diff --git a/modelad_test_config.yaml b/modelad_test_config.yaml
new file mode 100644
index 00000000..28a54bed
--- /dev/null
+++ b/modelad_test_config.yaml
@@ -0,0 +1,17 @@
+destination: &dest syn51498092
+staging_path: ./staging
+gx_folder: none
+gx_table: none
+datasets:
+  - biomarkers:
+      files:
+        - name: biomarkers
+          id: syn61250724.1
+          format: csv
+      final_format: json
+      provenance:
+        - syn61250724.1
+      destination: *dest
+      custom_transformations: 1
+      column_rename:
+        agedeath: age_death
diff --git a/src/agoradatatools/etl/transform/__init__.py b/src/agoradatatools/etl/transform/__init__.py
index ef000e81..2bbd6b9d 100644
--- a/src/agoradatatools/etl/transform/__init__.py
+++ b/src/agoradatatools/etl/transform/__init__.py
@@ -16,6 +16,7 @@
 )
 from agoradatatools.etl.transform.team_info import transform_team_info
 from agoradatatools.etl.transform.proteomics import transform_proteomics
+from agoradatatools.etl.transform.biomarkers import transform_biomarkers
 
 __all__ = [
     "transform_distribution_data",
@@ -28,4 +29,5 @@
     "transform_rnaseq_differential_expression",
     "transform_team_info",
     "transform_proteomics",
+    "transform_biomarkers",
 ]
diff --git a/src/agoradatatools/etl/transform/biomarkers.py b/src/agoradatatools/etl/transform/biomarkers.py
new file mode 100644
index 00000000..d820e0b5
--- /dev/null
+++ b/src/agoradatatools/etl/transform/biomarkers.py
@@ -0,0 +1,46 @@
+"""
+This module contains the transformation logic for the biomarkers dataset.
+This is for the Model AD project.
+"""
+
+import pandas as pd
+from typing import Dict
+
+
+def transform_biomarkers(datasets: Dict[str, pd.DataFrame]) -> pd.DataFrame:
+    """
+    Takes a dictionary of dataset DataFrames, extracts the biomarkers
+    DataFrame, and transforms it into a DataFrame grouped by
+    'model', 'type', 'age_death', 'tissue', and 'units'.
+
+    Args:
+        datasets (Dict[str, pd.DataFrame]): Dictionary of dataset names mapped to their DataFrame.
+
+    Returns:
+        pd.DataFrame: A DataFrame containing biomarker data modeled after intended final structure.
+    """
+    biomarkers_dataset = datasets["biomarkers"]
+    group_columns = ["model", "type", "age_death", "tissue", "units"]
+    point_columns = ["genotype", "measurement", "sex"]
+
+    missing_columns = [
+        col
+        for col in group_columns + point_columns
+        if col not in biomarkers_dataset.columns
+    ]
+    if missing_columns:
+        raise ValueError(
+            f"Biomarker dataset missing columns: {', '.join(missing_columns)}"
+        )
+
+    biomarkers_dataset = biomarkers_dataset.fillna("none")
+    data_rows = []
+
+    grouped = biomarkers_dataset.groupby(group_columns)
+
+    for group_key, group in grouped:
+        entry = dict(zip(group_columns, group_key))
+        entry["points"] = group[point_columns].to_dict("records")
+        data_rows.append(entry)
+
+    return pd.DataFrame(data_rows)
diff --git a/src/agoradatatools/process.py b/src/agoradatatools/process.py
index 75854767..46232143 100644
--- a/src/agoradatatools/process.py
+++ b/src/agoradatatools/process.py
@@ -1,5 +1,4 @@
 import logging
-import typing
 from typing import Union
 
 import synapseclient
@@ -13,11 +12,14 @@
 from agoradatatools.reporter import ADTGXReporter, DatasetReport
 from agoradatatools.constants import Platform
 
+
 logger = logging.getLogger(__name__)
 
 
 # TODO refactor to avoid so many if's - maybe some sort of mapping to callables
-def apply_custom_transformations(datasets: dict, dataset_name: str, dataset_obj: dict):
+def apply_custom_transformations(
+    datasets: dict, dataset_name: str, dataset_obj: dict
+) -> Union[DataFrame, dict, None]:
     if not isinstance(datasets, dict) or not isinstance(dataset_name, str):
         return None
     if dataset_name == "biodomain_info":
@@ -59,6 +61,8 @@ def apply_custom_transformations(datasets: dict, dataset_name: str, dataset_obj:
     if dataset_name in ["proteomics", "proteomics_tmt", "proteomics_srm"]:
         df = datasets[dataset_name]
         return transform.transform_proteomics(df=df)
+    if dataset_name == "biomarkers":
+        return transform.transform_biomarkers(datasets=datasets)
     else:
         return None
 
