I don't think its not used because there are no "standarts in data analisys and workflows" as you say. The main reason is the purpose and cost. What you want to do with NGS in clinical analysis is a big factor. Do you yourself has an idea how you can use NGS in your clinical medicine studies? And although sequencing is getting cheaper and cheaper, yet, the whole process of sample prep, sequencing and data analysis is still expensive.

Dear Abhijeet Singh, thank you for your opinion.

1. Of course i agree with you regarding costs. NGS testing is not a cheep approach.

2. Regarding purposes. Unfortunately in my country NGS is not popular because of cost. But in the field of onclogy (molecular profiling of tumors) many people have enough funds for pesonalization their treatment and covering all expences for targeted medicine.

3. The main direction of NGS implimentation that works in real life of people is myeloid panels (targeted DNA panels) and sometimes comprehencive cancer panels (like qiagen provides).

4. Today my general direction is 16S metagenomics testing with NGS as preventive factor (colon cancer). As well as prognostic factor in transplantation. It is not validated protols now, but we work at this. The price in the case of 16S metegenomics is about 100 USD or less (depends on loading in 1 run). I hope that in the nearest future we reached the validation because we have not bad results. This year and 2020 will show us the real results.

We do NGS for panels and exomes for hereditary disease as well as panels for oncology. The amount of genes that have to be analysed and might be contributing makes it very hard or impossible to realise the testing with other methods like Sanger. If you create small enough panels and have a throughput that use a sequencer to capacity it is also quite cost effective given that you take into account the labor that you save by multiplexing many samples.

I also don't concur with your opinion that there are no standards. There are many software solutions out there and different sequencing machines, but in the end it comes down to the quality of your results. And these are standardised. There are also best practice pipelines and Reference samples that can be used for validation.

Have a look at these:

Article ACMG clinical laboratory standards for next-generation sequencing

Article Best practices for benchmarking germline small-variant calls...

Article Standards and Guidelines for Validating Next-Generation Sequ...

Dear Daniel Becker, thank you a lot for your participation.

Yes, may be I was incorrect regarding standards. But regarding clinic I have to notify that we have recommendation and national standards. Indeed, in the case of recommendation we have enough volume of information, but (in my country) we haven't any standard protocol for diagnostics and treatment of cancer (and other) patients with help of NGS-based approaches.

On the base on my experience the brst way for introduction of a new methodology is approval by national standards. In our case we use NGS not so frequent as we have to. That is the main problem as I think.

Do you have the same situation? Some ways to solve it? Now it is cheep enough to use in routine clinical practice in the field of oncology as I think.

Thank you for examples of standards. I saw a few another todays morning. I am going to improve my base in this field.

I think there is a same story about Maldi tof ms.

This machine and technology was used by researchers but now many countries use it in hospitals.

In the best of my knowledge if you make a laboratory of information of genes in your country, it can be use easily with very lowest price.

Regards.

Dear Alireza Mordadi thank you for your answer.

I am not sure how it evolved here, but finding SNVs with NGS and just confirming the few relevant ones with sanger is faster and cheaper than to do a broad search with sanger. So if sanger is an accepted method, you can do NGS as "screening" in the background and report your sanger findings/confirmations.

The variant you report is the same and so is any downstream diagnostic or treatment.

The more people do it this way, the more popluar it gets, the higher the change of NGS becoming a standard

Dear Daniel Becker, thank you again for your comments. Your opinion is important. Now in my country the costs on Sanger and MiSeq based NGS is 30 USD per 800 bp and 200 USD per cancer panel (24 samples in 1 run) respectively.

Of course, Sanger is a gold standard and 30 USD for 1 SNP it is conviniend price. It is routine in our National Cancer Center to provide any patient a possibility to check tumor for KRAS, NRAS, EGFR for free (covered by goverment) by Sanger. It is ok in the case of known diagnosys and clear understanding of treatment strategy on the base on national standardts, ESMO or NCCN recommendations.

Unfortunately, in the majority of cases we receive as a result - resistant clones. ctDNA monitoring is not introduced in routine practice yet. On the other hand we can reseive tumor profile on the base on NGS testing and combine all received data to improve strategy. In the case of Sanger it is about 100-150 USD for several SNPs.

Hi Andrei S. Babenka ,

In my country (India) NGS is widely used in many clinical cases including oncology and hereditary genetic diseases.

There are private molecular diagnostics labs, who provides NGS based tests at reasonable rates.

To mention about the absence of "standards" there is an autonomous body, CAP, which sets a set of standards, which are to be maintained while performing NGS based tests.

you can refer this link for more info: https://www.cap.org/member-resources/precision-medicine/next-generation-sequencing-ngs-worksheets

The following link have details about NGS based tests performed by a private molecular diagnostic company :

https://diagnostics.medgenome.com/complete-testlist