Long insert whole genome sequencing for copy number variant and translocation detection.
As next-generation sequencing continues to have an expanding presence in the clinic, the identification of the most cost-effective and robust strategy for identifying copy number changes and translocations in tumor genomes is needed. We hypothesized that performing shallow whole genome sequencing (WGS) of 900-1000-bp inserts (long insert WGS, LI-WGS) improves our ability to detect these events, compared with shallow WGS of 300-400-bp inserts. A priori analyses show that LI-WGS requires less sequencing compared with short insert WGS to achieve a target physical coverage, and that LI-WGS requires less sequence coverage to detect a heterozygous event with a power of 0.99. We thus developed an LI-WGS library preparation protocol based off of Illumina's WGS library preparation protocol and illustrate the feasibility of performing LI-WGS. We additionally applied LI-WGS to three separate tumor/normal DNA pairs collected from patients diagnosed with different cancers to demonstrate our application of LI-WGS on actual patient samples for identification of somatic copy number alterations and translocations. With the evolution of sequencing technologies and bioinformatics analyses, we show that modifications to current approaches may improve our ability to interrogate cancer genomes.
Integrated Cancer Genomics Division, Translational Genomics Research Institute, Phoenix, AZ, 85004, USA, Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, 85004, USA and Cancer Treatment Centers of America, Medical Oncology, Goodyear, AZ, 85338, USA.
Winnie S
WS
Liang
Jessica
J
Aldrich
Waibhav
W
Tembe
Ahmet
A
Kurdoglu
Irene
I
Cherni
Lori
L
Phillips
Rebecca
R
Reiman
Angela
A
Baker
Glen J
GJ
Weiss
John D
JD
Carpten
David W
DW
Craig
D056915:DNA Copy Number Variations; D015723:Gene Library; D015894:Genome, Human; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D009369:Neoplasms / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*; D014178:Translocation, Genetic