SMURF-seq for fast, multiplexed copy number profiling with long-read sequencers

We present SMURF-seq, a protocol to efficiently sequence short DNA molecules on a long-read sequencer by randomly ligating them to form long molecules. Applying SMURF-seq using Oxford Nanopore Technologies MinION yields up to 30 countable fragments per read at present, which generates multiple copy number profiles in a single run at a reduced time and cost. More broadly, SMURF-seq expands the utility of long-read sequencers for read-counting applications, which do not benefit from increased read length.

[1]  Martin Kircher,et al.  High‐throughput DNA sequencing – concepts and limitations , 2010, BioEssays : news and reviews in molecular, cellular and developmental biology.

[2]  Michael Wigler,et al.  Genome-wide copy number analysis of single cells , 2012, Nature Protocols.

[3]  Nevenka Dimitrova,et al.  Optimizing sparse sequencing of single cells for highly multiplex copy number profiling , 2015, Genome research.

[4]  J. Sebat,et al.  Representational oligonucleotide microarray analysis: a high-resolution method to detect genome copy number variation. , 2003, Genome research.

[5]  Kenny Q. Ye,et al.  Strong Association of De Novo Copy Number Mutations with Autism , 2007, Science.

[6]  N. Loman,et al.  A complete bacterial genome assembled de novo using only nanopore sequencing data , 2015, Nature Methods.

[7]  Ji Huang,et al.  [Serial analysis of gene expression]. , 2002, Yi chuan = Hereditas.

[8]  S. Koren,et al.  Nanopore sequencing and assembly of a human genome with ultra-long reads , 2017, bioRxiv.

[9]  M. Wigler,et al.  Circular binary segmentation for the analysis of array-based DNA copy number data. , 2004, Biostatistics.

[10]  David A. Matthews,et al.  Real-time, portable genome sequencing for Ebola surveillance , 2016, Nature.

[11]  J. Kendall,et al.  SMASH, a fragmentation and sequencing method for genomic copy number analysis , 2016, Genome research.

[12]  Derek Y. Chiang,et al.  High-resolution mapping of copy-number alterations with massively parallel sequencing , 2009, Nature Methods.

[13]  Heng Li.  Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM , 2013, 1303.3997.

[14]  J. Troge,et al.  Tumour evolution inferred by single-cell sequencing , 2011, Nature.

[15]  J. Hicks,et al.  Potential of Aqueous Humor as a Surrogate Tumor Biopsy for Retinoblastoma , 2017, JAMA ophthalmology.

[16]  N. Navin,et al.  Clonal Evolution in Breast Cancer Revealed by Single Nucleus Genome Sequencing , 2014, Nature.