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April 23, 2024
7 min. read

Decision Factors: Choosing Between APP Quality Reporting Options

Jordan Gage, VP of Client Delivery & Analytics
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Time is ticking! 2024 marks the final year for Accountable Care Organizations (ACOs) to submit quality data through the Centers for Medicare and Medicaid Services (CMS) Web Interface (WI). Come 2025, a new chapter in Alternative Payment Model (APM) Performance Pathway (APP) Quality Reporting is required. This signals a significant shift in how Medicare ACOs will report on their quality measures.

Understand Your Options for APP Quality Reporting

Our goal is to equip you with the knowledge and insights necessary to choose the reporting method that best aligns with your organization's structure and resources. This article outlines the three APP Quality Reporting options, along with the pros and cons of each, for you to consider. You’ll also get a peer perspective from Nebraska Health Network on the challenges they encountered as they progressed through their selection process. By understanding the options and their nuances, ACOs can ensure a smooth transition and continued success in the evolving landscape of quality reporting.

Let’s begin with what you need to know: Starting Q1 2026, all ACOs must leverage one of three reporting options:

Electronic Clinical Quality Measures (eCQMs): This method leverages the electronic patient-level data from Certified Electronic Health Record Technology (CEHRTs) output in the Quality Reporting Document Architecture (QRDA). It requires complete reporting on all patients seen by each ACO participating provider, across all payers, Medicare or not.

Clinical Quality Measures (CQMs): Similar to eCQMs in purpose, CQMs require reporting on all patients, all payers. However, CQMs allow for manual data or supplemental data abstraction for patient medical records.

Medicare Clinical Quality Measures (Medicare CQMs): This option is the same as the CQMs but requires that an ACO only submit quality data for Medicare ACO assigned and assignable beneficiaries, versus all patients.

Understanding the differences between these options is crucial for organizations to make an informed decision about the best APP Quality Reporting option for their needs.

Evaluate Your APP Quality Reporting Options

Choosing the optimal APP Quality Reporting option hinges on examining and evaluating the strengths and weaknesses of each approach. Let's dissect eCQM, CQM, and Medicare CQM across key categories to help guide your decision:


  • eCQM: This method often requires the most significant upfront investment. Factors include electronic health record (EHR) fees for generating QRDA files, collaborating with each ACO EHR vendor for correct and timely file output, and establishing a process to transfer large patient datasets. While initial setup is resource-intensive, ongoing maintenance is expected to be significantly lower.
  • CQM & Medicare CQM: These options could require lower upfront time and costs but would likely come at the potential expense of ongoing maintenance, particularly as EHRs undergo system updates and measures evolve.


  • eCQM: Reporting heavily relies on the cooperation of participating provider EHR vendors to accurately output measure data.
  • CQM & Medicare CQM: Both options offer more flexibility to pull and aggregate data across EHRs, however, with CMS actively pushing for a complete switch to electronic reporting, familiarizing yourself with eCQMs now could prove advantageous in the long run.


  • eCQM: Identifying and correcting missing or inaccurate data presents a challenge with eCQMs. This option might lead to an inaccurate picture of patient care and hinder maximizing quality scores.
  • CQM & Medicare CQM: With these two options, data flows through the measure engine within a population health analytics vendor’s environment, mirroring the current ACO data validation process. This facilitates easier identification and correction of bad data, ensuring higher quality information.


  • eCQM: Inconsistency across how data is stored in the EHR, and mapped by the EHR vendor to the QRDA-I output file, could potentially result in lower performance scores with eCQM.
  • CQM: With this option, it may be easier to pull or incorporate non-standard data fields, possibly resulting in a higher more complete score.
  • Medicare CQM: In addition to the flexibility in the format in which the data is received, this option offers the potential for higher or more representative performance scores, as it’s only focused on your Medicare ACO patients.

Looking into these factors can help you make an informed decision about the APP Quality Reporting option that best aligns with your goals and resource constraints.

The majority of MSSP ACOs are still working through the requirements for eCQM.


Peer Perspective: Nebraska Health Network on considering the eCQMs challenges

At Koan Health we understand the approaches surrounding healthcare analytics are rooted in the recognition that as eCQMs become the eventual mandate, evaluating and planning will be critical steps. While this transition demands considerable effort and may not initially seem like the optimal starting point, it is essential for future readiness and ongoing success. Therefore, easing into this process while taking advantage of other reporting options such as Medicare CQMs will likely be the optimal solution to be fully ready for electronic quality reporting in the future.

To gain a peer perspective of the challenges Medicare ACOs face with the upcoming shift to new quality reporting standards, we spoke with Sara Ausedmore-Matteo, project manager at Nebraska Health Network (NHN). Through this insightful conversation, NHN identified four key challenges:

1. EMR Vendor Participation & Cooperation

EMR vendor participation is one of our primary requirements for all patient data. eCQMs rely heavily on EMR vendors to generate QRDA-I files, a specific data format for quality reporting.