@@ -186,7 +190,7 @@ def process_dataset(
 
 def create_data_manifest(
     syn: synapseclient.Synapse, parent: synapseclient.Folder = None
-) -> typing.Union[DataFrame, None]:
+) -> Union[DataFrame, None]:
     """Creates data manifest (dataframe) that has the IDs and version numbers of child synapse folders
 
     Args:
diff --git a/tests/test_assets/biomarkers/input/biomarkers_duplicated_input.csv b/tests/test_assets/biomarkers/input/biomarkers_duplicated_input.csv
new file mode 100644
index 00000000..b0091d2f
--- /dev/null
+++ b/tests/test_assets/biomarkers/input/biomarkers_duplicated_input.csv
@@ -0,0 +1,5 @@
+model,type,measurement,units,age_death,tissue,sex,genotype
+ModelA,TypeA,1,A,1,TissueA,male,genotype1
+ModelA,TypeA,1,A,1,TissueA,male,genotype1
+ModelA,TypeA,1,A,1,TissueA,male,genotype2
+ModelA,TypeA,1,A,1,TissueA,male,genotype2
diff --git a/tests/test_assets/biomarkers/input/biomarkers_extra_column.csv b/tests/test_assets/biomarkers/input/biomarkers_extra_column.csv
new file mode 100644
index 00000000..2e0b287f
--- /dev/null
+++ b/tests/test_assets/biomarkers/input/biomarkers_extra_column.csv
@@ -0,0 +1,3 @@
+model,type,measurement,units,age_death,tissue,sex,genotype,extra
+ModelA,TypeA,1,A,1,TissueA,male,genotype1,extra1
+ModelA,TypeA,2,A,1,TissueA,male,genotype1,extra1
diff --git a/tests/test_assets/biomarkers/input/biomarkers_good_test_input.csv b/tests/test_assets/biomarkers/input/biomarkers_good_test_input.csv
new file mode 100644
index 00000000..72e5b23f
--- /dev/null
+++ b/tests/test_assets/biomarkers/input/biomarkers_good_test_input.csv
@@ -0,0 +1,7 @@
+model,type,measurement,units,age_death,tissue,sex,genotype
+ModelA,TypeA,1,A,1,TissueA,male,genotype1
+ModelA,TypeA,2,A,1,TissueA,male,genotype1
+ModelA,TypeA,3,A,2,TissueA,male,genotype2
+ModelA,TypeB,4,A,2,TissueA,male,genotype1
+ModelA,TypeB,5,A,3,TissueA,male,genotype1
+ModelA,TypeB,6,A,3,TissueA,male,genotype2
diff --git a/tests/test_assets/biomarkers/input/biomarkers_missing_column.csv b/tests/test_assets/biomarkers/input/biomarkers_missing_column.csv
new file mode 100644
index 00000000..f3099769
--- /dev/null
+++ b/tests/test_assets/biomarkers/input/biomarkers_missing_column.csv
@@ -0,0 +1,3 @@
+model,type,measurement,units,age_death,tissue,sex
+ModelA,TypeA,1,A,1,TissueA,male
+ModelA,TypeA,2,A,1,TissueA,male
diff --git a/tests/test_assets/biomarkers/input/biomarkers_missing_input.csv b/tests/test_assets/biomarkers/input/biomarkers_missing_input.csv
new file mode 100644
index 00000000..e1b0a8d0
--- /dev/null
+++ b/tests/test_assets/biomarkers/input/biomarkers_missing_input.csv
@@ -0,0 +1,4 @@
+model,type,measurement,units,age_death,tissue,sex,genotype
+ModelA,TypeA,1,A,1,TissueA,male,genotype1
+ModelA,TypeA,,A,1,TissueA,male,genotype1
+,TypeA,1,A,1,TissueA,male,genotype1
diff --git a/tests/test_assets/biomarkers/input/biomarkers_none_input.csv b/tests/test_assets/biomarkers/input/biomarkers_none_input.csv
new file mode 100644
index 00000000..fda48b74
--- /dev/null
+++ b/tests/test_assets/biomarkers/input/biomarkers_none_input.csv
@@ -0,0 +1,10 @@
+model,type,measurement,units,age_death,tissue,sex,genotype
+ModelA,TypeA,1,A,1,TissueA,male,genotype1
+ModelA,TypeA,none,A,1,TissueA,male,genotype1
+ModelA,TypeA,NA,A,1,TissueA,male,genotype1
+ModelA,TypeA,nan,A,1,TissueA,male,genotype1
+ModelA,TypeA,N/A,A,1,TissueA,male,genotype1
+none,TypeA,1,A,1,TissueA,male,genotype1
+none,TypeA,1,A,1,TissueA,male,NA
+NA,TypeA,1,A,1,TissueA,male,genotype1
+ModelA,NA,1,A,1,TissueA,male,genotype1
diff --git a/tests/test_assets/biomarkers/output/biomarkers_duplicated_output.json b/tests/test_assets/biomarkers/output/biomarkers_duplicated_output.json
new file mode 100644
index 00000000..35acca28
--- /dev/null
+++ b/tests/test_assets/biomarkers/output/biomarkers_duplicated_output.json
@@ -0,0 +1,31 @@
+[
+    {
+        "model": "ModelA",
+        "type": "TypeA",
+        "age_death": 1,
+        "tissue": "TissueA",
+        "units": "A",
+        "points": [
+            {
+                "genotype": "genotype1",
+                "measurement": 1,
+                "sex": "male"
+            },
+            {
+                "genotype": "genotype1",
+                "measurement": 1,
+                "sex": "male"
+            },
+            {
+                "genotype": "genotype2",
+                "measurement": 1,
+                "sex": "male"
