Description
SHOW NOTES:
January 15, 2026
How two labs took on in-house sequencing
Understanding Tumor Markers for Breast Cancer (Free registration required)
bioAffinity Technologies' Laboratory maintains CAP accreditation
Next-Generation Sequencing – Molecular Oncology Committee
Hosted on Ausha. See ausha.co/privacy-policy for more information.
Transcription
Two labs take different paths to bringing next-generation sequencing in-house and a conversation with Dr. Neil Lindman on what labs should consider as sequencing expands, coming up next. This is the Path News Network Daily Edition, powered by the College of American Pathologists. I'm Stevan Borel. It's Thursday, January 15th, and here are the latest headlines. headlines. Bringing next-generation sequencing in-house doesn't have to look the same for every lab. A recent CAP Today report highlights two laboratories that took different paths to in-house NGS, one moving fast, the other building gradually, but with the same goal, faster results and better patient care. At Florida Cancer Specialist, Dr. Jennifer Gass launched NGS by an ambitious approach that helped accelerate everything that followed. As she puts it, quote, jumping headfirst into something difficult made it easier to bring additional tests online more quickly. At Centara Healthcare, Dr. David Seidman describes a more step-by-step strategy, one built over time as experience grew. He says, quote, that steady approach ultimately allowed the lab to exceed what they initially set out to perform. Read more by visiting the CAP Today link in the show notes. And for patients with advanced or metastatic breast cancer, tumor markers can play a role. But experts say it's important to understand what they can do and can't do. Tumor markers are not used to diagnose breast cancer or detect recurrence. Instead, they help clinicians monitor how cancer responds to treatment in later stages of the disease. In a recent issue of Patient Power, Dr. Allison Shamless, a member of the CAP Clinical Chemistry Committee, says tumor markers work best when paired with imaging and biopsy over time. Quote, tumor markers are most useful to follow the patient's cancer course after diagnosis. A Texas-based laboratory is reaffirming its commitment to quality after maintaining one of the most respected Distinctions in Laboratory Medicine. Precision Pathology Laboratory Services, part of BioAffinity Technologies, has successfully maintained its College of American Pathologists accreditation following a rigorous on-site inspection. Chief Operating Officer Dr. Xavier Reveles says the recognition reflects the team's dedication to excellence saying, quote, Earning CAP accreditation is a testament to our laboratory team's commitment to the highest standards in laboratory medicine. And finally, as more laboratories explore bringing next-generation sequencing in-house, ensuring reliable and consistent results is critical. The CAP's proficiency testing programs support laboratories across the full spectrum of NGS, helping labs validate performance as testing grows more complex. Here is a re-airing of my discussion with Dr. Neil Lindman, chair of the CAP Molecular Oncology Committee on what laboratories should consider as they bring next-generation sequencing in-house. Dr. Lindman, the CAP recently expanded its next-generation sequencing proficiency testing menu. Why is the development of these new programs important and how do they address emerging scientific or clinical needs?
Molecular oncology is a relatively new field, and it's grown a tremendous amount in the last two decades, basically since about 2004, 2005. There are scores of medications that cannot be given without understanding a specific genetic change in a specific cancer type. It's part of the FDA labeling in the United States. It's part of labeling in other countries, and it's just good medical science. You can make an individual test for every one of those things, in which case we would have high risk. hundreds of different tests that we ran, where you can do them all with one. And so next generation sequencing is that technology that enables you to detect both small alterations and large ones across dozens of genes, hundreds of genes, every single gene, my whole genome sequencing, the whole scope of the genetic compliment of a person, which is called their genome. And so that technology, which was a research method about 15 years ago and was unproven and innovative is now standard of care being used. all over the place in small hospital labs and private commercial labs and in big academic centers as well. But since all of these tests are are used to determine therapy and the field has evolved literally in 10 or 15 years, it's not yet matured to the place where a lot of other tests are different centers have developed them differently. And so more than ever or than anywhere proficiency testing and quality assurance is needed because different tests in different centers, even for the same markers, might not get the same results. So that's why the NGS portfolio that the CAP offers for proficiency testing is growing rapidly.
How do these NGS programs help laboratories strengthen quality, consistency, and accuracy when interpreting genomic data?
