Next-Generation Sequencing in MLS Practice

What if the future of diagnostics isn't just coming? What if it's already here, hidden in the strands of DNA and decoded by the medical laboratory scientists? Welcome to another episode of LabCast. my name is daniel your host for today and i'm joined by my co-host jesus tommy singh today we are diving into one of the most revolutionary technologies transforming modern lab practice

Next Generation Sequencing, or NGS for short. It is no longer just for research labs. It is shaping everyday diagnostics and medical laboratory scientists are at the heart of it. If you've ever wondered how genomics fits into your bench work, what skills you need to stay ahead, or where NGS is headed next, this episode is your guide. And thankfully, we have Mr. Emmanuel Owoeye. to explore these subjects with us now before we continue here is a little introduction about our guests

Emmanuel Oweye is a molecular biologist with a strong interest in next-generation sequencing and its role in modern diagnostics. He is trained and taught molecular biology and bioinformatics. helping others understand the emerging lab technologies. Emmanuel is passionate about bridging science and healthcare through education and accessible genomic tools. You're welcome Mr. Emmanuel.

Thank you, Mr. Daniel. Hello, everybody. Thank you also for joining us today. So to kick things off, when someone hears next generation sequencing, what should they picture? is it like a method a tool or a revolution or all of the above uh so for me i want them to i want people to hear of mgs and think it's It's a tool? Yes. However, it's a tool that is currently changing the way we see diseases. It's changing the way we approach genetic sequences.

So, yeah, it's a tool and also a revolution. All right, so NGS is more than just a method, you understand? It's more than a tool. Imagine prior to now, we relied on... uh morphological classification of diseases we understand without really paying attention to uh the molecular mechanisms that actually uh the molecular undertones that are responsible for the change in diseases but now with the advent of

uh naturation sequencing that has made sequencing of uh genesis sequences faster and easier we've been able to understand the molecular mechanisms responsible for different diseases so yeah it's a tool for consider the fact that it's change it is changing our sequence it is also a revolution like a dual well let me say multi-purpose or multi-facet um phenomena

All right. How would you describe the journey from Chinese genetic testing to NGS? Because I know that there must be a revolutionary history behind us. Was it a gradual or more of a scientific leap? It's a little bit of both, you understand. Usually, when we talk about sequencing before the advent of this, we used to talk more about SANGA sequencing, SANGA sequencing, SANGA sequencing. SANGA sequencing leads the foundation for whatever national sequencing will do.

you know how they say uh something worked so that the next could fly so saga sequencing did uh it worked crowd it probably ran for next generation sequencing so you know to be able to fly so it's a gradual build-up based on the little advances, the little changes that we could make to SANGA sequencing until next generation sequencing just.

you know it came up and blew all over the earth. The Human Genome project was primarily done with Sanger sequencing and that cost a whole lot of money and a whole lot of time you understand but now if we are going to use NGS to do the same thing on the Imaginium projects, it will cost us less and it will cost us less time. It cost us less money and less time. So yeah, it's a leap that was founded.

on gradual processes let's look at it that way it's a leap ngs itself is a leap but then it was built on the gradual progress that was made from traditional genetic testing

That's very interesting and very noteworthy. But in genomic, we hear about a lot of things coming up recently. What would you say are some of the most exciting breakthroughs that NGS is enabling right now in the field of genomics? What is that thing or what are those things that they are so exciting and, you know? It's really interesting to look forward to regarding NGS and genomics. So, for me...

When we talk about amazing breakthroughs that NGS has enabled, I'm going to first talk about real-time disease surveillance. For example, COVID-19, the COVID pandemic that happened in 2020. I feel like... most of the prevention, most of the things we could do to prevent the worldwide spread. was as a matter of the sequencing the engineering sequencing technology that was available then you understand initially we had the main string the alpha string and then

if we notice that, oh, there's another strain that is probably a little bit of morphological changes or a little bit of a change in the molecular mechanism behind the sequences. And before you knew it, we were able to have more than six strains. We had the Pan-African, we had the Delta, we had the Omicron. Like, I don't think there has ever been any viral pathogen that, you know.

uh made that kind of leap into humans and we were able to you know we were able to pick different variants uh within a very short period of time so and most of this was actually uh can be attributed to the mid-generation sequence that was available. Then another thing is cancer genetics, especially precision oncology, are proud to understand the molecular mechanisms that different cancer cells have.

