CorePlus Details Its Use Of Artificial Intelligence For Prostate Cancer

by Jondavid Klipp | Oct 15, 2020 | AI, Artificial Intelligence, CorePlus

CorePlus Details Its Use Of Artificial Intelligence For Prostate Cancer

Last month, LE briefly noted that CorePlus Servicios Clínicos y Patológicos LLC (Carolina, Puerto Rico) had become the first independent lab in the Americas to begin using artificialintelligence-assisted (AI) pathology for prostate cancer diagnostics. This month wegot in touch with CorePlus President Mariano de Socarraz to find out more.

Can you describe CorePlus?
We opened our CLIA-certified laboratory in Carolina, Puerto Rico in 2008. We currently have 115 employees, including four pathologists. CorePlus is full-service independent laboratory. Among our specializations is uropathology. We process approximately 3,000 prostate cancer cases (~36,000 slides) per year, representing more than half of all outpatient prostate cancer biopsies performed in Puerto Rico.

Is operating a lab in Puerto Rico different than in mainland United States?
No. Puerto Rico is a U.S. territory that must follow all federal lab regulations, including CLIA. Medicare and Medicaid insurance cover the majority of the 3.2 million people living in Puerto Rico and the biggest private insurer is Triple-S, which is an independent licensee of the Blue Cross Blue Shield Association. The biggest difference is probably reimbursement rates, which are substantially lower in Puerto Rico.

Among the competing clinical labs in Puerto Rico are Laboratorio Clinico Toledo and Laboratorios Borinquen. Anatomic pathology labs include Hato Rey Pathology and Puerto Rico Pathology. Quest Diagnostics has had a reduced presence following the damage to its lab facilities from Hurricane Maria in 2017. LabCorp transports specimens to its labs in Florida.

When did CorePlus transition to digital pathology?
We began digitizing slides using 3DHISTECH scanners in mid-2019. By late 2019 we had completed validation and by early 2020 our pathologists were reading digitized images for all our pathology cases, including all routine histopathology and stains.

What type of computer screens do your pathologists read the digital slide images from?
CorePlus validated the Dell UltraSharp 49 Curved Monitor – U4919DW. It’s a high-end, business grade monitor with a Delta E of <2 (color difference perception) and an aspect ratio of 32:9:0. This aspect ratio is the equivalent of two 27-inch monitors running at 2K.

And how did you get involved with AI-assisted pathology?
In August 2018, I read about a validation study conducted by University of Pittsburgh Medical Center which used an AI-based algorithm to detect and characterize prostate cancer from digitized slides. This study [recently published in The Lancet Digital Health] showed that an AI-based algorithm demonstrated 98% sensitivity and 97% specificity at detecting prostate cancer from 1,600 different tissue slide images that had been collected from 100 patients seen at UPMC who were suspected of having prostate cancer. It even spotted six potentially malignant slides that expert pathologists had failed to identify initially. This interested me, so I contacted the company that developed the algorithm, Israel-based Ibex Medical Analytics. We ran our own validation studies on 1,301 digitized prostate tissue slides and found results similar to those at UPMC. Overall accuracy was 99.4% with 96.9% specificity and 96.5% sensitivity.

How have you integrated AI into your pathology lab?
Our pathologists continue to read digitized images for every prostate tissue slide prepared by our lab. But starting in June, we also began sending digitized images of each slide to the Ibex cloud. Ibex runs its AI-based algorithm on each slide which provides 100% quality control on all prostate cases. This serves as a digital second opinion for our pathologists.

What happens when there is a discrepancy between the pathologist’s exam and the algorithm?

The pathologist goes back and reviews the slide(s) and/or orders an immunohistochemistry. I believe that we have reduced the potential for a misdiagnosis on prostate cancer biopsies to much less than 1%. This is significant given that even an expert uropathologist can miss 3%. So the AI
algorithm is acting as a failsafe that is catching cases that might otherwise be missed.

Was there any reluctance from your pathologists as you transitioned to digital pathology and AI for prostate?
The pathologists were always fully engaged in the transition. Our pathologists say they would never go back to the microscope, especially given their ability to read digitized slides at home during the pandemic. We have analyzed over 1,000 prostate biopsy cases using digital pathology with AI assistance to date. In real world practice it has helped identify lesions that would otherwise have been missed.

Will you apply AI-based algorithms to other cancers?
Yes, we are planning to start using an Ibex algorithm for second reads on all breast cancer cases within the next few weeks.

