Product Code:  MGM929
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Whole Genome / Whole Exome Sequencing

Whole Genome and Exome Sequencing using NGS have been widely accepted to speed up and reduce the cost of sequencing genomes for basic research as well as use of genomic data for a wide range of applications : genome wide association studies for complex diseases, variant calling to identify clinically actionable mutations and other specialized areas like identification of mutations that accumulate and give rise of tumor neo-antigens and shared antigens. At MedGenome we routinely perform Whole Genome Sequencing and Exome Sequencing and analyses using best practices.

Table 1 : Sample types processed for WGS/WES at MedGenome.

Sample TypeDNA (WGS/WES/Targeted)
Extracted Nucleic AcidMinimum: 200 ng (WGS/WES) 50 ng (Targeted)
Frozen Cell PelletsMinimum 1 x 106 cells (ship on dry ice)
Frozen Tissues30 mg frozen tissue or 20 mg stabilized tissue (ship on dry ice)
FFPE Slides5 slides (10 μM thick) 250 mm2
Curls5 curls (10 μM thick)
Single-cellFresh or cells in sample prep agent

Table 2: Deliverables for analyses of WGS/WES data

Standard Analysis OfferingAdvance Analysis Offering
Data QC (Read orientation, quality distribution, base distribution and GC distribution for all reads)CNV analysis
Alignment to the reference genomePathway analysis
Coverage analysisDeep variant annotation
Variant calling (germline/somatic calling)Mutational burden analysis
Variant AnnotationVariant interpretation

WGS germline calling validation

Total number of SNPs and Indels predicted using different flavour of GATK on two different datasets

DatasetGermline Variant Caller#of SNPs#of IndelsTotal
Gold StandardGiAB3,193,799391,6213,585,420
Illumina HiSeq XGATK - Lite - 2.3.9 -UC3,191,291380,7683,572,059
Sentieon - 3.5 -HC3,213,528393,8033,607,331
Sentieon - 3.5 -UC3,230,950379,2203,610,170
GATK - 3.6 -HC3,184,106388,1923,572,298
GATK - 3.6 -UC3,191,477376,6883,568,165
Illumina HiSeq 2500 PublicData (NIST)GATK - Lite - 2.3.9 -UC3,198,322383,9523,582,274
Sentieon- 3.5 -HC3,215,682397,5773,613,259
Sentieon - 3.5 -UC3,242,040386,3973,628,437
GATK - 3.6 -HC3,186,676393,3003,579,976
GATK - 3.6 -UC3,198,478383,9173,582,395

Sensitivity for SNV detection of our pipeline exceeded 99% at 30X-50X WGS coverage and was over 99% for the detection of Indels at 50X WGS coverage.



Figure 2 : Validation of WGS/WES pipelines using Gold Standard datasets

Results from our analysis meet industry standards and FDA challenge results.

We have recently added the 10X Chromium platform to our offerings and can perform 10X linked reads Whole Genome Sequencing, and analysis as well as de-novo analysis using the 10X software solutions.

Sample Report

Sample Test Report

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Tags: Whole Exome Sequencing, Exome, Exome sequencing, genetic, genetic tests, mutations, DNA

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