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AI-Assisted Genomic Variant Detection for Public Health

What it is for

Healthcare
  • GATK is used by the Public Health Laboratory for mutation tracking, antimicrobial resistance analysis, and outbreak comparison — supporting epidemiological investigation and public health response, not direct clinical care for individual patients.

NYC Automated Decision Systems — GATK

Research & Development
  • GATK supports public health laboratory workflows that contribute to disease surveillance research, including the identification of genomic variants used to track pathogen evolution and transmission during outbreaks.

NYC Automated Decision Systems — GATK

Run by
Department of Health and Mental Hygiene (DOHMH)
Where
No fixed location
Kept
Not stated by the NYC Office of Technology and Innovation.
Shared with
Accountable organization
Your copy
You cannot see the data it holds about you. What you can do

What it is for

HealthcareResearch & Development

The Genome Analysis Toolkit (GATK) is used by the NYC Department of Health and Mental Hygiene's Public Health Laboratory to identify genetic mutations in biological samples collected as part of disease surveillance and outbreak investigation. It compares aligned DNA sequencing data against a reference genome to call variants, supporting tasks like resistance analysis and outbreak strain comparison. No personally identifying information is collected or disclosed — the system operates on biological specimens, not individual health records. Results are used by laboratory scientists to inform public health responses.

What it collects and what happens to it

Data taken in

About a measurement
Anonymized data
  • Aligned DNA sequencing reads generated through public health laboratory workflows, representing the genetic content of biological samples. These are numeric base-call measurements with quality scores from sequencing instruments, not linked to any personally identifying information.

NYC Automated Decision Systems — GATK

Operational data
Anonymized data
  • A reference genome sequence serving as the standard baseline for variant comparison, along with curated known variant site resources from public consortia used for recalibration. These are population-level biological reference datasets with no link to any individual.

NYC Automated Decision Systems — GATK

Processing

Classification & Prediction
  • GATK applies naive Bayes classification to distinguish true genomic variants from sequencing errors in aligned reads. This statistical classification is used to produce a filtered set of high-confidence variant calls from raw sequencing data.

NYC Automated Decision Systems — GATK

What it does

Deciding (Analytical AI)
Human decides
  • GATK classifies aligned sequencing bases as true sequence or erroneous data using a naive Bayes model, producing variant calls that laboratory scientists review and interpret to inform public health decisions. The system is supervised — scientists retain decision authority over final conclusions.

NYC Automated Decision Systems — GATK

Outputs

About a measurement
Anonymized data
  • Identified genomic variants relative to the reference sequence — including single nucleotide variants and insertions/deletions — used for mutation tracking, antimicrobial resistance analysis, and outbreak strain comparison. Output is de-identified biological measurement data with no personally identifying information attached.

NYC Automated Decision Systems — GATK

Run by

Department of Health and Mental Hygiene (DOHMH)
  • The Public Health Laboratory within the Disease Control division of the NYC Department of Health and Mental Hygiene deploys GATK to perform genomic variant analysis on biological samples for disease surveillance and outbreak investigation.

NYC Automated Decision Systems — GATK

Built by

Not stated by the NYC Office of Technology and Innovation.

Kept for

Not stated by the NYC Office of Technology and Innovation.

Shared with

Available to the accountable organization
  • Variant call outputs are accessible to laboratory staff and public health scientists within the NYC Department of Health and Mental Hygiene for disease surveillance, resistance analysis, and outbreak investigation purposes.

NYC Automated Decision Systems — GATK

Not available to me
  • Genomic variant data produced by GATK is not available to individuals. The system processes de-identified biological samples and its outputs are internal laboratory results used exclusively for public health surveillance — not accessible to the public or data subjects.

NYC Automated Decision Systems — GATK

Stored

Not stated by the NYC Office of Technology and Innovation.

How to read the colours

Can it identify you?

Anonymized data
Data about people with the link to who is broken. Stripped of identifiers, blurred, aggregated, or noised so this system can’t reasonably tie a record back to an individual.
Pseudonymous data
Each person’s data is tied to a token (hash, ID, template) that lets this system recognise the same person across events, but the token itself doesn’t reveal a name. Reidentification is possible with extra information.
Identifiable data
The data either contains a direct identifier (name, address, account name, recognisable face or voice, plate number) or carries a token this system uses to look up legal identity during processing.

Who completes the loop?

Human decides
This mode suggests; a person decides what to do next. The AI is always advisory — a human is in the loop on every decision. Example: a triage tool ranks cases for a clinician who chooses which to see first.
Human executes
This mode decides; a person carries out the result. Example: an optimizer plans the day’s trash-collection routes, and drivers run them.
Autonomous
This mode decides and acts on its own. No person reviews each decision or carries out the resulting action.

Definitions from the DTPR standard. Amber is about your data, violet about who decides. The fuller the shape and the deeper the colour, the more identifying the data or the less a person is involved.

What you can do

Ask about this system

Questions go to the NYC Office of Technology and Innovation, not the vendor.

Your rights

  • Right to Be Informed of AI UseThe NYC automated decision systems register provides public notice that GATK is in use by the Department of Health and Mental Hygiene. As the system processes de-identified biological samples and does not make decisions about identifiable individuals, there is no individual notification mechanism. Members of the public may consult the NYC AI register for information about this system.
  • Right to Algorithmic TransparencyGATK is open-source software maintained by the Broad Institute, and its methods are publicly documented at https://gatk.broadinstitute.org. The NYC AI register also discloses that the system uses naive Bayes classification for variant calling. Interested members of the public may review the technical documentation on the Broad Institute's website.

Risks and safeguards

  • Reputational harmVariant misclassification could lead to incorrect attribution of a pathogen strain to an individual sample source or outbreak cluster, potentially affecting public health decisions about outbreak containment or individual notification.Safeguard: The system is supervised — laboratory scientists review all variant calls before they are acted upon. GATK uses known variant site resources from public consortia for recalibration to reduce false positive rates. The open-source methodology is peer-reviewed and widely validated in the scientific community.