The personal genome browser

originally published in

1. Liran Juan,
2. Mingxiang Teng,
3. Tianyi Zang,
4. Yafeng Hao,
5. Zhenxing Wang,
6. Chengwu Yan,
7. Yongzhuang Liu,
8. Jie Li,
9. Tianjiao Zhang and
10. Yadong Wang*

INTRODUCTION

Advances in high-throughput sequencing technologies have brought us into individual genome era. Population-level sequencing efforts, such as the 1000 Genomes Project and the UK10K Project (http://www.uk10k.org), have led to an explosive growth of individual genome sequencing data. The whole genome sequencing followed by functional and phenotypic analysis is projected to become a routine clinical practice in the near future. However, how to visualize and annotate individual genomes based on the existing knowledge to support clinical practices remains a critical challenge.

Principles of the PGB design

• The PGB aims at visualizing and annotating the individual genome variants and their effects on molecular traits and organismal phenotypes. The fundamental principle of the PGB design is based on genetic–molecular–phenotypic model which is a broadly accepted approach to annotate genetic variants. The model logically includes three layers: (i) variants of individual genomes; (ii) molecular traits associated with individual genomic variants, such as changes to genes and regulatory elements; (iii) phenotypes associated with genetic variants and molecular traits, e.g. diseases or drug interactions. This model can systematically interpret and annotate the personal genome.
• In order to support functional annotation of individual genomes, the PGB integrates 30 bioinformatics knowledge bases Then, an individual genome variants centred approach is designed to visualize the individual genome. The PGB displays the individual genome variants and associated molecular traits/phenotypes from the whole genome scale to single nucleotide scale, with reference to genome information simultaneously updated on the background of the same page. These features allow the PGB to perform comprehensive functional annotation and individual genomes visualization.

The PGB functionality

• The PGB consists of a reference genome panel and an individual genome panel sharing the same genomic coordinate system and reference sequence The reference genome panel displays common annotations of comparative genomics, genes and ribonucleicacids (RNAs), regulation, variations and repeats and phenotype/disease associations, etc. Individual genome panel  highlights variants and their functions of user specified individual genomes. The two panels can be merged together to facilitate users to reorder and compare tracks across the panels . In Select Individual window , users can upload personal genome variants files to the PGB, and specify personal genome to be illustrated in the individual genome panel.

The screenshots

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http://nar.oxfordjournals.org/content/early/2014/05/05/nar.gku361.long