Jan 18

Helping to feed the world with Genotyping by Sequencing

Many areas critical to improved agricultural production require robust and scalable genotyping platforms to enable the mapping of traits in plants and livestock as part of marker assisted selection (MAS) and marker assisted breeding (MAB) programmes.

Pile of Red Tomato.

Such programmes have helped improved drought, frost and parasite resistance in plants and improved yields.

Historically, these projects have involved the sequencing of parental genotypes using whole genome shotgun (WGS) sequencing. However, this can prove prohibitively expensive and resource intensive due to the complexity of sequencing de novo genomes.

In contrast, genotyping by sequencing (GBS) is a unique and cost-efficient technique developed and patented by Keygene, which reduces the genome complexity to certain regions which can be sequenced for a large number of samples.

According to Wolfgang Zimmermann, Sequencing Business Manager, Genomics, LGC – the scale of the efficiency increase is hard to comprehend; GBS delivers a large number of the useful SNPs in all samples of an analysed batch at just 1% of the cost – significantly opening up new applications and species.

Having secured a license for the commercial offering and use of GBS technology across all species and geographies, our sequencing experts have been working hard to further optimise the technique. This has led to the development of a self-tuning variant of the GBS technique (normalised GBS, or nGBS) that enhances the efficiency of the process and ensures selected loci are reliably sequenced across large sample batches using next-generation sequencing (NGS).

nGBS makes use of a normalisation process developed by LGC to exclude sequences for conserved repeats that code for organelle such as chloroplasts and mitochondria. This normalisation process is applicable to any genome regardless of size, methylation pattern, and type as well as abundance of repetitive elements.

This enables deeper sequencing of the remaining DNA and increases the number of single nucleotide polymorphisms (SNPs) identified from around 15,000 to up to 50,000.

Following a bioinformatics analysis, these SNPs can then be used to develop genotyping arrays or PCR- and KASP- based panels for downstream applications.

Zimmermann was keen to stress that if high quality DNA can be extracted then the technique can be used for nearly any species. Fortunately, LGC’s DNA extraction group have made a name for themselves extracting purified high molecular weight DNA from even the toughest of samples.

 

To learn more about LGC’s GBS services, and to downlown our latest application note visit here.

Jan 13

Toy Safety: proficiency testing to ASTM F963-16

On 20 October, 2016 ASTM International published ASTM F963-16 Standard Consumer Safety Specification for Toy Safety, an updated version of ASTM F963-11. The aim of this revision is to address various issues relating to toy safety, ideally highlighting and eliminating many potential hazards from toys intended for use by children under the age of 14.

baby toys collection isolated on white

A significant number of updates have been introduced to strengthen this standard, through the design, manufacturing and marketing of children’s toys, as well as addressing possible hazards that that may not be immediately apparent to consumers.

 

 

 

 

 

The following proficiency testing (PT) samples allow you to monitor your analysis against the 2016 version of ASTM F963 and EN71 equivalent where applicable:

 

Area updates ASTM Clause EN71 equivalent PT Sample Available in round(s)
Projectile toys 4.21 and 8.14 4.17 12 TY069 & TY071
Battery operated toys 4.25 15 TY070
Heavy elements 4.3.5 3 All rounds
Magnets 4.38 and 8.25 4.23 14 TY070
Sound producing toys 4.5 4.20 13 TY070 & TY072

For more information on our toy testing PT scheme please see Scheme Documentation.

To participate in any of the rounds please complete the Application Form and email it to ptcustomerservices@lgcgroup.com.

To order a copy of the standard ASTM F963-16, please visit the ASTM website.

By Wayne Gaunt, Technical Manager, Proficiency Testing
LGC Standards

Source:  ASTM F963-16, Standard Consumer Safety Specification for Toy Safety, ASTM International, West Conshohocken, PA, 2016, www.astm.org.

Jan 11

SSR conversion service: a convenient upgrade for 21st century challenges of how to feed the world

LGC’s recent launch of a full SSR conversion service allows convenient identification of potential SNP markers around microsatellites/SSR’s and converts them to KASP SNP genotyping assays. The SNP conversion will be carried out by the genomics team in Berlin who have recently topped their DNA sequencing services for the seventh time in nine years.

snpidentification_shadowSSRs are commonly used by researchers and plant breeders to introgress superior traits in terms of higher yields and productivity, better insect and disease resistance and improved nutrition.