We used to rely on morphological changes. We used to rely on the changes in the cells. We had to first look at the cellular hallmarks. So we couldn't attack cancer cells before. before it became full-blown cancer. You understand? But now we are able to understand some molecular mechanisms. We are able to understand genetic changes. We are able to understand mutations in some tumor suppressor genes.

as well as phone cogens and then we can predict that oh you have a mutation in this tumor suppressor gene it's expected that further down the line you will uh yeah genetically predisposed to this form of cancer we are able to introduce lifestyle changes for people who have not developed cancer and for people that have developed cancer we are able to precision oncology is coming onto the screen now where we can tailor

treatments to individual types of cancers and also another thing is the CRISPR-Cas9 system that is widespread that is currently coming up onto the scene now is because hope.

we are now able to you know sequence these people's genes we are we are able to understand that okay this gem this mutation is what's responsible for this disease so we are able to you know sequence an alternative gene that we can use to introduce probably the knockoff or the knockouts to knock off knocking in aging or knock out the defective gene so here precision oncology real-time pathogen testing as surveillance and prevention

as well as non-invasive parental testing. If your child is going to be genetically predisposed to some diseases, we're able to just get a very minute cell in a non-invasive manner and then we're able to test.

we're able to predict we're able to uh you know advise you on the kind of genetic challenges if possible that your unborn child we have so yeah i feel like for me those breakthroughs are very mind-blowing and measure sequencing thank you mind-blowing innovations through ngs it's so amazing solving human problems in so many ways so you know um when we talk about ngs you mentioned it as a tool as a scientific clip so what kind of equipment or software

does a lab need to actually perform in GS? And how different is this from what we are used to in a routine lab? So first things first. for you to do your next generation sequencing you need a sequencer that is built on the next generation sequencing platform I think currently the two mainstream ones are Illuminar Sequencers and Oxford Nanopore. They are based on the same parallel sequencing technology.

okay another thing for measuring sequencing is parallel sequencing technology you're able to sequence uh a genome uh using parallel a parallel we're able to do multiple uh assays at the same time so you have the Illumina and the oxford nano4 and then you need the basic setup for a molecular lab you need your high quality effects you need your reagents for your library preparation and

a lot of computational infrastructure. As a matter of fact, if you're setting up a sequencing lab, you will need a lot of computational infrastructure because whatever it is you're... uh sequencers are putting out you will need uh computational power as well as by informatics you understand to be able to analyze whatever data you are getting so and

why do you need a lot of computational power data skill and complexity are wide apart for SANGA sequencing SANGA sequencing is usually accurate for between 500 approximately 500 space you understand compared to ngs where you're sequencing millions you understand so your data skills are

the data scale is wide and then the complexity is also a lot. So typically in sequence for NGS, the first thing you have to do that is like, I feel like this step is the bedrock of whatever you're doing in molecular biology. sample extraction extraction of your nucleic acid whether rna or dna from your from the cell then quantification and quality checks you don't want to start

your next processes unless you are sure that you've extracted high quality DNA and high quality and a significant quantity of DNA. You can't trade one for one. you need it to be high quality and you need the quantity to be optimal and then the next thing is you do your library preparation you fragment your nucleic acid whether DNA or RNA then you add your adapters and then you run your sequencing again

Most of your heavy work, the heavy lifting comes after your sequencing. That's when we talk about, you align your reads, you do the gradient calling, interpret your results, and then you talk about... different bioinformatics analysis that can come into play. Whatever it is you want to do, you now have your data. You now have your sequencing data. It's up to you to do whatever it is you want to do with it.

right that's so robust so speaking about workflow right what kind of sample are we dealing with here is it like a raw human sample what kind of sample what kind of origin and can you briefly describe from sample to analysis what are the steps to take

and walk us through a typical day in the life of a molecular biologist working on NGA's Microsoft tool or something. Okay. For me, I do more with... viral samples edema of viral particles so i'm going to be using a day in the life of somebody working as a virologist so i think the first thing you do is uh whatever kind of samples usually i do with blood samples particularly the serum from the blood so uh you get the serum and then you know different organizational matter is for us we log

the we log the samples so we assign a code to it the name okay we assign a code i like to tell people that once your sample gets to my lab i don't know your name i only assign a code to it and throughout the processes, I only know, I can only refer to you by your code. So after that, you do your nuclear acid destruction, usually with the advent of different kits, different commercial kits now.

I don't think there's any lab that uses the traditional method. So most people use kids. And then after your DNA instruction, you use, you do your quality check, the quantification of the quality check. For us, I think I'm only familiar with the NanoDrop quantification system. And then after that, you're done with the nucleotide description.

