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

Arne De Roeck,Svenn D’Hert,Peter De Rijk,Jasper Van Dongen,Liene Bossaerts,Mojca Strazisar,Wouter De Coster,Christine Van Broeckhoven,Rita Cacace,Kristel Sleegers,Tim De Pooter

doi:10.1186/s13059-019-1856-3

Arne De Roeck, Svenn D’Hert + Show 9 more

Open Access

https://doi.org/10.1186/s13059-019-1856-3

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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.

Highlights

Half of the human genome is estimated to consist of repetitive DNA elements
We focused our analyses on an ABCA7 variable number of tandem repeats (VNTRs), for which we recently discovered that expanded alleles are a strong risk factor for Alzheimer’s disease [22]
Apart from Subject01 which we sequenced during the PromethION optimization phase, all sequencing datasets had a similar distribution of quality and an overall median identity to the reference genome of 86% (Additional file 1: Figure S4)

Summary

Introduction

Half of the human genome is estimated to consist of repetitive DNA elements. These are categorized as interspersed repeats (e.g., Alu, LINE elements, and segmental duplications) and tandem repeats (TRs). The latter includes short tandem repeats (STRs; a.k.a. microsatellites) which have 1–6-bp motifs and variable number of tandem repeats (VNTRs; a.k.a. minisatellites) with repeat unit length > 6 bp. We know of approximately 50 TRs that affect disease, primarily neurological. STRs are involved in rare diseases with high penetrance due to repeat expansions, and VNTRs are mostly associated with common complex disorders [2, 3].

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