Because a lot of these tests are still internally developed, but there are commercial products on the market now. Not only is the analytical chemistry part of the test somewhat variable from place to place, but the interpretation and the data analysis can be quite variable. I like to say each sample that I run my next generation sequencing panel gives me 20 million individual sequences of DNA to read. These two eyes cannot read 20 million pieces of information. And I'm used to using a microscope, but it won't work. And so we need essentially computer tools to process that data into something that we can interpret. That's called a pipeline. And it's a bunch of sequential computer programs. There's not one program in a pipeline. It's a dozen or more. And they refine that, if you will, raw information. raw sequence data into something that these two eyes can actually make some sense out of, and hopefully a little bit of brain behind the eyes. But all the pipelines are different. And so even two identical chemistry systems doing the same assay with the same sample even, if they have different pipelines which are much less standardized than the chemistry is even, you can get different outputs. Having some external comparison system like the PT system, where I see what other labs around the country are getting, helps me understand do I have a problem or not, or a limitation or not with my pipeline that I need to address. And so I think it's actually really important to be able to make sure that when I'm sending back to my patients and their providers is accurate.
Now, the CAP's in silico bioinformatics program takes a different approach to proficiency testing. So can you explain what these programs are and why they're significant for advancing precision medicine?
So I alluded to it with the last answer. I've been building up to it. There are really two components to this. There's the chemistry piece that generates sequence files that are raw and need to be refined. And then there's a pipeline that refines them into what is eventually going to get put in the report or taken out of the report or edited in some way. And each of those impact. the quality of the final product. The only practical way to test all of the scenarios that are needed to make sure that the pipeline is working properly involve generating data files as if they came from a true chemistry sample that was tested and then running those through the pipeline. There's a biomarker that's important for giving immune checkpoint inhibitors in cancer What they do is they unlock the immune system to recognize a tumor as foreign, and then use the body's immune system to destroy the tumor almost as if the tumor was an infection. To engineer that in a lab is crazy hard because it's a pattern of injury across the 3 billion, 3 billion with a B bases in every cell. And you have to put that pattern at random spots. But then if I'm going to give that sample to everyone, it's got to be the same for everybody. And it's just chemically impractical. So either I can get a cancer sample that actually has mismatch repair deficiency, but those are hard to get. But I can simulate it with a computer file. Okay? I can write a program that will create electronic mutations in a data file. that match the pattern i want to see and then give that file back to all the labs and so in silico pt is needed in order to identify these kinds of biomarkers that are not simple to engineer
And before we close, do you have any final thoughts on the future of next generation sequencing and the role of in silico programs in supporting laboratories and genomic medicine?
So one of the challenges with the in silico PT is that each lab needs to have a computer scientist basically in order to use it. There's two approaches. One is their standard commercial systems. They're assays that are manufactured by companies. They make output files. We have a process to receive the common ones, mutate them and send them back. But the companies, particularly in the world of FDA and FDA systems are locked, they're closed. So one of the things about an FDA system is they don't want the labs tinkering with it and changing it. But in order to get those intermediate files out, mutate them and put them back. You have to unlock it. So we had a series of meetings actually with FDA, believe it or not, to try and explain to them what we were doing and to see if they might consider encouraging the companies to take a different view. And that didn't work. So then you need people who are just going to like hack the code. Or you have assays that were just developed outside of FDA by a individuals that happen to have a good computational biology team that's capable of doing that. It's not a trivial thing to do, not every place has someone who can pull that off. Certainly if we believe next generation sequencing is going to be done in every hospital and every clinic in America, like that's a unique skill set. So one of the problems with the in silico for the future is we just don't have enough people with the right skills to implement it. And so either the systems have to change to make it easier to implement, or we have to grow a generation of people that have the skills to do it. Or I guess we can find a way somehow to make it easier. But I do think it is the only viable solution to scaling the PT that we need for the different use cases of next-generation sequencing without harvesting cancers. And I mean, there's all sorts of rules about that. People, you know, they have their tumor out. They don't want it going to someone else that's going to sell it and start using it. That's just not the point of it here. So it's hard to get the real samples.
