Category: News

From Ancestry to Disease Risk: What is Extracted DNA used for?

Posted on by Dora Katona

As DNA testing becomes more accessible and cost-effective, its applications in research, healthcare, and direct-to-consumer services, such as microbiome and ancestry testing, continue to expand. At Isohelix, we’re proud to support this growth by providing high-quality DNA collection and stabilization solutions. Whether you’re studying rare inherited disorders, using genomics to tailor drug treatments for patients, or helping consumers explore their ancestral roots, the success of your genetic analysis starts with reliable sample collection.

In this article, we examine key application areas where DNA collection plays a pivotal role, ranging from lifestyle genomics to cancer diagnostics. Read on to learn more about:

  • Unlocking Complex Traits with GWAS
  • Calculating Genetic Health Risks
  • Pharmacogenetics and Pharmacogenomics
  • Carrier Screening for Inherited Disorders
  • Lifestyle genomics
  • Microbiomics

Unlocking Complex Traits with GWAS

What is GWAS used for?

Genome-wide association studies (GWAS) compare genetic differences between samples from donors with and without a disease or trait, to find links. The primary genetic variations researchers look for are single nucleotide polymorphisms (SNPs), which represent a difference in a single nucleotide and are the most common type of genetic variation. SNPs commonly occur between genes, where they can be used as biological markers to help scientists locate genes associated with a disease or trait, within a gene, or in a regulatory region near a gene where they may affect the gene function and play a direct role in the trait or disease.

Multi-center GWAS projects often collect DNA from large numbers of individuals, utilizing high-throughput genotyping platforms, such as SNP arrays, to identify associations between SNPs and traits. These studies extract DNA from large cohorts, often over a wide geographical area, that must be collected and preserved to ensure consistent quality across the study.

Historically, DNA was collected from blood for GWAS studies, but as DNA collection and stabilization technology have improved for saliva and buccal swabs, these sample types are now commonly used.  Saliva collection is a safe and non-invasive process, and saliva collection kits can be mailed to donors for self-collection at home. Read more about how Isohelix saliva collection kits are replacing blood sampling at https://isohelix.com/saliva-instead-of-blood/.

Calculating Genetic Health Risks

Predictive genetic testing enables individuals to understand their risk of developing a specific condition or disease. Identifying genetic risk factors can encourage earlier lifestyle interventions or further clinical screening. A polygenic risk score is used to estimate the genetic risk for a trait or disease by combining the effects of multiple SNPs. Polygenic Risk Scores (PRS) are often generated using genome-wide association study (GWAS) data, which can come from SNP array data generated from DNA samples.

For example, Polygenic Risk Scores (PRS) have been widely used in breast cancer research to stratify risk and inform screening and prevention strategies. Integrating PRS into clinical practice enables healthcare providers to deliver more accurate risk assessments, personalized prevention strategies, and optimized screening programs.

Pharmacogenetics and Pharmacogenomics

What’s the difference between pharmacogenetics and pharmacogenomics? Although the terms are often used interchangeably, pharmacogenetics is a subset of pharmacogenomics, which focuses on understanding how genetic variations influence an individual’s drug response. By contrast, pharmacogenomics refers to the investigation of the collective influence of the entire genome on a drug response.

Pharmacogenetic/genomic testing is revolutionizing precision medicine by helping clinicians prescribe drugs that are more likely to be effective for patients and less likely to cause side effects based on the patient’s genetic makeup.

Knowing a patient’s genotype at a specific locus can help doctors select the correct medication and dosage. For example, variants in the CYP2C19 gene affect how a patient metabolizes clopidogrel, a commonly prescribed blood thinner[i].

Pharmacogenetic/genomic testing is revolutionizing precision medicine by helping clinicians prescribe drugs that are more likely to be effective for patients. and less likely to cause side effects based on the patient’s genetic makeup.

The broader approach of Pharmacogenomics evaluates all genetic interactions, allowing healthcare professionals to design treatment plans that require multiple medications. With the drug Trastuzumab, variations in the HER2 gene[ii], along with other genes that affect drug metabolism and immune function, can impact a patient’s response.

