Contact: Ruibang Luo, Jingcheng Zhang
Email: [email protected], [email protected]

Governome is an owner-governed genomic data management system based on blockchain, it designed to empower individuals with absolute control over their genomic data during data sharing.

This repository showcases the available applications of the current version of Governome, including data preprocessing for whole-genome data, individual variant query, cohort study, GWAS analysis, and forensics. Additionally, this repository demonstrates how data owners and hospitals upload information and provide proofs to participate in the workflow of Governome.

All the homomorphical computation modules in Governome are based on the excellent library tfhe-go, and all the zk-SNARKs modules in Governome are based on gnark.

• Introduction
• Installation
  • Install go 1.21
  • Get Governome source code
• Data Preprocessing
• Quick Start
  • Upload a SegKey and generating a proof
  • Individual variant query
  • Cohort study
  • Single SNP GWAS
  • Forensics
• Usage
  • Data Preprocessing
  • Upload a SegKey and generating a proof
  • Individual variant query
  • Cohort study
  • Single SNP GWAS
  • Forensics

Download and install Golang from the official website (https://golang.org/dl/).

# Download the latest Golang version 1.21 by visiting the official website (https://golang.org/dl/) and, 
# copying the download link for the Linux tarball.
# An example is shown below:
wget https://golang.org/dl/go1.21.10.linux-amd64.tar.gz

# Extract the downloaded tarball to your preferred local directory. In this example, we'll use `$HOME/.local`:
mkdir -p $HOME/.local
tar -xvzf go1.21.10.linux-amd64.tar.gz -C $HOME/.local

# Remove the tarball after extraction
rm go1.21.10.linux-amd64.tar.gz

# Set up your Go workspace and environment variables
## Create the required directory structure:
mkdir -p $HOME/go/{bin,src,pkg}

## add link to bashrc or .profile
## add the GOPATH,GOROOT to your `~/.bashrc` or `~/.profile`
echo 'export GOPATH=$HOME/go
export GOROOT=$HOME/.local/go
export PATH=$PATH:$GOROOT/bin:$GOPATH/bin' >> ~/.bashrc
source ~/.bashrc

## Verify the installation
## You will get "go version go1.21.10 linux/amd64" if installed successfully
go version

You can clone this repo as following:

mkdir Governome_RootFolder
cd Governome_RootFolder
git clone [email protected]:HKU-BAL/Governome.git
cd Governome

# $Governome_DIR is path of Governome
Governome_DIR=$(pwd)

We advise to create a root folder and organize the data in the following way to ensure the efficiency of accessing and processing data:

Governome_RootFolder/
    ├── Plaintext_Data/
    ├── Individuals/
    ├── Phenotype/
    ├── Segments_Enc_Data/
    └── ...

Here you need to update the defaultPath for the root folder.

In Governome, we process whole-genome data based on VCF (Variant Call Format) files. We have chosen 1000 Genomes dataset for benchmarking, and you can download the individual list here. Specifically, considering that the original VCF files can be overly cumbersome, we provide a simplified version that only retains the rsID and genotype columns. You can download this simplified data here or the preprocessed version here. If you find the whole-genome data too large, you can download a simplified version based on chromosome 20 from here. Please note that, at this moment, modify the Seg_num in ./auxiliary/params.go to 1024 or 2048.

In Governome, data is stored in encrypted form. If you have already downloaded the preprocessed data, please ignore this step. To encrypt the raw data, you need to run the following command:

cd ${Governome_DIR}/examples/data_process/
go run main.go -seg

# the raw data is available at ${Governome_RootFolder}/Segments_Enc_Data

Since the 1000 Genomes dataset does not provide short tandem repeat loci, we have chosen to randomly generate this data for the 2504 individuals and encrypt it. Here is an example code:

cd ${Governome_DIR}/examples/data_process/
go run main.go -str -strenc

For the sake of demonstration, we have omitted the process of collaboratively generating the public key and evaluation key in ThFHE. You can generate the public and private key pair for TFHE first to facilitate subsequent computations:

cd ${Governome_DIR}/examples/data_process/
go run main.go -genkey

If you want to see how multi-parties collaboratively generating the public key and evaluation key in ThFHE, you can turn to here for a Simple Demo.

This module demonstrates how, as a data owner, you will generate the ciphertext and zero-knowledge proofs that need to be submitted for a query. Please ensure that you have executed the corresponding command for generating the public and private key pair for TFHE.

cd ../user_proof
go run main.go -rsid ${Your Target rsID} -user ${DataOwner Name, e.g. HG00096} -id ${1 or 2, 1 for owners, 2 for hospitals}

go run main.go -all -rsid ${Your Target rsID} 

go run main.go -all -segID ${Your Target appID or segID} 

Noted that b and c are prepared for subsequent demonstrations, which take time. If you simply want to experience the full functionality of Governome, please ignore them.

