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.
NEW SwabCatcher tubes are used alongside RapiDri DNA and RNA Swab Kits designed to simplify the swabs transition through sample processing. The Tubes are also available pre-filled with BuccaLyse DNA and RNA stabilization buffer for room temperature shipping.
No more Swab retrieval issues
Automation, HT and Manual compatible
Barcoded for traceability
CE-IVD Certified
Fully transport tested to 95kPa
Product Information
SwabCapture L/00/50 50 x SwabCatcher 5ml collection tubes and caps(empty)
RapiDri RD-01 200 x RapiDri swabs SwabCatcher with drying pouch
BuccaLyse BEK/L/05/50 50 x BuccaLyse SwabCatcher collection tubes pre-filled with 0.5ml buffer
BuccalFix BFX/L/05/50 50 x BuccalFix SwabCatcher collection tubes pre-filled with 0.5ml buffer
At Isohelix we use our extensive knowledge in product design, regulatory, safety & commercial markets to design products that make it easy for our customers to collect high quality nucleic acid samples from saliva, buccal cells, and stool samples.
Isohelix will be present at the upcoming Festival of Genomics & Biodata in London, Booth #79, from 24th to the 25th of January. Join us to explore our latest products in Sample Collection, Stabilization, and Purification technologies.
Isohelix will be attending ASHG in Washington on Booth #1922 from 1 st – 5 th November. We are looking forward to seeing you to hear about your projects and to introduce our existing and new products for Sample Collection, Stabilization, and Purification devices.
Isohelix will be exhibiting at Medica in Dusseldorf from 13th – 16th November. We will be in Exhibit Hall 1, Booth G11-6. Alongside our existing products we will be launching a number of new products for Sample Collection, Stabilisation and Purification.
Sake brewing is an inherently microbial-driven process, and requires careful management in order to encourage the proliferation of microbes that contribute to the process while minimising the influence of microbes that may cause spoilage.
On the Surface
Using Isohelix SK-3S Buccal Swabs and BuccalFix DNA Stabilization Buffer, the study collected surface samples from various locations within the brewery, such as floors, brewing materials, and brewing equipment. DNA from the samples were extracted and underwent microbiome analysis using 16S gene sequencing.
Full of Flavour
The study found that microbes present in raw materials and brewing equipment both contributed to the microbial profile of the brewing starter culture used for fermentation. Beneficial microbes from the environment, such as lactic acid bacteria, help to control the brewing process, preventing the growth of undesirable microbes while in turn contributing to the flavour profile of the final product. This study also demonstrates the suitability and efficacy of Isohelix’s swab and stabilization products for use in environmental microbiome investigations.
Isohelix is pleased to announce that it has commenced engagement with the U.S. Food and Drug Administration (FDA) to progress the full regulatory approval of the GeneFix® Saliva DNA Collectors into the USA for their use in molecular and genetic diagnostics.
A study using Isohelix SK-2S Buccal Swabs has discovered that wine tasting has a washing effect on the tongue which causes lower microbiome diversity in professional wine tasters. This also affects how people taste, explaining why people can drink the same bottle of wine and perceive different flavours!
Washing Effect
Using the Isohelix SK-2S Buccal Swabs, the study collected DNA samples from the tongues of both professional wine tasters & non-professionals to compare the microbiome profiles between the two groups. They found that samples collected after wine tasting sessions had a lower microbial diversity than those taken prior to the tasting event. Therefore the study concluded that wine tasting sessions have a washing effect on the tongue, directly affecting microbiome diversity.
Sparkling Wine
As well as discovering the washing effect that wine has on the microbial diversity on the tongue, the study also discovered that this effect is increased when tasting sparkling wines! The comparison of bacterial diversity between samples collected before and after wine tasting, along with the presence of new bacterial taxa, indicated the direct effect of wine on the microbiome of frequent wine tasters, particularly in those tasting sparkling wines.
Putting Taste to the Test
In addition, results from an accompanying questionnaire found that having a long career in wine tasting effected taste perception compared to non-wine tasters, particularly in bitter or acidic food & drink. Results from these data suggest that changes in the microbial profile of the tongue have an effect on how we taste, giving some explanation as to why people can drink the same bottle of wine and perceive different flavours!
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