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Bio-informatics for medical laboratory technologists
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2.7 years ago
Kizuna • 780
France, Paris

Hi Biostars Users,

I am writing here to know your opinion and if possible have some advices. I am currently preparing the syllabus of bio-info course for medical lab technology students. After discussion with the dean, he pointed out that the course has to fit with what the actual practice of medical lab students. He is not interested in opening new research horizons for students, ...

What do you think? What topics fit the most with the practice of medical lab technologists ?

All ideas and suggestions are welcomed,

Best

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I'm moving this to the forum, which I suspect is a better fit.

Anyway, could you define a bit more what sorts of roles a "medical lab technologist" fills in France? Given the differences in how the medical practice is structured between countries, knowing that will help increase how much on-target advice others can give.

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Moreover, do these student know any programming language? I would explain some statistics tool (R or SPSS, depending on their computational background), and the online resources such as medline, the ncbi databases, etc...

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No they do not have any programming background... they can work in hospital labs, to perform haematological, biochemical, bacterial tests and even genetic tests such as paternity testing, forensic..

medline, ncbi databases is a good alternative.. SNPs, haplotype analysis... what else do you think might be interesting ??

Thanks

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they can work in hospital labs, to perform haematological, biochemical, bacterial tests and even genetic tests such as paternity testing, forensic..

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As they do not have any computational background I would recommend mostly focusing on using bioinformatics databases: GenBank, Pubmed, Mitelman database, Cancer Gene Census, ... As for browsing and manipulating genomic data, the UCSC genome browser + Galaxy combination could be quite efficient and easy to learn.

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3.7 years ago
aurelien.t • 30
France

Hi,

I'm a resident in a french hospital genetic lab. Our technical team is very interested in the development of NGS in our lab, but as you say for your students, they have no programming skills, and we lack of relevant available training in bioinformatics for them.

So we started to make some kind of courses, and the most interesting things are the final uses of bioinformatics : the principle of the main steps of a NGS bioinformatic pipeline, the main formats of files, how to extract data from UCSC,...

The goal is that they can perform the technical validation of NGS in routine.

We really focus on constitutional genetic, but I'm very interested by what you'll can do !

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2.4 years ago
Garan • 570
United Kingdom

In the NHS diagnostic labs, the Genetic Technologists can sometimes report variants (up to and including targeted NGS panels) and collect evidence of the possible pathogenic status of the variant. This would mainly be trawling various databases (such as HGMD, dbSNP, OMIM, EXaC, Decipher) or using some online tools such as SIFT, Polyphen. Our NGS VCF files are annotated by Alamut Batch (although we have also used Annovar and other annotation sources such as Biomart), and the GTs use Alamut Visual / USCS genome browser to investigate the variants.

Possibly guidelines on the limitations of these databases / tools, something on the frequency of the variants in the various databases, maybe some information on constructing a family history and what genotypes you would be expecting. Something about compound Hets, CNVs (and how to find them, possible available tools like Conifer, ExomeDepth, XHMM etc, problems with using read depth when using amplicon based libraries), an idea of how a basic variant caller works, a rough guide on how the alignment against a reference genome works (just a general overview, you don't have to go into the guts of BWA MEM).

I should point out that most of the more complex reporting is done by the Clinical Scientists so many of the variants will already be characterised.

Overall more on the application of the tools rather than how to construct pipelines - which would be great but at what point do you stop?

Not sure how the French genetic labs are set up, but the UK labs are moving towards having dedicated Bioinformatics staff to set up the NGS analysis.

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4.9 years ago
alexcd201403 • 30
USA

well, aurelien.t is very helpful. I think it's quite right for you just directly go some medical labs and try to ask some technologists' opinions, do some research, you will find a lot. while in here, you have to waite so long for the answers.

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