That's all we have for today. You can find us on Apple Podcasts, Amazon Music or Spotify. Subscribe on your favorite platform. Look for more news like this in our weekly weekly newsletters published every Tuesday and Thursday. We're back tomorrow at 5 a.m. Eastern with more CAP News. For The Daily Edition, I'm Stevan Borel. Have a great day
Description
SHOW NOTES:
January 15, 2026
How two labs took on in-house sequencing
Understanding Tumor Markers for Breast Cancer (Free registration required)
bioAffinity Technologies' Laboratory maintains CAP accreditation
Next-Generation Sequencing – Molecular Oncology Committee
Hosted on Ausha. See ausha.co/privacy-policy for more information.
Transcription
Two labs take different paths to bringing next-generation sequencing in-house and a conversation with Dr. Neil Lindman on what labs should consider as sequencing expands, coming up next. This is the Path News Network Daily Edition, powered by the College of American Pathologists. I'm Stevan Borel. It's Thursday, January 15th, and here are the latest headlines. headlines. Bringing next-generation sequencing in-house doesn't have to look the same for every lab. A recent CAP Today report highlights two laboratories that took different paths to in-house NGS, one moving fast, the other building gradually, but with the same goal, faster results and better patient care. At Florida Cancer Specialist, Dr. Jennifer Gass launched NGS by an ambitious approach that helped accelerate everything that followed. As she puts it, quote, jumping headfirst into something difficult made it easier to bring additional tests online more quickly. At Centara Healthcare, Dr. David Seidman describes a more step-by-step strategy, one built over time as experience grew. He says, quote, that steady approach ultimately allowed the lab to exceed what they initially set out to perform. Read more by visiting the CAP Today link in the show notes. And for patients with advanced or metastatic breast cancer, tumor markers can play a role. But experts say it's important to understand what they can do and can't do. Tumor markers are not used to diagnose breast cancer or detect recurrence. Instead, they help clinicians monitor how cancer responds to treatment in later stages of the disease. In a recent issue of Patient Power, Dr. Allison Shamless, a member of the CAP Clinical Chemistry Committee, says tumor markers work best when paired with imaging and biopsy over time. Quote, tumor markers are most useful to follow the patient's cancer course after diagnosis. A Texas-based laboratory is reaffirming its commitment to quality after maintaining one of the most respected Distinctions in Laboratory Medicine. Precision Pathology Laboratory Services, part of BioAffinity Technologies, has successfully maintained its College of American Pathologists accreditation following a rigorous on-site inspection. Chief Operating Officer Dr. Xavier Reveles says the recognition reflects the team's dedication to excellence saying, quote, Earning CAP accreditation is a testament to our laboratory team's commitment to the highest standards in laboratory medicine. And finally, as more laboratories explore bringing next-generation sequencing in-house, ensuring reliable and consistent results is critical. The CAP's proficiency testing programs support laboratories across the full spectrum of NGS, helping labs validate performance as testing grows more complex. Here is a re-airing of my discussion with Dr. Neil Lindman, chair of the CAP Molecular Oncology Committee on what laboratories should consider as they bring next-generation sequencing in-house. Dr. Lindman, the CAP recently expanded its next-generation sequencing proficiency testing menu. Why is the development of these new programs important and how do they address emerging scientific or clinical needs?
Molecular oncology is a relatively new field, and it's grown a tremendous amount in the last two decades, basically since about 2004, 2005. There are scores of medications that cannot be given without understanding a specific genetic change in a specific cancer type. It's part of the FDA labeling in the United States. It's part of labeling in other countries, and it's just good medical science. You can make an individual test for every one of those things, in which case we would have high risk. hundreds of different tests that we ran, where you can do them all with one. And so next generation sequencing is that technology that enables you to detect both small alterations and large ones across dozens of genes, hundreds of genes, every single gene, my whole genome sequencing, the whole scope of the genetic compliment of a person, which is called their genome. And so that technology, which was a research method about 15 years ago and was unproven and innovative is now standard of care being used. all over the place in small hospital labs and private commercial labs and in big academic centers as well. But since all of these tests are are used to determine therapy and the field has evolved literally in 10 or 15 years, it's not yet matured to the place where a lot of other tests are different centers have developed them differently. And so more than ever or than anywhere proficiency testing and quality assurance is needed because different tests in different centers, even for the same markers, might not get the same results. So that's why the NGS portfolio that the CAP offers for proficiency testing is growing rapidly.
How do these NGS programs help laboratories strengthen quality, consistency, and accuracy when interpreting genomic data?
