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Precise detection of de novo single nucleotide variants in human genomes

2018; National Academy of Sciences; Volume: 115; Issue: 21 Linguagem: Inglês

10.1073/pnas.1802244115

1091-6490

Laura Gómez-Romero, Kim Palacios-Flores, José Luis Reyes, Delfino García, Margareta Boege, Guillermo Dávila, Margarita Flores, Michael C. Schatz, Rafael Palacios,

Genomic variations and chromosomal abnormalities

Significance The precise location of variants in the human genome is of utmost importance. We present a unique approach, coverage-based single nucleotide variant (SNV) identification (COBASI), which uses only perfect matches between the reads of a sequence project and a reference genome to detect and accurately identify de novo SNVs. From the perfect matches, a representation of the read coverage per nucleotide along the genome, the variation landscape, is generated. SNVs are then pinpointed as significant changes in coverage and de novo SNVs can be identified with high precision. The performance of COBASI was analyzed using simulations and experimentally validated by sequencing de novo SNVs identified from a parent–offspring trio. We propose this pipeline as a useful tool for different genomic applications.