2011 Fiscal Year Final Research Report
Development of genome-partitioning technologies for next generation sequencing
| Project/Area Number |
21249024
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| Research Category |
Grant-in-Aid for Scientific Research (A)
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| Allocation Type | Single-year Grants |
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| Section | 一般 |
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| Research Field |
Human genetics
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| Research Institution | Yokohama City University |
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Principal Investigator |
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| Co-Investigator(Kenkyū-buntansha) |
MIYAKE Noriko 横浜市立大学, 医学部, 准教授 (40523494)
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| Project Period (FY) |
2009 – 2011
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| Keywords | 分子遺伝学 |
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| Research Abstract |
The advent and frequent update of next generation sequencers(NGSs) can attain the appropriate accuracy for mutation analysis and push disease-related genome analysis into the new stages. We now use Illumina Genome Analyzer(GA) IIx and Hiseq2000 which can produce as much as 60-Gb and 600-Gb sequences in one run, respectively. To focus on genes, we utilized exon capture methods such as SureSelect(Agilent). The current NGS protocol uses 100-108-bp pair-end reads and usually produces 8-9 Gb sequences(per one sample) could be enough for analysis of the whole exome : 90% of exome bait regions are covered by 8-10 reads or more. Sequences are aligned using MAQ, BWA, Novoalign and commercial-based NextGENe software all of which are able to extract nucleotide changes and small insertions/deletions. The most critical step is the priority scheme selecting variants. We have been successful in addressing culprit mutations in several diseases.
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[Journal Article] Mutations in POLR3A and POLR3B encoding RNA polymerase III subunits cause an autosomal recessive hypomyelinating leukoencephalopathy2011
Author(s)
Saitsu H, Osaka H, Sasaki M, Takanashi J, Hamada K, Yamashita A, Shiina M, Kondo Y, Nishiyama K, Tsurusaki Y, Miyake N, Doi H, Ogata K, Inoue K, Matsumoto N.
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Journal Title
Am J Hum Genet
Volume: 90(1)
Pages: 86-90
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[Journal Article] Exome sequencing reveals a homozygous SYT14 mutation in adult-onset autosomal recessive spinocerebellar ataxia with psychomotor retardation2011
Author(s)
Doi H, Yoshida K, T Yasuda, Fukuda M, Fukuda Y, Morita H, Ikeda S-i, Kato R, Tsurusaki Y, Miyake N, Saitsu H, Sakai H, Miyatake S, Shiina M, Nukina N, Koyano S, Tsuji S, Kuroiwa Y, Matsumoto N.
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Journal Title
Am J Hum Genet
Volume: 89(2)
Pages: 320-327
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[Journal Article] Dominant negative mutations in α-II spectrin cause early onset West syndrome with severe cerebral hypomyelination spastic quadriplegia, and developmental delay2010
Author(s)
Saitsu H, Tohyama J, Kumada T, Egawa K, Hamada K, Okada I, Mizuguchi T, Osaka H, Miyata R, Furukawa T, Haginoya K, Hoshino H, Goto T, Hachiya Y, Yamagata T, Saitoh S, Nagai T, Nishiyama K, Nishimura A, Miyake N, Komada M, Hayashi K, Hirai S, Ogata K, Kato M, Fukuda A, Matsumoto N.
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Journal Title
Am J Hum Genet
Volume: 86(6)
Pages: 881-889
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[Journal Article] Loss of decorin dermatan sulfate impairing collagen bundle formation in a new type of Ehlers-Danlos syndrome2010
Author(s)
Miyake N, Kosho T, Mizumoto S, Furuichi T, Hatamochi A, Nagashima Y, Arai E, Takahashi K, Kawamura R, Wakui K, Takahashi J, Kato H, Yasui H, Ishida T, Ohashi H, Nishimura G, Shiina M, Saitsu H, Tsurusaki T, Doi H, Fukushima Y, Ikegawa S, Yamada S, Sugahara K, Matsumoto N.
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Journal Title
Hum Mut
Volume: 31(8)
Pages: 966-974
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[Journal Article] Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome2010
Author(s)
Ng S, Bigham A, Buckingham K, Hannibal M, McMillin M, Gildersleeve H, Beck A, Tabor H, Cooper G, Mefford H, Lee C, Turner E, Smith J, Rieder M, Yoshiura K, Matsumoto N, Ohta T, Niikawa N, Nickerson D, Bamshad M, Shendure J.
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Journal Title
Nat Genet
Volume: 42(9)
Pages: 790-793
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[Journal Article] SMOC1 is essential for ocular and limb development in humans and mice
Author(s)
Okada I, Hamanoue H, (denotes equal contribution) Terada K, Tohma T, Megarbane A, Chouery E, Abou-Ghoch J, Jalkh N, Cogulu O, Ozkinay F, Horie K, Takeda J, Furuichi T, Ikegawa S, Nishiyama K, Miyatake S, Nishimura A, Mizuguchi T, Niikawa N, Hirahara F, Kaname T, Yoshiura K-i, Tsurusaki Y, Doi H, Miyake N, Furukawa T, Matsumoto N, Saitsu H.
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