Test development, optimization and validation of a WGS pipeline for genetic disorders
Abstract Background With advances in massive parallel sequencing (MPS) technology, whole-genome sequencing (WGS) has gradually evolved into the first-tier diagnostic test for genetic disorders. However, deployment practice and pipeline testing for clinical WGS are lacking. Methods In this study, we...
| Main Authors: | , , , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2023-04-01
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| Series: | BMC Medical Genomics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12920-023-01495-x |
| _version_ | 1797849853155344384 |
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| author | Ziying Yang Xu Yang Yan Sun Yaoshen Wang Lijie Song Zhihong Qiao Zhonghai Fang Zhonghua Wang Lipei Liu Yunmei Chen Saiying Yan Xueqin Guo Junqing Zhang Chunna Fan Fengxia Liu Zhiyu Peng Huanhuan Peng Jun Sun Wei Chen |
| author_facet | Ziying Yang Xu Yang Yan Sun Yaoshen Wang Lijie Song Zhihong Qiao Zhonghai Fang Zhonghua Wang Lipei Liu Yunmei Chen Saiying Yan Xueqin Guo Junqing Zhang Chunna Fan Fengxia Liu Zhiyu Peng Huanhuan Peng Jun Sun Wei Chen |
| author_sort | Ziying Yang |
| collection | DOAJ |
| description | Abstract Background With advances in massive parallel sequencing (MPS) technology, whole-genome sequencing (WGS) has gradually evolved into the first-tier diagnostic test for genetic disorders. However, deployment practice and pipeline testing for clinical WGS are lacking. Methods In this study, we introduced a whole WGS pipeline for genetic disorders, which included the entire process from obtaining a sample to clinical reporting. All samples that underwent WGS were constructed using polymerase chain reaction (PCR)-free library preparation protocols and sequenced on the MGISEQ-2000 platform. Bioinformatics pipelines were developed for the simultaneous detection of various types of variants, including single nucleotide variants (SNVs), insertions and deletions (indels), copy number variants (CNVs) and balanced rearrangements, mitochondrial (MT) variants, and other complex variants such as repeat expansion, pseudogenes and absence of heterozygosity (AOH). A semiautomatic pipeline was developed for the interpretation of potential SNVs and CNVs. Forty-five samples (including 14 positive commercially available samples, 23 laboratory-held positive cell lines and 8 clinical cases) with known variants were used to validate the whole pipeline. Results In this study, a whole WGS pipeline for genetic disorders was developed and optimized. Forty-five samples with known variants (6 with SNVs and Indels, 3 with MT variants, 5 with aneuploidies, 1 with triploidy, 23 with CNVs, 5 with balanced rearrangements, 2 with repeat expansions, 1 with AOHs, and 1 with exon 7–8 deletion of SMN1 gene) validated the effectiveness of our pipeline. Conclusions This study has been piloted in test development, optimization, and validation of the WGS pipeline for genetic disorders. A set of best practices were recommended using our pipeline, along with a dataset of positive samples for benchmarking. |
| first_indexed | 2024-04-09T18:50:54Z |
| format | Article |
| id | doaj.art-afe51f6315e5483190495461e1c34d35 |
| institution | Directory Open Access Journal |
| issn | 1755-8794 |
| language | English |
| last_indexed | 2024-04-09T18:50:54Z |
| publishDate | 2023-04-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Medical Genomics |