Real-time PCR (qPCR) is often used in pharmacogenetics, where a fast turnaround time is necessary, and a single or small number of genes are being investigated. For pharmacogenomics, whole genome SNP arrays provide genotype information on hundreds of thousands of loci. Blood and/or saliva samples can be used to generate genotyping data with both technologies.

Carrier Screening for Inherited Disorders

Carrier screening identifies individuals who may pass on harmful genetic conditions such as cystic fibrosis, spinal muscular atrophy, or Tay-Sachs disease. Historically, carrier screening was limited to a select number of tests, primarily offered to individuals or populations at higher risk. However, the use of carrier screening and its role in reproductive health is changing rapidly as genetic analysis tools, such as high-density microarrays, next-generation sequencing (NGS), and powerful bioinformatics, become more sophisticated. A single DNA sample can now be used to screen hundreds of disorders.

Lifestyle genomics

From ancestry testing to athletic performance and appearance traits, lifestyle genomic testing has exploded in popularity. Consumers are using at-home DNA collection of saliva or buccal swabs to uncover where their ancestors came from, how their bodies process nutrients, or whether they’re genetically predisposed to faster recovery from exercise. An ancestry company may use SNP genotyping to map thousands of genetic markers, comparing them to global population databases to infer ancestral origins.

Microbiomics

Consumer microbiome testing has rapidly gained popularity in recent years, offering individuals a window into the complex communities of bacteria, fungi, and other microorganisms living in their gut. Using at-home stool collection kits, consumers can submit samples for sequencing and analysis, revealing how their microbiome may influence digestion, immunity, skin health, mood, and even weight management.

Many testing providers pair results with personalized diet or supplement recommendations based on the individual’s microbial profile. The accuracy of microbiome insights relies on high-quality, well-preserved samples, making robust DNA collection and stabilization methods essential to ensure reliable sequencing data.

Isohelix DNA Collection and Stabilization

 At Isohelix, we understand the importance of high quality DNA collection, extraction and preservation.  Our GeneFixTM collection features high-yielding sample collectors that seamlessly integrate with our expanding range of Isohelix DNA collection, extraction and stabilization kits. These genetic sampling kits are specifically designed to provide exceptional DNA purity and yield, whether for life science research, molecular diagnostics, or forensic applications.

Visit our website to find out more: https://isohelix.com/

[i] Brown SA, Pereira N. Pharmacogenomic Impact of CYP2C19 Variation on Clopidogrel Therapy in Precision Cardiovascular Medicine. J Pers Med. 2018 Jan 30;8(1):8. doi: 10.3390/jpm8010008. PMID: 29385765; PMCID: PMC5872082.

[ii] Zakaria NH, Hashad D, Saied MH, Hegazy N, Elkayal A, Tayae E. Genetic mutations in HER2-positive breast cancer: possible association with response to trastuzumab therapy. Hum Genomics. 2023 May 18;17(1):43. doi: 10.1186/s40246-023-00493-5. PMID: 37202799; PMCID: PMC10193616.

Further Reading

  • Genome Wide Association Studies (GWAS)

Milona, M., et al. Association of Three Genetic Loci with Molar Incisor Hypomineralization in Polish Children. J. Clin. Med. 2024, 13, 857. https://doi.org/10.3390/jcm13030857

  • Genetic health risks

Mitchell, Brittany L., et al. “Polygenic risk scores derived from varying definitions of depression and risk of depression.” JAMA psychiatry 78.10 (2021): 1152-1160. https://doi.org/10.1001/jamapsychiatry.2021.1988

  • Pharmacogenetics

Lind, Penelope A., et al. “Clozapine efficacy and adverse drug reactions among a nationwide study of 1021 Australians prescribed clozapine: The ClozaGene Study.” Schizophrenia Bulletin (2024): sbae065. https://doi.org/10.1093/schbul/sbae065