+            },
+            {
+                "genotype": "genotype2",
+                "measurement": 1,
+                "sex": "male"
+            }
+        ]
+    }
+]
\ No newline at end of file
diff --git a/tests/test_assets/biomarkers/output/biomarkers_extra_column_output.json b/tests/test_assets/biomarkers/output/biomarkers_extra_column_output.json
new file mode 100644
index 00000000..3561d90f
--- /dev/null
+++ b/tests/test_assets/biomarkers/output/biomarkers_extra_column_output.json
@@ -0,0 +1,21 @@
+[
+    {
+        "model": "ModelA",
+        "type": "TypeA",
+        "age_death": 1,
+        "tissue": "TissueA",
+        "units": "A",
+        "points": [
+            {
+                "genotype": "genotype1",
+                "measurement": 1,
+                "sex": "male"
+            },
+            {
+                "genotype": "genotype1",
+                "measurement": 2,
+                "sex": "male"
+            }
+        ]
+    }
+]
\ No newline at end of file
diff --git a/tests/test_assets/biomarkers/output/biomarkers_good_test_output.json b/tests/test_assets/biomarkers/output/biomarkers_good_test_output.json
new file mode 100644
index 00000000..e1beeda8
--- /dev/null
+++ b/tests/test_assets/biomarkers/output/biomarkers_good_test_output.json
@@ -0,0 +1,68 @@
+[
+    {
+        "model": "ModelA",
+        "type": "TypeA",
+        "age_death": 1,
+        "tissue": "TissueA",
+        "units": "A",
+        "points": [
+            {
+                "genotype": "genotype1",
+                "measurement": 1,
+                "sex": "male"
+            },
+            {
+                "genotype": "genotype1",
+                "measurement": 2,
+                "sex": "male"
+            }
+        ]
+    },
+    {
+        "model": "ModelA",
+        "type": "TypeA",
+        "age_death": 2,
+        "tissue": "TissueA",
+        "units": "A",
+        "points": [
+            {
+                "genotype": "genotype2",
+                "measurement": 3,
+                "sex": "male"
+            }
+        ]
+    },
+    {
+        "model": "ModelA",
+        "type": "TypeB",
+        "age_death": 2,
+        "tissue": "TissueA",
+        "units": "A",
+        "points": [
+            {
+                "genotype": "genotype1",
+                "measurement": 4,
+                "sex": "male"
+            }
+        ]
+    },
+    {
+        "model": "ModelA",
+        "type": "TypeB",
+        "age_death": 3,
+        "tissue": "TissueA",
+        "units": "A",
+        "points": [
+            {
+                "genotype": "genotype1",
+                "measurement": 5,
+                "sex": "male"
+            },
+            {
+                "genotype": "genotype2",
+                "measurement": 6,
+                "sex": "male"
+            }
+        ]
+    }
+]
\ No newline at end of file
diff --git a/tests/test_assets/biomarkers/output/biomarkers_missing_output.json b/tests/test_assets/biomarkers/output/biomarkers_missing_output.json
new file mode 100644
index 00000000..f736159a
--- /dev/null
+++ b/tests/test_assets/biomarkers/output/biomarkers_missing_output.json
@@ -0,0 +1,35 @@
+[
+    {
+        "model": "ModelA",
+        "type": "TypeA",
+        "age_death": 1,
+        "tissue": "TissueA",
+        "units": "A",
+        "points": [
+            {
+                "genotype": "genotype1",
+                "measurement": 1.0,
+                "sex": "male"
+            },
+            {
+                "genotype": "genotype1",
+                "measurement": "none",
+                "sex": "male"
+            }
+        ]
+    },
+    {
+        "model": "none",
+        "type": "TypeA",
+        "age_death": 1,
+        "tissue": "TissueA",
+        "units": "A",
+        "points": [
+            {
+                "genotype": "genotype1",
+                "measurement": 1.0,
+                "sex": "male"
+            }
+        ]
+    }
+]
\ No newline at end of file
diff --git a/tests/test_assets/biomarkers/output/biomarkers_none_output.json b/tests/test_assets/biomarkers/output/biomarkers_none_output.json
new file mode 100644
index 00000000..f9272cb3
--- /dev/null
+++ b/tests/test_assets/biomarkers/output/biomarkers_none_output.json
@@ -0,0 +1,74 @@
+[
+    {
+        "model": "ModelA",
+        "type": "TypeA",
+        "age_death": 1,
+        "tissue": "TissueA",