Joris Parmentier, Product Marketing Manager, LGC, states, “LGC is committed to using our science for a safer world. In line with this our genomics expertise is being used as part of global breeding programmes with the aim of increasing global food production by 30% by 2050.

“Our science and technology identifies converts and screens the SNP sequences for  these desirable traits. We do this at an industrial scale, quicker, better and more cost-effectively for our customers. Our SSR conversion service is a convenient way to convert outdated SSR markers to new high throughput SNP genotyping and benefit from the advantages of SNP marker assisted selection.

“We can help our customers screen more samples, which in turn means confirmation of key markers more quickly, getting the crop with the improved trait to the market faster and resulting in a competitive advantage for our customers.

“Through collaborations with for example the African Orphan Crop Consortium (AOCC) LGC has been involved in bringing new tools and advancements in analysis techniques to developing countries. SSRs are extensively used – particularly in crops such as cocoa, sugar cane and coffee that are important sources of income in these countries. Our SSR conversion service ensures that the advantages of SNPs are made available globally to help those contributing to efforts to feed the world.”

For more on LGC’s SSR service click here.

Dec 12

Foreign particulate matter in pharmaceuticals

There has been a recent rise in the number of pharmaceutical product recalls due to the presence of Foreign Particulate Matter (FPM), and its effect on product efficacy and safety.

FPM is either inherent (from the product itself), intrinsic (from the production process), or extrinsic (contaminating particles from outside). There is a regulatory requirement for manufacturers to thoroughly investigate any incidents involving FPM and to determine its origin. In doing so the manufacturer needs to be able to demonstrate that they have a thorough understanding of their manufacturing process and control of the composition of their final product. Detection and analysis of FPM is a critical part of product development and quality control, and today forms a routine part of most upstream processing.

 

lgc_fpm

 

LGC has a proven track record in FPM analysis having carried out numerous FPM investigations involving active pharmaceutical ingredients, excipients, final dosage forms, process and packaging materials. Our services cover particle counting and morphology categorisation, identification of unknowns, root-cause determination and the development of bespoke FPM methodologies and reference libraries.

This rapid turnaround service allows our customers to complete their investigations in a timely and efficient manner. All investigations need to be fit for purpose and our study managers are able to call upon a wide range of FPM characterisation techniques including light microscopy, infrared (FT-IR and NIR) microscopy, scanning electron microscopy (SEM-EDX), x-ray diffraction and mass spectrometry. In addition to commercially available libraries we have assembled extensive component, product and contamination reference libraries.

To find out more about our expertise, please view our webinar on demand and download our fact sheet.

 

View webinar >>> 

lgc_view-webinar_on-demand

 

Download fact sheet >>>

lgc_foreign_particulate_matter_fact_sheet

 

 

Dec 07

Total Polar Compounds in frying oil

TRIAL SAMPLE: 796 (February 2017)

Oils and fats represent one of the three major classes of food constituents together with carbohydrates and proteins. Deep-fat frying is one of the most popular cooking procedures and leads to the production of both desirable and undesirable compounds. The cooking process affects the physicochemical characteristics and quality of the frying medium and the fried product itself.

French fries

The quality of oils and fats during the frying process has a major influence on the quality of the final product. Thermal processing of frying oils leads to oxidative and hydrolytic reactions i.e. hydrolysis and polymerisation and these chemical and physical changes lead to the formation of many volatile and non-volatile decomposition products. The majority of the non-volatile compounds formed during frying are, for convenience, classified as “Total Polar compounds” (TPC) and the formation of such compounds during repeated frying has been shown to increase with the degree of oil unsaturation.

The determination of the percentage of Total polar compounds (% TPC) is one of the most reliable methods for monitoring the quality changes in oils during the frying process and it reflects the degradation of the oil after repeated use. In order to protect consumers, several countries and International bodies have issued recommendations or a regulation which set maximum limits for the percentage of TPC, and regulates the use of oils & fats subjected to frying. Countries that control the quality of frying oil include:

 

A/A COUNTRY LEGISLATION/RECOMMENDATION LIMITS %TPC
1 France Legislation 25
2 Germany Recommendations by the German Society for Fat Science (DGF) 24
3 Italy Legislation 25
4 Poland Legislation 25
5 Spain Legislation 25
6 Brazil Recommendation 25
7 South Africa Regulation 25

 

The Food Safety & Standards Authority of India (FSSAI) released a statement dated 23rd September 2016, which addresses the issue of or repeated use of edible oils in cooking and frying of food by amending current standards (Food Products Standards and Food additives-FSS) to set a maximum limit for % TPC.

