Journal Article

Hidden biases in germline structural variant detection

Carroll, Andrew, Pan, Bohu, Sedlazeck, Fritz J., Gibbs, Richard A., Hong, Huixiao, Sahraeian, Sayed Mohammad Ebrahim, Zarate, Samantha, Mohiyuddin, Marghoob, Khayat, Michael M., Zheng, Yuanting, Shi, Leming

2021

Overview

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.

• Publisher: BioMed Central,Springer Nature B.V,BMC
• Subject: Animal Genetics and Genomics / Base Sequence / Bias / Bioinformatics / Biomedical and Life Sciences / Chromosome Mapping / Consortia / Datasets / DNA / DNA sequencing / Evolutionary Biology / Families & family life / family / Gene mapping / genome / Genomes / Genomic Structural Variation / Genomic variability / genomics / Genomics - methods / Genotyping / Germ Cells / High-Throughput Nucleotide Sequencing - methods / Human Genetics / Life Sciences / Microbial Genetics and Genomics / Next-generation sequencing / Nucleotide sequence / Parents & parenting / phenotype / Plant Genetics and Genomics / Reproducibility / SEQC2 Article Collection / Sequence Analysis, DNA / Structural variations