Makale detayı · 2009
Sequence and structural variation in a human genome uncovered by short read massively parallel ligation sequencing using two base encoding
- Yıl
- 2009
- Tür
- preprint
Veri kaynağı ayrımı
- YÖKSİS YÖKSİS makale kaydı
- YÖKSİS dergi adı Genome Research
- Katalog eşleşmesi (ISSN) Genome Research
- OpenAlex OpenAlex zenginleştirmesi (özet, atıf, konular)
Özet
OpenAlex · İngilizce
We describe the genome sequencing of an anonymous individual of African origin using a novel ligation-based sequencing assay that enables a unique form of error correction that improves the raw accuracy of the aligned reads to >99.9%, allowing us to accurately call SNPs with as few as two reads per allele. We collected several billion mate-paired reads yielding approximately 18x haploid coverage of aligned sequence and close to 300x clone coverage. Over 98% of the reference genome is covered with at least one uniquely placed read, and 99.65% is spanned by at least one uniquely placed mate-paired clone. We identify over 3.8 million SNPs, 19% of which are novel. Mate-paired data are used to physically resolve haplotype phases of nearly two-thirds of the genotypes obtained and produce phased segments of up to 215 kb. We detect 226,529 intra-read indels, 5590 indels between mate-paired reads, 91 inversions, and four gene fusions. We use a novel approach for detecting indels between mate-paired reads that are smaller than the standard deviation of the insert size of the library and discover deletions in common with those detected with our intra-read approach. Dozens of mutations previously described in OMIM and hundreds of nonsynonymous single-nucleotide and structural variants in genes previously implicated in disease are identified in this individual. There is more genetic variation in the human genome still to be uncovered, and we provide guidance for future surveys in populations and cancer biopsies.
Konular
Atıflar
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527 atıf
OpenAlex cited_by_count (önbellek / veritabanı)
Yerel katalogda bu makaleye atıf yapan 11 yayın (OpenAlex referans eşleşmesi; tam dünya listesi değildir).
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- Mapping copy number variation by population scale genome sequencing 2011
- Haplotype resolved genome sequencing of a Gujarati Indian individual 2011
- Characterization of missing human genome sequences and copy number polymorphic insertions 2010
- Alu repeat discovery and characterization within human genomes 2011
- Shouji: a fast and efficient pre-alignment filter for sequence alignment 2019
- Sensitive and fast mapping of di base encoded reads 2011
- Fast and accurate mapping of Complete Genomics reads 2015
- The Role of Next Generation Sequencing in Genetic Counseling 2015
- Gene Expression Changes in Crops Induced by Nanomaterial Exposure 2026