How does your lab get compensated for using digital pathology and AI to improve accuracy?
We do not get additional compensation and that is the problem with the current CPT-based feefor-service reimbursement model. AI increases accuracy and reduces utilization of immunohistochemistry and there ought to be some coding mechanism that fairly compensates labs that use it.
In the meantime, the increased efficiency that the combination of digital pathology and AI provides has helped offset the initial technology investment and development cost. In addition, the increased accuracy at CorePlus through its use of AI should lead to more clients. Knowing that 100% of prostate cancer cases sent to CorePlus are getting an AI second opinion should raise urologists’ confidence in our lab.

How will AI affect the practice of pathology over the long term?
After our current use of digital pathology and AI as a second read tool, I anticipate it will progress to be used as a triage tool and finally for primary reads with the supervision of a pathologist. The role of pathologists will evolve away from time at the traditional microscope toward selecting the
right AI algorithm to apply to a digitized slide and reviewing results in combination with a patient’s medical record to form a diagnosis.

Switching gears, is CorePlus performing Covid-19 PCR testing?
We started Covid-19 PCR testing on the Roche cobas 6800 platform in late April. CorePlus has been on an allocation of seven kits per week (equal to 1,344 tests). To compensate for the test reagent shortage, we began pooled testing for three specimens at a time in July. This has expanded our capacity to about 4,000 tests per week and we are preparing to increase our pool size to six specimens, which will double our capacity to 8,000 tests per week.

How do you see the Covid-19 pandemic ending?
It is not going away any time soon, even with a vaccine. Population immunity may take years.

Survey Reveals Huge Gap Between “Have” and “Have Not” Labs

by Jondavid Klipp | Oct 15, 2020 | Covid Testing, COVID-19, PCR Testing

Survey Reveals Huge Gap Between “Have” and “Have Not” Labs

The latest Laboratory Economics Covid-19 Survey of Labs showed that 71% of labs were currently performing Covid-19 PCR testing and another 3% planned to soon add this capability, while 26% were not doing this testing. Those labs that are performing Covid-19 PCR testing reported that they expect their overall test volume (including both Covid and non-Covid testing) this year to increase by an average of 59% with a median of 10%.

The benefits garnered by labs doing Covid-19 PCR testing will soon be enlarged as many labs are in the process of switching to combo tests that detect Covid-19 and influenza A/B from a single patient specimen (CPT 87636). New combo PCR tests for Covid-19, influenza A/B and respiratory syncytial virus (RSV) are also being introduced (CPT 87637).

Meanwhile, the “Have Nots” that do not perform Covid-19 PCR testing are expecting average volume growth of only 1% with a median of 0%. The “Have Nots” surveyed were comprised entirely of local pathology groups and physician-office-based labs.

“The downturn in patient office visits has decreased lab volumes and caused many to furlough or completely lay off certain areas of staff. The labs that are thriving are those that have been fast and flexible enough to add Covid testing,” said a surveyed lab executive from Florida.

“The Covid pandemic has introduced new healthcare delivery platforms, such as telemedicine, that do not enable the same amount of referral laboratory testing. Despite offering an electronic order and convenient online scheduling at local patient service centers, we are seeing an increase in patient no-shows and test orders are not being completed,” noted a lab executive from Texas.

National Covid-19 PCR test volumes have quadrupled since LE’s initial Covid-19 survey conducted back in early May. Volumes might be even higher if not for continued supply shortages. Our most recent survey
showed that 59% of labs had shortages in PCR-based Covid-19 test kits. Pipette tips (45%) and collection swabs/specimen transport media (41%) are also currently in short supply.

The Laboratory Economics Covid-19 Survey of Labs was emailed to approximately 6,000 pathologists, laboratory directors, managers and executives between September 30 and October 13. We received complete responses from 124 individuals, including 44% from local independent pathology groups/labs, 25% from national pathology/commercial lab companies, 23% from hospital-based labs and pathology groups, 6% from academic medical centers, and 2% from physician office labs.

Spotlight Interview With Aegis Sciences CEO Frank Basile

by Jondavid Klipp | Sep 15, 2020 | Aegis Sciences Corp.

Spotlight Interview With Aegis Sciences CEO Frank Basile

Aegis Sciences Corp. (Nashville, TN) performs some 20 million toxicology tests per year, making it one of the nation’s largest toxicology labs. On April
15, Aegis launched Covid-19 PCR testing with an initial capacity to perform up to 3,500 tests per day. Laboratory Economics recently spoke with Chief Executive Frank Basile, MD, to discuss Aegis and its Covid-19 testing strategy.

