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!
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.
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.
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.
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:
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.
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 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.
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/
[1] Facts and figures | Breast Cancer UK
[2] Office for National Statistics. Deaths registered in England and Wales: 2022-2023
We were delighted to see that two recent, high-profile studies looking at the effects of spaceflight on astronauts’ microbiomes chose Isohelix buccal swabs to collect their valuable samples.
In the Nature paper, “Longitudinal multi-omics analysis of host microbiome architecture and immune responses during short-term spaceflight,” published by Tierney et. al., (2024), the team used Isohelix swabs to collect samples from three microbial ecosystems (oral, nasal, and skin), before and after a 3-day mission to space.
Using paired metagenomics and metatranscriptomics alongside single-nuclei immune cell profiling, the team characterized microbiomes before, during and after spaceflight. The study revealed shifts in the microbiome and immune response during short term spaceflight; although most microbiome alterations were transient, longer-term shifts were observed in the astronaut’s oral microbiomes.
Another Nature paper, “Spatial multi-omics of human skin reveals KRAS and inflammatory responses to spaceflight”, Park et al (2024), also looked at the effects of short-duration spaceflight on the skin. The study applied a wide range of -omics methods, and as part of this study, Isohelix swabs were used to collect samples of astronauts’ skin microbiomes. Metagenomics and metatranscriptomics analyses were then performed on the skin swab samples. A key finding was that post-flight samples showed significant up-regulation of genes related to inflammation and KRAS signalling across all skin regions.
The results from these two important studies can help guide spacecraft design and response countermeasures for astronauts on future missions, and we are excited to see Isohelix products being used to expand our knowledge in this area.
Isohelix swabs feature a unique swab matrix and quick-release surface that maximises nucleic acid yields. Swab batches are ethylene oxide treated and routinely tested for human DNA contamination, making them ideal for capturing precious nucleic acid samples.
CLICK HERE TO FIND OUT MORE ABOUT ISOHELIX BUCCAL SWABS FOR NUCLEIC ACID COLLECTION OF ORAL AND SKIN MICROBIOME SAMPLES
Isohelix also offer stabilization reagents for buccal swabs that offer long term sample stability prior to isolation
The body of research using Isohelix products is growing all the time. One that caught our attention recently was, “Exploring the legacy of African and Indigenous Caribbean admixture in Puerto Rico” by Taiye Winful et al. (2023).
The goal of this study was to assess the biogeographic origins of African descendant Puerto Ricans and to investigate the potential for Indigenous ancestry within this community.
2ml saliva samples were collected from self-identified African descendant Puerto Ricans residing in Puerto Rico using Isohelix Genefix™ collection kits. GeneFix kits are ideal for collecting samples from study participants in remote communities 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.
When the samples reached the lab, DNA was extracted using the Isohelix Genefix Saliva-Prep 2 DNA kit, which uses a precipitation method to isolate high yields of pure DNA. The mitochondrial genomes of these individuals were sequenced, and Y chromosome haplogroups were genotyped for samples donated from males. Summary statistics, comparative analyses, and network analysis were used to assess diversity and variation in haplogroup distribution between the samples and comparative populations.
Results from the mitochondrial haplogroups showed that 66% had African, 5% had European, and 29% had Indigenous American matrilines. The Y chromosome analysis showed that 52% had African, 28% had Western European, 16% had Eurasian, and 4% had Indigenous American patrilines.
This study successfully used Isohelix GeneFix and Saliva-Prep kits to collect and extract DNA from saliva samples from study participants across Puerto Rico. The genomic analysis of these saliva samples have contributed to understanding how African descendants and Indigenous American admixture have shaped present-day communities.
CONTACT US to find out how we can help with your sample collection and DNA extraction needs.
High molecular weight (HMW) DNA is important for applications that require the use of very long DNA molecules, such as long read sequencing. Long-read sequencing enables the detection of variants that are often difficult to resolve with short reads, such as structural variants, complex rearrangements, and variants in highly repetitive regions.
In order to fully take advantage of long-read sequencing, high quality, high molecular weight (HMW) input DNA is required. Traditional DNA extraction methods often result in fragmented DNA samples. If these shorter fragments are not removed, the average length of sequencing reads, and subsequent effectiveness of long-read analyses are reduced.
To address this requirement, Isohelix has developed the Mag-Filter HMW Clean Up Kit, which employs magnetic beads alongside specialized size selection chemistry to isolate high molecular weight DNA fragments from extracted DNA samples, while removing smaller DNA fragments and other contaminants from samples.
