Best configuration workstation for our lab

Question

[vasanthmandla]

Hello,

We currently have Ion torrent S5 sequencer in our lab. We wanted to use it for NIPT (Noninvasive prenatal testing) and later on we want to use it for clinical exome and whole exome sequencing.

Q1) Is it best to have a workstation if so, kindly suggest the best possible configuration for the above applications

Q2) OR is it best to use AWS for the analysis rather than buying a workstation (we are planning to use the AWS to store the raw data), we do not have any server at present.

Thanks in advance.

[cpad0112]

2) NIPT panel is a small panel. I would rather go with on-premises server.

[vasanthmandla]

Hi cpad0112,

Yes, currently we are focusing on NIPT but we eventually want to use it for other applications too.

Answer 1

[GenoMax]

we are planning to use the AWS to store the raw data

Then it may be best to use AWS to do compute (if your budget/local security restrictions allow it). a) You will be paying for moving data around, if you want to analyze locally. b) You will have the flexibility to use a different configuration if compute needs change with size of data c) you will not need to worry about system admin, if you are only going to spin VM up when needed. d) you will only pay for resources you will use.

Answer 2

[Michael]

These questions come up all the time, even though people should ask their IT support about them. Some important points here: New Work Station for the Lab

About your thoughts on using AWS or edit (other open clouds), I know this depends on the jurisdiction, but if you do that in Europe you can already start saving and looking for a very good lawyer to keep you out of jail (maybe a bit exaggerated, but processing human data in uncertified cloud solutions is pretty much out of the question).

[GenoMax]

but if you do that in Europe you can already start saving and looking for a very good lawyer to get you out of jail.

Surely that is not a blanket case? Whether one likes it or not cloud computing is the future (even funding agencies are embracing it). Can you point to EU policies/laws that prohibit this (there may be country specific restrictions but entire EU sounds a bit unrealistic). I am curious to know.

[Jean-Karim Heriche]

Indeed, this is a bit exaggerated. The laws vary by country and in the absence of clear guidance, most people take the safest path of keeping clinical data within the hospital's walls. However, there's a lot of activity within the various European Open Science Cloud (EOSC) projects on sensitive data to figure out what's possible and come up with guidelines. As an example, in the EOSC-Life project, we're running a cloud-based sensitive data project. Similar things are also happening in the context of GA4GH. Obstacles multiply if you attempt to do any kind of cross-border work. For example if you want to use cloud resources in Germany, the only legally binding documents are in German. Then lawyers from other countries won't allow you to sign them because they don't understand them and a translation is not legally binding. And that's not saying anything about what kind of data you can or can not move across borders.

[Michael]

There is a similar infrastructure in Norway called TSD: https://www.sigma2.no/sensitive-data-services These are in fact "cloud infrastructures" for exactly doing these kind of things, and they are made to comply with European and national legislation for sensitive data. There are indeed different ways of making a cloud.

[Michael]

Also, note that I am not arguing against "cloud" here (that would be utterly stupid, however my original wording might have been less clear) or whether strict data privacy legislation is "good" or "bad". I am just saying that it is good to be aware of legal implications of your actions regarding data that belong to others.

[GenoMax]

I will respond here instead since both Michael Dondrup and Jean-Karim Heriche have interesting comments above.

I went looking a bit to see what the situation is in EU. I found this report that seems to consider/allow use of cloud computing even in clinical setting. https://www.enisa.europa.eu/publications/cloud-security-for-healthcare-services/at_download/fullReport

No doubt there will be interesting legal issues (case of translation mentioned being one). Unless people find a way to work across borders we may end up with more silos/difficulty in facilitating health care across EU.

[Michael]

Excellent, thanks. The conclusion of this report is, IMO, if one reads through it, and understands all implications and technical challenges, then carefully analyzes the task at hand, conferes with legal council and clarifies institutional responsibility, one could set out to finally plan migration of sensitive data into a cloud solution. In short, way above my pay grade.

[4galaxy77]

Perhaps because this is 'Noninvasive prenatal testing' and sounds clinical rather than strictly research?

[vasanthmandla]

Hello 4galaxy77,

Yes, this is for clinical use only.

[Michael]

Note: this comment is off-topic, because OP is seemingly located in India.

Of course, I am not a lawyer and I am not saying anything against cloud computing. Look through the GDPR for example https://gdpr-info.eu/ and then explain to me how human genetic data is not human personal data (following which I cannot even process personal in the USA) for me and then please give me a blanket guarantee that I'm safe to process clinical data like that without the fear of prosecution :)

Article 9:

1. Processing of personal data revealing racial or ethnic origin, political opinions, religious or philosophical beliefs, or trade union membership, and the processing of genetic data, biometric data for the purpose of uniquely identifying a natural person, data concerning health or data concerning a natural person’s sex life or sexual orientation shall be prohibited.

2. Paragraph 1 shall not apply if one of the following applies:

[...] (h) processing is necessary for the purposes of preventive or occupational medicine, for the assessment of the working capacity of the employee, medical diagnosis, the provision of health or social care or treatment or the management of health or social care systems and services on the basis of Union or Member State law or pursuant to contract with a health professional and subject to the conditions and safeguards referred to in paragraph 3;

1. Personal data referred to in paragraph 1 may be processed for the purposes referred to in point (h) of paragraph 2 when those data are processed by or under the responsibility of a professional subject# to the obligation of professional secrecy under Union or Member State law or rules established by national competent bodies or by another person also subject to an obligation of secrecy under Union or Member State law or rules established by national competent bodies#.

# personal comment: don't think this applies to Jeff Bezos

So there is European regulations and member states may even set stricter requirements. However, this drags us off topic slightly, because I think OP is situated in India and other rules may very well apply there.