  • Carrier screening

Rajan-Babu, Indhu-Shree, et al. “Defining the performance parameters of a rapid screening tool for FMR1 CGG-repeat expansions based on direct triplet-primed PCR and melt curve analysis.” The Journal of Molecular Diagnostics 18.5 (2016): 719-730. https://doi.org/10.1016/j.jmoldx.2016.05.002

  • Lifestyle Genomics

Kazan, H.H., Bulgay, C., Zorba, E. et al. Exploring the relationship between caffeine metabolism-related CYP1A2 rs762551 polymorphism and team sport athlete status and training adaptations. Mol Biol Rep 51, 841 (2024). https://doi.org/10.1007/s11033-024-09800-2

  • Microbiomics

Saifon, W., Sensorn, I., Trachu, N. et al. Gastrointestinal microbiota profile and clinical correlations in advanced EGFR-WT and EGFR-mutant non-small cell lung cancer. BMC Cancer 22, 963 (2022). https://doi.org/10.1186/s12885-022-10050-3

Self-Control and DNA Methylation: How Your Choices Influence Biological Aging

Posted on by Dora Katona

A study in Clinical Epigenetics by Willems et al (2024), examined whether self-control is associated with buccal and saliva DNA-methylation (DNAm) measures of biological aging, and whether biological aging measured in buccal DNAm is associated with self-reported health status.

The study found that in older participants (57–72 years), lower self-control was associated with more advanced biological aging, but this was not the case in young adults, adolescents or children. These associations were present even after correcting for possible confounders such as socioeconomic contexts, BMI, or genetic correlates of low self-control. The results also indicated that both advanced biological age and a faster pace of aging as measured by buccal DNAm, were associated with more self-reported disease.

The findings are consistent with the hypothesis that self-control is associated with health via pathways that accelerate biological aging in midlife and older age. 

We were excited to see that Isohelix SK-1S buccal swabs and Dri-Capsules were used to collect buccal and saliva samples for methylation profiling.

SK-1S buccal swab and Dri-Capsule

Click here to see other publications that used Isohelix products to investigate methylation status: https://isohelix.com/publications/

Read the open-access paper here: https://doi.org/10.1186/s13148-024-01637-7

Can Peanut Butter Boost Strength and Cognitive Function?

Posted on by Dora Katona

We are excited to see that the Isohelix RapiDri Buccal Swab Kit has been selected as the sample collection method for an Australian study investigating the effects of peanut butter supplementation on physical function, cognitive function, body composition, nutritional status, and DNA telomere length in older adults.

In the “Capacity of Older Individuals after Nut Supplementation (COINS) study,” buccal cell samples from participants’ inner cheeks will be collected using the Isohelix RapiDri Buccal Swab Kit, following the procedure outlined in the kit. RapiDri is an easy-to-use buccal swab that includes a quick-drying pouch that stabilizes DNA and acts as a secure transport pack. Cell samples will be processed and analyzed for DNA telomere length using the quantitative PCR method.

Alongside the DNA analysis, participants will undergo various physical and cognitive function assessments, body composition, and nutritional status analyses.

Once available, the results will indicate whether daily peanut butter intake improves physical function, cognitive health, and overall well-being in older adults.

We can’t wait to see the results of the study when they are published!

For more details on the study, click here.

How Genetics and Caffeine Shape Cognitive Performance: Insights from a New Study

Posted on by Dora Katona

Check out this hot-off-the-press publication by Kapellou et al. from St Mary’s University in London, where questionnaires, cognitive tests, and genotyping were used to investigate the interactions between genetics and habitual caffeine consumption on cognitive performance.

Healthy participants completed questionnaires on sociodemographic, health, and lifestyle factors and caffeine and alcohol intake.

They were then subjected to cognitive tests to assess social and emotional cognition, memory, attention, and executive function.

Finally, DNA was collected remotely from participants using an Isohelix RapiDri™ Swab kit. DNA was extracted and samples were genotyped at loci associated with caffeine metabolism and response, using TaqMan® SNP genotyping assays.

The findings suggest an association between genetic caffeine metabolism, habitual caffeine intake, and cognitive function in terms of social cognition and executive function.