Samples prepared using the Mag-Filter HMW Clean Up Kit are perfect for NGS and long-read sequencing applications.
The Mag-Filter HMW kit removes low molecular weight DNA while safeguarding high molecular weight DNA integrity. High purity HWM DNA is achieved through DNA sample cleanup and size selection.
The Mag-Filter HMW kit is optimized for use with extracted saliva samples but can be used on DNA from a variety of sample sources, such as buccal swabs. It can also be used to increase sample purity, allowing the use of valuable samples with initially low purity that might otherwise fail quality control checks.
The kit is simple to use and can cleanup samples for library prep in less than one hour. All kit components are non-hazardous, and gel separation is not required. The kit protocol can also be easily adjusted to accommodate varying sample volumes; the protocol is fully scalable, from small manually processed sample batches up to plate-based high throughput automation.
2023 was a busy year for Isohelix™ and our customers. In this blog, we present examples of how studies reported in peer-reviewed publications used Isohelix™ products to solve their sampling challenges.
We’ve highlighted four studies where Isohelix™ technologies were used to make groundbreaking discoveries in the world of biomedical research. In each of these studies, Isohelix™ sample collection products were used to collect DNA samples which were then analyzed using highly sensitive genetic analyses such as single nucleotide polymorphism (SNP) genotyping, genome wide association studies (GWAS), and next generation sequencing (NGS) analyses.
The Australian Genetics of Bipolar Disorder (BD) Study investigates a nation-wide cohort of adults living with bipolar disorder. The study aims to identify genetic risk factors influencing BD, medication treatment response, and adverse drug reactions (ADRs). Key goals are to characterize the patterns and costs of healthcare usage in BD and to examine the relationship between genetic risk and symptom severity. This article describes the study design and sample characteristics and summarises data collected on BD symptoms, psychiatric comorbidities, and medication use.
A significant strength of the study is its sample size; it’s the largest population-based study of adults living with BD in Australia. Study participants are based throughout Australia, with many living in rural or remote communities. Saliva samples are collected using Isohelix™ GeneFix™GFX-02 2 mL Saliva Collection Devices which stabilize DNA and RNA at room temperature for up to 60 months, then mailed to QIMR Berghofer via prepaid Australia Post. Following DNA extraction, genotyping is conducted using the Illumina Global Screening Array V.2.0.
The study demonstrates that Australians with BD are motivated to participate in genetically focused research studies if given the opportunity and provided with simple and effective sample donation protocols. GeneFix™ Saliva Collectors are ideal for this type of project as their reagents are non-toxic, and the collectors are easy to use as they have a unique funnel design that prevents buffer spillages or flow-back.
The results highlight the high rate of comorbidities and adverse drug reactions among adults living with bipolar disorder in the general Australian population and pave the way for future genomic analyses to identify genetic variants influencing pharmacotherapy treatment response and side effects.
The Hong Kong Genome Project (HKGP) is the first large-scale genome sequencing (GS) project in the Hong Kong Special Administrative Region. The project aims to sequence 45,000-50,000 genomes in five years, providing participants with diagnoses and personalized treatments and driving the application and integration of genomic medicine into routine clinical care.
For each participant, 6 mL of blood is obtained and stored in two 3-mL EDTA-containing anticoagulation tubes. For buccal swabs, the RapiDri Pouch kit is used to collect cells from inside the cheek, and saliva samples are collected using the GeneFix™ Saliva DNA Collection and Stabilization Kit. DNA from saliva samples has been shown to be comparable to DNA from blood in many downstream applications[iii] and DNA from saliva samples collected using GeneFix™ kits is stable at room temperature for over five years, avoiding the high cost and logistical challenges of cold chain transport.
This paper describes the establishment of a robust genome sequencing workflow for the project. The laboratory analyses approximately 350-500 samples per week. During the first 24 months of the project, 12,937 participants and their family members were recruited, and the laboratory has been adapted to facilitate the latest technologies, e.g., long read sequencing and multi-omics.
This paper describes the Avoidant Restrictive Food Intake Disorder – Genes and Environment study (ARFID-GEN), which is designed to expand the discovery of genetic and environmental contributions to ARFID risk. The goal of the study is to deliver actionable findings that can be transformed into clinically meaningful insights. This will be achieved by advancing the understanding of the genetic architecture of ARFID relative to other eating disorders and other psychiatric, neurodevelopmental, and metabolic disorders and traits.