The next thing you need to do is your library preparation for your NGS. You fragment DNA if it's already fragmented. You do your PCR amplification. PCR is another... technique that revolutionized molecular biology. In case you don't know, Kareemulis is one of my heroes. I like the guy a lot. Big ups to him for the PCR technique.

then you do your PCR application and clean up. And yeah, please, if you are going to be doing NDS, you need to actually pay attention to your PCR application and the clean up step. Very important. and then you incubate your samples. Then after that, you do your library selection for your NGS and then you normalize concentrations.

And then once you are done preparing like those, you load it into your NGS equipment. And then you input your sample sheets. You set the parameters that varies from kit to kit. And then you start your sequencing. And at that point, I want to believe, as we always say, the rest is in the hand of God. Whether your wrong will be successful or not is between your processes, the machine and God.

then after that you just keep monitoring your room you know it's time to check if everything is going properly and hopefully before you close that day your run is ready if not you can leave it to run till the next day is expected that your uh your facility has uh is it possible power supply so that nothing shuts down mid-run so that is actually the end of

whatever it is you are going to do what is next is your bioinformatic analysis you understand that your run is done you just have to do the quality then read the alignments to the reference you know And then if there's differences, variations, check them out through variants, calling, and then check your, quantify your gene expression. And that is all. The rest is for the clinicians or the owner of data.

Usually, you might not own the data you're working with. You're probably sampling for people. So you let them know that, oh, this is your results, and then they are able to do whatever it is they want to do with their data.

wow wow wow that sounds that sounds very interesting i'm sure it's a lot of work but yeah it still sounds very interesting and personally i would love to experience what it's what it is like you know being in a molecular lab like that even here in nigeria and so i'd just like to ask that you you share with us some real life examples of you know

something that you've experienced whereby NGS made a critical difference in diagnosing or treating a patient and other facilities in Nigeria that carries out these processes do we have facilities you know that actively carry out these processes using ngs yes I know at the HDD Lab in Radyman's University, I know they have a next generation sequencer. In Kabbalah, in Kabbalah Tech in Ibado, they also have a next generation sequencer.

I think Naima in Yaba, Lagos, they also have one. So off the top of my, those are three facilities in Nigeria that I can point to that they have. Yeah. Okay.

And I also want you to share with us a story that just shows how NGS makes a difference. in the diagnosing and treating of patients as we have it today, as opposed to the normal traditional systems of diagnosis that we are used to. How does NGS make such a difference? Have you experienced any situation whereby you knew for a fact that if it wasn't for, you know, the use of NGS, the situation or the story would have ended quite differently?

okay so for that i don't have any personal experience but i'm going to uh answer the question from the perspective of somebody working on cancer genetics up till now your chances of surviving cancer is dependent on the early detection the earlier they detect it before it becomes uh before it metastasizes the better your chances of surviving is unfortunately Most of our classification of cancer is dependent on the... We actually depend on it having taken root first. You understand?

we have to see if it has affected organs we need to check for morphological changes in the cells but now we are able to you know understand the molecular mechanisms behind some of these changes you understand If your tumor suppressor gene is a mutant strain, meaning it's not a white type, it's kind of defective. Even if you don't have cancer now, we are able to say, oh, down the line.

you are expected to have it. You understand? Or if you have some oncogenes that are kind of being expressed abnormally, especially the operation of some oncogenes. we're able to tell you that oh you are at the you have a genetic predisposition to distance also a lot of genetic diseases genetic defects diabetes

maturity onset of onset diabetes will be young for people that are familiar history. And also, I think in Nigeria, one way we are using, I won't say it's Nigerian sequencing per se, but it's a molecular technique. and the AMPS PCR as well as the conventional PCR is prenatal diagnosis for sickle cell testing. Now we do have to wait for the child to be born before we say oh you have sickle cell.

