Genome sequencing clinical interpretation help

Question

[vinch]

Hey there!

I'm beginner in bioinformatics, but need to analyse sequencing data of a child with ASD. Now I have few questions and will be appreciate for any help, contact or advise.

1. Can you please suggest a service, or a company that can make interpretation of raw full genome sequencing data (100x). VCF, CRAM, FASTQ available. Clinically there is an Autism Spectrum Disorder (ASD) symptoms, so it would be awesome, if the specialist/company have an experience in finding reasons of neurologic disorders, but I will be happy for any recommendation.
2. I tried promethease - it's easy and useful. As i understand promethease compares genome data to SNpedia database. Maybe somebody knows, what database are also need to be processed to make research completed? clinvar? something else? some alternative for automatic database analysis like promethease?
3. Usually geneticists want some text result of sequencing, and I can't understand how can 1gb vcf file with ~20k genes be converted to pdf? Does somebody have an example of such text result?

Thank you for attention

[cpad0112]

There are several companies that furnish clinical interpretation of data starting with raw data: sophia genetics, pieriandx, DNAstar, OncoDNA etc. In addition, NGS products (kits, panels, machines etc) selling companies like qiagen (QCI), Agilent offer end-to-end clinical interpretation services and they charge per report. Clinical annotation is in the context of the disease panel. Annotations are panel specific.

Text results in general can be reported as defined by standards like FHIR (earlier HL-7) CG templates. Reach out to some one local who knows how to report clinical variants within legal framework.

Answer 1

[swbarnes2]

Your best bet is a geneticist. But honestly, I do not expect that genetics will tell you anything about an autistic person that you couldn't learn better by observing the person and talking to them.

A geneticist should understand what a vcf is.