The most widely used targeted resequencing method
IGATech has been a reliable, professional and helpful service provider since the start of our collaboration. In addition, their staff has always been friendly and willing to exchange knowledge and experiences.
Variations in mtDNA sequence can be reliably obtained "gratis" by using any exome sequence capture kit. This possibility offers the prospect of using exome sequencing as a comprehensive single diagnostic test to detect pathogenic point mutations both in coding nuclear genes and in mitochondrial DNA. A minimum per-mtDNA-base coverage threshold of 20X ensures that the vast majority of mtDNA SNVs are detected. Coverage correlates with the relative amount of mtDNA in the original genomic DNA sample, thus majorly depending on the tissue from which DNA was isolated.
we perform exome capture and resequencing of other species, including mouse, bovine, canine and zebrafish
We use different commercialy available exome capture systems (Illumina/NimbleGen/Agilent). Upon the sample QC, DNA fragmentation, barcoding and targeted enrichment, libraries are sequenced in a paired-end mode on a HiSeq2500 producing 125 bp reads or on a NextSeq 500 producing 75 bp or 150 bp reads. Sequencing depth is optimized to meet your requirements.
In our continuous commitment to implement the state-of-the-art procedures we are optimizing library preparation with 10XGenomics Chromium System, which uses the power of linked-reads to fully resolve genic phasing, structural variation, and detect variants in previously inaccessible and complex regions of the exome.
The exome and targeted sequencing service provided by IGATech are of high quality. They also provide a substantial and versatile bioinformatics support that is very helpful for prioritizing exome sequence variants.
DATA ANALYSIS
We developed a pipeline that fully automates the process of variant detection from alignment of produced reads to identification and annotation of SNPs and short indels to reveal common and rare variants. The pipeline was benchmarked on the NA12878, Genome in a Bottle Consortium reference material of the US National Institute of Standards and Technology, to assess variant-call accuracy.
Standard bioinformatic analysis includes:
- Base calling and demultiplexing
- Alignment to reference sequence
- Quality control and improvement of reads
- Variant calling and annotation
- Quality Control - on-target and coverage statistics and metrics, asses the efficiency and the lack of bias in the enrichment process before performing downstream analysis of the sequence data
- Variant summary report including variant functional annotation, its clinical significance (ClinVar), phenotype ontology data (HPO), prediction of possible impact of an amino acid substitution on the protein structure and function (SIFT, PolyPhen, LRT, MutuationTaster, PhyloP and GERP++scores), dbSNP identifiers, allele frequencies (1000 Genomes Project, NHLBI-ESP 6500 exome project and ExAC), and many other information
- Annotated SNPs and small InDels in an Excel-compatible file
Advanced bioinformatic analysis includes:
- Family trio analysis - for de novo mutations, deleterious recessive mutations and genes which may be affected by compound heterozygosity to rapidly identify a short list of candidate mutations (results in an Excel-compatible file).
- Matched tumor/normal pair analysis - to identify germline and somatic mutations useful for the diagnosis, treatment and prevention of cancer (results in an Excel-compatible file)
- Identification of mitochondrial DNA variants
We also provide full support on study design to ensure correct sequencing and bioinformatics strategies are used to meet your project goals. Our expert will consult with you about your specific requirements, and will also be your technical resource and point of contact for the length of your project.
