How genotyping is aiding in the fight against malaria

mosquitoe-1548975_19203.2 billion people across 106 countries and territories, live in areas at risk of malaria transmission. The serious and sometime fatal mosquito-borne disease is caused by the Plasmodium parasite – in 2015, malaria caused 212 million clinical episodes, and 429,000 deaths.

Malaria has been a public health problem in Brazil ever since it was brought to the region during its colonization. By the 1940s it is estimated that six to eight million infections and 80,000 malaria-related deaths occurred every year in the country.

Due to a concerted series of malaria control policies, Brazil has recorded a 76.8% decrease in malaria incidence between 2000 and 2014 – and effort which the country was praised by the WHO.  In 2014, there were 143,910 of microscopically confirmed cases of malaria and 41 malaria-related deaths.

Part of Brazil’s malaria control policy involves the use of primaquine – a medication first made in 1946, to treat and prevent malaria. It is particularly effective against the Plasmodium vivax parasite that is prevalent in the Brazil.

Unfortunately primaquine can induce haemolytic anaemia in glucose-6-phosphate dehydrogenase (G6PD)-deficient individuals and may lead to severe and fatal complications. 330 million people worldwide are affected with G6PD deficiency, with recent studies suggesting the prevalence of the deficiency could be as high as 10% in Brazil.

Recently, molecular biologists from LGC enabled a cutting edge study in collaboration with researchers from Brazil and the London School of Hygiene and Tropical Medicine.

The researchers looked for mutations in a sample of 516 male volunteers that could be used as clinical indicators for G6PD deficiency that could lead to complications in people prescribed with primaquine.

Blood samples were collected from around Brazil at hospitals during surgeries, as well as using the local Brazilian radio stations to ask people to come and submit blood.

Needing a fast and efficient way to generate results in high throughput, the team turned to LGC’s integrated genomics toolkit to facillitate the research. Each sample was screened against 24 KASP assays to assess the genetic bases of G6PD deficiency. In combination with the IntelliQube®,a fully automated point and click PCR system;  the team collected the data in roughly three hours of instrument time and one hour hands on time.

KASP is a flexible, highly specific genotyping technology, which can be used to determine SNPs and InDels.  KASP uses unlabelled oligonucleotide primers, which gives the technology a cost advantage and allows more data to be generated, increasing data quality.

The data indicates that approximately one in 23 males from the Alto do Juruá could be G6PD deficient and at risk of haemolytic anaemia if treated with primaquine. The authors conclude that routine G6PDd screening to personalize primaquine administration should be considered – particularly as complete treatment of patients with vivax malaria using chloroquine and primaquine, is crucial for malaria elimination.

The teams are continuing their collaboration to help further research in to treatments for malaria, and we can’t wait to see more!

To access the paper, please click here, or to see the IntelliQube in action and learn more about this automated PCR instrument click here.

 

 

Sources:

Malaria. (2017, July 13). Retrieved August 8, 2017, from https://www.cdc.gov/malaria/about/index.html

Maia, U. M., Batista, D. C., Pereira, W. O., & Fernandes, Thales Allyrio Araújo de Medeiros. (n.d.). Prevalence of glucose-6-phosphate dehydrogenase deficiency in blood donors of Mossoró, Rio Grande do Norte. Retrieved August 8, 2017, from http://www.scielo.br/scielo.php?pid=S1516-84842010000500017&script=sci_arttext&tlng=en

 

This blog post was originally published on the Biosearch Technologies blog.

Accelerating rice improvement in South Asia

WP_20180515_009Diversity is the spice of life and is also key to breeding rice that delivers increased yields. Rice is a crucial staple food for about half a billion people in Asia, but it suffers from diseases that reduce yields, destroy harvests and put food security and livelihoods at risk. But there is hope – by tracking DNA markers of natural genetic variants through generations of crosses, breeders can identify better combinations that enrich crop vitality and resilience leading to more reliable and sustainable rice production.

collaborative project between Bangor University and LGC with a university partner in India (SKUAST), a research institute in Pakistan (NIBGE) and, in Nepal, a government research centre (NARC) and a private seed company (Anamolbiou) is addressing this challenge and has already identified over a million new markers in rice. They can reveal linkage to genes and patterns of diversity that help rice breeders select for a wide range of resistance genes to improve many different varieties. The project continues to develop these markers into more KASP assays that will be made available in publicly searchable databases.

Modern disease-resistant varieties are not always well adapted to specific environments, so breeders aim to incorporate markers for both biotic and abiotic stress resistance as well as yield components into locally accepted varieties that may already possess value traits, such as aroma. Molecular markers such as Simple Sequence Repeats (SSRs) in rice were developed in the 1990s for marker-assisted selection (MAS) and these are still used by some rice breeders in Asia to improve selection efficiency. Smaller breeding companies do not have all the resources (i.e. trained personnel, instrumentation for extraction or genotyping) to use such markers in-house. They can benefit from a service-based approach such as LGC Genomics’ genotyping service using KASP technology that offers a lower cost per data point and is faster to implement or use in their own lab. KASP assays offer greater sensitivity, speed, and safety than the older techniques, such as SSRs, when carried out in breeders’ own labs.

WP_20180515_007The collaboration with Bangor University and partners has already developed new methods to identify suitable SNP and InDel markers that can replace existing SSRs in target breeding crosses which have been adopted by Nepalese breeders. Now, a broader survey of suitable SNPs and InDel markers, across a set of 130 publically available rice genome sequences selected for geographic diversity, is discovering novel markers that are relevant to both Indica and Japonica rice backgrounds.

Before the research team started this project there was a choice of 2055 useful KASP assays that breeders could use, depending on their breeding strategy, but this project has increased the choice to over 245,000 potential markers that should benefit a wider range of rice breeding programs. This increase in the number of KASP assays enables the project and research community to utilize KASP technology on a scale that was only available to big breeding companies before this project. It’s exciting times for rice breeding!

Bangor University and partners plan to make thousands of the rice markers from this project available in the form of a searchable database so that rice breeders can easily find the most suitable options to replace their target SSRs in existing programs or to identify the appropriate loci for a range of possible new crosses. LGC will also offer them as validated KASP assays on its website. The large database of validated KASP assays produced by this project will thus give rice breeders the ability to carry out genomic selection (GS) with many thousands of loci across their populations, enabling smaller breeders to benefit from the same genomic scale technologies that generally require significant resource investment to develop on their own. The availability of this marker set to the public sector, and the services provided by LGC Genomics, will enable rice breeders of all sizes to apply genomic tools to accelerate their MAS and GS breeding programs to develop new rice varieties that will improve food security.

To learn more about our KASP genotyping services click here.

 

This blog originally appeared on the Biosearch Technologies blog.