As the world is consumed by the ongoing pandemic, it is easy to forget that there are investigators all around the globe that continue to make important discoveries in human medicine. Below are a few examples that remind us there are those that persevere in their chosen fields of study despite the trying times. At Golden Helix, we continue to support these investigations with our VarSeq, VSClinical, and SVS software. We are constantly innovating and improving our platforms to meet the needs of the scientific community. Read on to see how dedicated scientists all over the world are using our products to enable precision medicine!
Pathogenic Somatic Alterations in Advanced HPV-negative Cell Squamous Laryngeal Carcinoma Revealed Via Targeted Next Generation Sequencing
A team of Bulgarian investigators conducted a study using targeted NGS techniques to better understand the genetic landscape of advanced laryngeal squamous cell carcinomas (LSCC). There have been few studies that focus specifically on LSCC because this type of cancer is usually included in broader studies of cancers of the head and neck. In this study, they focused on LSCC’s to better understand the molecular mechanisms involved in the cancerogenesis of this aggressive disease. Since LSCC’s can occur in any of the three anatomical regions in the larynx, the team also took account of which region the tumors had originated. Using VSClinical for their variant analysis, they successfully identified pathogenic variants in 27 cancer-associated genes and also demonstrated slight differences in the mutational profiles of tumors from each of the three regions of the larynx. The team is hopeful that further targeted NGS investigations will help to select and develop more precise treatment approaches to LSCC’s in the future.
Radke Kaneva & Colleagues, Medical University – Sofia Bulgaria / Published in Genetika
MITO-FIND: A Study in 390 Patients to Determine a Diagnostic Strategy for Mitochondrial Disease
Mitochondrial diseases present a diagnostic challenge because they present with a wide range of clinical features and underlying genetic causes. Traditional diagnostic approaches have mostly relied on tissue biopsies and other invasive procedures aimed at finding the disease-causing DNA variant. Researchers in Canada employed VSClinical as they assessed the value of incorporating the recent innovations in bioinformatics data analysis of NGS data as a less invasive first approach to diagnosis. In this two-part study, they first retrospectively investigated what they termed as the “Traditional Diagnostic Pathway” from patients who had previously been assessed for a mitochondrial disease. The second part was called the “Next Generation Sequencing Pathway” which was a prospective view of how applying NGS techniques could have affected the initial diagnosis. Their study supports recent findings that including a “genomics first” approach combined with other techniques may serve as an effective first step in diagnosing mitochondrial diseases.
Aneal Khan, Marina Kerr & Colleagues, University of Calgary / Published in Molecular Genetics & Metabolism
Genetic Control of CCL24, POR, and IL23R Contributes to the Pathogenesis of Sarcoidosis
Sarcoidosis is a disease of unknown cause that is characterized by tiny collections of inflammatory cells (also known as granulomas) that can form in any part of the body. It is a genetically complex condition. Researchers in Japan utilized SVS software to perform a genome wide association study (GWAS) which is thought to be the first study of its kind of sarcoidosis in an Asian population. Since ethnicity is known to play a role in the prevalence and clinical features of sarcoidosis, the team compared their Japanese study group to a control group of samples taken from subjects in the Czech Republic. They were able to identify three loci (two of which were novel) in their meta-analysis of the Japanese samples when compared to the Czech cohorts. The data indicated a genome-wide significant association with sarcoidosis. Their findings supported the concept that differences in genetic background can determine ethnic differences in sarcoidosis prevalence and phenotypes.
Akira Meguro & Colleagues, Yokohama City University / Published in Communications Biology
Simplifying Detection of Copy Number Variations in Maturity Onset Diabetes of the Young
Investigators in Canada published a paper demonstrating the value of detecting copy number variants (CNV’s) to determine their effect on maturity onset diabetes of the young (MODY). Their work also showcased the role improved bioinformatics tools play in today’s precision medicine focus. The team examined a group of patients clinically suspected to have MODY but had tested negative for pathogenic mutations using a targeted panel. Using VarSeq’s industry-leading CNV calling tool, they re-examined the NGS data, specifically looking for CNV’s. In this study, individuals were identified as having heterozygous CNVs, thus allowing them to be re-classified from “mutational negative” to “CNV positive”. For those reclassified, quality of life and management decisions were impacted which allowed for a more personalized and effective treatment. The team hopes this combined bioinformatics and NGS approach will result in an easier, more cost-effective method alternative to the standard practice of using multiple detection methods to identify pathogenic CNVs. They also are hopeful their method will improve the diagnostic capability of genetic testing for MODY moving forward.
Robert Hegele, John Robinson & Colleagues, Robarts Research Institute / Published in the Canadian Journal of Diabetes
Compound Heterozygous Splicing CDON Variants Result in Isolated Ocular Coloboma
Researchers at the Medical College of Wisconsin were presented the opportunity to take a deeper look at the genetic causes of a developmental defect in an affected, non-consanguineous family. Ocular coloboma refers to a condition where there is a gap in one or more tissues in the eye, causing the tissue to not fully develop in utero. Using SVS to perform their trio analyses on two affected siblings and their parents, the team was able to identify compound heterozygous donor splice site variants in the CDON gene. They hope their discovery will lead to further investigations of the inherited genetic causes of ocular coloboma.
Linda Reis & Colleagues, Medical College of Wisconsin / Published in Clinical Genetics
Genome-wide Association Analysis of 17,019 Korean Women Identifies Variants Associated with Facial Pigmented Spots
Korean investigators employed SVS software in their GWAS study aimed at discovering the genetic association of facial pigmented spots in a large cohort of Korean women. Skin pigmentation has been studied in populations of European and African descent, but little is known how this data translates to Asian populations. In this study, the team used two types of imaging methods to measure and assess facial pigmentation: UV light imagine and polarized light. After the visual characterization of the pigmented spots was complete, the team then utilized the power of DNA analysis to identify the genetic effect on the presence of these spots in the Korean study population. While confirming the indicated association between previously identified variants in African, Japanese and Latino populations, the team identified two additional variants of significance that were not previously reported. Although further investigation is needed, the team hopes this discovery will lead to more studies of this type to better understand the formation of pigmented facial spots in women of Korean descent.
Joong-Gon Shin & Colleagues, LG Household & Healthcare/ Published in the Journal of Investigative Dermatology