3,000 children and adults with ARFID from the United States are included in the study. Efficient online phenotyping of children and adults with ARFID including environmental exposures is combined with at-home saliva sampling, and samples are genotyped to analyze single nucleotide polymorphism (SNP) – based heritability, genome wide association studies, genetic correlations (rgs), and copy number variations (CNVs).
Eligible children are asked to complete a questionnaire on their symptoms and provide a saliva sample using Isohelix™ saliva collection kits, which are non-toxic and easy for children to use at home as they have a unique funnel design that prevents buffer spillages or flow-back. The kits are provided with return packaging for mailing to the lab for analysis.
The aim is to identify genome-wide significant loci for ARFID, informative rgs, implicated CNVs, and environmental precipitants. Ultimately, the work will hopefully yield information on critical biological pathways that may point toward drug discovery or repurposing that could aid in reversing the tenacity and lethality of these illnesses.
This study explored surface bacterial communities in four global subway facilities using 16S rRNA gene amplicon sequencing of DNA extracted from swabs.
Isohelix™ Buccal swabs can be used to collect surface DNA from environmental sources as well as from buccal samples. Indoor surface samples for Busan City were collected twice per site using Isohelix™ DNA/RNA buccal swabs (SK-2S, Isohelix) moistened with sterile 1 mL of phosphate-buffered saline. Samples were collected for 3 min from each site in a 100 cm2 area as recommended in a previous study[vi]. The microbiome was analysed based on the 16S rRNA gene.
Samples collected in Korea were analysed alongside comparable samples obtained from previous studies in Boston[vii], Moscow[viii], and Mexico City[ix].
The study showed that the surface bacterial diversities and taxonomic profiling of the studied subway station surface environments were similar. Most of the predominant phylotypes were Gram-positive microorganisms that probably originated from human and outdoor sources.
The above studies are just a few of the projects that have used Isohelix™ sample collection and stabilization products to collect samples from research study participants or the environment, for genomic analysis.
[i] Lind, Penelope A., et al. “Preliminary results from the Australian Genetics of Bipolar Disorder Study: A nation-wide cohort.” Australian & New Zealand Journal of Psychiatry 57.11 (2023): 1428-1442. https://journals.sagepub.com/doi/epub/10.1177/00048674231195571
[ii] Chu, Annie TW, et al. “The Hong Kong genome project: building genome sequencing capacity and capability for advancing genomic science in Hong Kong.” J Transl Genet Genom 2023;7:196-212 https://www.oaepublish.com/articles/jtgg.2023.22
[iii] “New Saliva-Prep2 Isolates High Purity Genomic DNA using GeneFixTM Collectors”, Isoghelix Application Note GSPN: January 2019
[iv] Bulik, Cynthia M., et al. “ARFID Genes and Environment (ARFID-GEN): study protocol.” BMC psychiatry 23.1 (2023): 863. https://bmcpsychiatry.biomedcentral.com/articles/10.1186/s12888-023-05266-x
[v] Kim J, Bae S, Park S, Shukla SK, Yoo K. Investigation of Surface Bacterial Diversities and Compositions in the Global Subway Facilities. Atmosphere. 2023; 14(1):140. https://doi.org/10.3390/atmos14010140
[vi] Jansson, L.; Akel, Y.; Eriksson, R.; Lavander, M.; Hedman, J. Impact of swab material on microbial surface sampling. J. Microbiol. Methods 2020
[vii] Hsu, T.; Joice, R.; Vallarino, J.; Abu-Ali, G.; Hartmann, E.M.; Shafquat, A.; DuLong, C.; Baranowski, C.; Gevers, D.; Green, J.L. Urban transit system microbial communities differ by surface type and interaction with humans and the environment. Msystems 2016, 1, e00018-16
[viii] Klimenko, N.S.; Tyakht, A.V.; Toshchakov, S.V.; Shevchenko, M.A.; Korzhenkov, A.A.; Afshinnekoo, E.; Mason, C.E.; Alexeev, D.G. Co-occurrence patterns of bacteria within microbiome of Moscow subway. Comput. Struct. Biotechnol. J. 2020, 18, 314–322
[ix] Hernández, A.M.; Vargas-Robles, D.; Alcaraz, L.D.; Peimbert, M. Station and train surface microbiomes of Mexico City’s metro (subway/underground). Sci. Rep. 2020, 10, 8798