Participants were grouped into ‘fast’ and ‘slow’ metabolizers:

  • ‘Fast’ metabolizers consumed significantly more caffeine than ‘slow’ metabolizers.
  • ‘Slow’ metabolizers performed better than ‘fast’ metabolizers in emotion recognition among high-caffeine consumers.
  • “Fast’ metabolizers performed better than ‘slow’ metabolizers in the executive function domain, but only within moderate caffeine consumers.

The study confirms that the association between caffeine and cognition is domain-specific, with social and emotional cognition and executive linked to habitual intake. It also replicates previous findings that ‘fast’ metabolizers consume more caffeine. More research in natural environments using larger cohorts is needed to confirm these findings and understand how habitual caffeine may influence cognitive function based on individual genotypes.

Rapidly extract DNA for sensitive applications with Buccalyse Direct-to-PCR kits

Posted on by Dora Katona

We are always thrilled to see our products cited in peer-reviewed publications.

This month, we would like to share some publications in which our popular Buccalyse Direct-to-PCR (BEK) kits (sometimes referred to as Buccalyse DNA Release kits) have been used to rapidly extract DNA for applications such as PCR and microarray analysis:

“Advancing human genotyping: The Infinium HTS iSelect Custom microarray panel (Rita) development study” Matute et al (2024)

The objective of this research was to assess the sensitivity, repeatability, reproducibility, accuracy, and precision of an HTS iSelect Custom panel called ‘Rita’, a custom SNP microarray panel developed using Illumina Infinium HTS technology. Designed for high-throughput genotyping, the panel efficiently facilitates the analysis of over 4000 markers associated with health, lifestyle, and forensic factors.

Studies revealed consistent panel performance across different batches and operators, with no significant deviations in call rates or genotyping results. The evaluation confirmed the Rita microarray as a robust, high-throughput genotyping tool, underscoring its potential in genetic research and forensic applications.

Samples for the study were extracted from buccal swabs using the Buccalyse DNA Release Kit. The sensitivity study showed that it is possible to obtain more than a 99 % call rate when working with as little as 0.78 ng of DNA.

The ability to a lower DNA input increases the assay’s utility in forensic laboratories, where casework samples may sometimes contain small amounts of genetic material.

Genes Involved in Susceptibility to Obesity and Emotional Eating Behavior in a Romanian Population Vranceanu et al, (2024)

This study examined the relationship between six obesity-related genes (CLOCK, FTO, GHRL, LEP, LEPR, MC4R) and their impact on measures of obesity and emotional eating behavior in 220 Romanian adults.

Buccal cells were collected from the lateral wall of the oral vestibule and sent for processing in a UK laboratory using the Rapidri Swab kit. DNA was then extracted from the buccal cells using Buccalyse, and genotype analysis was performed using the ABI7900 real-time thermocycler system.

The analysis revealed significant variability in obesity-related phenotypes and emotional eating behaviors across different genotypes. The study provides a foundation for targeted interventions to prevent and reduce obesity and suggests potential strategies for gene expression modulation to mitigate the effects of emotional eating.

“Systemic immunity shapes the oral microbiome and susceptibility to bisphosphonate-associated osteonecrosis of the jaw.” Kaylan et al (2015)

Osteonecrosis of the jaw (ONJ) is a rare but serious adverse drug effect linked to long-term and/or high-dose exposure to nitrogen-bisphosphonates (N-BP). The objective of this investigation was to assess the relationship linking immune function, N-BP exposure, the oral microbiome, and ONJ susceptibility.

To investigate the oral microbiome, Isohelix DNA swabs were used to obtain microbial DNA by running the swab along an area of the outer gumline of subjects. DNA was extracted using the Isohelix Buccalyse DNA extraction kit and stored at −20°C until analysis.

The oral microbiome was characterized by 454 pyrosequencing of the 16S rRNA gene in 93 subjects stratified by N-BP exposure and a history of ONJ.

The oral microbiome was found to be unlikely to cause ONJ. Instead, individuals with bisphosphonate-associated ONJ lacked immune resiliency, which impaired their capacity to respond adequately to the immunological stress of N-BP.