it's possible that when the mother is pregnant you just take some fatal samples through the mother's body and then they test it and then they are able to you know prepare the parents before they give it like oh we've don't type in for your child to notice that your child is probably is either a carrier or your child is suffering from circle cell disease so these are the options available for treatments like this part i mentioned

i think there's already an fda pro-crispar treatment which is like a definitive cure for sickle cell and if you can't afford that uh there's bone marrow transplant if you can't afford that there are drugs you have to take you understand you just have to monitor your child so we are now able to you know advise people before they have to deal with the food our disease is done we are able to prepare their minds

for you wow thank you very much for that sir thank you so much i i love how really eye opening all of this is and um to to to just add to all that you've said you know you've talked about how this thing has just impacted the the healthcare system especially you've mentioned about cancer and

oncology and in how we approach the diagnosis of all those illnesses. So how has the rise of NGS changed the responsibilities or skill sets of the modern medical laboratory scientist, what are those skills or what are those responsibilities, actually not or and, what are the skills and responsibilities that a modern medical laboratory scientist

must embrace you know to to really go with this next generation sequencing thing and not be left behind so uh the truth is we don't have the infrastructure we nigeria as a country we don't have the infrastructure for ngs it's not a widespread so we can't crucify people for not knowing it yet however uh for now i think what all of us can do is you understand understand the data service we should learn some bioinformatic analysis even if we

can sequence with ourselves we consent to the centers that can do it and then we do our analysis we should be able to do maybe variant calling understand the little little things like as one of my professors wherever you are, do delete it, you can do and let it be known that you can do it. You understand? So it's more about the bioinformatics aspects, then also the wrong quality control, your sequencing data.

you understand bioinformatics how to use different bioinformatics tools and pipelines and how to manipulate your sequences your data and then uh probably as i always like to tell people join a community of scientists. If you have a community of scientists, you are able to, you know, discuss new techniques.

if there's any new phenomenon that's coming up in science you can always you have uh you have someone to talk to about it so yeah for now the data savvy learn by informatics tools and pipelines Thank you so much for that. Embracing new dynamics as they're coming is very very paramount in any field of practice.

So, you know, sensitive issues, just like the one you mentioned regarding sickle cell and genetic counselling, can actually cause medical legal cases if not handled well. with the rise of ngs how are labs navigating sensitive issues like genetic privacy and also Incidental findings, confidentiality, informed consent of the patients. How are labs navigating these sensitive issues to avoid medical legal cases? Okay, so first things first.

for each organization, if you're dealing with a data that is a sensitive sequencing data, the first thing is, I think you need to have a bioethics committee, you need to have a committee of scientists.

and they decide okay how do we you know protect these people's data and then you need to get consent forms you need what your clients need to understand that oh this is why according to us uh we are going to have to sequence your data this it's possible that these are the things we find and if we find them do you want to know i think there was a time i did a course on i think it's uh sequencing i think specifically cancer sequencing

And they mentioned that we have two types of variants. We have a variant of significance, which is capable of causing, which has deleterious effects or capable of causing diseases. And then we have a variant that is in significance.

uh you actually sequence you need to let the patients know that oh we are going to be doing this and it is possible that these are the things we will find if you find evidence of significance other than what you came to check for do you want to know or not you know because if if i if i'm already feeling like i have very i have a very short time to leave because of a tumor and then you do another sequencing and find another one

and you come and tell me it feels like you're just trying to shorten my life yes so uh you should let them know beforehand that oh possibilities these are the possible things if you find them do you want to know if not Okay, do you have a guardian or someone else like a nest of kin that you think we should tell, that will probably be able to tell you in a more familiar manner?

especially when you are dealing with these things, you need a lot of transparency with the people, especially for interning parents. If you are sequencing, if you are running sequences, sequencing for. an unborn child you need to let the parents know these are the things but I feel like everything should you know be handled by a bioethics committee an in-house bioethics committee that have a set of rules and policies guiding them

So it kind of makes it easy for the scientists to do their role. The community will be in charge of, you know, these are the kind of information we put out there, and these are the kind of concerns that we've gotten from the patients. for you to be able to do this thing. Yes, yes, yes. The importance of working with ethical approval and informed consent can't be overemphasized.

so you know you mentioned you took a particular course to keep updated in your field of interest in your field of practice so can you help our dear listeners to also mention places where they can take these courses. What kind of courses are we even talking about here to become more proficient in NGS in a clinical laboratory setting?

So the first thing that is needed is a strong foundation in molecular biology. That cannot be overemphasized. Whatever it is you're going to be doing as a molecular biology. You need to understand the core principles of molecular biology, essential dogma, and stuff like that. And then followed by hands-on training in NGS workflows.

