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7.8 years ago
blueberry
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0
Hello! I'm totally new here and new to next-gen sequencing so please be understanding if my question is obvious. :) I need to know what exactly I can read from next-generation sequencing data, what I can find there that can be important for the diagnosis of genetic disease. I'm sure I can learn what are the gene names, number of the chromosomes, genotypes but what types of mutations can I read from it? All of them or only specific? What else can I learn? What can be useful information for a doctor? There's a lot of information on the Internet, a lot of articles and I can't find any specific, precise information. Is there any literature that I can learn from?
Sequencing is a technique to read the sequence of nucleic acids (DNA). Information that one can derive from that sequence is going to be dependent on the kind of analysis that is being done with that raw sequence. By looking at raw sequence data one can learn nothing since that is just a string of A/C/G/T.
Sounds like you are a physician yourself. You may find a book like this useful (The Busy Physician’s Guide To Genetics, Genomics and Personalized Medicine By Kevin M. Sweet, Ron C. Michaelis).
You may also be interested in this perspective by Dr. Robert Green (PI of the MedSeq project).
Thanks a lot! That's very helpful. :)
First of all, what type of NGS? That's a rather broad term. Talking about RNA-seq, chip-seq, whole genome sequencing, whole exome sequencing, targeted gene panel sequencing,...? I assume NGS is a synonym for illumina sequencing in most cases. I do not like the term NGS but it's so damn popular that I'll have to accept that :p can't we talk about massive parallel sequencing by synthesis instead? ;)
So true. I actually like your terminology. I'm going to start using it. :)
As for blueberry's question, it is so vast, vague and muddled that it is impossible to answer. Here is an attempt, assuming that the question is about Exome-Seq data and the variants found in this data. NCBI has tried to categorize all human SNPs in one database, dbSNP. NCBI has also tried to categorize all clinically relevant SNPs in one database, ClinVar.