Using generative adversarial networks for genome variant calling from low depth ONT sequencing data

• Published in: Scientific reports Vol. 12; no. 1; p. 8725
• Main Authors: Yang, Han, Gu, Fei, Zhang, Lei, Hua, Xian-Sheng
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 30.05.2022; Nature Publishing Group; Nature Portfolio
• Subjects: 631/114/1305; 631/114/2397; 692/308/2056; Coronaviruses; COVID-19 - genetics; DNA sequencing; Genome, Human; Genomes; Humanities and Social Sciences; Humans; multidisciplinary; Polymorphism, Single Nucleotide; SARS-CoV-2 - genetics; Science; Science (multidisciplinary); Sequence Analysis, DNA - methods; Severe acute respiratory syndrome coronavirus 2
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-022-12346-7

Genome variant calling is a challenging yet critical task for subsequent studies. Existing methods almost rely on high depth DNA sequencing data. Performance on low depth data drops a lot. Using public Oxford Nanopore (ONT) data of human being from the Genome in a Bottle (GIAB) Consortium, we trained a generative adversarial network for low depth variant calling. Our method, noted as LDV-Caller, can project high depth sequencing information from low depth data. It achieves 94.25% F1 score on low depth data, while the F1 score of the state-of-the-art method on two times higher depth data is 94.49%. By doing so, the price of genome-wide sequencing examination can reduce deeply. In addition, we validated the trained LDV-Caller model on 157 public Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) samples. The mean sequencing depth of these samples is 2982. The LDV-Caller yields 92.77% F1 score using only 22x sequencing depth, which demonstrates our method has potential to analyze different species with only low depth sequencing data.