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NGS Services

NGS & Bioinformatics

MedGenome offers a wide range of fast, high quality and cost efficient next generation sequencing (NGS) services to advance our clients’ genomic analysis needs.
We operate a CLIA-certified, CAP-accredited and ISO 15189-certified NGS lab in California. Our state-of-the-art facility is equipped with the latest Illumina NGS platforms including MiSeq, HiSeq 2500 and HiSeq X10.

Whole Genome Sequencing

Whole Genome Sequencing (WGS) provides complete information on genetic makeup of organisms, enabling researchers to study variations within the species and compare them with others which can help in solving unanswered puzzles in the genomics and providing fuel for research for biomarker discovery and personalized medicine.

WGS can reveal germline variation, somatic variation, copy number variation, changes in transposable elements, and structural variants.

Whole Exome Sequencing (WES)

Also known as targeted exome capture, Whole Exome Sequencing sequences the protein coding sequences of the genome (exomes) rather than the complete genome. It is estimated that the protein coding regions of the human genome constitute about 85% of the disease-causing mutations.

Exome sequencing is done to identify the functional variation that is responsible for both Mendelian and common diseases. Most of the diseases or phenotypes are caused by variations in coding regions, and so it is an alternative for whole genome sequencing based on a research question.

RNA Sequencing

RNA sequencing (RNA-Seq) is a powerful technique that allows researchers to study the complete transcriptome profiling. A transcriptome is a complete set of transcripts, which includes their quantities as available in the cell, for specific physiological conditions. A complete understanding of the transcriptome gives enormous information on the functional components of the genome, molecular components of cell, tissues and knowledge on disease development.

Different technologies such as hybridization-based, and sequence-based approaches, and specialised microarrays have also been used earlier to study the transcriptome, but they were found to not be very effective for large volumes of data. Development of RNA-Seq based on the high-throughput DNA sequencing method has solved that problem to a great extent.

miRNA Sequencing

miRNA Sequencing is also a type of RNA-Seq with the difference being that the input is enriched for small RNAs. miRNA-Seq enables researchers to study tissue-specific expression patterns, isoforms of miRNAs, disease relationships and to find out novel uncharacterized miRNAs.

With unprecedented sensitivity and dynamic range, small RNA sequencing methods allow for the most accurate detection and quantification of rare small RNA sequences.

ChIP Sequencing

ChIP-seq is a powerful method to map transcription factor binding sites and histone modification status on a genome-wide scale. This technique is a combination of chromatin immunoprecipitation assays with sequencing.

Main steps in the ChIP-seq include cross-linking a protein to chromatin, shearing the chromatin, using a specific antibody to precipitate the protein of interest with its associated DNA, reverse cross linking and finally purifying the associated DNA fragments.

Methyl Sequencing

Methyl sequencing is an approach developed to study the cysteine methylation patterns across the genome. Researchers are focusing on this technique as cysteine methylation has a remarkable effect on expression of genes, and is also linked to chromosomal stability and cellular differentiation.

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.

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 in what is done with 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. Bioinformatics Services

Sample Requirements
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%

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