A highly annotated whole-genome sequence of a Korean individual

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Abstract
The genome of an anonymous Korean male has been sequenced using a broad spread of genomic techniques. This combinatorial approach allows for detailed characterization of sequence and structural variation. The first four individual genomes to have been determined spanned three distinct ethnic groups: a Yoruba African, northwest European (Craig Venter and James Watson) and Han Chinese. This new work, together with another Korean sequence reported elsewhere, adds the Altaic ethnic grouping to the list. Human genome sequences have so far been reported for individuals with ancestry in three distinct geographical regions: a Yoruba African, two individuals of northwest European origin, and a person from China. Here, using a combination of methods, a highly annotated, whole-genome sequence is provided for a Korean male. Recent advances in sequencing technologies have initiated an era of personal genome sequences. To date, human genome sequences have been reported for individuals with ancestry in three distinct geographical regions: a Yoruba African, two individuals of northwest European origin, and a person from China1,2,3,4. Here we provide a highly annotated, whole-genome sequence for a Korean individual, known as AK1. The genome of AK1 was determined by an exacting, combined approach that included whole-genome shotgun sequencing (27.8× coverage), targeted bacterial artificial chromosome sequencing, and high-resolution comparative genomic hybridization using custom microarrays featuring more than 24 million probes. Alignment to the NCBI reference, a composite of several ethnic clades5,6, disclosed nearly 3.45 million single nucleotide polymorphisms (SNPs), including 10,162 non-synonymous SNPs, and 170,202 deletion or insertion polymorphisms (indels). SNP and indel densities were strongly correlated genome-wide. Applying very conservative criteria yielded highly reliable copy number variants for clinical considerations. Potential medical phenotypes were annotated for non-synonymous SNPs, coding domain indels, and structural variants. The integration of several human whole-genome sequences derived from several ethnic groups will assist in understanding genetic ancestry, migration patterns and population bottlenecks.