Technically, that is the best place. In a country like Nigeria, where we don't have a lot of facilities with sequencers, I think the next thing you should do is bioinformatics courses. Elix Bargin Institute in Obumosho, Ohio State. It's one of the best places where you can actually learn to informatics analysis, vaccine design, peptide design.

you know, a whole lot of things. As long as you want to deal with Informatics, yes, Elixbauer Institute is one of the best places where you can do it. And also you have resources online, especially on Coursera and Udemy. also for bioinformatics courses and when we're talking about the uh ethical considerations in molecular biology and genetics you'll find a lot of materials on that on cacera so yeah thank you

All right. Yeah. And still on that, you know, you've spoken about what needs to be known before going into this field.

but also what steps can we take to increase the accessibility and affordability of next generation sequencing? especially in resource-limited settings, in developing countries, what steps can we take? What roles can international collaborations play in bridging this gap?

i mean there are so many countries we don't have to think so far we can you know look at our dear nation nigeria and just consider how far we are even in the healthcare space how do we then begin to chart a course that then leads us to actually integrating this NGS into our healthcare processes? So for me, I have always held the opinion that for innovation to thrive in a community, we need the government of the day to be really particular about.

working with people that want to enable it. First things first, I believe for NGS to take hold in Nigeria, I think the country can afford to actually set up NGS facilities. this one in this geopolitical zone for a start you understand if we set up ngs uh facilities in asia uh scientists go there they do their work helps with the kind of quality data, quality sequencing data that your country can put out. You can publish more on NGS.

and if you can publish more ngs it signals to foreign investors that oh this place is a viable ground for this investment that is when you cannot tell them oh we want to come in set up with us but uh in a place where the government of the is no uh they are not helping and i don't think any institution in nigeria can willingly can all actually put down money to set up an NGS platform, an NGS facility. It's too expensive. It's a whole lot of Azure. The monetary burden is kind of a lot.

however if you're already using it if foreigners if expatriates can see that oh you're already working with it it kind of signals to them that oh yeah you are good for it you are good for the money you understand they can always do it and also international collaborations will come but please let's be sincere a collaborator will rather set up

an ngs platform in his own country than give it to another country that they are not even sure that you people will utilize it very well let's be sincere yeah so i feel like uh a lot of it falls on the government The government should increase the funding for education, especially the science, technology, engineering and mathematics. Those three things, those four areas, you need to increase funding for them.

uh for molecular biology nigeria probably has the lowest uh part of our budgets we allocated less than i think less than one or less than two percent of our total budget research and development in the molecular in the molecular sense and that's not even caught in it it's not even caught in it for is that even caught in it for the education budget not to talk the general education budget don't talk of the science

budget alone on the molecular research and development so yeah i feel like the government can do more and they need to do better if nigeria is going to be on the same to be able to say yes we are doing this using next generation sequences i i really i must say that i love how you said like we should be sincere with ourselves because at the end of the day it all boils down to the government of the day

and how you know all these policies are actually shaping um the healthcare system the educational system and what seems to be the priority of our leaders It's something that we must get right before anybody even comes from outside to invest in all these things for us. And as we begin to close...

How do you see next generation sequencing evolving over the next decade? Will it become as routine as, for instance, full blood count? As NGS continues to advance, how do we see the innovations emerging in the next decade? So, will it become routine?

yes will it become as written as full blood counts uh not in this decade and i don't think not in the next you know but yes it will become written uh let's look at uh the human genome project that cost us uh a whole lot of millions to do okay when i say a lot of millions a whole lot of millions of dollars Let's put it like that. But now we could actually, using the same Saga sequencing, we can do it for approximately $8,000. You understand? So yes, with more advanced names.

with more technological advancement, the cost of producing initial sequencer and automation is going to reduce. The cost will reduce. the automation, the things we can do remotely will increase and once we are able to strike that balance here, definitely NGS will become, you know, it becomes a more routine procedure.

not totally routine. I want to believe not totally routine because even the Sanger sequencing that has become routine in Nigeria, we can still boast of, I don't think we can boast of 10 facilities with a Sanger sequencer. yes it's going to become more recent than it currently is well well well it has been an interesting conversation so far

So we have another interesting segment known as this or that, whereby you can only choose one option. Ready? Let's go. So WebLab or Byinformatics? Byinformatics. Genome or Microbial genome? Human genome. DNA sequencing or RNA sequencing? RNA sequencing. Single cell sequencing or bulk sequencing? I'll choose single cell. Choices so far. Teaching NGS or doing NGS? This is a tie.

that's interesting so you must be a teacher at art obviously from our conversation so far it showcased that and that's a wrap on today's deep dive into the world of ngs also known as Next Generation Sequencing, a powerful tool shaping the future of diagnostics and medical laboratory science. Huge thanks to our guest. Mr. Emmanuel Oweye for breaking it all down in such a relatable way. We hope this episode sparked some level of curiosity in you.

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Until next time, stay curious, stay informed. Bye bye.