Hidden biases in germline structural variant detection.

TitleHidden biases in germline structural variant detection.
Publication TypeJournal Article
Year of Publication2021
AuthorsKhayat, MM, Sahraeian, SMohammad E, Zarate, S, Carroll, A, Hong, H, Pan, B, Shi, L, Gibbs, RA, Mohiyuddin, M, Zheng, Y, Sedlazeck, FJ
JournalGenome Biol
Volume22
Issue1
Pagination347
Date Published2021 Dec 20
ISSN1474-760X
KeywordsBase Sequence, Bias, Chromosome Mapping, Genomic Structural Variation, Genomics, Germ Cells, High-Throughput Nucleotide Sequencing, Sequence Analysis, DNA
Abstract

BACKGROUND: Genomic structural variations (SV) are important determinants of genotypic and phenotypic changes in many organisms. However, the detection of SV from next-generation sequencing data remains challenging.

RESULTS: In this study, DNA from a Chinese family quartet is sequenced at three different sequencing centers in triplicate. A total of 288 derivative data sets are generated utilizing different analysis pipelines and compared to identify sources of analytical variability. Mapping methods provide the major contribution to variability, followed by sequencing centers and replicates. Interestingly, SV supported by only one center or replicate often represent true positives with 47.02% and 45.44% overlapping the long-read SV call set, respectively. This is consistent with an overall higher false negative rate for SV calling in centers and replicates compared to mappers (15.72%). Finally, we observe that the SV calling variability also persists in a genotyping approach, indicating the impact of the underlying sequencing and preparation approaches.

CONCLUSIONS: This study provides the first detailed insights into the sources of variability in SV identification from next-generation sequencing and highlights remaining challenges in SV calling for large cohorts. We further give recommendations on how to reduce SV calling variability and the choice of alignment methodology.

DOI10.1186/s13059-021-02558-x
Alternate JournalGenome Biol
PubMed ID34930391
PubMed Central IDPMC8686633
Grant ListUM1 HG008898 / HG / NHGRI NIH HHS / United States

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