Clinical Genotyping

Targeted resequencing - focused assessment of key genes

With targeted resequencing, a subset of genes or regions of the genome are isolated and sequenced. Targeted approaches using NGS converge time, expenses, and data analysis on specific areas of interest. Such targeted analysis can focus on any region, i.e. specific genes of interest (panels), targets within genes or mitochondrial DNA, that are most likely to be involved in the phenotype under study.

Targeted approaches can also deliver much higher coverage levels, allowing identification of variants that would be too rare and too expensive to identify with whole-genome or Sanger sequencing.

GENE PANEL SEQUENCING

Targeted gene sequencing panels are useful tools for analyzing specific mutations in a given sample. By focusing on the genes most likely to be involved, these panels conserve resources and minimize data analysis considerations.

Panels can be predesigned containing important genes or gene regions known to be associated with a disease or phenotype, selected from publications and expert guidance. Predesigned panels are available for preconception carrier testing for severe, recessive childhood diseases, cancer, inherited disorders, cardiac conditions, and autism.

On the other hand, custom designs offer you the possibility to target regions of the genome relevant to your specific research interests. Custom targeted sequencing is the most suitable option for examining genes in specific pathways, or for follow-up experiments from genome-wide association studies or whole-genome sequencing.

Clinical exome sequencing

The clinical exome targets all protein-coding regions harboring disease-causing variants. Panel provides comprehensive coverage of ~5000 genes, present in HGMD, OMIM and ClinVar, associated with known clinical phenotypes. You can analyze all of the genes on the panel or choose to focus on a specific subset. This comprehensive test has a superior diagnostic yield in comparison to traditional approach of testing single genes or using low-density microarrays, and is becoming a common molecular diagnostic test for individuals with rare genetic disorders.  

In addition to variants in the coding regions, exome-sequencing offers the possibility of the detection of mitocondrial DNA (mtDNA) variants “gratis” from the exome off-capture reads. Variations in mtDNA sequence can be reliably obtained 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.

sequencing - DATA ANALYSIS - reporting

If not otherwise specified, we generate enough raw sequence data per patient so that at least 95% of targeted region is covered >20X. We developed a fully automated pipeline, benchmarked on the NA12878, Genome in a Bottle Consortium reference material of the US National Institute of Standards and Technology, which detects 99% of all DNA variants (SNPs, small indels and CNVs) within the targeted region of the genome.

Standard bioinformatic analysis includes:

• Base calling and demultiplexing
• Alignment to reference sequence
• Quality control and improvement of reads
• Variant calling and annotation
• On-target and coverage statistics and metrics
• 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 mtDNA variants 

CLINICAL Interpretation service

Besides variant identification, we also provide clinical exome data interpretation. In order to identify the potential disease-causing variants, a series of filters that are specific for each patient (family history, any differential diagnoses, and all relevant components of the patient's condition) are applied during the analysis. Data are presented to our Clinical Genomics Board which includes molecular geneticists, clinical geneticists, genetic counselor and bioinformatician. The Board reviewes and interprets the data, and releases the final report. In case no clearly causal variant is identified, the other potential disease-causing variants are kept for eventual future reanalysis as new findings are published in the literature. Additional sequencing of other family members may be recommended in order to assist with analysis and interpretation.

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.Extraction of genomic DNA from blood, saliva and buccal swabs can be provided.