Because a lot of these tests are still internally developed, but there are commercial products on the market now. Not only is the analytical chemistry part of the test somewhat variable from place to place, but the interpretation and the data analysis can be quite variable. I like to say each sample that I run my next generation sequencing panel gives me 20 million individual sequences of DNA to read. These two eyes cannot read 20 million pieces of information. And I'm used to using a microscope, but it won't work. And so we need essentially computer tools to process that data into something that we can interpret. That's called a pipeline. And it's a bunch of sequential computer programs. There's not one program in a pipeline. It's a dozen or more. And they refine that, if you will, raw information. raw sequence data into something that these two eyes can actually make some sense out of, and hopefully a little bit of brain behind the eyes. But all the pipelines are different. And so even two identical chemistry systems doing the same assay with the same sample even, if they have different pipelines which are much less standardized than the chemistry is even, you can get different outputs. Having some external comparison system like the PT system, where I see what other labs around the country are getting, helps me understand do I have a problem or not, or a limitation or not with my pipeline that I need to address. And so I think it's actually really important to be able to make sure that when I'm sending back to my patients and their providers is accurate.
Now, the CAP's in silico bioinformatics program takes a different approach to proficiency testing. So can you explain what these programs are and why they're significant for advancing precision medicine?
So I alluded to it with the last answer. I've been building up to it. There are really two components to this. There's the chemistry piece that generates sequence files that are raw and need to be refined. And then there's a pipeline that refines them into what is eventually going to get put in the report or taken out of the report or edited in some way. And each of those impact. the quality of the final product. The only practical way to test all of the scenarios that are needed to make sure that the pipeline is working properly involve generating data files as if they came from a true chemistry sample that was tested and then running those through the pipeline. There's a biomarker that's important for giving immune checkpoint inhibitors in cancer What they do is they unlock the immune system to recognize a tumor as foreign, and then use the body's immune system to destroy the tumor almost as if the tumor was an infection. To engineer that in a lab is crazy hard because it's a pattern of injury across the 3 billion, 3 billion with a B bases in every cell. And you have to put that pattern at random spots. But then if I'm going to give that sample to everyone, it's got to be the same for everybody. And it's just chemically impractical. So either I can get a cancer sample that actually has mismatch repair deficiency, but those are hard to get. But I can simulate it with a computer file. Okay? I can write a program that will create electronic mutations in a data file. that match the pattern i want to see and then give that file back to all the labs and so in silico pt is needed in order to identify these kinds of biomarkers that are not simple to engineer
And before we close, do you have any final thoughts on the future of next generation sequencing and the role of in silico programs in supporting laboratories and genomic medicine?
So one of the challenges with the in silico PT is that each lab needs to have a computer scientist basically in order to use it. There's two approaches. One is their standard commercial systems. They're assays that are manufactured by companies. They make output files. We have a process to receive the common ones, mutate them and send them back. But the companies, particularly in the world of FDA and FDA systems are locked, they're closed. So one of the things about an FDA system is they don't want the labs tinkering with it and changing it. But in order to get those intermediate files out, mutate them and put them back. You have to unlock it. So we had a series of meetings actually with FDA, believe it or not, to try and explain to them what we were doing and to see if they might consider encouraging the companies to take a different view. And that didn't work. So then you need people who are just going to like hack the code. Or you have assays that were just developed outside of FDA by a individuals that happen to have a good computational biology team that's capable of doing that. It's not a trivial thing to do, not every place has someone who can pull that off. Certainly if we believe next generation sequencing is going to be done in every hospital and every clinic in America, like that's a unique skill set. So one of the problems with the in silico for the future is we just don't have enough people with the right skills to implement it. And so either the systems have to change to make it easier to implement, or we have to grow a generation of people that have the skills to do it. Or I guess we can find a way somehow to make it easier. But I do think it is the only viable solution to scaling the PT that we need for the different use cases of next-generation sequencing without harvesting cancers. And I mean, there's all sorts of rules about that. People, you know, they have their tumor out. They don't want it going to someone else that's going to sell it and start using it. That's just not the point of it here. So it's hard to get the real samples.
