At Golden Helix, we are proud to support researchers and clinicians worldwide who push the boundaries of precision medicine. Our VarSeq software continues to be instrumental in the analysis and interpretation of genetic data, enabling groundbreaking discoveries and advancements. Recently, several papers have been published that showcase the power and versatility of VarSeq in various research domains, from neurodegenerative diseases to pharmacogenomics. In this blog post, we highlight some of these significant studies, demonstrating how VarSeq is helping researchers uncover novel genetic insights and contributing to the development of personalized medicine.
Primary Microgliopathy Presenting as Degenerative Dementias: A Case Series of Novel Gene Mutations from India
Introduction: Microglia exert a crucial role in homeostasis of white matter integrity, and several studies highlight the role of microglial dysfunctions in neurodegeneration. Primary microgliopathy is a disorder where the pathogenic abnormality of the microglia causes white matter disorder and leads to a neuropsychiatric disease. Triggering receptor expressed on myeloid cells (TREM2), TYRO protein tyrosine kinase binding protein (TYROBP) and colony-stimulating factor 1 receptor (CSF1R) are genes implicated in primary microgliopathy. The clinical manifestations of primary microgliopathy are myriad ranging from neuropsychiatric syndrome, motor disability, gait dysfunction, ataxia, pure dementia, frontotemporal dementia (FTD), Alzheimer’s dementia (AD), and so on. It becomes imperative to establish the diagnosis of microgliopathy masquerading as degenerative dementia, especially with promising therapies on horizon for the same. We aimed to describe a case series of subjects with dementia harbouring novel genes of primary microgliopathy, along with their clinical, neuropsychological, cognitive profile and radiological patterns. Methods: The prospective study was conducted in a university referral hospital in South India, as a part of an ongoing clinico-genetic research on dementia subjects, and was approved by the Institutional Ethics Committee. All patients underwent detailed assessment including sociodemographic profile, clinical and cognitive assessment, pedigree analysis and comprehensive neurological examination. Subjects consenting for blood sampling underwent genetic testing by whole-exome sequencing (WES). Results: A total of 100 patients with dementia underwent genetic analysis using WES and three pathogenic variants, one each of TREM2, TYROBP, and CSF1R and two variants of uncertain significance in CSF1R were identified as cause of primary microgliopathy. TREM2 and TYROBP presented as frontotemporal syndrome whereas CSF1R presented as frontotemporal syndrome and as AD. Conclusion: WES has widened the spectrum of underlying neuropathology of degenerative dementias, and diagnosing primary microglial dysfunction with emerging therapeutic options is of paramount importance. The cases of primary microgliopathy due to novel mutations in TREM2, TYROBP, and CSF1R with the phenotype of degenerative dementia are being first time reported from Indian cohort. Our study enriches the spectrum of genetic variants implicated in degenerative dementia and provides the basis for exploring complex molecular mechanisms like microglial dysfunction, as underlying cause for neurodegeneration.
“The variants to the reference were called using the Genomic Analysis Tool Kit. The variants were annotated and filtered using the Golden Helix VarSeq analysis workflow implementing the American College of Medical Genetics (ACMG) guidelines for interpretation of sequence variants. This includes comparison against the gnomAD population catalog of variants in 730,947 exomes and 76,215 genomes and 1000 Genomes Project Consortium of 2,500 genomes, the NCBI ClinVar database and multiple lines of computational evidence on conservation and functional impact.”
Genotypes and phenotypes of motor neuron disease: an update of the genetic landscape in Scotland
Abstract
Background
Using the Clinical Audit Research and Evaluation of Motor Neuron Disease (CARE-MND) database and the Scottish Regenerative Neurology Tissue Bank, we aimed to outline the genetic epidemiology and phenotypes of an incident cohort of people with MND (pwMND) to gain a realistic impression of the genetic landscape and genotype–phenotype associations.
Methods
Phenotypic markers were identified from the CARE-MND platform. Sequence analysis of 48 genes was undertaken. Variants were classified using a structured evidence-based approach. Samples were also tested for C9orf72 hexanucleotide expansions using repeat-prime PCR methodology.
Results
339 pwMND donated a DNA sample: 44 (13.0%) fulfilled criteria for having a pathogenic variant/repeat expansion, 53.5% of those with a family history of MND and 9.3% of those without. The majority (30 (8.8%)) had a pathogenic C9orf72 repeat expansion, including two with intermediate expansions. Having a C9orf72 expansion was associated with a significantly lower Edinburgh Cognitive and Behavioural ALS Screen ALS-Specific score (p = 0.0005). The known pathogenic SOD1 variant p.(Ile114Thr), frequently observed in the Scottish population, was detected in 9 (2.7%) of total cases but in 17.9% of familial cases. Rare variants were detected in FUS and NEK1. One individual carried both a C9orf72 expansion and SOD1 variant.
