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Exome sequencing or Trio analysis Rapid and Cost-effective Solution for Exome Analysis

Exome sequencing is the most effective way of studying coding regions of the genome. Humans have about 20.000 protein-coding genes, constituting only about 1,5% of the genome but up to 85% of disease-causing mutations can be located within exome.

Exome sequencing enables to identify common variants (SNV), copy-number variants (CNV), small insertions or deletions (InDel) and even rare de-novo mutations.

SEQme s.r.o., Dlouha 176, 26301 Dobris, Czech Republic www.seqme.eu | ngs@seqme.eu

Exome from 855 EUR

… worth

thinking about!

SEQme Service lab

• Project design

• Direct consulting with our lab specialists and

bioinformaticians

• Fast sample turnaround

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Four trios were analyzed in this study, all with comparable results. Data were provided as vcf files, variant tables including annotation, and detailed laboratory report. SEQme does not perform clinical interpretation of obtained results.

Example data

Standard exome trio analysis using Ion AmpliSeq™ Exome RDY panel on Ion Proton, ~ 90 million 200 bp-reads, average read depth ~ 110×, 99% alignment to reference sequence.

Optimal pooling Three exome libraries

in equimolar ratio (coefficient of variation

3,6%)

Coverage More than 90 % bases covered at least 20×

Chromosome coverage: Excellent uniformity

Variant calling: At your

fingertips

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SEQme s.r.o., Dlouha 176, 26301 Dobris, Czech Republic www.seqme.eu | ngs@seqme.eu

When ordering exome sequencing, SEQme recommends sending samples from complete trios, typically a child and his or her parents, whenever possible. Having data for a complete trio significantly increases the odds of a definitive result (when compared to a single exome sequencing) namely because of:

• More accurate variant calling at all positions

• Enhanced ability to make variant calls in low-coverage regions

The accuracy of variant calling is improved, because at any given position you are effectively sampling four independent alleles, two from each parent, a total of six times. Variant calling is performed on all sequenced family members. This allows for more accurate calls in all three family members, but especially in the child, whose variants—with the exception of de novo changes—are inherited from his or her parents. The second factor that contributes to increased success with trios is the enhanced ability to make calls in low-coverage regions. Variant calling from next-generation sequencing data requires adequate read depth. However, in the case of multiple sequenced family members and for the same reasons as described above, it is possible to call variants at suboptimal coverage levels, thus improving sensitivity with minimal negative impact on specificity. An example of this scenario is presented in a simplified alignment view from IGV. None of the three sequenced family members are covered to an adequate depth for accurate variant calling when viewed individually, but when processed in combination, the top and bottom samples are correctly called for heterozygous changes.

Why Exome Trio?

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SEQme s.r.o., Dlouha 176, 26301 Dobris, Czech Republic www.seqme.eu | ngs@seqme.eu

Interested in exome sequencing?

SO-010 Trio whole exome sequencing (Includes Sample QC, Exome library prep for 3 samples, Ion Proton single end sequencing, 200 bp, 60-80 million reads, vcf file + annotation)

SO-020 Duo whole exome sequencing (Includes Sample QC, Exome library prep for 2 samples, Ion Proton single end sequencing, 200 bp, 60-80 million reads, vcf file + annotation)

Contact us ! Petr Vacha, ngs@seqme.eu, cell: +420-606153030 See also www.seqme.eu for sample submission guidelines, pricing etc.

Testimonials Romana M., VUVeL Brno, Czech Republic Thank you for your complex services regarding our Next-Gen seq project. I deeply appreciate especially pre-project consultation and help with data analysis. We will definitely continue in this cooperation. Nicklas B., Chalmers University of Technology, Sweden I am very content with the data you provided, so it is quite likely that I will use your sequence service in the future. Inga M., Department of Zoology, Swedish Museum of Natural History Thanks for the great support so far already, this is really an asset.

You know what you want. We know how to do it.