Robust Benchmark Structural Variant Calls of An Asian Using the State-of-Art Long Fragment Sequencing Technologies

Du, Xiao; Li, Lili; Liang, Fan; Liu, Sanyang; Zhang, Wenxin; Sun, Shuai; Sun, Yuhui; Fan, Fei; Wang, Linying; Liang, Xinming; Qiu, Weijin; Fan, Guangyi; Wang, Ou; Yang, Weifei; Zhang, Jiezhong; Xiao, Yexiang; Wang, Yan; Wang, Depeng; Qu, Su; Chen, Fang; Huang, Jie

doi:10.1101/2020.08.10.245308

Cited by 4 publications

(5 citation statements)

References 55 publications

(56 reference statements)

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“…Meanwhile, many variants in complex regions such as xMHC and segmental duplications were reported, which are difficult for the read-alignment strategies. Another contribution of our benchmark is that we extend the variant types to complex structural variants, compared to previous studies 7, 8, 11, 53 . Nevertheless, our benchmark also has several limitations.…”

Section: Discussionmentioning

confidence: 99%

“…Thus, authoritative and comprehensive variant benchmarks are crucial for precisely understanding genetic variations in clinical samples. Many variant benchmarks and genomic reference materials have been established for the community to evaluate their variant detection pipelines during the past decades [5][6][7][8][9][10][11][12][13][14][15] . For example, the Genome in a Bottle (GIAB) Consortium developed seven reference materials and high-confidence benchmarks for both small variants 10 and structural variants 7 , prompting the pipeline evaluation in genomic analysis.…”

Section: Introductionmentioning

confidence: 99%

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Haplotype-resolved assemblies and variant benchmark of a Chinese Quartet

Jia

Yang

et al. 2022

Preprint

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As the state-of-the-art sequencing technologies and computational methods enable investigation of challenging regions in the human genome, an update variant benchmark is demanded. Herein, we sequenced a Chinese Quartet, consisting of two monozygotic twin daughters and their biological parents, with multiple advanced sequencing platforms, including Illumina, BGI, PacBio, and Oxford Nanopore Technology. We phased the long reads of the monozygotic twin daughters into paternal and maternal haplotypes using the parent-child genetic map. For each haplotype, we utilized advanced long reads to generate haplotype-resolved assemblies (HRAs) with high accuracy, completeness, and continuity. Based on the ingenious quartet samples, novel computational methods, high-quality sequencing reads, and HRAs, we established a comprehensive variant benchmark, including 3,883,283 SNVs, 859,256 Indels, 9,678 large deletions, 15,324 large insertions, 40 inversions, and 31 complex structural variants shared between the monozygotic twin daughters. In particular, the preciously excluded regions, such as repeat regions and the human leukocyte antigen (HLA) region, were systematically examined. Finally, we illustrated how the sequencing depth correlated with the de novo assembly and variant detection, from which we learned that 30 X HiFi is a balance between performance and cost. In summary, this study provides high-quality haplotype-resolved assemblies and a variant benchmark for two Chinese monozygotic twin samples. The benchmark expanded the regions of the previous report and adapted to the evolving sequencing technologies and computational methods.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Haplotype-resolved assemblies and variant benchmark of a Chinese Quartet

Jia

Yang

et al. 2022

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

“…Meanwhile, many variants in complex regions such as xMHC and segmental duplications were reported, which are di cult for the readalignment strategies. Another contribution of our benchmark is that we extend the variant types to complex structural variants, compared to previous studies 7,8,11,53 . Nevertheless, our benchmark also has several limitations.…”

Section: Discussionmentioning

confidence: 99%

“…Thus, authoritative and comprehensive variant benchmarks are crucial for precisely understanding genetic variations in clinical samples. Many variant benchmarks and genomic reference materials have been established for the community to evaluate their variant detection pipelines during the past decades [5][6][7][8][9][10][11][12][13][14][15] . For example, the Genome in a Bottle (GIAB) Consortium developed seven reference materials and high-con dence benchmarks for both small variants 10 and structural variants 7 , prompting the pipeline evaluation in genomic analysis.…”