That's all we have for today. You can find us on Apple Podcasts, Amazon Music or Spotify. Subscribe on your favorite platform. Look for more news like this in our weekly weekly newsletters published every Tuesday and Thursday. We're back tomorrow at 5 a.m. Eastern with more CAP News. For The Daily Edition, I'm Stevan Borel. Have a great day
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Description
SHOW NOTES:
January 15, 2026
How two labs took on in-house sequencing
Understanding Tumor Markers for Breast Cancer (Free registration required)
bioAffinity Technologies' Laboratory maintains CAP accreditation
Next-Generation Sequencing – Molecular Oncology Committee
Hosted on Ausha. See ausha.co/privacy-policy for more information.
Transcription
Two labs take different paths to bringing next-generation sequencing in-house and a conversation with Dr. Neil Lindman on what labs should consider as sequencing expands, coming up next. This is the Path News Network Daily Edition, powered by the College of American Pathologists. I'm Stevan Borel. It's Thursday, January 15th, and here are the latest headlines. headlines. Bringing next-generation sequencing in-house doesn't have to look the same for every lab. A recent CAP Today report highlights two laboratories that took different paths to in-house NGS, one moving fast, the other building gradually, but with the same goal, faster results and better patient care. At Florida Cancer Specialist, Dr. Jennifer Gass launched NGS by an ambitious approach that helped accelerate everything that followed. As she puts it, quote, jumping headfirst into something difficult made it easier to bring additional tests online more quickly. At Centara Healthcare, Dr. David Seidman describes a more step-by-step strategy, one built over time as experience grew. He says, quote, that steady approach ultimately allowed the lab to exceed what they initially set out to perform. Read more by visiting the CAP Today link in the show notes. And for patients with advanced or metastatic breast cancer, tumor markers can play a role. But experts say it's important to understand what they can do and can't do. Tumor markers are not used to diagnose breast cancer or detect recurrence. Instead, they help clinicians monitor how cancer responds to treatment in later stages of the disease. In a recent issue of Patient Power, Dr. Allison Shamless, a member of the CAP Clinical Chemistry Committee, says tumor markers work best when paired with imaging and biopsy over time. Quote, tumor markers are most useful to follow the patient's cancer course after diagnosis. A Texas-based laboratory is reaffirming its commitment to quality after maintaining one of the most respected Distinctions in Laboratory Medicine. Precision Pathology Laboratory Services, part of BioAffinity Technologies, has successfully maintained its College of American Pathologists accreditation following a rigorous on-site inspection. Chief Operating Officer Dr. Xavier Reveles says the recognition reflects the team's dedication to excellence saying, quote, Earning CAP accreditation is a testament to our laboratory team's commitment to the highest standards in laboratory medicine. And finally, as more laboratories explore bringing next-generation sequencing in-house, ensuring reliable and consistent results is critical. The CAP's proficiency testing programs support laboratories across the full spectrum of NGS, helping labs validate performance as testing grows more complex. Here is a re-airing of my discussion with Dr. Neil Lindman, chair of the CAP Molecular Oncology Committee on what laboratories should consider as they bring next-generation sequencing in-house. Dr. Lindman, the CAP recently expanded its next-generation sequencing proficiency testing menu. Why is the development of these new programs important and how do they address emerging scientific or clinical needs?
Molecular oncology is a relatively new field, and it's grown a tremendous amount in the last two decades, basically since about 2004, 2005. There are scores of medications that cannot be given without understanding a specific genetic change in a specific cancer type. It's part of the FDA labeling in the United States. It's part of labeling in other countries, and it's just good medical science. You can make an individual test for every one of those things, in which case we would have high risk. hundreds of different tests that we ran, where you can do them all with one. And so next generation sequencing is that technology that enables you to detect both small alterations and large ones across dozens of genes, hundreds of genes, every single gene, my whole genome sequencing, the whole scope of the genetic compliment of a person, which is called their genome. And so that technology, which was a research method about 15 years ago and was unproven and innovative is now standard of care being used. all over the place in small hospital labs and private commercial labs and in big academic centers as well. But since all of these tests are are used to determine therapy and the field has evolved literally in 10 or 15 years, it's not yet matured to the place where a lot of other tests are different centers have developed them differently. And so more than ever or than anywhere proficiency testing and quality assurance is needed because different tests in different centers, even for the same markers, might not get the same results. So that's why the NGS portfolio that the CAP offers for proficiency testing is growing rapidly.
How do these NGS programs help laboratories strengthen quality, consistency, and accuracy when interpreting genomic data?