Buccalyse offers researchers a robust, user-friendly tool that consistently delivers reliable results. Its widespread adoption in diverse studies reflects its quality and adaptability, making it an indispensable asset for advancing research in genetics, microbiome studies, and forensic science.

Summary

The above publications feature DNA extracted using the Buccalyse Direct-to-PCR kit being used in a range of molecular biology applications including (but not limited to) genotyping using SNP micorarrays and PCR methods, and 454 pyrosequencing of the 16S rRNA gene for microbiome characterization.

The Buccalyse Direct-to-PCR Kit has been specially formulated to produce high DNA yields from buccal swabs. The kit is a quick and simple one-tube alternative to existing DNA isolation methods when extracting DNA for use in PCR reactions. The yield of DNA from a single buccal swab using Buccalyse is generally around 2 to 4ug from an adult.

CLICK HERE TO FIND OUT MORE ABOUT BUCCALYSE

Meet Isohelix at ASHG 2024 in Denver!

Posted on by Dora Katona

Isohelix is delighted to be attending ASHG 2024 in Denver from November 5 to 9. Join us at Booth #775!

We can’t wait to hear about your projects and introduce you to our innovative solutions for sample collection, stabilization, and purification.

Come by to discuss how our products can enhance your research efforts. We look forward to connecting with you at the event!

GeneFix™ Saliva collection devices used in large Japanese GWAS study on dental caries

Posted on by Dora Katona

What are Genome-wide association studies (GWAS)?

GWAS studies are genomic studies that test hundreds of thousands of genetic variants across many genomes, to find those statistically associated with a specific trait. GWAS have a range of applications including understanding the underlying biology of  a phenotype, estimating the heritability of a trait, investigating genetic correlations and making clinical predictions.

Advantages and Disadvantages of GWAS

GWAS can identify associations but doesn’t typically pinpoint causal relationships, so further studies are usually required to confirm findings and explore their biological significance.

GWAS Studies to investigate dental caries and
peridontal disease

Genome wide association studies (GWAS) play a crucial role in understanding the mechanisms underlying dental caries and periodontal disease. There are large variations in genetics and lifestyles across ethnicities, and although large-scale genome-wide association studies (GWAS) on dental caries and periodontal disease have been conducted extensively, few studies focus on Asian populations.

The recent study,  “Genome-wide association meta-analysis identifies two novel loci associated with dental caries” by Nogawa et al., used genome data from 45,525 Japanese individuals to conduct a GWAS, assessing the self-reported history of dental caries and periodontal disease of study participants. A meta-analysis was then performed by integrating our results with those from a previous large-scale GWAS predominantly involving European populations.

Although no new loci associated with periodontal disease were identified, two novel loci associated with dental caries were discovered. The findings contribute to understanding the mechanisms underlying dental caries and periodontal disease.

We were delighted that this study used GeneFix Saliva collection devices to collect and stabilize DNA in saliva samples collected from participants. Genotyping was executed employing various Illumina Infinium BeadChips.

The GeneFix™ range of DNA/RNA products has been designed to maximize the yields and purity of DNA/RNA collected and stabilized from saliva. GeneFix kits are ideal for collecting samples from study participants at home or in the clinic, as they are non-toxic, simple to use, and contain a reagent that stabilizes DNA at room temperature for up to 60 months. After sample collection, kits can be mailed to the lab for DNA extraction.

GeneFix Saliva Collection Products Used for Ground-Breaking Breast Cancer Research

Posted on by Dora Katona

Between 1993 and 2018[1] breast cancer rates in women increased by 24%, and in the UK in 2022, breast cancer was the most common cause of death for women between 35-49 and 50-64 years of age.[2]

We are delighted to see Isohelix products used for Breast Cancer research, with two recent UK-based studies using GeneFix Saliva collection devices to collect and stabilize DNA in saliva samples collected from study participants:

  • BRCA Direct: A Digital Pathway for BRCA-Testing in Breast Cancer
  • Breast Cancer Risk Assessment in Younger Women (BCAN-RAY) study

GeneFix Saliva Collection Products

The GeneFix™ range of DNA/RNA products has been designed to maximize the yields and purity of DNA/RNA collected and stabilized from saliva. GeneFix kits are ideal for collecting samples from study participants at home or in the clinic, as they are non-toxic, simple to use, and contain a reagent that stabilizes DNA at room temperature for up to 60 months. After sample collection, kits can be mailed to the lab for DNA extraction.
Read on to learn about recent studies using GeneFix products for Breast Cancer Research.

