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.

Highlights of our services are:

  • Support with experimental design
  • Experienced in processing a wide range of sample types with options for low input and/or degraded samples
  • End to end solutions for extraction, library preparation, sequencing and bioinformatics analysis
  • Provide basic and advanced bioinformatics analysis and data interpretation

Whole Genome Library Prep, Sequencing, and Analysis Service Offerings

Source Library Prep Options Analysis Offering
  • Cells
  • Tissues
  • Blood
  • FFPE
  • Curls
  • Purified gDNA
  • Illumina Truseq Nano
  • Illumina Truseq PCR-free
  • Illumina DNA Kit (Nextera Flex)
  • Nextera XT
Standard Analysis:
  • Data QC (Read orientation, quality distribution, base distribution and GC distribution for all reads)
  • Alignment (BAM file)
  • Variant Annotation (germline/somatic)
  • Somatic Mutation Analysis and Interpretation
Advanced Analysis:
  • Denovo Whole Genome Assembly
  • Low Frequency Variant Analysis
  • Joint Genotyping
  • Structural Variant Calling
  • CNV Analysis - Tumor/Normal, Germline
  • HMW gDNA
  • Blood
  • 10X Whole Genome Linked reads
    (check for service availability)
Long-range analyis of phasing of SNVs, indels, and structural variants

Whole Exome Library Prep, Sequencing, and Analysis Service Offerings

Source Library Prep Options Analysis Offering
  • Cells
  • Tissues
  • Blood
  • FFPE
  • Curls
  • Purified gDNA
  • Agilent SureSelect Whole Exome - Mouse and Human
    (Kapa, IDT and other WES kits are available upon request)
Standard Analysis:
  • Data QC (Read orientation, quality distribution, base distribution and
    GC distribution for all reads)
  • Alignment (BAM file)
  • Variant Annotation (germline/somatic)
  • Somatic Mutation Analysis and Interpretation
Advanced Analysis:
  • Low Frequency Variant Analysis
  • Structural Variant Calling
  • CNV Analysis - Tumor/Normal, Germline
  • Mutational Burden Analysis

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 WGS coverage and was over 99% for the detection of Indels at 50X WGS 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.

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