1. A comparison of tools for copy-number variation detection in germline whole exome and whole genome sequencing data
- Author
-
Migle Gabrielaite, Mathias Husted Torp, Malthe Sebro Rasmussen, Sergio Andreu-Sánchez, Filipe Garrett Vieira, Christina Bligaard Pedersen, Savvas Kinalis, Majbritt Busk Madsen, Miyako Kodama, Gül Sude Demircan, Arman Simonyan, Christina Westmose Yde, Lars Rønn Olsen, Rasmus L. Marvig, Olga Østrup, Maria Rossing, Finn Cilius Nielsen, Ole Winther, and Frederik Otzen Bagger
- Subjects
Cancer Research ,whole genome sequencing (WGS) ,Bioinformatics ,Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,Whole genome sequencing (WGS) ,Copy-number variation (CNV) ,bioinformatics ,copy-number variation (CNV) ,Benchmark ,Article ,whole exome sequencing (WES) ,benchmark ,structural variant ,Oncology ,SDG 3 - Good Health and Well-being ,Structural variant ,RC254-282 ,Whole exome sequencing (WES) - Abstract
Simple Summary Copy-number variations (CNVs) have important clinical implications for several diseases and cancers. We reviewed 50 popular CNV calling tools and included 11 tools for benchmarking in a reference cohort encompassing 39 whole genome sequencing (WGS) samples paired current clinical standard—SNP-array based CNV calling. For nine samples we also performed whole exome sequencing (WES), to address the effect of sequencing protocol on CNV calling. Furthermore, we included Gold Standard reference sample NA12878, and tested 12 samples with CNVs confirmed by multiplex ligation-dependent probe amplification (MLPA). Tool performance varied greatly in the number of called CNVs and bias for CNV lengths. Some tools had near-perfect recall of CNVs from arrays for some samples, but poor precision. We suggest combining the best tools also based on different methodologies: GATK gCNV, Lumpy, DELLY, and cn.MOPS. Abstract Copy-number variations (CNVs) have important clinical implications for several diseases and cancers. Relevant CNVs are hard to detect because common structural variations define large parts of the human genome. CNV calling from short-read sequencing would allow single protocol full genomic profiling. We reviewed 50 popular CNV calling tools and included 11 tools for benchmarking in a reference cohort encompassing 39 whole genome sequencing (WGS) samples paired current clinical standard—SNP-array based CNV calling. Additionally, for nine samples we also performed whole exome sequencing (WES), to address the effect of sequencing protocol on CNV calling. Furthermore, we included Gold Standard reference sample NA12878, and tested 12 samples with CNVs confirmed by multiplex ligation-dependent probe amplification (MLPA). Tool performance varied greatly in the number of called CNVs and bias for CNV lengths. Some tools had near-perfect recall of CNVs from arrays for some samples, but poor precision. Several tools had better performance for NA12878, which could be a result of overfitting. We suggest combining the best tools also based on different methodologies: GATK gCNV, Lumpy, DELLY, and cn.MOPS. Reducing the total number of called variants could potentially be assisted by the use of background panels for filtering of frequently called variants.
- Published
- 2021