NGS Software is Bridging the Gap Between Discovery and Practical Application
Researchers, clinicians, and scientists need cutting-edge solutions to better understand the complexities of human genetics. By delivering high-quality analysis tools and advancing the interpretation of genomic data, Golden Helix bridges the gap between discovery and practical application. Our NGS technologies play a critical role in accelerating genetic insights, supporting the development of more precise diagnostics, treatments, and innovations in personalized medicine.
Below are three recent studies that highlight how the application of Golden Helix’s software has supported groundbreaking advancements in human genetic research.
Comprehensive germline and somatic profiling of high-risk Thai breast cancer via next-generation sequencing
Background: The genetic landscape of breast cancer varies across ethnic groups, but Thai breast tumors have remained largely uncharacterized. This study aimed to address that gap by analyzing germline and somatic mutations in high-hereditary-risk Thai breast cancer patients.
Objectives: To identify germline and somatic mutation patterns in high-risk Thai breast cancer patients and explore how they compare to other ethnic groups.
Subjects & Methods: Germline and somatic sequencing was performed on 1,676 high-risk Thai breast cancer patients using a 36-gene panel and a 501-gene tumor panel, with findings compared to other ethnic cohorts.
Results:
- Germline pathogenic or likely pathogenic mutations were found in 13% of patients, with BRCA1 and BRCA2 being the most commonly affected genes.
- Somatic profiling revealed TP53 as the most frequently mutated gene, especially in HER2+ and triple-negative breast cancer (TNBC) subtypes, while MAP3K1 and GATA3 mutations were more common in HR+/HER2− tumors.
- Clinically actionable mutations were identified in 75.56% of tumors.
- Mutation patterns, such as lower PIK3CA mutation rates and distinct BRCA1/2 mutation distributions, differed from Western and Chinese cohorts.
Conclusions: This is the first study to report both germline and somatic mutational profiles in Thai breast cancer patients. The findings highlight common mutated genes, oncogenic pathways, clinically actionable variants, subtype-specific alterations, and clinical impact. The study also revealed genetic differences between Thai and other ethnic groups, as well as divergent somatic profiles in germline carriers and non-carriers. The identified germline and somatic mutations provide deeper insight into potential therapeutic targets and could guide the development of custom genetic panels in clinical practice. This study underscores the importance of routine genetic sequencing for advancing precision cancer therapies in Thailand.
“Genomic DNA extraction from peripheral blood, sequencing, and variant interpretation were performed as described in the Cancer Genomics Thailand project23. Briefly, genomic DNA from blood samples was sequenced using a custom 36-core cancer panel that encompasses all exons and ± 50 bp of intron–exon boundaries in the target genes (see Supplementary Table 1). Ion Torrent next-generation sequencing technology (Ion S5 XL sequencer; Thermo Fisher Scientific, Waltham, MA, USA) was used for library preparation and sequencing. Raw reads were mapped to the GRCh37 reference genome via Ion Torrent Suite software v5.16.1 (Thermo Fisher Scientific). Germline variants were called and annotated using JSI SeqPilot SeqNext (JSI Medical Systems, New York, NY, USA). The P/LP germline variants were interpreted and classified according to the 2015 ACMG-AMP standards guideline57 and the ACMG/ClinGen guideline58, using Golden Helix VS Clinical software. All SNVs and indels were validated by Sanger sequencing, and CNVs were confirmed by digital MLPA.”
Novel Variant of the Desert Hedgehog Gene in an Indian Patient of 46, XY Gonadal Dysgenesis with Peripheral Neuropathy
Background: 46, XY gonadal dysgenesis (GD) is a rare disorder of sex development; only five cases worldwide have linked GD and peripheral neuropathy to mutations in the Desert Hedgehog (DHH) gene. This report presents the first such case documented in India.
Objectives: To report a novel DHH gene mutation associated with 46, XY gonadal dysgenesis and severe peripheral neuropathy in an Indian patient.
Subjects & Methods: A retrospective clinical and genetic analysis was performed on a 30-year-old woman with primary amenorrhea, severe peripheral neuropathy, and family history, using clinical exome sequencing.
Results:
- The patient had a 15-year history of impaired temperature sensation, Charcot’s joints, distal muscle wasting, and amputations.
- Ultrasound revealed a rudimentary pelvic structure with absent uterus; clinical exome sequencing identified a novel homozygous missense mutation (c.553T>C; p.Ser185Pro) in exon 2 of the DHH gene.
- Her family history included a sister with similar features and absent reproductive structures, and a father with sensory neuropathy.