As a Data Owner, you are highly interested in your own genotype data. To fulfill this, you can initiate a query to Governome to gain insights into your health condition. Governome provides a module specifically designed for this purpose. You can use the following command to perform the query:

cd ../data_owner_query/
go run main.go -rsid ${Your Target rsID} -user ${DataOwner Name, e.g. HG00096}

For the sake of demonstration, the parameters used here are highly insecure. If you wish to use secure parameters, please add the statement -toy=false. If you have executed b, you may also choose to add -read and -verify to read and verify the proofs from a file.

As the head of a pharmaceutical company, you and your team intend to develop a new drug based on a specific target SNP. However, you are uncertain about the true correlation between the target and the disease over a specific population. In this regard, you can initiate a distribution query to Governome regarding this target. The command is as follows:

cd ../querySingleSnp/
go run main.go -rsid ${Your Target rsID} -cohort ${Your interested population, e.g. EUR}

And you will obtain the result of how the distribution of different genotypes. Similarly, you can set -toy=false to use secure parameters, and add -read and -verify to read and verify the proofs from a file.

After obtaining the distribution of Single SNPs, you are not satisfied with simple statistical results and wish to conduct further refined analysis. You want to select a population and perform GWAS analysis on the target population to determine associations using p-values. Governome provides a module for this purpose, and you can execute the following command:

cd ../gwas/
go run main.go -rsid ${Your Target rsID} -cohort ${Your interested population, e.g. EUR}

Noted that the the Phenotype comes from Hail, you can download it here. The default Phenotype is CaffeineConsumption. If you want to change it, you can modify the Phenotype file by yourself. Similarly, you can set -toy=false to use secure parameters, and add -read and -verify to read and verify the proofs from a file.

As authority/law enforcement agency, you have encountered individuals with unidentified identities in your jurisdiction. To determine their identities, you can use the 13 Short Tandem Repeat (D3S1358, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, D16S539, THO1, TPOX, CSF1PO, D7S820) in Governome's auxiliary data block to confirm their identities. Here, the individual's identity is no longer represented by strings like HG00096 but is standardized as integers from 0 to 2503. You can run the following command:

cd ../search_person/
go run main.go -groundtruth ${Your Target Person's ID, 0 ~ 2503}

Here, you can use -GroundTruth to set the individuals of interest. If you do not wish to perform the query on individuals from the 1000 Genomes dataset, you can set it to -1, and we will randomly generate such individuals for you. Similarly, you can set -toy=false to use secure parameters, and add -read and -verify to read and verify the proofs from a file if you have executed c.

  -genkey
    	Whether to generate the keys
  -path string
    	Root FilePath (default "../../..")
  -precomputed
    	Whether owner choose to precompute the access token
  -seg
    	Whether to preprocess the data to segments
  -str
    	Whether to generate the str data
  -strenc
    	Whether to encrypt the str data
  -toy
    	Whether using Toy Parameters (default true)

  -all
    	Whether include all Individuals
  -begin int
    	Begin ID when generate all
  -end int
    	Begin ID when generate all (default 2504)
  -id int
    	1 or 2, 1 for owners, 2 for hospitals (default 1)
  -precomputed
    	Whether owner choose to precompute the access token
  -rsid string
    	Target Site in rsID (default "rs6053810")
  -segID int
    	AppID or SegID for all individual (default -1)
  -user string
    	User Name in 1kGP (default "HG00096")

  -precomputed
    	Whether owner choose to precompute the access token
  -read
    	Whether read Data from file, not suitable for toy params
  -rsid string
    	Target Site in rsID (default "rs6053810")
  -toy
    	Whether using Toy Parameters (default true)
  -user string
    	User Name in 1kGP (default "HG00096")
  -verify
    	Whether verifying the proofs

  -cohort string
    	Population, in 'AFR', 'AMR', 'EAS', 'EUR', 'SAS', 'ALL' (default "ALL")
  -precomputed
    	Whether owner choose to precompute the access token
  -read
    	Whether read Data from file, not suitable for toy params
  -rsid string
    	Target Site in rsID (default "rs6053810")
  -toy
    	Whether using Toy Parameters (default true)
  -verify
    	Whether verifying the proofs

  -cohort string
    	Population, in 'AFR', 'AMR', 'EAS', 'EUR', 'SAS' (default "EUR")
  -precomputed
    	Whether owner choose to precompute the access token
  -read
    	Whether read Data from file, not suitable for toy params
  -rsid string
    	Target Site in rsID (default "rs6053810")
  -toy
    	Whether using Toy Parameters (default true)
  -verify
    	Whether verifying the proofs

  -groundtruth int
    	GroundTruthID in 1kGP
  -precomputed
    	Whether owner choose to precompute the access token
  -read
    	Whether read Data from file, not suitable for toy params
  -toy
    	Whether using Toy Parameters (default true)
  -verify
    	Whether verifying the proofs