How many Covid-19 PCR tests is Aegis currently performing?
We are currently performing an average of about 10,000 tests per day with capacity of up to 30,000 tests per day. We’re using the PerkinElmer RNA/DNA extraction system and ThermoFisher’s QuantStudio 7 analyzer for testing.

Who are your Covid-19 clients?
We’ve added over 1,000 new clients over the past 12 weeks, including urgent care centers, surgery centers, nursing homes, doctor’s offices, correctional facilities and colleges and universities. We also have state contracts with Tennessee, Louisiana and Oklahoma. We placed a moratorium on new client starts in July in order to maintain a 24-hour turnaround time from specimen pickup to result reporting. This was recently lifted as we have increased capacity.

Are private payers matching Medicare’s reimbursement rate of $100 for Covid-19 PCR testing?

Yes, in the majority of cases. Medicaid, however, in some states is paying significantly below and/or are not credentialing because they insist on an “in-state bricks and mortar” presence which is slightly impractical during the pandemic. Additionally, certain payers are denying claims, paying the patient, or not responding at all. This is a significant problem and appears to be in direct conflict with the CARES Act.

Describe the NIH grant that Aegis was awarded and how it will be used.
Aegis has received a $6.6 million grant from the National Institutes of Health (NIH) under its Rapid Acceleration of Diagnostics (RADx) program. The grant funding will be used to expand our molecular lab from 3,000 square feet to 18,000 square feet. We’ll also be moving to Thermo Fisher’s highthroughput KingFisher Flex system for RNA/DNA extraction into the lab. We plan to increase our capacity to 60,000 Covid-19 PCR tests per day by September 30. In addition, we are developing a multiplexed Covid-19 + Flu A/B assay which will be available early October.

Any plans for pooled testing?
We have looked at it. However, we’re currently seeing positivity rates of around 10%, which makes pooled testing less feasible. Pooled testing is best suited for discrete population testing of groups expected to have positivity rates of <5%. Aegis serves clients nationwide that range from pre-surgery testing (low positivity rate) to walk-in clinics and correctional facilities (higher positivity rate). Our lab TAT averages less than 24 hours. Samples would have to be segregated to take advantage of pooled testing, leading to workflow complexity and potentially overall increases in TAT.

Has Aegis experienced any supply shortages?
Supplies haven’t been a limiting factor for us. We spent five weeks prior to launch getting our supply chain in order. For example, we diversified key supplies by validating specimen transport media from multiple vendors.
Rapidly finding and retaining good people has been the biggest challenge we have needed to overcome. Over the past 12 weeks we have hired over 200 employees, and will continue to hire more, especially for specimen accessioning and processing positions in the lab. Our current overall employee count is 1,051.

Describe your new Covid-19 antibody test.
On August 31, Aegis launched a Covid-19 antibody test that utilizes dried blood spot specimens. The test allows samples to be taken by fingerstick and should be popular for testing children and others. Samples are sent to our lab without the need for an invasive blood draw or additional processing at the collection site. We validated the test in accordance with FDA Emergency Use Authorization (EUA) requirements and it showed 99.9% specificity and 96.1% sensitivity. Demand for antibody testing has
been slow so far, but that is likely to change after a Covid-19 vaccine becomes available. Antibody testing could be used to determine if previous exposure to the virus occurred or to see if an individual that received a vaccine elicited an immune response. We expect this to become an important test later this year and into next year, especially as we bring additional product enhancements to market.

Have your toxicology test volumes bounced back from the lows?
Our toxicology volumes bottomed in mid-April but have since rebounded to approximately 80% to 85% of pre-pandemic levels. I expect we’ll be back to nearly 100% of “pre-pandemic” levels sometime by year’s end.

Do you think Covid-19 will come back in a severe way this fall/winter?
I expect cases to spike up, along with other respiratory infections, this coming fall and winter, although masking might limit the upsurge.

Publicly-Traded Lab Revenue Falls 1.4% In First-Half 2020

by Jondavid Klipp | Sep 15, 2020 | BioReference Labs, Labcorp, Quest Diagnostics, Sonic Healthcare

Publicly-Traded Lab Revenue Falls 1.4% In First-Half 2020

On a combined basis, 20 publicly-traded labs reported a revenue decrease of 1.4% to $9.8 billion during the first six months of 2020 (after adjusting for acquisitions), according to financial reports collected by Laboratory Economics.

