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Old 09-10-2013, 03:00 AM   #1
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Default PubMed: Genome Reference and Sequence Variation in the Large Repetitive Central Exon

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Genome Reference and Sequence Variation in the Large Repetitive Central Exon of Human MUC5AC.

Am J Respir Cell Mol Biol. 2013 Sep 6;

Authors: Guo X, Zheng S, Dang H, Pace RG, Stonebraker JR, Jones CD, Boellmann F, Yuan G, Haridass P, Fedrigo O, Corcoran DL, Seibold MA, Ranade SS, Knowles MR, O'Neal WK, Voynow JA

Abstract
Despite modern sequencing efforts, the difficulty in assembly of highly repetitive sequence has prevented resolution of human genome gaps, including some in the coding regions of genes with important biological functions. One such gene, MUC5AC, encodes a large, secreted mucin, which is one of the two major secreted mucins in human airways. Currently, the MUC5AC region contains a gap in the human genome reference (hg19) across the large, highly repetitive and complex central exon. This exon region is predicted to contain imperfect tandem repeat sequences and multiple conserved cysteine-rich (CysD) domains. To resolve the MUC5AC genomic gap, we utilized high-fidelity, long polymerase chain reaction, followed by Pacific Biosciences' single molecule real time (SMRT®) sequencing. This technology yielded long sequence reads and robust coverage that allowed for de novo sequence assembly spanning the entire repetitive region. Furthermore, we used SMRT Sequencing of PCR amplicons covering the central exon to identify genetic variation in four individuals. The results demonstrated the presence of segmental duplications of CysD domains, insertions/deletions (indels) of tandem repeats, and single nucleotide variants. Additional studies demonstrated that one of the identified tandem repeat insertions is tagged by non-exonic single nucleotide polymorphisms. Taken together, these data illustrate the successful utility of SMRT Sequencing long reads for de novo assembly of large repetitive sequences to fill the gaps in the human genome. Characterization of the MUC5AC gene and the sequence variation in the central exon will facilitate genetic and functional studies for this critical airway mucin.


PMID: 24010879 [PubMed - as supplied by publisher]



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