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:
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.
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.
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.
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.
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.
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.
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.
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.
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.
Isohelix will be exhibiting at ESHG 2024 June 1st – 4th in Berlin, at Booth #652. Alongside our New Product launches for DNA Collection and Isolation, we will also have our development team available to discuss any technical matters that might help in your research or diagnostics. Please visit us anytime.
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.
HMW DNA Cleanup and Size Selection
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.
Saliva DNA samples spiked with DNA ladder and processed using the Mag-Filter Clean-Up Kit demonstrate effective removal of small DNA fragments.
HMW DNA from saliva and buccal swab samples
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.
GFX-01
Simple to Use HMW DNA Preparation
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.
GeneFix™ Saliva Collection Devices are used to collect samples for a large population-based study in Australia
The Hong Kong Genome Project uses GeneFix™ Saliva Collection Devices to collect saliva samples and the RapiDri Pouch kit for buccal swabs.
Isohelix™ saliva collection kits are used to collect saliva from a large cohort of children in the USA
Isohelix™ Buccal Swabs are used to swab surfaces to collect DNA from bacterial communities in subway facilities
STUDY 1 : Preliminary results from the Australian Genetics of Bipolar Disorder Study: A nation-wide cohort[i]
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.
GFX-02
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.
STUDY 2 : The Hong Kong genome project: building genome sequencing capacity and capability for advancing genomic science in Hong Kong[ii]
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.
RapiDri Swab
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.
STUDY 3 : Avoidant Restrictive Food Intake Disorder Genes and Environment (ARFID-GEN): study protocol[iv]
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).
SK-2S
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.
STUDY 4 : Investigation of Surface Bacterial Diversities and Compositions in the Global Subway Facilities[v]
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.
SK-2S
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.
Summary
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.
Tell us about how Isohelix™ products helped your study by emailing us at info@isohelix.com!
References
[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
[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
Increasing numbers of saliva samples are being collected remotely from study participants for use in genetic testing, so the need for safe, simple and easy to use sample collection, stabilization and transportation is growing rapidly.
Studies have shown that DNA samples from swabs can degrade rapidly without the correct stabilization. SaliFix™ Collectors contain 1ml of preservation reagent that is designed to maintains DNA integrity and yields whilst preventing bacterial growth long term, yet provides easy and easy device for Saliva DNA collection, stabilization, and transport.
SaliFix™ Collectors are specifically designed for collecting Saliva samples in various environment including at home, in clinic or remotely. The foam swabs effectively maximizes saliva collection, even from donors who may find it difficult to produce saliva.
The SaliFix™ kit also includes the SwabCatcher format for improved Sample Handling
The NEW SwabCatcher tube simplifies sample processing and cuts down on cross-contamination as the cap holds the swab tightly after screwing the cap onto the tube. This removed the tedious process choice of having to cut the swab tip and or manually using tweezers to remove the swab prior to processing. This makes the tube ideal for high-throughput processing using automated instruments, and further the tubes are barcoded for easy sample tracking.
SwabCatcher tubes are leakproof and fully transport tested to 95kPa to allow mailing and storage, and the reagents are non-hazardous.
Agarose gel analyzed by electrophoresis. Saliva DNA isolated from SaliFixTM collection devices using the Isohelix Saliva-Prep-2 kit (GSPN-50), shows high quality DNA with no degradation.
DNA collected using SaliFix™ collectors is of high yield and purity, and suitable for all downstream analyses.
Saliva Swab DNA Collection Kit
All-in-one saliva DNA collection, stabilization, and transport device.
Uses the NEW Swab-Catcher for easy handling and automated-processing.
Simple collection at home, in clinic. a viable alternative to blood collection.
Instant stabilization maximises DNA yields allowing RT shipping and storage in a non-hazardous format.
Optimized for extraction using Isohelix DNA extraction and other kits.
Product Information
SFX/LS/1/50 SaliFix™ saliva collection tubes prefilled with 1ml SaliFix™ buffer and individually wrapped, foam saliva swabs.
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