Genetics and Genomics Lab

Introduction:

Genetics and Genomics Lab has many unique features in the field of Genetics and Biotechnology research.  The main objective of this lab is to provide a quality DNA analysis services to the researchers in UVAS as well as other research organizations throughout the country. The ability to sequence and analyze entire genome has created a revolution in biomedical research.
We are now investigating entire gene networks, background effects, the role of single nucleotide polymorphisms and structural variants across the genome, modeling genotype-phenotype relationships and much more. Genetics and Genomics Lab is providing technical help and meaningful research facilities to the students who want the opportunity. Plus we are offering some unique services which are not being offered by any other institute in the country.

DNA Core facility Request Form

Scope of the Lab

DNA/RNA extraction

Genetics and Genomics Lab offers a lot of services starting from DNA/ RNA extraction. For this purpose we accept a variety of samples like blood, tissue, hair, urine samples. Extraction is confirmed by using gel electrophoresis.

Qualitative and Quantitative PCR

PCR is a powerful amplification technique that can generate an ample amount of a specific segment of DNA from only a small amount of starting material (i.e., DNA template or target sequence). Sometimes there are pitfalls that complicate the reaction
Genetics and Genomics Lab also provide services of qualitative PCR and quantitative PCR. For this purpose we have latest version of ABI ProFlex PCR systems and ABI 7500 Real time PCR system.

DNA Quantification/ UV/VIS Spectroscopy

Quantification of DNA is a very important step especially when we have to perform different techniques such as PCR, RFLP, RAPD and sequencing. We use two most widespread methods for quantification of DNA

• By comparison of an aliquot of the extracted sample with standard DNA of known concentration using gel electrophoresis
• Spectrophotometric determination. By using these methods we gain information for nucleic acid quantity, quality and purity of the extracted samples

We can help you to analyze your samples on a spectrophotometer using the cuvettes. We have a state of the art UV/VIS spectrophotometer i.e., Eppendorf biospectrometer. It gives high quality analysis using very low sample volume, producing accurate and reliable results.

DNA Sequencing

DNA sequencing refers to sequencing methods for determining the order of the nucleotide beses in a molecule of DNA. Genetics and Genomics Lab provides the facility of DNA sequencing based on the principle of Sanger sequencing using capillary-based ABI-3500 Genetics analyzer and providing more than 99% accurate results. Sample should be highly purified and accurately quantified.

DNA Fragment analysis:

Genetics and Genomics Lab provides high quality DNA Fragment analysis and genotyping facility on the basis of finding SNP and DNA microsatellite. We are always available for troubleshooting and analysing your data.

Speed Gene Test:

The identification of the 'speed gene' is the first known characterization of a gene contributing to a specific athletic trait in thoroughbred horses and has the potential to transform decision-making processes in the global bloodstock industry. Horses with a specific mutation in the gene called myostatin (MSTN) have improved athletic performance.
Speed gene Test results tell racehorse owners and trainers if a horse is ideally suited to racing over short, middle, or middle-to-long distances. They could potentially optimize their purchasing and training decisions and enter their horses in the most suitable races. The test is also anticipated to help make more precise breeding decisions to maximize the genetic potential and value of their horses.

Projected height test

The Projected Height Test predicts the mature height of horses at withers from birth. Based on DNA analysis of the LCORL/NCAPG gene region and the sex of the horse. The Projected Height Test can be used to complement other selection tools to shortlist stallions and mares most likely to produce the desired results. The potential outcomes from any breeding combination can be predicted if the genetic type of the stallion and mare are known. We at Genetics and Genomics lab offering this unique service and predicting the results with a greater success rate.

Horse Gate Test

Genetics and Genomics Lab is offering the facility of gait test. The horse industry should benefit from the applications of gait analysis by improving the profitability of racing and riding activities.

Parentage Analysis

DNA parentage testing is a valuable tool which allows breeders to select elite animals with confidence, knowing that their ancestry is correct. Breeders can use this information to access genetic progress and confirm parentage when selling elite animals. It increases the validity and value of a pedigree. We are providing the facility of parentage analysis, supported by a highly experienced staff team.

A1/A2 Genotyping of Dairy Animals

Bovine milk is regarded as nature’s perfect food due to presence of vital nutrients. However some peptides are generated after proteolytic digestion of β-casein that have opioid properties and may increase the risk of chronic diseases. There are 13 genetic variants of bovine beta-casein. Out of these A1 and A2 are the most common in dairy cattle breeds. The A1 and A2 variants differ only at position 67, which is histidine in A1 or proline in A2 milk. A1 β casein could be responsible for several health disorders like diabetes, coronary heart disease etc. while A2 β-casein is generally considered safe for human consumption. That is why we are offering A1/A2 genotyping of dairy animals by identifying allelic distribution of A1A2 alleles.

