Nov 16, 2019

NanoSatellite: accurate characterization of expanded tandem repeat length and sequence through whole genome long-read sequencing on PromethION

Genome Biology
Arne De RoeckKristel Sleegers

Abstract

Technological limitations have hindered the large-scale genetic investigation of tandem repeats in disease. We show that long-read sequencing with a single Oxford Nanopore Technologies PromethION flow cell per individual achieves 30× human genome coverage and enables accurate assessment of tandem repeats including the 10,000-bp Alzheimer's disease-associated ABCA7 VNTR. The Guppy "flip-flop" base caller and tandem-genotypes tandem repeat caller are efficient for large-scale tandem repeat assessment, but base calling and alignment challenges persist. We present NanoSatellite, which analyzes tandem repeats directly on electric current data and improves calling of GC-rich tandem repeats, expanded alleles, and motif interruptions.

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Mentioned in this Paper

Sitting Root Test
Genome
Nucleic Acid Sequencing
Alzheimer's Disease
Tandem Mass Spectrometry
ABCA7 protein, human
Evaluation
Protein Domain
Analysis
Alleles

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