Because a lot of these tests are still internally developed, but there are commercial products on the market now. Not only is the analytical chemistry part of the test somewhat variable from place to place, but the interpretation and the data analysis can be quite variable. I like to say each sample that I run my next generation sequencing panel gives me 20 million individual sequences of DNA to read. These two eyes cannot read 20 million pieces of information. And I'm used to using a microscope, but it won't work. And so we need essentially computer tools to process that data into something that we can interpret. That's called a pipeline. And it's a bunch of sequential computer programs. There's not one program in a pipeline. It's a dozen or more. And they refine that, if you will, raw information. raw sequence data into something that these two eyes can actually make some sense out of, and hopefully a little bit of brain behind the eyes. But all the pipelines are different. And so even two identical chemistry systems doing the same assay with the same sample even, if they have different pipelines which are much less standardized than the chemistry is even, you can get different outputs. Having some external comparison system like the PT system, where I see what other labs around the country are getting, helps me understand do I have a problem or not, or a limitation or not with my pipeline that I need to address. And so I think it's actually really important to be able to make sure that when I'm sending back to my patients and their providers is accurate.
Now, the CAP's in silico bioinformatics program takes a different approach to proficiency testing. So can you explain what these programs are and why they're significant for advancing precision medicine?
So I alluded to it with the last answer. I've been building up to it. There are really two components to this. There's the chemistry piece that generates sequence files that are raw and need to be refined. And then there's a pipeline that refines them into what is eventually going to get put in the report or taken out of the report or edited in some way. And each of those impact. the quality of the final product. The only practical way to test all of the scenarios that are needed to make sure that the pipeline is working properly involve generating data files as if they came from a true chemistry sample that was tested and then running those through the pipeline. There's a biomarker that's important for giving immune checkpoint inhibitors in cancer What they do is they unlock the immune system to recognize a tumor as foreign, and then use the body's immune system to destroy the tumor almost as if the tumor was an infection. To engineer that in a lab is crazy hard because it's a pattern of injury across the 3 billion, 3 billion with a B bases in every cell. And you have to put that pattern at random spots. But then if I'm going to give that sample to everyone, it's got to be the same for everybody. And it's just chemically impractical. So either I can get a cancer sample that actually has mismatch repair deficiency, but those are hard to get. But I can simulate it with a computer file. Okay? I can write a program that will create electronic mutations in a data file. that match the pattern i want to see and then give that file back to all the labs and so in silico pt is needed in order to identify these kinds of biomarkers that are not simple to engineer
And before we close, do you have any final thoughts on the future of next generation sequencing and the role of in silico programs in supporting laboratories and genomic medicine?
So one of the challenges with the in silico PT is that each lab needs to have a computer scientist basically in order to use it. There's two approaches. One is their standard commercial systems. They're assays that are manufactured by companies. They make output files. We have a process to receive the common ones, mutate them and send them back. But the companies, particularly in the world of FDA and FDA systems are locked, they're closed. So one of the things about an FDA system is they don't want the labs tinkering with it and changing it. But in order to get those intermediate files out, mutate them and put them back. You have to unlock it. So we had a series of meetings actually with FDA, believe it or not, to try and explain to them what we were doing and to see if they might consider encouraging the companies to take a different view. And that didn't work. So then you need people who are just going to like hack the code. Or you have assays that were just developed outside of FDA by a individuals that happen to have a good computational biology team that's capable of doing that. It's not a trivial thing to do, not every place has someone who can pull that off. Certainly if we believe next generation sequencing is going to be done in every hospital and every clinic in America, like that's a unique skill set. So one of the problems with the in silico for the future is we just don't have enough people with the right skills to implement it. And so either the systems have to change to make it easier to implement, or we have to grow a generation of people that have the skills to do it. Or I guess we can find a way somehow to make it easier. But I do think it is the only viable solution to scaling the PT that we need for the different use cases of next-generation sequencing without harvesting cancers. And I mean, there's all sorts of rules about that. People, you know, they have their tumor out. They don't want it going to someone else that's going to sell it and start using it. That's just not the point of it here. So it's hard to get the real samples.
