The first Irish genome and ways of improving sequence accuracy

Abstract

Whole-genome sequencing of an Irish person reveals hundreds of thousands of novel genomic variants. Imputation using previous known information improves the accuracy of low-read-depth sequencing.

Figure 1

Personal genomes sequenced so far. Each male (yellow) or female (pink) sequenced is shown in the approximate geographical position of their ethnic origin. The name or codename and ethnicity of the individual sequenced, the date of publication, the sequencing platform used, the coverage and the reference are given for each genome. Platforms: 3730xl (Applied Biosystems by Life Technologies, Carlsbad, CA, USA); Complete Genomics Analysis Platform (CGA) Complete Genomics, Mountain View, CA, USA); FLX (Roche, Basel, Switzerland); Genome Analyzer (GA) (Illumina, San Diego, CA, USA); Heliscope (He6licos BioScience, Cambridge, MA, USA); SOLiD (Applied Biosystems by Life Technologies).

Figure 2

The influence of read-depth on discovering personal genomic variants. Sequences included in our analysis are represented by blue squares, with names or codenames as shown in Figure 1. The lines indicate correlations; the YH genome (red square) was not included in the correlation analysis because it is thought to be an outlier, possibly owing to its higher percentage of single-end-read sequencing. (a) Higher read-depth sequencing can reveal more SNPs, as shown by the positive correlation between read-depth and number of SNPs detected. (b) The ratio of heterozygous to homozygous SNPs shows a positive relationship with read-depth of sequencing, suggesting that high-depth sequencing can detect heterozygous SNPs better.