Repetitive DNA and next-generation sequencing: computational challenges and solutions

Abstract

Repetitive DNA sequences are abundant in a broad range of species, from bacteria to mammals, and they cover nearly half of the human genome. Repeats have always presented technical challenges for sequence alignment and assembly programs. Next-generation sequencing projects, with their short read lengths and high data volumes, have made these challenges more difficult. From a computational perspective, repeats create ambiguities in alignment and assembly, which, in turn, can produce biases and errors when interpreting results. Simply ignoring repeats is not an option, as this creates problems of its own and may mean that important biological phenomena are missed. We discuss the computational problems surrounding repeats and describe strategies used by current bioinformatics systems to solve them.

What's in a genome? The C-value enigma and the evolution of eukaryotic genome content

“…An opposing interpretation is that sequence datasets for larger genomes are less complete than for smaller genomes, due to the inherent difficulties in sequencing and assembly of highly repetitive genomes (e.g. [23]). The presence of more non-coding DNA, much of which will be tightly compacted as heterochromatin, can also make it challenging to achieve truly complete coverage of a genome sequence.…”

Consensus Statement on next-generation-sequencing-based diagnostic testing of hereditary phaeochromocytomas and paragangliomas

“…Some NGS techniques, such as Ion Torrent (Life Technologies/ThermoFisher, Waltham, Massachusetts, USA), rely on single-nucleotide additions and can have a high error rate for indel detection (1%) 37 . Illumina platforms have high sensitivity (0.1%); however, false-positive errors have also been reported 37,38 . AT-rich regions and GC-rich regions are well known to be problematic in conventional PCR and Sanger sequencing 38 .…”

“…Illumina platforms have high sensitivity (0.1%); however, false-positive errors have also been reported 37,38 . AT-rich regions and GC-rich regions are well known to be problematic in conventional PCR and Sanger sequencing 38 . These areas can also be challenging for capture by target and WES probes and, therefore, tend to be underrepresented by NGS.…”

“…Efficient capture of exons and adjacent regions, quality of sequencing and error rates are influenced by the reagents and kits used in library preparation and exome capture, as well as by the chemicals and equipment used for sequencing 38 . For laboratories that adopt commercial NGS services or institutional core facilities for processing their samples, it is critical to ensure that every step of the protocol is performed following strict quality control standards, using reliable reagents and sequencers with low error rates.…”

Discovering and Genotyping Twilight Zone Deletions

“…They can be distinguished by their definition of discordant read, their clustering/grouping techniques, and their details in deriving predictions from groups of discordant reads. Note that handling of reads that became multiply mapped due to repetitive sequence often plays a major role [29], see for example [6] for a combinatorially principled approach.…”