That's all we have for today. You can find us on Apple Podcasts, Amazon Music or Spotify. Subscribe on your favorite platform. Look for more news like this in our weekly weekly newsletters published every Tuesday and Thursday. We're back tomorrow at 5 a.m. Eastern with more CAP News. For The Daily Edition, I'm Stevan Borel. Have a great day
Description
SHOW NOTES:
January 15, 2026
How two labs took on in-house sequencing
Understanding Tumor Markers for Breast Cancer (Free registration required)
bioAffinity Technologies' Laboratory maintains CAP accreditation
Next-Generation Sequencing – Molecular Oncology Committee
Hosted on Ausha. See ausha.co/privacy-policy for more information.
Transcription
Two labs take different paths to bringing next-generation sequencing in-house and a conversation with Dr. Neil Lindman on what labs should consider as sequencing expands, coming up next. This is the Path News Network Daily Edition, powered by the College of American Pathologists. I'm Stevan Borel. It's Thursday, January 15th, and here are the latest headlines. headlines. Bringing next-generation sequencing in-house doesn't have to look the same for every lab. A recent CAP Today report highlights two laboratories that took different paths to in-house NGS, one moving fast, the other building gradually, but with the same goal, faster results and better patient care. At Florida Cancer Specialist, Dr. Jennifer Gass launched NGS by an ambitious approach that helped accelerate everything that followed. As she puts it, quote, jumping headfirst into something difficult made it easier to bring additional tests online more quickly. At Centara Healthcare, Dr. David Seidman describes a more step-by-step strategy, one built over time as experience grew. He says, quote, that steady approach ultimately allowed the lab to exceed what they initially set out to perform. Read more by visiting the CAP Today link in the show notes. And for patients with advanced or metastatic breast cancer, tumor markers can play a role. But experts say it's important to understand what they can do and can't do. Tumor markers are not used to diagnose breast cancer or detect recurrence. Instead, they help clinicians monitor how cancer responds to treatment in later stages of the disease. In a recent issue of Patient Power, Dr. Allison Shamless, a member of the CAP Clinical Chemistry Committee, says tumor markers work best when paired with imaging and biopsy over time. Quote, tumor markers are most useful to follow the patient's cancer course after diagnosis. A Texas-based laboratory is reaffirming its commitment to quality after maintaining one of the most respected Distinctions in Laboratory Medicine. Precision Pathology Laboratory Services, part of BioAffinity Technologies, has successfully maintained its College of American Pathologists accreditation following a rigorous on-site inspection. Chief Operating Officer Dr. Xavier Reveles says the recognition reflects the team's dedication to excellence saying, quote, Earning CAP accreditation is a testament to our laboratory team's commitment to the highest standards in laboratory medicine. And finally, as more laboratories explore bringing next-generation sequencing in-house, ensuring reliable and consistent results is critical. The CAP's proficiency testing programs support laboratories across the full spectrum of NGS, helping labs validate performance as testing grows more complex. Here is a re-airing of my discussion with Dr. Neil Lindman, chair of the CAP Molecular Oncology Committee on what laboratories should consider as they bring next-generation sequencing in-house. Dr. Lindman, the CAP recently expanded its next-generation sequencing proficiency testing menu. Why is the development of these new programs important and how do they address emerging scientific or clinical needs?
Molecular oncology is a relatively new field, and it's grown a tremendous amount in the last two decades, basically since about 2004, 2005. There are scores of medications that cannot be given without understanding a specific genetic change in a specific cancer type. It's part of the FDA labeling in the United States. It's part of labeling in other countries, and it's just good medical science. You can make an individual test for every one of those things, in which case we would have high risk. hundreds of different tests that we ran, where you can do them all with one. And so next generation sequencing is that technology that enables you to detect both small alterations and large ones across dozens of genes, hundreds of genes, every single gene, my whole genome sequencing, the whole scope of the genetic compliment of a person, which is called their genome. And so that technology, which was a research method about 15 years ago and was unproven and innovative is now standard of care being used. all over the place in small hospital labs and private commercial labs and in big academic centers as well. But since all of these tests are are used to determine therapy and the field has evolved literally in 10 or 15 years, it's not yet matured to the place where a lot of other tests are different centers have developed them differently. And so more than ever or than anywhere proficiency testing and quality assurance is needed because different tests in different centers, even for the same markers, might not get the same results. So that's why the NGS portfolio that the CAP offers for proficiency testing is growing rapidly.
How do these NGS programs help laboratories strengthen quality, consistency, and accuracy when interpreting genomic data?
