Evaluation of Whole-Exome Enrichment Solutions: Lessons from the High-End of the Short-Read Sequencing Scale

Usera, Ana Díaz-de; Lorenzo-Salazar, José M.; Rubio-Rodríguez, Luis A.; Muñoz-Barrera, Adrián; Guillén‐Guío, Beatriz; Marcelino-Rodríguez, Itahisa; García‐Olivares, Víctor; Mendoza-Alvarez, Alejandro; Corrales, Almudena; Íñigo-Campos, Antonio; González-Montelongo, Rafaela; Flores, Carlos

doi:10.3390/jcm9113656

Cited by 16 publications

(13 citation statements)

References 58 publications

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“…The Nextera DNA Prep kit was used for WGS, except for six samples that were processed by Illumina DNA Prep. The same samples were processed with Nextera DNA Exome with a 350 bp insert size as described elsewhere 32 . The library quality control was carried out in a TapeStation 4200 (Agilent Technologies, Santa Clara, CA).…”

Section: Methodsmentioning

confidence: 99%

A benchmarking of human mitochondrial DNA haplogroup classifiers from whole-genome and whole-exome sequence data

García‐Olivares

Muñoz-Barrera

Lorenzo-Salazar

et al. 2021

Sci Rep

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The mitochondrial genome (mtDNA) is of interest for a range of fields including evolutionary, forensic, and medical genetics. Human mitogenomes can be classified into evolutionary related haplogroups that provide ancestral information and pedigree relationships. Because of this and the advent of high-throughput sequencing (HTS) technology, there is a diversity of bioinformatic tools for haplogroup classification. We present a benchmarking of the 11 most salient tools for human mtDNA classification using empirical whole-genome (WGS) and whole-exome (WES) short-read sequencing data from 36 unrelated donors. We also assessed the best performing tool in third-generation long noisy read WGS data obtained with nanopore technology for a subset of the donors. We found that, for short-read WGS, most of the tools exhibit high accuracy for haplogroup classification irrespective of the input file used for the analysis. However, for short-read WES, Haplocheck and MixEmt were the most accurate tools. Based on the performance shown for WGS and WES, and the accompanying qualitative assessment, Haplocheck stands out as the most complete tool. For third-generation HTS data, we also showed that Haplocheck was able to accurately retrieve mtDNA haplogroups for all samples assessed, although only after following assembly-based approaches (either based on a referenced-based assembly or a hybrid de novo assembly). Taken together, our results provide guidance for researchers to select the most suitable tool to conduct the mtDNA analyses from HTS data.

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Section: Methodsmentioning

confidence: 99%

A benchmarking of human mitochondrial DNA haplogroup classifiers from whole-genome and whole-exome sequence data

García‐Olivares

Muñoz-Barrera

Lorenzo-Salazar

et al. 2021

Sci Rep

Self Cite

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show abstract

“…The Nextera DNA Prep kit was used for WGS, except for six samples that were processed by Illumina DNA Prep. The same samples were processed with Nextera DNA Exome with a 350 bp insert size as described elsewhere (Díaz-de Usera et al, 2020). The library quality control was carried out in a TapeStation 4200 (Agilent Technologies, Santa Clara, CA).…”

Section: Samples Library Preparation and Sequencingmentioning

confidence: 99%

A benchmarking of human mitochondrial DNA haplogroup classifiers from whole-genome and whole-exome sequence data

García‐Olivares

Muñoz-Barrera

Lorenzo-Salazar

et al. 2021

Preprint

Self Cite

View full text Add to dashboard Cite

The mitochondrial genome (mtDNA) is of interest for a range of fields including evolutionary, forensic, and medical genetics. Human mitogenomes can be classified into evolutionary related haplogroups that provide ancestral information and pedigree relationships. Because of this and the advent of high-throughput sequencing (HTS) technology, there is a diversity of bioinformatic tools for haplogroup classification. We present a benchmarking of the 11 most salient tools for human mtDNA classification using empirical whole-genome (WGS) and whole-exome (WES) short-read sequencing data from 36 unrelated donors. Besides, because of its relevance, we also assess the best performing tool in third-generation long noisy read WGS data obtained with nanopore technology for a subset of the donors. We found that, for short-read WGS, most of the tools exhibit high accuracy for haplogroup classification irrespective of the input file used for the analysis. However, for short- read WES, Haplocheck and MixEmt were the most accurate tools. Based on the performance shown for WGS and WES, and the accompanying qualitative assessment, Haplocheck stands out as the most complete tool. For third-generation HTS data, we also showed that Haplocheck was able to accurately retrieve mtDNA haplogroups for all samples assessed, although only after following assembly-based approaches (either based on a referenced-based assembly or a hybrid de novo assembly). Taken together, our results provide guidance for researchers to select the most suitable tool to conduct the mtDNA analyses from HTS data.

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“…There are several commercial kits for whole exome enrichment. The most known kits are SureSelect (Agilent), TruSeq Capture (Illumina), xGen (IDT), Human Comprehensive Exome (Twist Bioscience), Seq-Cap EZ (Roche NimbleGen) [4][5][6][7][8][9]. Enrichment protocols are similar and are based on hybridization of exon sequences with biotinylated DNA or RNA probes with a subsequent capture by streptavidin-covered magnetic beads.…”

Section: Introductionmentioning

confidence: 99%

“…Most kits are designed to enrich the libraries for sequencing using the Illumina platform. However, earlier, we managed to adapt the enrichment protocol for sequencing using the MGI platform with the Agilent SureSelect Human All Exon V6 probes that previously showed slightly better performance in exome sequencing in several studies [4,[10][11][12][13].…”

Section: Introductionmentioning

confidence: 99%

Performance comparison of Agilent new SureSelect All Exon v8 probes with v7 probes for exome sequencing

et al. 2022

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Exome sequencing is becoming a routine in health care, because it increases the chance of pinpointing the genetic cause of an individual patient's condition and thus making an accurate diagnosis. It is important for facilities providing genetic services to keep track of changes in the technology of exome capture in order to maximize throughput while reducing cost per sample. In this study, we focused on comparing the newly released exome probe set Agilent SureSelect Human All Exon v8 and the previous probe set v7. In preparation for higher throughput of exome sequencing using the DNBSEQ-G400, we evaluated target design, coverage statistics, and variants across these two different exome capture products. Although the target size of the v8 design has not changed much compared to the v7 design (35.24 Mb vs 35.8 Mb), the v8 probe design allows you to call more of SNVs (+ 3.06%) and indels (+ 8.49%) with the same number of raw reads per sample on the common target regions (34.84 Mb). Our results suggest that the new Agilent v8 probe set for exome sequencing yields better data quality than the current Agilent v7 set.

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Evaluation of Whole-Exome Enrichment Solutions: Lessons from the High-End of the Short-Read Sequencing Scale

Cited by 16 publications

References 58 publications

A benchmarking of human mitochondrial DNA haplogroup classifiers from whole-genome and whole-exome sequence data

A benchmarking of human mitochondrial DNA haplogroup classifiers from whole-genome and whole-exome sequence data

A benchmarking of human mitochondrial DNA haplogroup classifiers from whole-genome and whole-exome sequence data

Performance comparison of Agilent new SureSelect All Exon v8 probes with v7 probes for exome sequencing

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