In light of the increasing concern, LGC Standards has included a new sample, total polar compounds in frying oil to the food chemistry proficiency testing scheme (QFCS). Palm oil was chosen as a material for this proficiency testing (PT) trial sample.  It is extensively used in commercial frying, fat spreads and generally in the food industry as it is the cheapest of all major edible oils and it is produced in the greatest quantity worldwide.  The fatty acid composition of palm oil is 50% saturated and 50 % unsaturated fat, it is relatively stable to oxidation and is naturally semi solid in room temperature, so does not require hydrogenation to become solid. You can find more details in Scheme Documentation.

By Savvas Xystouris, Technical/Development Manager, Proficiency Testing, LGC Standards

For more from LGC Standards, please click here.

Nov 17

New strict codes of practice for mitigating acrylamide formation

In September 2016, the E.U. Commission presented an amended regulation proposal for acrylamide, based on feedback from the stakeholders’ consultation. The Regulation is proposed to be made under Article 4 of Regulation (EC) No. 852/2004 on the hygiene of foodstuffs, and it sets out a requirement for food business operators to take account of strict new codes of practice for reducing acrylamide formation, as part of their food safety management systems.

The E.U. Commission has recommended that member states should continue the collection of acrylamide monitoring data and as with previous surveys, send the data to the European Food Safety Authority (EFSA).  Given the increased spotlight on acrylamide in both the EU and globally, it is certain that regulatory authorities will continue to monitor acrylamide levels in food, to determine whether further action/regulation is needed.

Many types of savoury snack in white dishes

Acrylamide is a process contaminant, formed in numerous baked or fried carbohydrate-rich foods as a result of high temperature cooking at >120 °C (248 °F). It is formed from reducing sugars and the amino acid asparagine (a building block of proteins) as part of the Malliard reaction.

The vast majority of evidence from animal studies suggests that acrylamide and its metabolite glycidamide are genotoxic and carcinogenic i.e. they have the potential to damage DNA and cause cancer.  However, the majority of human studies have not yet shown direct correlation with cancer therefore it is classified as a possible carcinogen in Group 2A by the International Agency for Research on Cancer (IARC). The intake of large amounts of acrylamide may also cause neurotoxic and hormonal disorders. Based on the results of monitoring in the Member States from 2007–2011, the EU Commission has set ‘indicative values’ for acrylamide in various food products. The most recent indicative values are laid down in Commission Recommendation (EC) No. 647/2013. In June 2015, EFSA published its first full risk assessment of acrylamide in food. The report reconfirmed previous evaluations, that acrylamide in food can potentially increase the risk of developing cancer for consumers in all age groups.

WHO/JEFCA: In 2010, the Joint Food and Agriculture Organization/World Health Organization Expert Committee on Food Additives (JECFA) concluded that acrylamide is a human health concern, suggested additional long-term studies and advised that exposure to acrylamide in food should be as low as reasonably practicable (ALARP).

CODEX: The Codex Alimentarius Commission (CAC) has developed a Code of Practice for the reduction of acrylamide in food to disseminate best practice to manufacturers.

USA: In 2016, the Food and Drug Administration (FDA) issued guidance to help the food industry reduce the amount of acrylamide in certain foods, but these are recommendations, not regulations.

CHINA: The China National Centre for Food Safety Risk Assessment (CFSA), published a paper for the Dietary exposure of the Chinese population to acrylamide, confirming it is a potential health concern for consumers, and recommending efforts should be made to reduce acrylamide in Chinese food. The EFSA & CFSA are due to sign an agreement on food safety in November 2016 during the China International Food Safety & Quality Conference/Expo jointly organised by the EFSA and EU Commission.

In light of the increasing concern, and the potential for higher demand for acylamide analysis, LGC Standards have included a new sample, for the analysis of acrylamide in snacks, to the food chemistry proficiency testing scheme (QFCS). Find out more in our scheme documentation.

