At Golden Helix, we’re proud to see how VarSeq is transforming the landscape of genetic research and clinical diagnostics. From variant annotation and filtering to in-depth visualization, VarSeq’s powerful suite of tools helps researchers uncover critical genetic insights with confidence and efficiency. In this blog post, we’re excited to showcase recent publications where VarSeq played a pivotal role in identifying novel genetic mutations and advancing our understanding of complex diseases.
Neonatal meconium aspiration syndrome associated with ABCA3 gene mutation and mycoplasma infection: a case report
Preterm infants are at high risk of developing respiratory distress syndrome (RDS). Mutations in the genes encoding for surfactant proteins B and C or the ATP-binding cassette transporter A3 (ABCA3) are rare but known to be associated with severe RDS and interstitial lung diseases. The exact prevalence of these mutations in the general population is difficult to determine, as they are usually studied in connection with clinical symptoms. Most cases are not captured due to variability in expression or diagnosis. It is estimated that they affect a small percentage of the population, with mutations in ABCA3 most commonly identified in association with severe lung diseases in newborns. Even heterozygous ABCA3-mutations can increase the risk and severity of RDS in neonates. The expression of these proteins is developmentally regulated, increases with gestational age, and is crucial for the function of pulmonary surfactant at birth. Additional lung stressors, such as meconium aspiration syndrome or pulmonary infections, can lead to a complex clinical picture associated with severe courses. This case report describes an extremely preterm female infant with suspected meconium aspiration syndrome, severe RDS, Mycoplasma pneumoniae infection, and a heterozygous ABCA3-mutation. The report discusses the clinical presentation, diagnostic evaluation, and therapeutic interventions, emphasizing the complexities associated with multiple pulmonary conditions in the context of extreme prematurity. At the limits of viability, therapeutic options for severe respiratory insufficiency are limited compared to older children. The developmental neurological prognosis following prolonged relative hypoxia is a crucial factor to consider in discussions about changing treatment goals. Particularly in severe cases, pulmonary infections and genetic changes in surfactant metabolism must be considered in newborns with RDS.
“Persistent ventilation problems and clinical suspicion of surfactant deficiency syndrome led to urgent genetic testing in the newborn. Therefore whole-exome sequencing (Twist Comprehensive Exome + Mitochondrial Panel (Twist Bioscience)) on NextSeq2000 (lllumina) as 2×150 bp „paired end reads” was performed on genomic DNA. Analysis of the target genes TBX4, BMPR2, SMAD9, ENG, ALK1, ABCA3, SFTPB, SFTPC, SFTPA1, SFTPA2, CSF2RA, CSF2RB, FLNA, FOXF1, NKX2-1, TTF-1, GATA2, SLC7A7, MARS, NPC2, NPB, FOXP1, TMEM173, CFTR in the SeqNext module (JSI, Germany) and genes related to the Genomics England PanelApp (https://panelapp.genomicsengland.co.uk/panels/) primary ciliary disorders (Version 1.42), surfactant deficiency (Version 1.11) and PanelApp Australia (https://panelapp.agha.umccr.org/panels/) Ciliary Dyskinesia (Version 1.38) identified the heterozygous missense mutation c.920C>T (p.Ala307Val) in exon 9 of the ABCA3-gene (Submission number: RCV004732503.1), after using the filtering programs varSEAK (JSI, Germany) and VarSeq (Golden Helix, USA).”
Whole-Exome Sequencing: Discovering Genetic Causes of Granulomatous Mastitis
Granulomatous mastitis (GM) is a rare, benign, but chronic and recurrent inflammatory breast disease that significantly impacts physical and psychological well-being. It often presents symptoms such as pain, swelling, and discharge, leading to diagnostic confusion with malignancy. The etiology of GM remains unclear, though autoimmune and multifactorial components are suspected. This study aimed to explore the genetic underpinnings of GM using whole-exome sequencing (WES) on 22 GM patients and 52 healthy controls to identify single nucleotide variants (SNVs) and copy number variations (CNVs) potentially linked to the disease. WES analysis revealed novel SNVs in six genes: BRCA2 (rs169547), CFTR (rs4727853), NCF1 (rs10614), PTPN22 (rs2476601), HLA-DRB1 (seven variants), and C3 (rs406514). Notably, most of these variants are associated with immune regulation and inflammatory pathways, supporting the hypothesis that GM is an autoimmune disease. However, all identified variants were classified as benign according to the American College of Medical Genetics and Genomics (ACMG) guidelines, necessitating further investigation into their potential functional effects. Despite conducting CNV analysis, no significant variations were identified. This study represents a foundational step in linking genetic predisposition to GM and highlights the need for integrating genetic, clinical, and functional data to better understand GM’s pathophysiology. Future research should focus on larger cohorts, functional studies, and exploring multifactorial contributors to GM, including hormonal and environmental factors.