Because a lot of these tests are still internally developed, but there are commercial products on the market now. Not only is the analytical chemistry part of the test somewhat variable from place to place, but the interpretation and the data analysis can be quite variable. I like to say each sample that I run my next generation sequencing panel gives me 20 million individual sequences of DNA to read. These two eyes cannot read 20 million pieces of information. And I'm used to using a microscope, but it won't work. And so we need essentially computer tools to process that data into something that we can interpret. That's called a pipeline. And it's a bunch of sequential computer programs. There's not one program in a pipeline. It's a dozen or more. And they refine that, if you will, raw information. raw sequence data into something that these two eyes can actually make some sense out of, and hopefully a little bit of brain behind the eyes. But all the pipelines are different. And so even two identical chemistry systems doing the same assay with the same sample even, if they have different pipelines which are much less standardized than the chemistry is even, you can get different outputs. Having some external comparison system like the PT system, where I see what other labs around the country are getting, helps me understand do I have a problem or not, or a limitation or not with my pipeline that I need to address. And so I think it's actually really important to be able to make sure that when I'm sending back to my patients and their providers is accurate.
Now, the CAP's in silico bioinformatics program takes a different approach to proficiency testing. So can you explain what these programs are and why they're significant for advancing precision medicine?
So I alluded to it with the last answer. I've been building up to it. There are really two components to this. There's the chemistry piece that generates sequence files that are raw and need to be refined. And then there's a pipeline that refines them into what is eventually going to get put in the report or taken out of the report or edited in some way. And each of those impact. the quality of the final product. The only practical way to test all of the scenarios that are needed to make sure that the pipeline is working properly involve generating data files as if they came from a true chemistry sample that was tested and then running those through the pipeline. There's a biomarker that's important for giving immune checkpoint inhibitors in cancer What they do is they unlock the immune system to recognize a tumor as foreign, and then use the body's immune system to destroy the tumor almost as if the tumor was an infection. To engineer that in a lab is crazy hard because it's a pattern of injury across the 3 billion, 3 billion with a B bases in every cell. And you have to put that pattern at random spots. But then if I'm going to give that sample to everyone, it's got to be the same for everybody. And it's just chemically impractical. So either I can get a cancer sample that actually has mismatch repair deficiency, but those are hard to get. But I can simulate it with a computer file. Okay? I can write a program that will create electronic mutations in a data file. that match the pattern i want to see and then give that file back to all the labs and so in silico pt is needed in order to identify these kinds of biomarkers that are not simple to engineer
And before we close, do you have any final thoughts on the future of next generation sequencing and the role of in silico programs in supporting laboratories and genomic medicine?
So one of the challenges with the in silico PT is that each lab needs to have a computer scientist basically in order to use it. There's two approaches. One is their standard commercial systems. They're assays that are manufactured by companies. They make output files. We have a process to receive the common ones, mutate them and send them back. But the companies, particularly in the world of FDA and FDA systems are locked, they're closed. So one of the things about an FDA system is they don't want the labs tinkering with it and changing it. But in order to get those intermediate files out, mutate them and put them back. You have to unlock it. So we had a series of meetings actually with FDA, believe it or not, to try and explain to them what we were doing and to see if they might consider encouraging the companies to take a different view. And that didn't work. So then you need people who are just going to like hack the code. Or you have assays that were just developed outside of FDA by a individuals that happen to have a good computational biology team that's capable of doing that. It's not a trivial thing to do, not every place has someone who can pull that off. Certainly if we believe next generation sequencing is going to be done in every hospital and every clinic in America, like that's a unique skill set. So one of the problems with the in silico for the future is we just don't have enough people with the right skills to implement it. And so either the systems have to change to make it easier to implement, or we have to grow a generation of people that have the skills to do it. Or I guess we can find a way somehow to make it easier. But I do think it is the only viable solution to scaling the PT that we need for the different use cases of next-generation sequencing without harvesting cancers. And I mean, there's all sorts of rules about that. People, you know, they have their tumor out. They don't want it going to someone else that's going to sell it and start using it. That's just not the point of it here. So it's hard to get the real samples.
That's all we have for today. You can find us on Apple Podcasts, Amazon Music or Spotify. Subscribe on your favorite platform. Look for more news like this in our weekly weekly newsletters published every Tuesday and Thursday. We're back tomorrow at 5 a.m. Eastern with more CAP News. For The Daily Edition, I'm Stevan Borel. Have a great day
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