BRCA-Direct: A Digital Pathway for BRCA-Testing in Breast Cancer

The BRCA-DIRECT study was funded by Cancer Research UK and affiliated with the Institute of Cancer Research, SHORE-C,  Manchester University Foundation Trust, and The Royal Marsden Foundation Trust. The study aimed to provide an easy way for patients with breast cancer to access genetic testing within the NHS.

The BRCA1, BRCA2, and PALB2 genes are associated with hereditary breast cancer, so Identification of a pathogenic variant in one of these genes can have health implications for patients and their relatives. This study examined the feasibility, safety, and acceptability of a digital information model.

Participants provided a saliva or blood sample and accessed a digital platform using a device connected to the internet.  Family history details were collected, and information was gathered about the general knowledge of BRCA testing. Participants were asked about their anxiety levels at different points in the process. Half of all those who took part saw digital information, and half booked a standard appointment with genetic counselors.

Participants were then randomized to receive their results digitally or by booking a telephone appointment with a genetic counselor. Everyone who had a positive result was then referred to their local clinical genetics team. If the digital pathway is successful, the concept could be expanded to other cancers and hospitals.

​We are looking forward to seeing the results of the study that has led to further funding for a pilot across North Thames GLH, funding by SBRI Healthcare/NHS England Cancer Programme: SBRI Healthcare – NHS Cancer Programme awards £12.1 million to accelerate new front-line innovations that detect and diagnose cancer earlier

The BCAN-RAY study

The Breast Cancer Risk Assessment in Younger Women (BCAN-RAY) study began in May 2023. BCAN-RAY is one of the first research studies in the world to identify new ways to predict the risk of younger women getting breast cancer. The study aims to evaluate a comprehensive breast cancer risk assessment strategy among a diverse ethnic and socioeconomic population of women aged 30–39 years without a strong family history of breast cancer.

Two hundred fifty women previously diagnosed with breast cancer without a strong family history of the disease will be studied alongside 750 women (control participants) in the same age group who have not had breast cancer and who also have no strong family history of the disease. 

Control participants will complete questionnaires about breast cancer risk factors, undergo low-dose mammograms, and donate a saliva sample, which is collected using Isohelix GeneFix Saliva Collection Kits. Saliva samples will be used to analyze the genetic makeup of participants and identify those at higher risk using a tool called a polygenic risk score, which is a powerful predictor of breast cancer risk.

Cancer tissue biopsy

The BCAN-RAY study should complete recruitment in May 2025, and we look forward to seeing the results.

The study is funded by Cancer Research UK via the International Alliance for Cancer Early Detection (ACED), The Christie Charity, and The Shine Bright Foundation. It is led by Manchester University NHS Foundation Trust, and delivered at The Nightingale Centre at Wythenshawe Hospital and breast oncology centers across Greater Manchester and Cheshire.

Please follow the link to the Sarah Harding Breast Cancer Appeal: A letter from Girls Aloud (christie.nhs.uk) 

Read our blog article about genomic analysis using saliva instead of blood: https://isohelix.com/saliva-instead-of-blood/

Find out how to simplify Saliva and Buccal Swab sample collection and processing: https://isohelix.com/how-to-simplify-saliva-and-buccal-swab-sample-collection-and-processing/

Click here to find out more about our GeneFix Saliva Collection Products: https://isohelix.com/genefix-saliva-dna-rna-collection/

References

[1] Facts and figures | Breast Cancer UK

[2] Office for National Statistics. Deaths registered in England and Wales: 2022-2023