“Variants were annotated and analyzed using databases and in silico tools, including gnomAD [59], ClinVar [60], dbSNP [61], OMIM [62], PolyPhen2 [63], and SIFT [64]. The Human Genome Variation Society nomenclature was applied via the VarSeq transcript annotation algorithm. CNVs were analyzed using ExomeDepth v1.1.16 software.”
Phenotypic variability in a family with an inherited KAT6A frameshift variant
KAT6A syndrome or Arboleda-Tham Syndrome (ARTHS; OMIM #616268) is a syndromic neurodevelopmental disorder mainly presenting with variable degrees of intellectual disability (ID) and developmental delay (DD), especially speech delay, hypotonia and autism spectrum disorders/behavioral problems. Multiple organ-systems including eyes, heart, gastrointestinal and neurological system can be involved. Other phenotypic features with a suggested association to KAT6A include immune dysfunction and pituitary anomalies. Initially, ID/DD was reported as universal in KAT6A syndrome; however, two children with normal assessment of intellect and development at age 10 and 11 years, were recently reported. KAT6A syndrome is caused by heterozygous pathogenic variants in KAT6A. Inherited variants are rare, and to our knowledge, only three inherited missense variants in KAT6A have been reported, whereas frameshift and nonsense variants have been inherited from mosaic parents only.
Here, we report a Danish family, where an inherited KAT6A frameshift variant c.2710dup (p.(Glu904Glyfs∗12)) show clinical variability in disease phenotype expression among three family members. The description includes an affected first child with premature pubarche (the first individual to our knowledge), a mildly affected second child with normal cognitive performance assessment (the third reported individual with normal assessment of cognition and KAT6A syndrome), and a self-sufficient adult family member. The description expands the phenotypic spectrum of KAT6A syndrome, and thus brings important knowledge for improved management and counselling of patients and families with this rare condition.
“Further data analysis of the exome was performed using VarSeq version 2.2.4 (Golden Helix). Data was filtered for autosomal dominant de novo variants, autosomal dominant paternally inherited variants with association to relevant phenotype or with a CADD score >30, and autosomal recessive inherited variants (homozygous/compound heterozygous). Analysis of copy number variants (CNVs) was not performed. Reference genome: hg38.”
Phenotypic and molecular characterization of the largest worldwide cluster of hereditary angioedema type 1
Hereditary angioedema type 1 (HAE1) is a rare, genetically heterogeneous, and autosomal dominant disease. It is a highly variable, insidious, and potentially life-threatening condition, characterized by sudden local, often asymmetric, and episodic subcutaneous and submucosal swelling, caused by pathogenic molecular variants in the SERPING1 gene, which codes for C1-Inhibitor protein. This study performed the phenotypic and molecular characterization of a HAE1 cluster that includes the largest number of affected worldwide. A geographically HAE1 cluster was found in the northeast Colombian department of Boyaca, which accounts for four unrelated families, with 79 suspected to be affected members. Next-Generation Sequencing (NGS) was performed in 2 out of 4 families (Family 1 and Family 4), identifying the variants c.1420C>T and c.1238T>G, respectively. The latter corresponds to a novel mutation. For Families 2 and 3, the c.1417G>A variant was confirmed by Sanger sequencing. This variant had been previously reported to the patient prior to the beginning of this study. Using deep-learning methods, the structure of the C1-Inhibitor protein, p.Gln474* and p.Met413Arg was predicted, and we propose the molecular mechanism related to the etiology of the disease. Using Sanger sequencing, family segregation analysis was performed on 44 individuals belonging to the families analyzed. The identification of this cluster and its molecular analysis will allow the timely identification of new cases and the establishment of adequate treatment strategies. Our results establish the importance of performing population genetic studies in a multi-cluster region for genetic diseases.
“Finally, the vcf files were generated through the Haplotyper algorithm (Sentieon) and analyzed using VarSeq v2.3.0 software (Golden Helix). The bioinformatics analysis was conducted following the guidelines established for the classification of pathogenicity as described by The American College of Medical Genetics (ACMG) guidelines [11].”
The success stories highlighted in this blog—ranging from neonatal respiratory disorders to rare inflammatory diseases and genetic syndromes—are a testament to VarSeq’s unparalleled capabilities in variant analysis and interpretation. Our software isn’t just a tool; it’s a catalyst for discovery, helping researchers and clinicians worldwide streamline their workflows and achieve breakthroughs faster and more accurately.