Burkitt’s Lymphoma
Burkitt’s lymphoma is an aggressive cancer of the white blood cells which occurs most often in children and young adults. It is a common form of malignancy in children in Equatorial Africa, and is also frequently associated with immunocompromised individuals, such as those suffering from AIDS.
This disease is associated with a chromosomal translocation, between chromosomes 8 and 14 of the myc gene. This gene is a regulator gene that codes for a transcription factor. In most cases of Burkitt’s lymphoma, the reciprocal translocation shifts the proto-oncogene myc from its normal position on chromosome 8 to a location closer to the enhancers of the antibody heavy chain genes on chromosome 14.
This t(8;14)(q24;q32) translocation causes the myc gene to be persistently expressed, resulting in continuous cell division without control or order. A defining feature of Burkitt’s lymphoma is the presence of this translocation between the myc gene and the IgH gene.
SynaSV™ is an MGRC online tool specifically designed to visualise structural variations. This powerful application can be used to visualise translocation mutations.
Here, we showcase how SynaSV™ can be used to view and identify structural variations in the IgH-myc gene fusion.
With MGRC’s genetic screening services, mutations such as the IgH-myc gene fusion are detected for common and rare genetic disorders. Early screening of this disease will enable the cancer to be identified when it is still localised. This would enable target therapy to be more effective.
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Click here, to submit your query.
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On the result page, it is displayed that the two highest scoring matches are two different targets. Select these targets by clicking on the respective check boxes. A structural variation graph will appear.

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From the graph, it can be observed that that the query (middle) is split across a breakpoint, where the first part matches to chromosome 8 (top) and the second part to chromosome 14 (bottom).

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In the structural variation graph, the statistics table indicates that the structural variation is an inter-chromosomal translocation.

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Malaysia-based company completes genomics milestone

Kuala Lumpur, 17 November 2011 Malaysian Genomics Resource Centre Berhad (MGRC) today announced that it has successfully completed its 100th human genome from a diverse mix of Malaysian, European and Australian individuals.

The results of the data generated from these genomes has helped in efforts to identify and compare highly represented patterns of common and clinically-relevant genetic variations within Malaysian and other populations, and to establish robust bioinformatics protocols for the reference-based analysis of genomic information.

MGRC Chief Scientific Officer, Dr Stephen Rudd, explained, “By reaching this milestone, MGRC has clearly demonstrated its capabilities in sequencing and analysing human genomes. It also further highlights the fact that genomics technologies and expertise are available in Malaysia for both the local and international life sciences community.”

The experience of analysing 100 human genomes has enabled MGRC to enhance its analytical pipelines and its proprietary Human Genome Browser. This puts the Company in the position of now being able to sequence and analyse a human genome in less than two weeks.

These pipelines are already being used in the MyGenome Project to characterise patterns of human genetic variation in the Malaysian population. The MyGenome Project is a collaborative effort among Ministry of Science, Technology and Innovation (MOSTI), Malaysia Genome Institute (MGI), and MGRC. It was launched in November 2010 and it involves the deep sequencing and comprehensive bioinformatics analysis of 25 genomes from ethnic groups in Malaysia.

About Malaysian Genomics Resource Centre Berhad
Malaysian Genomics Resource Centre Berhad (MGRC) provides genome sequencing, bioinformatics analysis, and genetic screening services. The company�s expertise is in the rapid sequencing and analysis of large volumes of genetic data. Since 2004, MGRC has developed extensive experience in the sequencing and analysis of human, animal, plant and microbial genomes, including large complex de novo genome assembly, for customers in Malaysia and overseas. Today MGRC operates one of the largest computational centres for genetic analysis in the region.

 
Can We Detect Non-Halal Elements in Food?
It was recently reported that the Department of Islamic Development Malaysia (JAKIM) had confirmed that a particular brand of dairy product was non-halal after it was found to contain porcine DNA. This discovery not only affects consumers of the product but also renders other products, which use it as an ingredient, non-halal. This clearly highlights a case of inaccurate food labelling, an issue which is of great concern to most consumers of edible products.
Consumers come from various backgrounds and unique lifestyles, especially in a multicultural country like Malaysia. Many people are committed to observing food restrictions, which could be due to religious principles, lifestyle, food allergies or medical requirements. For these consumers, food labels are imperative in helping them make the right purchase. With this in mind, it is essential that food manufacturers accurately and truthfully label their products. To protect the rights of consumers, the sources and composition of all products have to be properly tested and verified prior to the products being sold. For this purpose, DNA-based methods can be employed to identify and detect traces of contamination in a product. Using specific DNA sequence regions, primers or probes unique to specific meat or plant species can be designed.
A suitable sequence region to use for probe design is the mitochondrial DNA (mtDNA) of various animals or plants. The mtDNA sequence is often used in population genetics studies as its gene content is believed to be strongly conserved. The existence of multiple copies of mtDNA in the cell also makes DNA amplification relatively easier. Using the cytochrome b sequence of Sus scrofa (wild pig) as an example, users can submit the sequence as a query on SynaProbe™ to design unique probe sequences to detect traces of pork. The specificity of these probes can be further verified with SynaHybridise™ to ensure accurate identification and detection of the targeted porcine species. In the example, the hybridisation of the probe to various breeds and isolates of the meat samples highlights the success of the probe in identifying the meat species, regardless of its breed.
The designed short sequences display much flexibility in terms of their application. Polymerase chain reaction (PCR) is already commonly employed in laboratory testing to provide specific and sensitive detection of trace contaminants in food products. While PCR is a hugely popular option, users may also consider microarray testing. The inclusion of hundreds to thousands of probes per microarray chip might potentially allow for the simultaneous detection of multiple contaminants within a product, resulting in a shortened testing time.
To design unique probe sequences specific to an animal or plant species:
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Click here, then click on .

