1M-PI Protocols

Our Multi-Omics Data

Protocols Precision Begins at the Source

Every sample within the 1M-PI is collected, processed, and analyzed using meticulously standardized protocols, purpose-built to ensure reproducibility, precision, and cross-site comparability. These protocols are validated across our certified omics laboratories in the USA, Türkiye, and South Korea. They will be uniformly implemented in our upcoming facilities in the UK and India, set to launch by Q1 2026. This harmonized approach forms the cornerstone of a globally scalable and scientifically rigorous data ecosystem.

Specimens Analyzed

  • Whole blood (Genomics)

  • Whole blood (Transcriptomics)

  • Plasma (Proteomics)

  • Plasma (Metabolomics)

  • Plasma (Lipidomics)

  • Saliva (Metagenomics)

  • Stool (Metagenomics)

  • Urine (Metabolomics)

Omics Data Generated

  • Genomics (Whole Genome Sequencing)

  • Epigenomics

  • Transcriptomics

  • Proteomics

  • Metabolomics

  • Lipidomics

  • Oral Metagenomics

  • Gut Metagenomics

Sample Collection Protocols

To ensure the highest standards of sample integrity and traceability, all collection procedures follow a unified, rigorously defined protocol.

Key pre-collection requirements include

  • Clear Sample Labeling: Full identifiers—name, surname, and date—must be clearly written on both collection tubes and transport bags to ensure traceability and compliance.

  • Informed Consent Compliance: Verify validity of consent forms, with specific guidance for minors and legal guardians to ensure ethical and legal compliance.

  • Storage and Shipping Protocols: Adhere to strict temperature control and logistics guidelines, including the use of dry ice for samples requiring -80°C storage, timely dispatch, and hygienic handling procedures throughout the chain of custody

Blood Collection

  • EDTA Tubes:

    • Collect 3.5 mL, then invert 5–6 times.

    • Aliquot 0.5 mL x2 (whole blood) &
      0.25 mL x 4–5 (plasma from centrifuge).

    • Preservation: Store at -80°C

  • PAXgene Tubes:

    • Immediately invert 20–30 times due to RNA fragility.

    • Preservation: Store at -80°C


Stool Collection

  • Contamination Control: Utilize a sterile paper sheet.

  • Homogenization: Ensure complete dissolution of fecal matter by vigorously shaking the sample in DNA/RNA shield.

  • Preservation: Store at +4°C (up to 72 hours at home), followed by long-term storage at -80°C.

Saliva Collection

  • Pre-Collection Fasting: Adhere to strict fasting rules (no food, drink, or brushing within 30 minutes).

  • Stabilization: Collect 2 mL, then immediately add stabilizing solution from the red cap tube.

  • Preservation: Store at +4°C (up to 72 hours at home), followed by long-term storage at -80°C.

Urine Collection

  • Transfer System: Use the specialized vacuum transfer mechanism.

  • Tube Identification: Use specific tube colors (yellow cap, blue cap collector).

  • Preservation: Store at +4°C (up to 24 hours at home), followed by long-term storage at -80°C.


Informed Consent & Data Sharing

We protect participants' rights and privacy at every step.

All participants must submit signed consent forms. Unsigned or incomplete forms are not accepted.

Clear sample labelling (name, date) is mandatory.
Unlabeled samples are rejected.

Participants can choose to grant access to their multi-omics data for research and development activities.

Participants gain access to their personal multi-omics data for personal health insights and preventive care.

All participants provide informed consent aligned with global ethics standards and GDPR.
Consent includes:

Longitudinal follow-up
(~10% of cohort)

Use of de-identified data

Personal Data Access &
Data sharing for R&D activities

Longitudinal Multi-Omics Data Generation

Enables dynamic tracking of health over time, uncovering early disease signals and personalized intervention opportunities

7/24 Assistance

Information & Real time support for all concerns and questions including.

  • Captures temporal changes in molecular profiles, revealing cause-effect relationships and disease progression pathways.
  • Enhances predictive modeling and treatment response monitoring by integrating individual baseline and follow-up data.

Multi-Omics Data Generation Pipelines

Genomics (WGS)

  • gDNA extraction with QIAamp kit

  • Library prep via Illumina PCR-Free kits

  • Sequencing on NovaSeq 6000/X Plus

  • Variant calling via DRAGEN Germline Pipeline

Whole Blood Transcriptomics

  • RNA isolation with PAXgene Qiasymphony / RNeasy (manual)

  • QC by NanoDrop + TapeStation (RIN >5)

  • Library: Illumina Stranded Total RNA with Ribo-Zero Plus

  • Uses RNaseH-based rRNA depletion

Plasma Proteomics












Plasma Lipidomics

  • Plasma extraction via BUME method

  • Internal Standards: Avanti LipidoMIX

  • UHPLC: Accucore C30 Column (Vanquish system)

  • MS: Orbitrap Exploris 240, deep scan, stepped collision energies

Plasma & Urine Metabolomics

  • LC/MS-based plasma metabolomics

  • Internal standards: L-Valine-d8, L-Phenyl-d5-alanine

  • Data processed with Compound Discoverer 3.3

  • Filters for compound detection, peak integration, pathway mapping

Oral & Gut Metagenomics

  • gDNA isolation via PowerFecal Pro DNA kit

  • Dual workflows for low- and high-input DNA

  • Taxonomic analysis with MetaPhlAn 3.0 and Kraken2


Data Analysis, Integration & Interpretation using AI & Systems Biology

All datasets are:

  • Structurally standardised for interoperability across AI platforms
  • Aligned with FAIR data principles (Findable, Accessible, Interoperable, Reusable)
  • Enriched with clinical, lifestyle, and biosensor metadata via the participant app

We follow 1M-PI data analysis pipeline:

  • Batch effect correction
  • Missing data imputation
  • Cross-platform normalisation

Clinical-Grade Quality Assurance for Multi-Omics Data Generation

Every data point generated is logged and auditable. Labs operate under the oversight of a central QA board within the 1M-PI Consortium.

Our labs follow internationally recognised standards:

ISO 15189

CLIA/CAP-equivalent QC for clinical omics

Sample traceability systems

QC & Data Handling

Quality Control

  • Pre-injection calibration checks
  • Internal standard mixes, blanks, QC samples used throughout
  • Use of SERRF QC correction

Data Analysis Tools

  • DRAGEN (WGS, RNAseq, Metagenomics)
  • Compound Discoverer 3.3 (Proteomics/Metabolomics)
  • Databases: mzCloud, ChemSpider, KEGG, Human Metabolome DB

Accessing Our Protocols For Approved Partners & Collaborators

We provide access to

  • Full SOPs for sample handling and processing
  • Metadata submission templates
  • Interoperability frameworks for integration with your systems