+        "units": "A",
+        "points": [
+            {
+                "genotype": "genotype1",
+                "measurement": "1",
+                "sex": "male"
+            },
+            {
+                "genotype": "genotype1",
+                "measurement": "none",
+                "sex": "male"
+            },
+            {
+                "genotype": "genotype1",
+                "measurement": "none",
+                "sex": "male"
+            },
+            {
+                "genotype": "genotype1",
+                "measurement": "none",
+                "sex": "male"
+            }, 
+            {
+                "genotype": "genotype1",
+                "measurement": "none",
+                "sex": "male"
+            }
+        ]
+    },
+    {
+        "model": "ModelA",
+        "type": "none",
+        "age_death": 1,
+        "tissue": "TissueA",
+        "units": "A",
+        "points": [
+            {
+                "genotype": "genotype1",
+                "measurement": "1",
+                "sex": "male"
+            }
+        ]
+    },
+    {
+        "model": "none",
+        "type": "TypeA",
+        "age_death": 1,
+        "tissue": "TissueA",
+        "units": "A",
+        "points": [
+            {
+                "genotype": "genotype1",
+                "measurement": "1",
+                "sex": "male"
+            },
+            {
+                "genotype": "none",
+                "measurement": "1",
+                "sex": "male"
+            },
+            {
+                "genotype": "genotype1",
+                "measurement": "1",
+                "sex": "male"
+            }
+        ]
+    }
+]
\ No newline at end of file
diff --git a/tests/transform/test_biomarkers.py b/tests/transform/test_biomarkers.py
new file mode 100644
index 00000000..280ce788
--- /dev/null
+++ b/tests/transform/test_biomarkers.py
@@ -0,0 +1,73 @@
+import os
+
+import pandas as pd
+import pytest
+
+from agoradatatools.etl.transform import biomarkers
+
+
+class TestTransformBiomarkers:
+    data_files_path = "tests/test_assets/biomarkers"
+    pass_test_data = [
+        (
+            # Pass with good fake data
+            "biomarkers_good_test_input.csv",
+            "biomarkers_good_test_output.json",
+        ),
+        (
+            # Pass with duplicated data
+            "biomarkers_duplicated_input.csv",
+            "biomarkers_duplicated_output.json",
+        ),
+        (
+            # Pass with none data
+            "biomarkers_none_input.csv",
+            "biomarkers_none_output.json",
+        ),
+        (
+            # Pass with missing data
+            "biomarkers_missing_input.csv",
+            "biomarkers_missing_output.json",
+        ),
+        (
+            # Pass with extra column
+            "biomarkers_extra_column.csv",
+            "biomarkers_extra_column_output.json",
+        ),
+    ]
+    pass_test_ids = [
+        "Pass with good fake data",
+        "Pass with duplicated data",
+        "Pass with none data",
+        "Pass with missing data",
+        "Pass with extra column",
+    ]
+    fail_test_data = [("biomarkers_missing_column.csv")]
+    fail_test_ids = [("Fail with missing column")]
+
+    @pytest.mark.parametrize(
+        "biomarkers_file, expected_output_file", pass_test_data, ids=pass_test_ids
+    )
+    def test_transform_biomarkers_should_pass(
+        self, biomarkers_file, expected_output_file
+    ):
+        biomarkers_df = pd.read_csv(
+            os.path.join(self.data_files_path, "input", biomarkers_file)
+        )
+        output_df = pd.DataFrame(
+            biomarkers.transform_biomarkers(datasets={"biomarkers": biomarkers_df})
+        )
+        expected_df = pd.read_json(
+            os.path.join(self.data_files_path, "output", expected_output_file),
+        )
+        pd.testing.assert_frame_equal(output_df, expected_df)
+
+    @pytest.mark.parametrize("biomarkers_file", fail_test_data, ids=fail_test_ids)
+    def test_transform_biomarkers_should_fail(
+        self, biomarkers_file, error_type: BaseException = ValueError
+    ):
+        biomarkers_df = pd.read_csv(
+            os.path.join(self.data_files_path, "input", biomarkers_file)
+        )
+        with pytest.raises(error_type):
+            biomarkers.transform_biomarkers(datasets={"biomarkers": biomarkers_df})