Conclusions
Our results provide an accurate summary of MND demographics and genetic epidemiology. We recommend early genetic testing of people with cognitive impairment to ensure that C9orf72 carriers are given the best opportunity for informed treatment planning. Scotland is enriched for the SOD1 p.(Ile114Thr) variant and this has significant implications with regards to future genetically-targeted treatments.
“On gene panel sequencing, depth of coverage (≥ 20X) was, on average, 98% across the regions of interest. After VarSeq variant filtering, 503 variants were identified in 339 samples. Variants (including benign variants and VUS) were identified in 278/339 (82.0%) of samples. Fifteen (15/339, 4.4%) had a variant meeting criteria for pathogenicity (Table 2). The number of pwMND with a VUS in an MND-associated gene was 88 (88/339, 25.9%). Of these, 38 individuals (38/339, 1.1%) had a VUS which met some pathogenic ACMG-AMP criteria (‘hot’ VUS). These are summarised in Supplementary Material 2. One patient had both a pathogenic missense variant and a pathogenic C9orf72 expansion. A further six individuals had two variants of interest (including VUS meeting some criteria for pathogenicity) and these are summarised in Supplementary Material 3.”
A comprehensive Thai pharmacogenomics database (TPGxD-1): Phenotype prediction and variants identification in 942 whole-genome sequencing data
Computational methods analyze genomic data to identify genetic variants linked to drug responses, thereby guiding personalized medicine. This study analyzed 942 whole-genome sequences from the Electricity Generating Authority of Thailand (EGAT) cohort to establish a population-specific pharmacogenomic database (TPGxD-1) in the Thai population. Sentieon (version 201808.08) implemented the GATK best workflow practice for variant calling. We then annotated variant call format (VCF) files using Golden Helix VarSeq 2.5.0 and employed Stargazer v2.0.2 for star allele analysis. The analysis of 63 very important pharmacogenes (VIPGx) reveals 85,566 variants, including 13,532 novel discoveries. Notably, we identified 464 known PGx variants and 275 clinically relevant novel variants. The phenotypic prediction of 15 VIPGx demonstrated a varied metabolic profile for the Thai population. Genes like CYP2C9 (9%), CYP3A5 (45.2%), CYP2B6 (9.4%), NUDT15 (15%), CYP2D6 (47%) and CYP2C19 (43%) showed a high number of intermediate metabolizers; CYP3A5 (41%), and CYP2C19 (9.9%) showed more poor metabolizers. CYP1A2 (52.7%) and CYP2B6 (7.6%) were found to have a higher number of ultra-metabolizers. The functional prediction of the remaining 10 VIPGx genes reveals a high frequency of decreased functional alleles in SULT1A1 (12%), NAT2 (84%), and G6PD (12%). SLCO1B1 reports 20% poor functional alleles, while PTGIS (42%), SLCO1B1 (4%), and TPMT (5.96%) showed increased functional alleles. This study discovered new variants and alleles in the 63 VIPGx genes among the Thai population, offering insights into advancing clinical pharmacogenomics (PGx). However, further validation is needed using other computational and genotyping methods.
“A BED file, containing the genomic coordinates of these 63 VIPGx genes listed in the PharmGKB database12 was downloaded from the UCSC genome database.13 Subsequently, the BCFtool (version 1.18) facilitated the extraction of these 63 VIPGx genes from raw VCF files, resulting in files named as “PGx-VCF files.” These files underwent comprehensive annotation and cataloging through Golden Helix VARSeq 2.5.0 (build 14,706-608a25a286) (Figure 1).”
“Out of 72,034 known variants, 464 were found to be significantly associated with the Pharmacokinetics/Pharmacodynamics (PK/PD) and toxicities of various drugs. Golden Helix VARSeq 2.5.0 (build 14706-608a25a286) used PharmGKB Variants 2019-06-19, GHI, to annotate these variants and their associations with PK/PD and toxicity.”
The recent publications from VarSeq users exemplify the transformative impact of advanced genomic analysis tools in modern research. These studies expand our understanding of complex genetic disorders and pave the way for innovative therapeutic approaches and personalized treatment strategies. At Golden Helix, we remain committed to supporting the scientific community with cutting-edge solutions like VarSeq, empowering researchers to continue making remarkable strides in genetic research. We are excited to see what future discoveries will emerge from the ongoing collaboration between Golden Helix and the global scientific community!