| spelling | doaj.art-afe51f6315e5483190495461e1c34d352023-04-09T11:29:10ZengBMCBMC Medical Genomics1755-87942023-04-0116111110.1186/s12920-023-01495-xTest development, optimization and validation of a WGS pipeline for genetic disordersZiying Yang0Xu Yang1Yan Sun2Yaoshen Wang3Lijie Song4Zhihong Qiao5Zhonghai Fang6Zhonghua Wang7Lipei Liu8Yunmei Chen9Saiying Yan10Xueqin Guo11Junqing Zhang12Chunna Fan13Fengxia Liu14Zhiyu Peng15Huanhuan Peng16Jun Sun17Wei Chen18College of Life Sciences, University of Chinese Academy of SciencesDepartment of Paediatrics, Pu’er People’s HospitalBGI Genomics, BGI-ShenzhenTianjin Medical Laboratory, BGI-Tianjin, BGI-ShenzhenTianjin Medical Laboratory, BGI-Tianjin, BGI-ShenzhenTianjin Medical Laboratory, BGI-Tianjin, BGI-ShenzhenTianjin Medical Laboratory, BGI-Tianjin, BGI-ShenzhenTianjin Medical Laboratory, BGI-Tianjin, BGI-ShenzhenTianjin Medical Laboratory, BGI-Tianjin, BGI-ShenzhenTianjin Medical Laboratory, BGI-Tianjin, BGI-ShenzhenTianjin Medical Laboratory, BGI-Tianjin, BGI-ShenzhenBGI-Wuhan Clinical Laboratories, BGI-ShenzhenTianjin Medical Laboratory, BGI-Tianjin, BGI-ShenzhenTianjin Medical Laboratory, BGI-Tianjin, BGI-ShenzhenTianjin Medical Laboratory, BGI-Tianjin, BGI-ShenzhenBGI Genomics, BGI-ShenzhenClinical Laboratory of BGI Health, BGI-ShenzhenTianjin Medical Laboratory, BGI-Tianjin, BGI-ShenzhenPu’er People’s HospitalAbstract Background With advances in massive parallel sequencing (MPS) technology, whole-genome sequencing (WGS) has gradually evolved into the first-tier diagnostic test for genetic disorders. However, deployment practice and pipeline testing for clinical WGS are lacking. Methods In this study, we introduced a whole WGS pipeline for genetic disorders, which included the entire process from obtaining a sample to clinical reporting. All samples that underwent WGS were constructed using polymerase chain reaction (PCR)-free library preparation protocols and sequenced on the MGISEQ-2000 platform. Bioinformatics pipelines were developed for the simultaneous detection of various types of variants, including single nucleotide variants (SNVs), insertions and deletions (indels), copy number variants (CNVs) and balanced rearrangements, mitochondrial (MT) variants, and other complex variants such as repeat expansion, pseudogenes and absence of heterozygosity (AOH). A semiautomatic pipeline was developed for the interpretation of potential SNVs and CNVs. Forty-five samples (including 14 positive commercially available samples, 23 laboratory-held positive cell lines and 8 clinical cases) with known variants were used to validate the whole pipeline. Results In this study, a whole WGS pipeline for genetic disorders was developed and optimized. Forty-five samples with known variants (6 with SNVs and Indels, 3 with MT variants, 5 with aneuploidies, 1 with triploidy, 23 with CNVs, 5 with balanced rearrangements, 2 with repeat expansions, 1 with AOHs, and 1 with exon 7–8 deletion of SMN1 gene) validated the effectiveness of our pipeline. Conclusions This study has been piloted in test development, optimization, and validation of the WGS pipeline for genetic disorders. A set of best practices were recommended using our pipeline, along with a dataset of positive samples for benchmarking.https://doi.org/10.1186/s12920-023-01495-xWhole genome sequencingGenetic disordersClinical diagnosisBioinformatics pipelines |
| spellingShingle | Ziying Yang Xu Yang Yan Sun Yaoshen Wang Lijie Song Zhihong Qiao Zhonghai Fang Zhonghua Wang Lipei Liu Yunmei Chen Saiying Yan Xueqin Guo Junqing Zhang Chunna Fan Fengxia Liu Zhiyu Peng Huanhuan Peng Jun Sun Wei Chen Test development, optimization and validation of a WGS pipeline for genetic disorders BMC Medical Genomics Whole genome sequencing Genetic disorders Clinical diagnosis Bioinformatics pipelines |
| title | Test development, optimization and validation of a WGS pipeline for genetic disorders |
| title_full | Test development, optimization and validation of a WGS pipeline for genetic disorders |
| title_fullStr | Test development, optimization and validation of a WGS pipeline for genetic disorders |
| title_full_unstemmed | Test development, optimization and validation of a WGS pipeline for genetic disorders |
| title_short | Test development, optimization and validation of a WGS pipeline for genetic disorders |
| title_sort | test development optimization and validation of a wgs pipeline for genetic disorders |
| topic | Whole genome sequencing Genetic disorders Clinical diagnosis Bioinformatics pipelines |
| url | https://doi.org/10.1186/s12920-023-01495-x |
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