References
EFSA Panel on contaminants in the food chain (CONTAM), ‘Scientific Opinion on acrylamide in food’, EFSA Journal, 13(6):4104, 2015. http://onlinelibrary.wiley.com/doi/10.2903/j.efsa.2015.4104/epdf, (accessed 17 October 2016)

EFSA, Acrylamide in food is a public health concern, 2015 https://www.efsa.europa.eu/en/press/news/150604, (accessed 20 October 2016)

International Agency for Research on Cancer (IARC), ‘EPIC Study: The Acrylamide Working group’, http://epic.iarc.fr/research/acrylamide.php  (accessed 17 October 2016)
Zhou Ping Ping et al., ‘Dietary exposure of the Chinese population to Acrylamide’, Biomed Environ Sci, Vol. 26 (6), 2013, pp.421-429. Available from cfsa.net.cn, (accessed 20 October 2016)

By Savvas Xystouris, Technical/Development Manager, Proficiency Testing.

For more from LGC Standards, please click here.

Nov 15

Underpinning measurements: written standards

Reference materials are a type of measurement standard used to validate analytical methods, establish traceability and support quality control. They are particularly important for analytical chemistry and clinical analysis as most analytical instrumentation is comparative so samples of known composition (reference materials) are needed to ensure accurate calibration.

A reference material (RMs) can either be a pure substance, e.g. an immunosuppressant certified for purity, or a matrix material, e.g. ‘drinking water’ containing a range of commonly found compounds.

logo_isoThe development, production, and certification of reference materials are supported by a number of ISO (International Organization for Standardization) Guides. These guides, adopted by over 160 countries, ensure that materials, products, processes and services are fit for purpose. In order to maintain their relevance and ensure their appropriateness, ISO Guides are revised every 5 years.

LGC scientists working as part of our UK National Measurement Laboratory and Designated Institute for chemical and bio-measurement function provide the UK representation on the ISO Reference Materials Committee (REMCO) and the chair of the UK Reference Material Working Group. Within these committees we have taken a leading role in the latest revisions of the reference material guides ISO Guide 34 (General requirements for the competence of reference material producers) and ISO Guide 35 (Reference materials – General and statistical principles for certification).

To support the evolving regulatory needs with the reference material field, such as the introduction of national accreditation schemes for reference material producers, ISO Guide 34 has not only been revised but has also been converted to an international standard in the 17000 series. This series includes well known accreditation standards such as ISO17025.

LGC has been instrumental in the conversion process, leading and coordinating the views of UK stakeholders to inform the international position and providing comments throughout the drafting and production stages. The parallel contributions LGC has been making in writing, editing and commenting on the revisions to ISO Guide 35 have also informed the development of this new standard.

The new standard (ISO17034 – General requirements for the competence of reference material producers) was published at the beginning of this month (01 November 2016) and represents a global consensus for reference material production. It will benefit the UK through increased acceptance of our reference materials overseas.

The degree of input into the production and revision of the ISO Guides for reference material production demonstrates the level of impact LGC has in its role as the UK National Measurement Laboratory and Designated Institute for chemical and bio-measurement on the best practise in the field, maintaining the position of UK reference material producers at a global level.

 

LGC is accredited to Guide 34 as a Reference Material Producer.

All our materials are available from LGC Standards. For further information please contact uksales@lgcstandards.com

 

LGC, the UK National Measurement Laboratory and Designated Institute for chemical and bio-measurement

 

Oct 14

Cell manufacturing: standardising the future of medicine

Today, on World Standards Day, we consider the need for standardisation in regenerative and personalised medicine to support healthcare developments and ensure the future of medicine arrives early.

m-tissue-cell-biology-culture-flasks-istock_000006300680mediumCell therapies, where living cells are transplanted into a patient, have significant potential to treat and change the course of diseases currently unaffected by existing medicines.

Cell therapies are being investigated for health issues such as prostate cancer, stroke, paralysis, loss of eyesight, Alzheimer’s and diabetes and the market is expected to grow to £5-10 billion by 2025. The UK is a world leader in this field and hundreds of millions of pounds are being invested in translating these therapies from a research environment into effective clinical applications, with the first cell-based therapies reaching clinical trials and the first products emerging onto the market.

