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.
|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|
|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|
|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.
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.