Our VarSeq software continues to support cutting-edge research, enabling scientists worldwide to explore the depths of genetic variants with precision and accuracy. In this blog, we highlight recent publications that leveraged VarSeq for impactful discoveries in pharmacogenomics and familial cancer studies, showcasing the vital role of our tools in advancing personalized medicine and genetic research.
Thai pharmacogenomics database −2 (TPGxD-2) sequel to TPGxD-1, analyzing genetic variants in 26 non-VIPGx genes within the Thai population
Next-generation sequencing (NGS) has transformed pharmacogenomics (PGx), enabling thorough profiling of pharmacogenes using computational methods and advancing personalized medicine. The Thai Pharmacogenomic Database-2 (TPGxD-2) analyzed 948 whole genome sequences, primarily from the Electricity Generating Authority of Thailand (EGAT) cohort. This study is an extension of the previous Thai Pharmacogenomic Database (TPGxD-1) and specifically focused on 26 non-very important pharmacogenes (VIPGx) genes. Variant calling was conducted using Sentieon (version 201808.08) following GATK’s best workflow practices. We then annotated variant call format (VCF) files using Golden Helix VarSeq 2.5.0. Star allele analysis was performed with Stargazer v2.0.2, which called star alleles for 22 of 26 non-VIPGx genes. The variant analysis revealed a total of 14,529 variants in 26 non-VIPGx genes, with TBXAS1 had the highest number of variants (27%). Among the 14,529 variants, 2328 were novel (without rsID), with 87 identified as clinically relevant. We also found 56 known PGx variants among the known variants (n = 12,201), with UGT2B7 (19.64%), CYP1B1 (8.9%), SLCO2B1 (8.9%), and POR (8.9%) being the most common. We reported a high frequency of intermediate metabolizers (IMs) in CYP2F1 (34.6%) and CYP4A11 (8.6%), and a high frequency of decreased functional alleles in POR (53.9%) and SLCO1B3 (34.9%) genes. This study enhances our understanding of pharmacogenomic profiling of 26 non-VIPGx genes of notable clinical importance in the Thai population. However, further validation with additional computational and reference genotyping methods is necessary, and novel alleles identified in this study should undergo further orthogonal validation.
Germline genetic variants in a case of familial cancer: RAD51D and four other co-segregated variants
Cancer is a multifactorial, multi-step process of pathogenesis; however, in the case of familial cancers, genetic aetiology can play a significant role. Identifying genetic variants in cancer patients having a strong family history of cancer as well as their unaffected blood relatives can unravel their role in predisposition to cancer. Here, we report the findings of whole-exome sequencing in a patient (77/F) diagnosed with ovarian cancer and her daughters (61/F) and (59/F) who were diagnosed with breast and ovarian cancers along with her asymptomatic son (53/M). All the four family members show segregation of RAD51D (rs200564819). Other incidental findings ADAMTS13 (rs142572218) and SYCE1 (rs201873178) genetic variants in proband and son, and LIAS (rs546751789) and PDHA1 (rs747051654) genetic variants in son have also been reported.
“… Golden Helix VarSeq 2.2.5 10(VarSeq™ Version 8.x) and GATK3 (Genome Assembly Toolkit 3) (McKenna et al. 2010) were used for the analysis and NGS-WES raw data were validated. The … Germline variant analysis by GATK3 and Golden …”
As these studies demonstrate, VarSeq is at the forefront of innovation in genetic analysis, empowering researchers to push the boundaries of knowledge and improve clinical outcomes. We are proud to be part of the journey toward personalized medicine, providing the tools that enable researchers to make significant strides in pharmacogenomics and cancer genomics. Stay tuned for more groundbreaking publications supported by VarSeq!