Due to the complex and non-uniform nature of cell populations, developing standardised approaches for the bioprocessing of cells is crucial. This will ensure cell therapy products are comparable throughout the manufacturing process and maintain product quality and safety on any changes in manufacturing.

As the UK National Measurement Laboratory and Designated Institute for chemical and bio-measurement, LGC plays a significant role in the International Organization for Standardization (ISO) Technical Committee (TC 276 Biotechnology) that is developing best practice guides and standards for bioprocessing and cell characterisation, leading the UK Delegation.

These guides and standards will improve the quality control and hence safety of cell-based products. They will support a more rapid progression of cell based therapies to the market place and make the future of medicine a reality for patients.

worldstandardsday2016_poster_midres-222x300Standards for cell characterisation and bioprocessing

LGC is involved in developing the following standards:

ISO 20391-1: Biotechnology – Cell Counting – Part 1: General guidance on cell counting methods

ISO 20391-2: Biotechnology – Cell Counting – Part 2: Experimental design and statistical analysis to quantify counting method performance

ISO TS 20399-3: Raw materials control for bioprocessing – Part 3: Best practice guide for developers

Manufacturing standardisation publications

Comparability, manufacturing, characterisation and controls. White Paper (2016) Regen Med. 11(5)483-492. DOI:10.2217/rme-2016-0053

 

 

 

LGC, the UK National Measurement Laboratory and Designated Institute for chemical and bio-measurement

Sep 21

Alzheimer’s disease diagnosis: the need for speed

Every three seconds there is a new case of dementia somewhere in the world.

Dementia is the broad term for brain disorders that affect memory, thinking, behaviour and emotion, and is a debilitating and currently incurable condition that affects 10.5 million people in Europe and over 46 million people globally. With an aging population this figure is set to rise to over 130 million by 2050.

The most common cause of dementia is Alzheimer’s disease, which represents about 70 % of all cases. To help patients access the most effective treatments and sources of support, early diagnosis is crucial. However, recent studies suggest only half of people with Alzheimer’s have been formally diagnosed and these cases are often only identified in the advanced stages through highly invasive tests such as lumbar punctures.

The key reasons for this are the lack of accuracy involved in the measurement of biomarkers currently used to indicate Alzheimer’s disease and the absence of alternative clinically-approved and non-invasive tools to diagnose and monitor disease progression.

In our role as the National Measurement Laboratory and Designated Institute for chemical and bio-measurement, scientists at LGC have recently started work on two European metrology projects that aim to address these critical measurement needs.

EMPIR_neurometNeuroMET (led by LGC) is a multidisciplinary project which combines the diverse expertise of a number of National Measurement Institutes (NMIs) together with clinicians and academics. This project aims to overcome the measurement challenges currently constraining clinical innovation and uptake in neurodegenerative disease diagnosis and treatment. It will challenge the performance of a number of non-invasive/minimally invasive approaches for early diagnostic and drug therapeutic monitoring, such as magnetic resonance imaging and blood analysis. Within Neuromet reference methods for protein biomarkers will be developed and their utility in protein standardisation of clinical measurements will be addressed. Finally, the application of novel statistical approaches to integrate clinical analytical and assessment data will enable for the first time the development of validated person centred outcome measures. By working directly with clinicians, the tools and protocols developed will be ready for direct implementation in partnering hospital laboratories and back into the clinic.

EMPIR_remindRecent studies strongly suggest that metal ions such as iron (Fe), zinc (Zn), copper (Cu), or aluminium (Al) are directly or indirectly involved in the development of Alzheimer’s. In collaboration with European NMIs, clinicians and academics, ReMIND (in which LGC is a project partner) aims to understand the role of metals and metal containing bio-molecules in Alzheimer’s development. This project will develop reference measurement procedures to provide measurement comparability between laboratories for established and potential biomarkers in cerebral spinal fluid, plasma and brain tissue using high accuracy inorganic mass spectrometry and Raman spectrometry approaches. This work will support reliable, comparable measurements in current diagnostic tests, enable extended studies into the uptake, metabolism and transport of metals to the brain to be performed, and further the development of population-based screening through blood testing.

