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Long-read genome sequencing identifies causal structural variation in a Mendelian disease

Genetics in Medicine volume 20, pages 159163 (2018) | Download Citation

The first two authors contributed equally to this work.

Abstract

Purpose

Current clinical genomics assays primarily utilize short-read sequencing (SRS), but SRS has limited ability to evaluate repetitive regions and structural variants. Long-read sequencing (LRS) has complementary strengths, and we aimed to determine whether LRS could offer a means to identify overlooked genetic variation in patients undiagnosed by SRS.

Methods

We performed low-coverage genome LRS to identify structural variants in a patient who presented with multiple neoplasia and cardiac myxomata, in whom the results of targeted clinical testing and genome SRS were negative.

Results

This LRS approach yielded 6,971 deletions and 6,821 insertions > 50 bp. Filtering for variants that are absent in an unrelated control and overlap a disease gene coding exon identified three deletions and three insertions. One of these, a heterozygous 2,184 bp deletion, overlaps the first coding exon of PRKAR1A, which is implicated in autosomal dominant Carney complex. RNA sequencing demonstrated decreased PRKAR1A expression. The deletion was classified as pathogenic based on guidelines for interpretation of sequence variants.

Conclusion

This first successful application of genome LRS to identify a pathogenic variant in a patient suggests that LRS has significant potential for the identification of disease-causing structural variation. Larger studies will ultimately be required to evaluate the potential clinical utility of LRS.

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Acknowledgements

The authors thank the research subject and clinical care teams for their participation in this research study; Chen-Shan (Jason) Chin for helpful discussions; and Primo Baybayan and Matt Boitano for PacBio library preparation and sequencing.

Author information

Affiliations

  1. Department of Pathology, Stanford University, Stanford, California, USA

    • Jason D Merker
    • , Zachary Zappala
    • , Laure Fresard
    • , Yanli Hou
    • , Kevin S Smith
    • , Stephen B Montgomery
    •  & Jillian G Buchan
  2. Stanford Medicine Clinical Genomics Service, Stanford Health Care, Stanford, California, USA

    • Jason D Merker
    • , Tam Sneddon
    • , Megan Grove
    • , Sowmi Utiramerur
    • , Jillian G Buchan
    •  & Euan A Ashley
  3. Pacific Biosciences, Menlo Park, California, USA

    • Aaron M Wenger
    • , Christine C Lambert
    • , Kevin S Eng
    • , Luke Hickey
    •  & Jonas Korlach
  4. Department of Genetics, Stanford University, Stanford, California, USA

    • Zachary Zappala
    • , Stephen B Montgomery
    • , James Ford
    •  & Euan A Ashley
  5. Department of Medicine, Stanford University, Stanford, California, USA

    • Daryl Waggott
    • , Matthew Wheeler
    • , James Ford
    •  & Euan A Ashley
  6. Stanford Center for Inherited Cardiovascular Disease, Stanford University, Stanford, California, USA

    • Daryl Waggott
    • , Matthew Wheeler
    •  & Euan A Ashley
  7. Stanford Cancer Institute, Stanford, California, USA

    • James Ford

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Competing interests

A.M.W., C.C.L., K.S.E., L.H., and J.K. are employees and shareholders of Pacific Biosciences, a company commercializing DNA sequencing technologies. The other authors declare no conflict of interest.

Corresponding author

Correspondence to Euan A Ashley.

Supplementary information

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Publication history

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DOI

https://doi.org/10.1038/gim.2017.86

Supplementary material is linked to the online version of the paper at http://www.nature.com/gim