Taiwan Biobank’s Purpose

The purpose of the Taiwan Biobank is to establish a human biological database specific to Taiwan, by combining information on lifestyle habits, environmental factors, and biological markers. The aim is to collect a vast amount of biological specimens and health information for biomedical research, and provide researchers from various fields in Taiwan with access to this information.

Since the announcement of the first complete human genome sequence in 2003, biomedical research worldwide has made significant progress. The Taiwan Biobank hopes to contribute to this progress by establishing a database of genome-related information to help biomedical researchers identify clues to combat the onset, progression, and treatment of diseases, and promote the future health of the Taiwanese people.

Any identifiable personal information is removed upon data release to ensure the protection of participant privacy. Researchers from various fields may apply for access to the data and conduct descriptive analyses to establish preliminary study hypotheses, which may serve as the basis for genetic medicine research.
 

Whole-genome Sequencing (WGS)

The Taiwan Biobank uses both Ion Proton and Illumina platforms for next-generation whole-genome sequencing of DNA samples extracted from blood. The WGS data allows for the comprehensive identification of genetic variations among the Taiwanese population and shall help researchers understand the relationship between health and disease at the genetic level.

Illumina

The Illumina platform combines sequencing-by-synthesis (SBS) with a patented fluorescence detection system. Base extension of the complementary strand incorporates fluorescent dye-labeled nucleotides which provide the readout for the base type, thus ensuring the final nucleic acid sequence quality. PCR-free libraries were sequenced on Illumina HiSeq 2500, HiSeq 4000 or NovaSeq 6000 instruments, generating 2×150bp reads. The resulting whole genome sequences were aligned to the human reference, hs38DH, and achieved an average depth of at least 30x.
 

Whole-genome Genotyping (WGG)

TWB Chip

The customized TWB chip is based on Thermo Fisher Scientific’s Axiom Genome-Wide CHB chip. About 650,000 single nucleotide polymorphisms (SNPs) related to cancer, drug response, drug metabolism, or with polymorphism in the Taiwanese population can be detected on the chip.

TWB 2.0 Chip

Based on the genotyping experience accrued from the original TWB chip and whole-genome sequence information from 1000 Taiwan Biobank participants, the National Center for Genome Medicine and Thermo Fisher Scientific jointly developed the TWB 2.0 genotyping chip specifically for the Taiwanese population. This chip contains approximately 750,000 SNPs that can be immediately applied to clinical and precision medicine research.

Imputation

Data from the TWB and TWB 2.0 chips are harmonized through a genotype imputation procedure. In addition, genome-wide associations with questionnaire items, physical examination data and biochemistry results are available.
 

DNA methylation data

DNA methylation data from blood cells was collected by the Illumina Infinium MethylationEPIC BeadChip whole-genome methylation analysis chip. This chip can directly detect the methylation status of over 850,000 individual CpG sites.
 

HLA typing

Human leukocyte antigen (HLA) is located on chromosome 6p and is associated with an individual's immune system. Class I (HLA-A, HLA-B, HLA-C) and class II (HLA-DPA1, HLA-DPB1, HLA-DQA1, HLA-DQB1, HLA-DRB1, HLA-DRB345) HLA loci was genotyped through next-generation sequencing with NXType assay kits. Using this experimental technique, up to 4-field HLA typing data for human leukocyte antigen can be obtained.
 

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WGS Data Analysis Toolchain

Illumina

Function	Tool	Version
Reads Mapping	BWA	0.7.17
Bam file operation	Samtools	1.9
SNV/INDEL calling(GRCh38)	GATK	4.1.0.0
Variation annotation(GRCh38)	Ensembl VEP	108