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From: steven perkins <>
Subject: [DNA] Article: Whole-genome sequencing and comprehensive variantanalysis of a Japanese individual using massively parallel sequencing
Date: Thu, 18 Nov 2010 17:55:28 -0500


http://www.nature.com/ng/journal/v42/n11/full/ng.691.html
http://www.nature.com/ng/journal/v42/n11/abs/ng.691.html#supplementary-information

Article

Nature Genetics 42, 931 - 936 (2010)

Published online: 24 October 2010 | doi:10.1038/ng.691

Whole-genome sequencing and comprehensive variant analysis of a
Japanese individual using massively parallel sequencing

Akihiro Fujimoto1,2, Hidewaki Nakagawa1, Naoya Hosono1, Kaoru Nakano1,
Tetsuo Abe1, Keith A Boroevich1, Masao Nagasaki3, Rui Yamaguchi3,
Tetsuo Shibuya3, Michiaki Kubo1, Satoru Miyano2,3, Yusuke Nakamura1,3
& Tatsuhiko Tsunoda1,2

Abstract

We report the analysis of a Japanese male using high-throughput
sequencing to ×40 coverage. More than 99% of the sequence reads were
mapped to the reference human genome. Using a Bayesian decision
method, we identified 3,132,608 single nucleotide variations (SNVs).

Comparison with six previously reported genomes revealed an excess of
singleton nonsense and nonsynonymous SNVs, as well as singleton SNVs
in conserved non-coding regions. We also identified 5,319 deletions
smaller than 10 kb with high accuracy, in addition to copy number
variations and rearrangements. De novo assembly of the unmapped
sequence reads generated around 3 Mb of novel sequence, which showed
high similarity to non-reference human genomes and the human
herpesvirus 4 genome.

Our analysis suggests that considerable variation remains undiscovered
in the human genome and that whole-genome sequencing is an invaluable
tool for obtaining a complete understanding of human genetic
variation.

--
Steven C. Perkins      
http://stevencperkins.com/
Online Journal of Genetics and Genealogy
http://jgg-online.blogspot.com/
Steven C. Perkins' Genealogy Page
http://stevencperkins.com/genealogy.html
Steven C. Perkins' Genealogy Blog
http://scpgen.blogspot.com/


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