Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding. Academic Article uri icon

Overview

abstract

  • 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.

authors

publication date

  • June 22, 2009

Research

keywords

  • Base Pairing
  • Computational Biology
  • Genetic Variation
  • Genome, Human
  • Ligases
  • Sequence Analysis, DNA

Identity

PubMed Central ID

  • PMC2752135

Scopus Document Identifier

  • 69749090013

Digital Object Identifier (DOI)

  • 10.1101/gr.091868.109

PubMed ID

  • 19546169

Additional Document Info

volume

  • 19

issue

  • 9