- Neurological testing confirmed severe motor and sensory deficits, and the mutation was classified as likely pathogenic based on conservation, functional predictions, and clinical phenotype.
Conclusions: This is the first reported case from India of 46, XY gonadal dysgenesis with severe peripheral neuropathy associated with a novel DHH mutation, expanding the genotypic spectrum linked to this rare syndrome.
“Clinical exome sequencing libraries were prepared using in-solution hybrid capture protocol for select genes harbouring known disease-causing mutations. Libraries were sequenced on Illumina NextSeq 550 platform using 2 × 150 bp read chemistry according to manufacturer’s instructions. Reads from the sequence output were aligned to the human reference genome (GRCh38) using the Burrows-Wheeler Aligner (BWA). Variants to the reference were called using the Genomic Analysis Tool Kit (GATK). The variants were annotated and filtered using the Golden Helix VarSeq analysis workflow implementing the ACMG guidelines for interpretation of sequence variants. This includes comparison against the gnomAD population catalogue of variants in 123,136 exomes, the 1000 Genomes Project Consortium’s publication of 2,500 genomes, the NCBI ClinVar database and multiple lines of computational evidence on conservation and functional impact. Clinical exome sequencing showed a missense variant (NM_021044.4) c.553T>C (P.Ser185Pro) detected in exon 2 of DHH gene in homozygous state [Figure 2]. The P.Ser185Pro variant is novel (not in any individuals) in 1 kg., as well as in our in-house database and in gnomAD. The gene DHH has a low rate of benign missense variation. The gene DHH contains two pathogenic missense variants, indicating that missense variants are a common disease mechanism in this gene with a high missense variants Z-Score of 1.64. The P.Ser185Pro missense variant is predicted to be damaging by both SIFT and PolyPhen2. The serine residue at codon 185 of DHH is conserved in all mammalian species. The nucleotide c. 553 in DHH is predicted conserved by GERP++ and PhyloP across 100 vertebrates. Further, the clinical phenotype of the proband matches with that of the disorder caused by pathogenic variants in DHH gene. For these reasons, this variant has been classified as Likely pathogenic.”
A genetic variant in SMAD7 acts as a modifier of LMNA-associated muscular dystrophy, implicating SMAD signaling as a therapeutic target
Background: Mutations in LMNA cause various muscular dystrophies (LMNA-MD) with wide phenotypic variability even among individuals with the same mutation, suggesting that genetic modifiers may influence disease severity.
Objectives: To identify and functionally test a genetic modifier influencing the severity of LMNA-associated muscular dystrophy.
Subjects & Methods: Whole-genome sequencing was performed on four siblings with the same LMNA mutation but differing disease severity, and functional studies were carried out in a Drosophila model.
Results:
- A novel SMAD7 variant was found only in severely affected siblings and enhanced muscle defects when modeled in Drosophila.
- Overexpression of wild-type SMAD7 rescued muscle function in flies, indicating that SMAD7 regulates disease severity.
- Elevated SMAD signaling was detected in human muscle biopsies from individuals with LMNA mutations, supporting a broader role for SMAD pathway dysregulation in LMNA-MD.
Conclusions: SMAD7 functions as a genetic modifier of LMNA-associated muscular dystrophy, and targeting SMAD signaling presents a potential therapeutic strategy for managing disease severity.
“Read mapping was performed with Burrows-Wheeler-Alignment Maximum Exact Matches (BWA-MEM) (GRCh37), and results were stored in the SAM/BAM format (42). HaplotypeCaller from Genome Analysis Toolkit was used for detection of single-nucleotide variants and small insertions/deletions (99). VarSeq (version 2.3; Golden Helix, Inc, Bozeman, Montana, USA) was used for variant annotation and filtering for quality control, proper phenotype segregation, minor allele frequency of <5% in the gnomAD and 1000 Genomes database (53, 100), and loss-of-function or missense mutations. Retained variants and the genes containing them were then prioritized and ranked using a combination of relevant tissue expression (GTEx), constraint metrics [missense z score and probability of loss of function intolerance (pLI)], conservation metrics [Genomic Evolutionary Rate Profiling (GERP) and PhyloP], in silico predictors of pathogenicity (SIFT, PolyPhen-2, MutationTaster, MutationAssessor, FATHMM, FATHMM-MKL, MetaSVM, and MetaLR), and PhoRank, a tool available in VarSeq modeled on the Phevor algorithm that combines phenotype, gene function, and disease information from many ontologies to prioritize disease-causing alleles (42–53).“
These studies demonstrate the real-world impact of Golden Helix’s solutions in advancing genetic research and clinical discovery. Explore how our tools can support your work — request a demo today.