Section: Introductionmentioning

confidence: 99%

Haplotype-resolved assemblies and variant benchmark of a Chinese Quartet

Jia

Li²,

Yang

et al. 2022

Preprint

Self Cite

View full text Add to dashboard Cite

As the state-of-the-art sequencing technologies and computational methods enable investigation of challenging regions in the human genome, an update variant benchmark is demanded. Herein, we sequenced a Chinese Quartet, consisting of two monozygotic twin daughters and their biological parents, with multiple advanced sequencing platforms, including Illumina, BGI, PacBio, and Oxford Nanopore Technology. We phased the long reads of the monozygotic twin daughters into paternal and maternal haplotypes using the parent-child genetic map. For each haplotype, we utilized advanced long reads to generate haplotype-resolved assemblies (HRAs) with high accuracy, completeness, and continuity. Based on the ingenious quartet samples, novel computational methods, high-quality sequencing reads, and HRAs, we established a comprehensive variant benchmark, including 3,883,283 SNVs, 859,256 Indels, 9,678 large deletions, 15,324 large insertions, 40 inversions, and 31 complex structural variants shared between the monozygotic twin daughters. In particular, the preciously excluded regions, such as repeat regions and the human leukocyte antigen (HLA) region, were systematically examined. Finally, we illustrated how the sequencing depth correlated with the de novo assembly and variant detection, from which we learned that 30 × HiFi is a balance between performance and cost. In summary, this study provides high-quality haplotype-resolved assemblies and a variant benchmark for two Chinese monozygotic twin samples. The benchmark expanded the regions of the previous report and adapted to the evolving sequencing technologies and computational methods.

show abstract

“…Genome in a Bottle (GIAB) and other efforts have established various whole-genome reference materials and defined benchmark calls and regions to benchmark germline small variants (SNVs and indels) [5][6][7][8] and structural variants (SVs) [9][10][11] . However, all these efforts on genomic reference materials only evaluated variants identified inside the benchmark regions.…”

Section: Introductionmentioning

confidence: 99%

Quartet DNA reference materials and datasets for comprehensively evaluating germline variants calling performance

Ren

Duan

et al. 2022

Preprint

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Current methods for evaluating the accuracy of germline variant calls are restricted to easy-to-detect high-confidence regions, thus ignoring a substantial portion of difficult variants beyond the benchmark regions. We established four DNA reference materials from immortalized cell lines derived from a Chinese Quartet including parents and monozygotic twins. We integrated benchmark calls of 4.2 million small variants and 15,000 structural variants from multiple platforms and bioinformatic pipelines for evaluating the reliability of germline variant calls inside the benchmark regions. The genetic built-in-truth of the Quartet family design not only improved sensitivity of benchmark calls by removing additional false positive variants with apparently high quality, but also enabled estimation of the precision of variants calls outside the benchmark regions. Batch effects of variant calling in large-scale DNA sequencing efforts can be effectively identified with the concurrent use of the Quartet DNA reference materials along with study samples, and can be alleviated by training a machine learning model with the Quartet reference datasets to remove potential artifact calls. Matched RNA and protein reference materials were also established in the Quartet project, thereby enabling benchmark calls constructed from DNA reference materials for evaluation of variants calling performance on RNA and protein data. The Quartet DNA reference materials from this study are a resource for objective and comprehensive assessment of the accuracy of germline variant calls throughout the whole-genome regions.

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Robust Benchmark Structural Variant Calls of An Asian Using the State-of-Art Long Fragment Sequencing Technologies

Cited by 4 publications

References 55 publications

Haplotype-resolved assemblies and variant benchmark of a Chinese Quartet

Haplotype-resolved assemblies and variant benchmark of a Chinese Quartet

Haplotype-resolved assemblies and variant benchmark of a Chinese Quartet

Quartet DNA reference materials and datasets for comprehensively evaluating germline variants calling performance

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