Among five national clinic al labs (Quest Diagnostics, LabCorp, Sonic, BioReference and Enzo), combined revenue fell by 3.1% (after adjusting for acquisitions). BioReference had the strongest revenue growth, up 18% to $421.8 million, driven by Covid-19 PCR testing. BioReference processed approximately 2.2 million Covid-19 PCR tests during the first six months of 2020.

Among 15 specialty and genetic testing labs, combined pro-forma revenue increased by 7.3%.

Pro-forma revenue growth was fastest at DermTech, up 98.4% to $2.4 million. Other fast-growing companies included Castle Biosciences, up 54.9% to $30.1 million; Guardant Health, up 47.7% to $133.8 million; and CareDx, up 39.6% to $80.2 million.

Top 25 Fastest-Growing Labs by Medicare Part B Volume of Services

Spotlight Interview With PathGroup CEO Ben Davis

by Jondavid Klipp | Sep 11, 2020 | PathGroup

Spotlight Interview With PathGroup CEO Ben Davis

Originally founded by pathologists in 1965, PathGroup (Brentwood, TN) has grown to become the nation’s largest privately-held lab company. PathGroup, which currently has 2,200 employees, is owned by Pritzker Private Capital, company management and pathologists. Laboratory
Economics recently spoke with long-time Chief Executive Ben Davis, MD, to discuss PathGroup and its growing role in Covid-19 testing.

When did PathGroup initiate Covid-19 PCR testing and how many are being performed?
We began Covid-19 PCR testing on April 1st with an initial capacity of 2,000 tests per day using the Hologic Panther and Roche cobas 6800 platforms. We are currently performing an average of about 7,500 tests per day with capacity of up to 14,000 tests per day. Demand is coming from physician clinics, state health departments, employers, schools, universities, hospitals and nursing homes. Peak demand came in early July when we received specimens in excess of our capacity for several days.

How have positivity rates trended?
On July 6 our positivity rate peaked at 17%. That’s dropped to a current average of about 10%, including 12.5% for patients under age 30 and 9% for those 30 and above.

What is your turnaround time for Covid-19 PCR testing?
Our turnaround time from specimen collection to result reporting is consistently 24 hours for all clients. We have limited new client additions in order to maintain a 24-hour turnaround time. The location of our main 150,000-square-foot lab—adjacent to Nashville International Airport—has also helped.

Could PathGroup do more Covid-19 PCR tests if it had more supplies?
Yes. The current shortages of specimen collection devices and test kits are keeping us below instrument capacity. We’ve kept in close touch with our suppliers on changing situations and plan accordingly.

Are most private insurers matching Medicare’s $100 reimbursement rate for Covid-19 PCR testing?
Yes.

Describe the NIH grant that PathGroup was awarded and how it will be used?
PathGroup has received a $20.75 million grant from the National Institutes of Health (NIH) under its Rapid Acceleration of Diagnostics (RADx) program. The grant funding will be used to purchase new high-throughput liquid handling, robot and automated testing equipment from Illumina, LGC, Hologic and Thermo Fisher. We also plan to hire an additional 100 to 200 employees with the goal of expanding our Covid-19 PCR testing capacity to 80,000 tests per day. Importantly, we’ll be diversifying our supply chain to mitigate risk against supply chain constraints as fall/winter approaches.

Which Covid-19 antibody test does PathGroup perform?
Roche’s cobas serum antibody test. We’re performing about 400 tests per day.

Have non-Covid-19 clinical and pathology test volumes bounced back from the lows?
Yes. In late March/early April, our volumes had declined temporarily by 75% with anatomic pathology case volume hit the hardest. But in May, as physician offices started re-opening and elective surgeries resumed, we saw a sharp rise in non-Covid-19 volumes that are currently back at 100% of pre-pandemic levels, maybe even a little higher.

What precautions have you taken for your employees?
About 15% to 20% of our 2,200 employees are currently working from home. All people entering our lab facilities have their temperature checked and must wear masks. We are also offering Covid-19 testing on a voluntary basis to any employee that requests one, whether symptomatic or asymptomatic.

Do you think Covid-19 will come back in a severe way this fall/winter?
I would not want to predict severity, but the disease is likely to continue to spread this coming fall/winter. A vaccine will help, but Covid-19 is not going away. One of my biggest fears is that the disease will adapt and mutate into a more virulent strain, such as SARS-CoV-1 in 2003 and the MERS-CoV in 2012.