The research developed under these two projects will support the development of earlier and more accurate methods for the diagnosis and monitoring of Alzheimer’s disease. This will improve the quality of life both for those affected and their families and ultimately reduce the significant global economic burden of Alzheimer’s care, estimated to be over US$1 trillion by 2018.

To find out more about these projects, contact the NMS Helpdesk.

Find out more about other European projects LGC is involved with.

September is World Alzheimer’s Month, an international campaign to raise dementia awareness and challenge stigma. #RememberMe #WAM

#chembiomeasurement

 

Sep 08

How certain can you be: the need for measurement uncertainty

Thousands of routine measurements are made each day. These measurements vary from clinicians making medical diagnoses, to providing evidence to protect our borders, to safeguarding the quality of our water. However, to have a real understanding of the value of any of these measurements you need to know both its quantity and its quality, i.e. how good the measurement really is and can you trust it?

This is demonstrated through the measurement uncertainty associated with each measurement.

Whenever a measurement is made there will always be some level of uncertainty or doubt about the result obtained. This is unavoidable and not due to mistakes in the application of the measurement method, but to the fact that all measurements are subject to variable factors which will contribute to the uncertainty in the result.

For example, when asked how long it takes to get home from work, you might say ‘about 45 minutes’. The ‘about’ indicates that you know the answer is not exactly 45 min – the true answer may lie anywhere between 40 and 50 minutes and depends on the traffic, the weather and a host of other factors. The range associated with the measurement (±5 minutes in this case) is the measurement uncertainty.

Measurement uncertainty allows individual measurement results to be meaningfully compared, for example to see whether a clinical limit has been exceeded or whether results produced before and after a drug intervention are genuinely different. In some cases, such as a quick screening test, a large measurement uncertainty may be acceptable but in others, for example monitoring the amount of a chemotherapy drug present in the body, a small measurement uncertainty is necessary. The impact on human health, the environment and the economy can be significant if measurement uncertainty is not sufficiently accounted for.

mu_thumbnail-of-flyer-1Recently clinical laboratories in the UK adopted the International Organisation for Standardization (ISO) standard 15189 (Medical laboratories – Requirements for quality and competence) which stipulates that measurement uncertainty is to be calculated for each clinical assay.

As the UK National Measurement Laboratory and Designated Institute for chemical and bio-measurement, we have considerable expertise in this field, and have been a leading exponent of calculating, and importantly reporting, measurement uncertainty for all quantitative measurement for many years. In this role we are providing support for clinical laboratories and informing the clinical community of the fundamentals of measurement uncertainty and will be running a specific training course in November to address this challenging topic.

 

If you have any further questions about measurement uncertainty or any of the courses, presentations or guides below please contact us.

 

Training courses

Measurement uncertainty for clinical testing laboratories, specific one-off training event for laboratory analysts and quality managers seeking accreditation to ISO 15189, 2 November 2016

Evaluating measurement uncertainty for chemical testing laboratories, scheduled training course on measurement uncertainty training in line with ISO principles, 12 October 2016

Find further information on LGC training courses on our website or contact us directly.

 

Upcoming presentations

BMSS Introduction to Mass Spectrometry Short Course, Eastbourne, UK, An introduction to small molecule quantitation, Chris Mussell, 13 September 2016 – this will contain a short section on measurement uncertainty

WADA-BIPM Symposium: Standards and Metrology for Anti-Doping Analysis, BIPM, Paris, France, “Bottom up” (GUM) approach to MU assignment for organic analytes, Chris Mussell, 28-29 September 2016

Waters UK Clinical Users Meeting, British Library, UK, Eschewing Obfuscation – Measurement Uncertainty & Mass Spectrometry, Chris Mussell, 19 October 2016

Advances in Clinical Analysis 2016, Chromatographic Society meeting, Burlington House, London, Measurement Uncertainty & Mass Spectrometry, Chris Mussell, 30 November 2016

 

Guides and webinars

Mass spectrometry and measurement uncertainty, Chris Mussell & Simon Cowen, webinar outlining basic concepts and approaches to measurement uncertainty estimation with examples

Evaluating measurement uncertainty in clinical chemistry, guide produced by LGC under the National Measurment System (NMS) that outlines ‘top-down’ approaches to uncertainty demonstrated by clinical analysis case studies

Guide to the expression of uncertainty in measurement, guide produced by the International Bureau for Weights and Measures (BIPM)

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