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On the results page, click on to verify the specificity of the selected probe sequence.

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Results generated show the number of matches to the probe accompanied by a list of matches. From the list of hits, the probe is demonstrated to match all types of Sus scrofa isolates and breeds.

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Fatty Foods Make You Want to Munch!
If you love French fries, burgers or deep-fried snacks, you had better read on.
A group of researchers has shown that eating fatty foods may make you want to munch even more. In the study, rats that tasted fat in their food kept on eating, thanks to endocannabinoids. Endocannabinoids are the body’s equivalent of cannabinoids, the active ingredient in marijuana, and are reportedly released in the brain and body.
Rats on a fat diet registered an increase in endocannabinoid activity, thus demonstrating a link to binge-eating. When given compounds that blocked the cellular ‘buttons’ triggered by the endocannabinoids, the rats stopped eating immediately. According to the lead researcher in this study, the findings may prove pivotal in assisting scientists to develop drugs that can combat binge-eating and similar weight-related conditions.
SynaTate™ is an online application that annotates and interrogates data to identify structural and functional motifs in query sequences with patterns stored in SynaBASE™, MGRC’s proprietary database. The analysis of the cannabinoid receptor 1 gene (endocannabinoid receptor) using SynaTate™ revealed that it has a potentially active region on the third forward reading frame. This frame encodes for the melanocyte-stimulating hormone receptor which produces the melanocyte-stimulating hormone (MSH). MSH is found in the brain and has been shown to have an effect on appetite. The findings open up the possibility of developing drugs that block the metabolism of intestinal endocannabinoids to treat binge-eating, obesity and other eating disorders.
Subsequently, the gene was compared against the SwissProt database using SynaCompare™. The comparison showed that the conserved region is the same in both rat and mouse, thus making the latter a suitable model for expression studies of the cannabinoid receptor 1 gene. This is especially useful as mice are cheaper and easier to obtain, and are ideal for genetic research.
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Click here to submit query.

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The results page shows that significance is predicted on the third forward reading frame, F3. Select the significance region on F3 by left clicking and dragging across. Right clicking within the selection will display a list of options. Select ‘Annotate nucleotide sequence’.

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The results show that the cannabinoid receptor 1 gene encodes for the melanocyte-stimulating hormone receptor. The receptor produces melanocyte-stimulating hormone (MSH) which has the ability to control appetite.

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Click here to compare the cannabinoid receptor 1 gene against the SwissProt database.

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The results show that mouse has the closest homology to rat. Click on the ‘Show’ button to view the respective graphs.

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The dot-plot graph shows a diagonal line, which indicates that there is homology between rat and mouse. These regions could be useful for studying the expression of the gene, with the aim of developing drugs to overcome weight-related problems.

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Improved version helps researchers with more complex bioinformatics analysis

Kuala Lumpur, 8 August 2011 – Malaysian Genomics Resource Centre Berhad (MGRC) has announced the extensive update of its comprehensive range of high-speed online bioinformatics analysis tools and reference databases. These free-to-use tools now offer users greater flexibility to perform complex analyses of genomic data with a very short turnaround time.

One of the major updates involves the seamless integration between SynaBlast-Mega and sequence data from NCBI’s GenBank database. MGRC’s SynaBlast-Mega bulk alignment tool enables users to search thousands of either nucleotide or protein sequences in a single submission. The tool now utilises the fullest set of DNA and protein sequences from GenBank. With this enhancement, SynaBlast-Mega users are able to submit up to 10MB of sequence query data, thus empowering them to analyse thousands of queries at one time.

To further improve its bioinformatics applications, MGRC has also included additional biological domains in its reference databases. While retaining a focus towards mammalian genomic information, complete datasets from fungal, bacterial, plant and invertebrate genomes have also been included. This Malaysia-based genome sequencing and analysis centre now operates with a storage capacity of more than 50 TB, as part of its commitment to provide state-of-the-art online sequence analysis tools to users throughout the world. The combination of integrated software tools and increased databases has seen a continued upswing in MGRC users from the United States, Europe, China and India. MGRC has also provided a version of the portal in Mandarin for Chinese users.

MGRC’s Chief Scientific Officer, Dr Stephen Rudd, explained, “The ability to easily perform complex searches and analyses of multiple sequences simultaneously using SynaBlast-Mega will greatly reduce the time taken by users to obtain results. Coupled with access to GenBank databases, our bioinformatics tools are primed to help scientists, researchers and bioinformaticians accelerate their downstream research and subsequently to make interesting new discoveries that are of significance. MGRC’s online applications are designed to be highly robust, versatile and all-encompassing. Much thought is also put into ensuring they are compatible with GenBank and other publicly-available reference databases, as well as being user-friendly.”

The enhanced and updated SynaBlast-Mega, and other online sequence analysis tools, can be freely accessed by the public at MGRC’s bioinformatics portal, www.mgrc.com.my.

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