That said, there is the all-or-nothing nature of eCQMs to think about. If even one EMR within an ACO's network cannot generate the required QRDA-I files, the entire eCQM reporting process fails. Standardization across EMR vendors is crucial, but unfortunately, it's not always present.

QRDA file inconsistencies can also happen. Even if EMRs can generate QRDA-I files, variations in how they interpret reporting logic can lead to inconsistencies. This can make accurate data analysis a challenge.

2. Prioritizing Data Security in an Expanding Data Pool

The switch to all-payer, all-patient reporting significantly expands the data pool ACOs need to manage. This raises concerns about data security, especially considering recent healthcare data breaches.

ACOs must find a way to balance reporting requirements with data security – to securely generate, transfer, and store a much larger volume of data while adhering to reporting mandates.

3. Managing Expectations for All-Payer, All-Patient Reporting

Reporting on all patients, regardless of payer status, introduces new complexities. ACOs need to coordinate with specialists to ensure they are aware of and able to fulfill reporting requirements for primary care services included in the eCQM measures.

Successful implementation of all-payer, all-patient reporting requires open communication and collaboration between ACOs and specialists.

4. Tackling Issues Can Be More Trouble

Troubleshooting issues with eCQMs can be more challenging than with CQMs. Limited visibility into data logic within EMRs can make it difficult to pinpoint the root cause of discrepancies.

While challenges exist, Sara’s insights offer keys to success - collaboration and proactive planning. By carefully considering EMR vendor capabilities, prioritizing data security, and fostering collaboration with specialists, ACOs can position reporting logic themselves for success in the new reporting landscape.

Success in eCQMs demands meticulous planning, coordination, and validation, all of which necessitate significant time and resources. Therefore, ACOs must embark on this planning journey, even if they initially opt for Medicare CQMs or CQMs for PY2025. Starting early ensures readiness and a smooth transition towards achieving their quality reporting goals.


Koan Health clients identified EMR vendor cooperation and costs associated with producing the required data for reporting as the two major challenges in their decision-making process.

NHN’s Decision for 2024 and Beyond

We also asked Sara about NHN’s final decision to go with dual reporting (WI & APP) for 2024 and the long-term vision of eCQMS. Here's what she shared:

Dual Reporting for 2024: In recognition of the complexities information will be important in future conversations with our ACO partners about reporting surrounding the new reporting options, we opted for a dual reporting approach for 2024 to allow for more time and further testing of the new processes. This means NHN will utilize the web interface for PY 2024 reporting in Q1-2025 while simultaneously working through Medicare CQMs throughout 2024. Dual reporting is an opportunity for NHN to compare performance and submit the optimal results to CMS.  

Taking a Phased Approach: Our decision to start with Medicare CQMs acknowledges the challenges of all-payer, all-patient reporting and allows for data collection in a larger beneficiary pool. This information will be instrumental in future conversations with our ACO partners regarding reporting changes and performance.

Long-Term Vision: Electronic Quality Measures. While a specific completion date from CMS is undetermined, we see this as an opportunity to begin paving the way for the ultimate goal of adopting full electronic reporting.

With our measured approach and gathering valuable data throughout 2024, we are hoping to position ourselves for a smoother transition to eCQMs in the future.


The majority of Koan Health clients have opted for Dual Reporting (CMS WI + APP) for PY 2024.


Making an Informed Decision on APP Quality Reporting

Selecting the right APP Quality Reporting option can feel a bit overwhelming, but it doesn't have to be. Koan Health provides expert guidance along with a proven approach to help you with your decision and transition. We encourage you to:

1. Self-Assess and Know Your ACO Needs

  • Data Capabilities: Evaluate your current infrastructure. Do you have the systems and resources to support the chosen reporting option?
  • Reporting Preferences: Consider the level of detail and specificity required. Prioritize a comprehensive assessment or a more streamlined approach.
  • Resource Allocation: Be realistic about the technical complexities and potential resource requirements involved.

2. Seek Advice from a Trusted Partner

By carefully considering your needs and leveraging a population health analytics partner like Koan Health, you can confidently choose the APP Quality Reporting option that positions your organization for success. The benefits of choosing Koan Health to support your decision-making include:

  • Client-Centric Approach: We provide a personalized analysis to recommend the APP Quality Reporting option that best suits your organization.
  • Qualified Registry Status: Our 2024 certification ensures we meet the highest CMS standards for ACO MIPS reporting.
  • Comprehensive Solutions: We offer all required eCQM and CQM measures, with ongoing updates based on annual specifications.
  • Proven Experience: We've been rigorously testing eCQM measures and have a well-established user interface and QRDA processing system.

Contact us to schedule a demo and explore our APP Quality Reporting process flow and technical capabilities.

Peer Perspectives: Nebraska Health Network (NHN)

How to Successfully Navigate the APP Quality Reporting Options  

How did you evaluate the options for APP Quality Reporting?

What were your biggest considerations in evaluating APP Quality Reporting?

How did you arrive at a decision for APP Quality Reporting?

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