NGS Services

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 Type DNA (WGS/WES/Targeted)
Extracted Nucleic Acid Minimum: 200 ng (WGS/WES) 50 ng (Targeted)
Frozen Cell Pellets Minimum 1 x 106 cells (ship on dry ice)
Frozen Tissues 30 mg frozen tissue or 20 mg stabilized tissue (ship on dry ice)
FFPE Slides 5 slides (10 μM thick) 250 mm2
Curls 5 curls (10 μM thick)
Single-cell Fresh or cells in sample prep agent
Table 2: Deliverables for analyses of WGS/WES data.
Standard Analysis Offering Advance Analysis Offering
Data QC (Read orientation, quality distribution, base distribution and GC distribution for all reads) CNV analysis
Alignment to the reference genome Pathway analysis
Coverage analysis Deep variant annotation
Variant calling (germline/somatic calling) Mutational burden analysis
Variant Annotation Variant interpretation

WGS germline calling validation

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

Dataset Germline Variant Caller #of SNPs #of Indels Total
Gold Standard GiAB 3,193,799 391,621 3,585,420
Illumina HiSeq X GATK - Lite - 2.3.9 -UC 3,191,291 380,768 3,572,059
Sentieon - 3.5 -HC 3,213,528 393,803 3,607,331
Sentieon - 3.5 -UC 3,230,950 379,220 3,610,170
GATK - 3.6 -HC 3,184,106 388,192 3,572,298
GATK - 3.6 -UC 3,191,477 376,688 3,568,165
Illumina HiSeq 2500 PublicData (NIST) GATK - Lite - 2.3.9 -UC 3,198,322 383,952 3,582,274
Sentieon- 3.5 -HC 3,215,682 397,577 3,613,259
Sentieon - 3.5 -UC 3,242,040 386,397 3,628,437
GATK - 3.6 -HC 3,186,676 393,300 3,579,976
GATK - 3.6 -UC 3,198,478 383,917 3,582,395

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


snpMetrics

indelMetrics

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.

Considering Genomic Research?
*
 
*
*
 


2019 © MedGenome • All Rights Reserved