Sex identification in Birds

The sex chromosomes in birds are designated as Z and W, and the male is homomorphic sex (ZZ) and the female is heteromorphic (ZW). In most avian species the Z chromosome is a large chromosome and it contains almost all the known sex-linked genes. The W chromosome is generally a much smaller micro-chromosome, containing a high proportion of repeat sequence DNA. CHD gene is found on both the Z and W chromosomes but the size of the gene on the W chromosome is smaller than the gene on the Z chromosome hence male and female birds are identified using their genetic information with almost 100% reliability.

Sample Submission Guidelines for DNA Sequencing:

•  Please provide the template in distilled water and it should be free of EDTA, salts, proteins, RNA or genomic DNA. The Genetic analyzers are very much sensitive to these contaminants so take a great care in template preparation
• Purify your template with any common procedure or by using kits.
• Run your template on agarose gel to check its purity size and concentration.
• Quantify purified DNA.
• Use 1.5ml eppendrof tubes, PCR tubes or 96-well PCR plates for pooling your samples.
• Templates should be provided at the following concentrations:

• Place your samples in a container of ice before sending us.
• For optimum results, purify the PCR product before sending for sequencing. Any method (including purification kits) that have potential to remove dNTPs, primers and excessive salts etc. can be used. 

Primers

• Primer concentration should be 3.0-5.0ρmol submitted for sequencing. Wrong information about concentration of primer and template may affect the sequencing reaction and consequently the data generated.
• Poor primer quality will result in poor sequence quality.
• A primer with a melting temperature too low for cycling conditions will not anneal to the template. Design primers with Tm's between 55-60oC.
• Secondary structure in the primer will cause the primer to self-anneal and not to the template.
• Mismatch between primer and primer annealing site on the 3' end of a primer can cause the sequencing reaction to fail. If a reaction fails with a standard primer, check if the DNA fragment/plasmid contains the primer binding site and that the site was not lost due to restriction digest and cloning of an insert.
• Multiple priming sites on a template will cause peaks that overlap one another. Base calling software will not be able to assign correct base.

Total quantity required

• Please provide atleast 10uL template and 5uL primer per reaction.
• Estimated time for results will be 4-5 working days and results will be sent via e-mail. If Soft copies of data on customers CD can also be provided if requested.
•  To view your results

            The electopherograms can be visualized using one of these software

• ABI Sequence scanner (Windows)
• BioEdit (Windows)
• Chromas (Windows)

Sample submission guidelines for DNA Fragment Analysis

• DNA samples must be clearly labeled and provide corresponding information on request form
• High quality DNA samples are an absolute necessity for good results.
• We recommend pooling different dyes after your PCR reaction.
• Please Prepare and submit samples in a 96 well plate or PCR tubes with appropriate concentrations.
• Please cover plate or tube with aluminum foil. If you are shipping your sample, please cover plate with cap strip.
• At least 25 base pair difference is recommended for two fragments pooled in a single well and labeled with same dye.
• Please provide at least 5mL of the PCR product.
• DNA fragments must be conjugated with one of the following dyes, VIC, HEX, NED, TET, PET, FAM.
• Estimated time for results will be 1-2 working days and results will be given via e-mail. Soft copies of data on customers CD can also be provided if requested.

Viewing your results

To view your results, use the following available software

• ABI Peak scanner (Window)

How to apply for these Services???

• Apply Directly

If you are applying directly please read the following instructions carefully and then fill the                request form.

• Attach Gel images of the samples along with complete information.
• There should be proper labeling on the sample tubes.
• Deposit the payment in the Account office by cross cheque in the favour of CLC UVAS or by submitting cash on the spot.
• In case of cross cheque please attach the copy of cheque along with the request form.
• Submit samples in sample collection room CLC UVAS Ravi campus Pattoki.

Apply Through HEC.

• If you are applying through HEC, you have to seek permission from HEC before sending your samples to us.
• All the applicants need to apply online. For this purpose please visit: eportal.hec.gov.pk
• Applicant needs to register himself or login (in case of an existing user).
• Enter the information and the details required for samples analysis. Also submit  scanned copies of the following documents:
• Summary of research proposal
• Approval letter of Research Synopsis/Proposal
• Consent Letter of incharge CLC  
• Brief profile of Research Supervisor
• Endorsement by research supervisor, head of department and Director (ORIC) must be    obtained at appropriate section of the prescribed application form.
• Submit your application at least 6 weeks before submission of samples.
• The ASI Management Committee will evaluate the application and decision of the Committee will be communicated to the applicant almost within 6 weeks from the date of submission of the application.
• In case additional information is required, the decision of the application may be delayed.
• For all the approved cases, HEC will issue award letter to the applicant.
• After getting the award letter, the applicant may send samples to Genetics and Genomics lab CLC for analysis.
• On receiving Analysis results from Genetics and Genomics lab, the researcher will fill the ‘Result Acceptance Voucher’ and ‘HEC Payment Form’ dully signed by supervisor, countersigned by your DIRECTOR ORIC/DEAN.
• We will send it to HEC for reimbursement of payment to CLC UVAS.
• Electronic copies of results will be sent to you through your provided Email address after 10 working days. It may take longer time if there arise some sort of technical issues