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Authors:
Jong Bhak1 and Sungwoong Jho1
Affiliations:
1. Genome Research Foundation, Suwon, 443-270, South Korea.
Contacts:
Unique Paper Identifier: 2011.11.05.01.01.JongBhak
Abstract
A Caucasian female human genome analyses are reported. It was sequenced using Illumina GA2 next generation sequencers and 90GB of short DNA fragments of ~90 base pairs were obtained. Overall coverage on to the reference human geome (HG19) was 99.2% with sequencing depth of 33 folds. 3.5 million SNPs, 200,000 short indels, 10,000 long structural variations, and 125,000 copy number variations were found. We found 10,000 non-synonymous mutations resulting in 100 genes affected by amino acid changes. Out of 100, we found 2 presumably critical mutations that resulted in some structural changes. The whole analysis was carried out by a bioinformatics pipeline called 'Genome Engine' which finished the whole analysis process in about 2 weeks, semi-automatically. The donor of the genome is Rosalynn Gill who donated all the rights and information associated with the data to the public as a part of PGP (Personal Genome Project). Gill's genome was the first publically available female human genome and the data were available from http://bioftp.org since April 2010 with analyses results. Here we present the second stage comparative analyses of her genome.
Introduction
NGS (next generation sequencers) produced many personal genomes in various research projects such as PGP (Personal Genome Project), 1000 genome project, YH genome project of China, Korean Genome Project (KGP) by Genome Research Foundation in Korea, Japanese genome project, and Indian genome project. By 2011, the number of genomes has increased from 10s in 2010 to hundreds. However, relatively few female human genomes have been competely publicized. In 2008, Leiden university announced that they had sequenced the first female human genome. However, the claimed to be the first female human genome data were not publicized nor its research report was announced by Nov. 2011. In the mean time, PGP has publicized the first female genome, Rosalynn Gill's, on the web in April 2010 with extensive analyses that were similar to the previous genomes such as James Watson, YH, and SJK. Gill was PGP number 9 and many of phenotypic and clinical data points were also public at the time of data publication.
The data have been used to be compared with various existing genomes and 10s of Korean genomes that have been available through KPGP (Korean Personal Genome Project). Here, we report the second stage analyses of PGP9 using automated genome pipeline called "Genome Engine". Genome Engine was developed to analyse the first Korean human genome in 2008. It is a personal genome analyzer with common functions such as detecting SNPs, Indels, SVs, CNVs, chart drawing functions, and genome browsing. The main idea of the second stage female genome analysis was to apply an already common genome analysis package to annotate it as much as possible with minimum effort.
Results
Results come here.
Acknowledgement
This work was supported by the GRF in-house program (XXXX).
References
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