess allele frequency and clinical relevance. A broad set of in silico prediction tools (including SIFT, PolyPhen-2, GERP++, PhyloP, GeneSplicer, NNSplice, and PWM splice predictors) was applied to evaluate the potential impact of amino-acid substitutions and splice-site alterations. All variants were annotated according to HGVS nomenclature conventions using the VarSeq transcript annotation workflow, ensuring consistency with the most frequently referenced transcripts in ClinVar.”
Citation: Zaher Z, Abdelmohsen G, Bahaidarah S, Baamer F, Abdulrhman Abdulkareem A, Alrefaei AF, Naseer MI and Abu-Elmagd M (2026) Case Report: A rare stop-gained MYZAP mutation is associated with atrioventricular septal defects in an Arabian family. Front. Cardiovasc. Med. 13:1866593. https://doi.org/10.3389/fcvm.2026.1866593
APOE genotype is associated with Ex vivo inflammatory responses in healthy individuals: Potential implications for Alzheimer’s disease
Background: APOE genotype influences Alzheimer’s disease risk through effects on lipid metabolism, amyloid and tau pathology, and immune regulation, with APOE4 associated with increased inflammation and disease risk while APOE2 is associated with protection.
Objective: This study investigated whether APOE genotype influences inflammatory responses by comparing basal and LPS-stimulated immune markers in healthy individuals, testing whether APOE4 and APOE2 carriers exhibit distinct immune profiles compared with APOE3 carriers.
Subjects and Methods: This study analyzed 91 healthy adults from the New York City area to examine the relationship between APOE genotype and inflammatory responses. Participants were genotyped for APOE variants, and basal and LPS-stimulated cytokine levels were measured in blood to assess differences in immune activity among APOE2, APOE3, and APOE4 carriers using statistical modeling.
Results: In 91 healthy adults, APOE4 carriers showed heightened LPS-stimulated inflammatory responses, including increased IL-1β and TNF-α levels, while APOE2 carriers showed reduced IL-1β responses, suggesting APOE genotype influences immune profiles associated with Alzheimer’s disease risk.
Conclusions: The study found that APOE genotype influences innate immune response profiles, with APOE4 carriers showing a heightened inflammatory response and APOE2 carriers exhibiting a reduced inflammatory response to immune stimulation, suggesting that genotype-specific inflammatory pathways may contribute to differences in Alzheimer’s disease risk.
How SVS Was Used: “Participants were genotyped at enrollment as described in previous publication (Hunter et al., 2020a). Five mL of whole blood was obtained in EDTA-coated collection tubes via venipuncture. The Global Screening Array-24.v1.0 was used to genotype APOE gene variant rs7412 with a genotyping call rate of 98.5%; only samples with a 95% genotype call rate or more were retained for analysis. TaqMan (Thermo Fisher Scientific, Waltham, MA) was used to genotype the variant rs429358 with a call rate of 99.3%. The TaqMan assay was used for rs429358 because a higher genotyping error rate than the Global Screening Array chip was found in our quality control step using samples with previously known APOE genotypes. Genotype data were analyzed with the Golden Helix SVS software (Golden Helix, Bozeman, MT). The genotypes did not deviate from the Hardy-Weinberg equilibrium.”
Citation: Joan Y. Song, et al. (2026). APOE genotype is associated with Ex vivo inflammatory responses in healthy individuals: Potential implications for Alzheimer’s disease,
Brain, Behavior, & Immunity – Health, Volume 56, 101307, https://doi.org/10.1016/j.bbih.2026.101307
