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TCR SEQUENCING

T-cells are the core components of our adaptive immune system. Once activated, they can directly kill cells that are foreign (cytolytic T-cells) or perform helper function (helper T-cells) to activate B-cells to make antibodies against foreign antigen. The activation of T-cells involve recognition of MHC-peptide complex by the T-cell receptors (TCR). Humans carry >109 T-cells, each expressing a unique TCR. This highly diverse repertoire of T-cells has the ability to recognize peptides originating from foreign elements such as invading pathogens and cancer cells. Each TCR recognize peptides in complex with MHC proteins presented on the surface of antigen presenting cells. Productive T-cell activation results in the clonal expansion of a specific T-cell and this expansion can be accurately determined by TCR sequencing. In cancer, TCR sequencing has predictive and prognostic value and can lead to the development of novel therapeutics such as engineered T-cells.

Analysis of T-cell population requires generation of large quantity of data to cover each and every unique TCR expressed by T-cells present in the population. This is achieved by next generation sequencing of genomic DNA from purified T-cells. Both α and β chain of the TCR are sequenced to determine clonal diversity of the complementary-determining regions (CDRs) of the individual receptor. The CDR1 and CDR2 regions contribute binding to MHC and the CDR3 region to the peptide presented by the MHC. The diversity in the CDR3 region can be assessed by sequencing the β chain of the TCR complex.

TCR Sequencing Process

Every sample is precious, and data integrity is paramount. We communicate with our customers at every stage of the sequencing process, to ensure that they receive the maximum value out of every sample.

We also recognize that the value our customers get is not in the sequencing alone; it’s the technologies within the sequencing. MedGenome is one of the few genomics research companies that provides turnkey solutions to our customers, offering robust bioinformatics services alongside NGS sequencing.

Sample Requirements
DNA RNA
CELLS Minimum 1e+6 cells required. Cells should be shipped in dry ice Minimum 1e+6 cells required. Cells should be frozen and pelleted and shipped in dry ice
TISSUE 30 mg of fresh or frozen tissue or 20 mg of stabilized tissue. The tissue should be immersed in Liq N2 and shipped in dry ice or should be

immersed in RNAlater RNA Stabilization Reagent or All protect Tissue Reagent

30 mg of fresh or frozen tissue or 20 mg of stabilized tissue. The tissue should be immersed in Liq N2 and shipped in dry ice or should be

immersed in RNAlater RNA Stabilization Reagent or All protect Tissue Reagent

FFPE 5 slides with 10um thick tissues and surface area of 250 mm2 8 slides with 10um thick tissues and surface area of 250 mm2
BLOCK Sufficient thickness to generate the optimal number of slides as required in FFPE row
whole genome sequencing 100 ng
whole exome sequencing 100 ng
RNA sequencing 0.2 ug of high quality RNA (RIN>8) or 1ug RNA (RIN<8)
RNA-TruSeq access libraries / Libraries from ffpe rna 10 ng of high quality RNA (RIN>8) or 50ng RNA (RIN<5)
truseq standed mrna library 100 ng high quality RNA (RIN>8) or 1ug RNA with RIN between 5 and 8.

 

Genome in a Bottle validation results for WGS & WES
Sample name analysis type variant type accuracy precision analytical sensitivity analytical specificity
Asian son (NA24631) WGS SNP 99.9972% 99.9972% 98.3605% 99.9993%
Asian son (NA24631) WGS INDEL 99.9990% 97.2113% 95.9767% 99.9996%
Asian son (NA24631) WES SNP 99.9987% 99.4271% 98.9305% 99.9996%
Asian son (NA24631) WES INDEL 99.9996% 97.4525% 94.9458% 99.9999%
Utah female (NA12878) WGS SNP 99.9986% 99.5894% 99.2871% 99.9995%
Utah female (NA12878) WGS INDEL 99.9991% 97.6290% 96.7742% 99.9996%
Utah female (NA12878) WES SNP 99.9990% 99.3678% 99.3030% 99.9995%
Utah female (NA12878) WES INDEL 99.9995% 93.7846% 96.4536% 99.9997%